ANNUAL REPORT

SIPPE REPORT 

ANNUAL REPORT 

2010-2011 

Shanghai Institute of Plant Physiology & Ecology 

Chinese Academy of Sciences


Director’s Report 

Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese 

Academy of Science (CAS), was formed by integration of the former 

Shanghai Institute of Plant Physiology and Shanghai Institute of 

Entomology on May 19 th , 1999. The mission of SIPPE is to achieve 

breakthrough in cutting knowledge of plant, insect and microbiology 

sciences and in the industrialization of agriculture and industrial 

biotechnology, to play a leading role in innovation in the national 

science and technology innovation system. Currently, SIPPE focuses on deciphering physiology 

and genetic basis of rice yield and quality, physiology and biotechnology in plant stress resistance 

improvement, systems biology of microbial metabolism and synthetic biology. 

SIPPE is always adhering to the “people-oriented” concept and pays a great attention to recruit 

the distinguished scientists. In 2010 and 2011, SIPPE made remarkable achievements in 

recruiting new principle investigators and organizing the research teams. Professor Jian-Kang 

Zhu (member of National Academy of Science in USA) obtained the national “Top One-Thousand- 

Outstanding-Talents Program” fund. Totally 9 principle investigators are supported by various 

funds including “Outstanding Young Investigator Fund” from NSFC, national “One-Thousand- 

Young-Talents Program” or CAS “One-Hundred-Talents Program”. One scientist was elected as 

the member of Academy of Sciences of Developing Countries and one has won the HLHL prize. 

With a good academic atmosphere, SIPPE has gained a number of important achievements in the 

last two years. More than 160 research papers including 13 papers in leading scientific journals 

such as Nature Genetics, Science, PNAS, Plant Cell and PLOS Genetics were published and 23 

patents have been authorized and a new crop variety has obtained the protection of new varieties. 

In addition, National Center of Plant Gene Research (Shanghai) was formally established, which 

will speed up the industrialization of plant biotechnology. The National Key Laboratory of Plant 

Molecular Genetics (NKLPMG) was evaluated as one of the "Excellent" laboratories by the 

Ministry of Science and Technology. 

In the next few years, SIPPE will allocate resources rationally, improve the supporting system and 

do its best to create new research mechanisms to build a first-class institution. 

On behalf of the Institute, I would like to acknowledge the enormous supports from our sponsor 

and funding agencies and thank our staff and students for their persistent hard working. I hope 

that we will make a new chapter in SIPPE history with greater degrees of enthusiasm, scientific 

ideas, pragmatic attitudes and morale. 

HongWei Xue

Content 

Introduction 

Introduction of SIPPE 

Institute Organization 

2010-2011 Progress 

Highlights of Achivements 

Projects 

Research Team Construction 

Cooperation and Extention 

2 

3 

12 

24 

25 

28 

INTRODUCTION 

Appendix 

Publication 

Major Event 

Representative Publications 

Committee 

30 

37 

41 

54

SIPPE 

Academic Degree Committee 

Advisory Committee Academic Committee 

Research Sector Administration Sector Supporting Sector 

Introduction 


研究所介绍 

Introduction of SIPPE 

2010-2011 SIPPE Report 

Institute Organization 

Shanghai Institute of Plant Institute Physiology Introduction 

and Ecology (SIPPE) is one of the institutions of the Shanghai Institutes 

for Biological Sciences (SIBS), Chinese Academy of Science (CAS). SIPPE was established by the integration 

of the former Shanghai Institute of Plant Physiology (SIPP) and Shanghai Institute of Entomology (SIE) on May 

Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Science (CAS), 

19 th , 1999. The former SIPP was initially evolved from the laboratory of Plant Physiology, Institute of Botany 

was formed by the integration of the former Shanghai Institute of Plant Physiology (SIPP) and 

of the Academia Sinica, which was founded at the town of Beipei, Chongqing on May 1 st , 1944. On January 

Shanghai Institute of Entomology (SIE) on May 19 th , 1999. The former SIPP was developed from the 

laboratory of Plant Physiology, Institute of Botany of the Academia Sinica, which was founded in 

23 rd , 1953, Institute of Experimental Biology, CAS, was separated from the Academia Sinica and became the 

Chongqing Beipei on May 1 st , 1944. On January 23 rd , 1953, Institute of Experimental Biology of 

predecessor of SIPP. It was the cradle of plant physiology and biochemistry in China, and one of the pioneer 

Chinese Academy of Science was separated from the Academia Sinica and became the predecessor 

institutions that carried out molecular genetic researches in plants and microbes. Tremendous achievements have 

of SIPP. Many famous plant physiologists worked in SIPP. It was the cradle of plant physiology and 

been made in the fields of photosynthesis and nitrogen fixation in the early years. Former SIE, one of the main 

biochemistry research in China, and one of the pioneer institutes that carried out molecular genetic 

researches in plants and microbes.Tremendous success has been achieved in the field of 

research institutions on entomology in China, was founded in 1959 and once made great progresses in insect 

photosynthesis and nitrogen fixation, etc. The former SIE, one of the main research institutes in 

taxonomy, physiology, toxicology, co-evolution, pesticide resistance and sex pheromones. 

entomology of China was founded in 1959 and has made great progress in insect taxonomy, 

physiology, toxicology, co-evolution, resistance and sex pheromone. 

The mission of SIPPE is to generate knowledge of plants, 

microbes and insects through creative research, to train scientists 

for the future, and to benefit the sustainable agriculture, ecological 

environments, bio-energy and bio-manufacturing requirements 

in China. Our research topics include, if not all, functional 

genomics and physiology, synthetic biology, developmental 

and evolutionary biology, and biotechnologies by using plants, 

microbes and insects as model organisms. 

National Key Laboratory of Plant Molecular Genetics 

National Center of Plant Gene Research (Shanghai) 

National Center for Gene Research,CAS 

Key Laboratory of Insect Development and Evolutionary Biology, CAS 

Key Laboratory of Synthetic Biology, CAS 

Laboratory of Photosynthesis and Environmental Biology 

Executive Office 

Aiming at the cutting edge of biological sciences in important physiological processes and 

interaction between plants, microorganisms and insects, SIPPE focus on original systematic and 

applied basic research to meet strategic requirements for sustainable agriculture, ecological 

By the end of 2011, there are 403 research scientists working at 

SIPPE including 51 professors, 55 associate professors and senior 

technicians. SIPPE now has 9 CAS academicians, 11 winners for 

the NSFC “National Outstanding Young Investigator Award”, three awardees for “the One-Thousand-Talents” 

environment, bio-energy and bio-manufacturing in China. The goal of SIPPE is to achieve 

schemes, and 28 awardees for the CAS “One-Hundred-Talents” program. The research capacity of SIPPE has 

breakthrough in deciphering molecular physiology and genetic basis of rice yield and quality, 

been continuously strengthened by the supports from the funding agencies of the National Natural Science 

physiology and biotechnology in plant stress resistance improvement, systems biology study of 

microbial metabolism and synthesis of artificial life system; to achieve substantial progress in functional 

Foundation of China (NSFC) and the Ministry of Science and Technology (MOST), Ministry of Agriculture 

genomics of important traits formation of plant, insects and micro-organisms, fine regulation of plants 

and CAS. In particular, three innovative research teams including “The system and synthetic biology research 

and insects development, metabolic and biosynthetic pathways in plant, insect and micro-organisms, 

of microbial metabolism” have been funded by NSFC, and three projects have won the MOST’s National Basic 

plant gene regulation in insect, disease and stress resistance, advanced biotechnology, etc.; to 

Research Program (“973”) and National Science and Technology Infrastructure Program supports. 

In the next five to ten years, SIPPE will continue to strengthen its research team by recruiting outstanding young 

scientists, to improve its institutional managements, and to improve its national and international competitiveness 

in plant, microbe and insect sciences. The Institute will expand its collaborations with local and international 

institutions and enterprises for related basic and translational research. In general, SIPPE will devote its efforts to 

establish itself as a world-recognized institution by reinforcing its both basic and applied research capacities. 

7 

Projects Management Office 

Crop Cultivation and Breeding Base 

Core Facility Center 

Phytotron 

Shanghai Entomological Museum 

2 

3

Introduction 


National Key Laboratory of Plant Molecular Genetics 

The National Key Laboratory of Plant Molecular Genetics (NKLPMG), the first national key laboratory for plant 

molecular biological research, was approved for its organization in 1986 and was officially founded in 1988. 

NKLPMG mainly focuses on the following research areas: (1) plant functional genomics; (2) plant molecular 

physiology and development; (3) plant biotechnology and genetic engineering. The current director of NKLPMG 

is Professor Hong-Wei Xue and the chairman of academic board is Professor Zhi-Hong Xu, an academician of 

the Chinese Academy of Sciences (CAS). 

NKLPMG comprises of an active and energetic research team. Currently, there are 24 research groups and 120 

staff in NKLPMG, including 5 academicians of the CAS, 1 honored as “the One-Thousand-Talents”, 6 honored 

as “National Outstanding Young Investigator” by NSFC, and 14 honored as “the One-Hundred-Talents”. 

In the past two years, through unremitting efforts of all members, NKLPMG has been undertaking a total of 205 

research projects, among which 78 were newly approved from the Ministry of Sciences and Technology (973 

and 863 programs), the National Plant Transgenic Program, the National Natural Science Foundation of China, 

etc. Moreover, NKLPMG has made great progress in the research of rice functional genomes, plant development 

and cell biology, plant hormone and signal conduction, plant nutrition and metabolism, and plant biotechnology. 

NKLPMG published 103 scientific papers, of which 67 appeared on the SCI indexed journals including Plant 

Cell, PNAS, EMBO J, Cell Res, Plant J, Plant Physiol, etc. In the same period of time, NKLPMG obtained 12 

patent licenses and is currently applying for additional 40 national and international patents. 

In 2011, NKLPMG obtained the top record of “Excellence” in the national key laboratory assessment organized 

by the Ministry of Science and Technology, representing considerable accumulations of systematic scientific 

researches and comprehensive advantages in plant molecular biology and molecular physiology for NKLPMG. 

NKLPMG will make further effort to produce innovative contributions to plant and agricultural sciences and aim 

to be a world-class laboratory of plant Science. 

Homepage of NKLPMG: http://www.nlpmg.labs.gov.cn/ 

XiaoYa Chen Academician Plant Secondary Metabolism and Cotton Biology 

YuDa Fang Professor Cell Biology of Plant Genome and Epigenome 

JiMing Gong Professor Mineral Nutrition and Phytoremediation 

FangQing Guo Professor Nitric Oxide Signal Transduction and Mechanisms of Senescence 

YuKe He Professor Plant Morphogenesis and Molecular Breeding 

ZuHua He Professor Plant Disease Resistance and Rice Functional Genomics 

Hai Huang Professor Plant Developmental Biology 

JiRong Huang Professor G-protein Signaling and Chloroplast Development 

LaiGeng Li Professor Cell Wall Formation and Biomass Biosynthesis Studies 

HongXuan Lin Academician The Genetics and Functional Genomics of Crop 

HongTao Liu Professor Light Regulated Development and Light Signal Transduction 

HuaLing Mi Professor Protein-Protein Interactions in Chloroplasts 

WeiHua Tang Professor Plant-Fungal Interaction and Plant Reproductive Biology 

JiaWei Wang Professor Plant Small Regulatory RNAs 

YongFei Wang Professor Ion Channel and Signal Transduction in Plant Cells 

QiGuang Wen Professor Ethylene Signal Transduction 

Han Xiao Professor Fruit Developmental Biology 

Fang Xie Professor Legume-Rhizobium Symbiotic Nitrogen Fixation 

HongWei Xue Professor Plant Hormones and Seed Development 

ZhenBiao Yang Professor Plant Cell Biology and Signal Transduction 

HongXia Zhang Professor Engineering Salt Tolerant Plants 

Peng Zhang Professor Cassava and Sweetpotato Biotechnology 

Peng Zhang Professor Structural Biology 

4 

5

Introduction 


Key Laboratory of Synthetic Biology, CAS 

The Key Laboratory of Synthetic Biology (KLSynB) is a key laboratory of the Chinese Academy of Sciences 

(CAS), established in December 2008 through reorganization of the Laboratory of Molecular Microbiology. 

KLSynB focuses on developing the theory of synthetic biology under the guidance of systems biology via 

integrative analysis and comprehensive characterization of various levels of biological systems, integrating the 

theory of systems biology with the tools of synthetic biology in order to guide the production of biomaterial, 

biomedical and bio-fuel molecules through modification and/or synthesis of novel or improved biosystems (cell 

factory and molecular machine), and innovating synthetic biology technologies and transforming the cuttingedge 

core techniques into engineering-oriented platform and related resource banks/databases for research and 

application. The current director of KLSynB is academician Guo-Ping Zhao and the chairman of academic board 

is academician Sheng-Li Yang. 

KLSynB currently consists of 67 permanent staffs including 12 principal investigators, 9 associated professors, 

21 assistant professors and 9 technicians. One professor is honored as academician, three as “the Distinguished 

Young Investigator” by NSFC, six as “the One-Hundred-Talents” of CAS, and four as the Pujiang Scholars of 

Shanghai. KLSynB has been supported by 104 grants with RMB 42 million from various sources of funding 

agencies during 2010-2011, including one from the National “973” program and one from the Creative Research 

Group of NSFC. Fifty-eight peer-reviewed SCI-sourced papers have been published. In 2011, KLSynB hosted an 

international conference of the Six-Academy Synthetic Biology Symposium. 

Key Laboratory of Insect Developmental and 

Evolutionary Biology, CAS 

The Key Laboratory of Insect Developmental and Evolutionary Biology (IDEB), CAS, was founded in 2009. 

The research topics conducted at IDEB are mainly focused on the genomics and functional genomics studies of 

insects, primarily the Bombyx mori and Drosophila melanogaster. The main mission of IDEB is to reveal the 

complexity of insect systematics, development, the interactions between insects and insects, and between insects 

and other organisms at the molecular and genetic levels. The acquired knowledge can be used for innovative 

insect pest managements and effective use of beneficial insects. In addition, IDEB will work together with the 

Shanghai Entomological Museum to train and educate graduates for advanced insect sciences, and to spread and 

broaden insect knowledge for public audience. The current director of IDEB is Professor Cheng-Shu Wang and 

the chairman of academic board is Professor Le Kang, a CAS academician. 

Currently, there are one academician, 8 professors and 8 associate professors plus more than 100 staff, postdocs 

and graduate students at IDEB. During 2010-2011, the scientists at IDEB have been involved in 60 research 

programs from the Ministry of Sciences and Technology (973 and 863 programs), National Natural Sciences 

Foundation of China, and CAS. More than 60 high profile papers have been published by IDEB members on 

the journals of PNAS, PLoS Genetics, Genome Biology, Development, Cell Research, JBC, etc. IDEB has 

established a close relationship with the Shanghai Key Lab of Chemical Biology, East China University of 

Science and Technology. IDEB successfully organized “The 3 rd International Symposium on Insect Physiology, 

Biochemistry and Molecular Biology” in 2011 in Shanghai. 

WeiHong Jiang Professor Microbial Metabolic Regulation and Enzyme Engineering Group 

LaiGeng Li Professor Group of Cell Wall Formation and Biomass Biosynthesis Studies 

Xuan Li Professor Bioinformatics Research 

ZhongJun Qin Professor Molecular Genetics of Actinomycetes and Genomic Engineering Group 

Yong Wang Professor Synthetic Biology for Natural products Development 

LiYou Xiao Professor Chemical Biology and Enzymology 

Chen Yang Professor Microbial Metabolic Engineering and Comparative Genomics Group 

Sheng Yang Professor Microbial Metabolic Regulation and Enzyme Engineering Group 

Peng Zhang Professor Cassava and Sweetpotato Biotechnology Group 

GuoPing Zhao Academician Microbial Functional Genomics Group 

ZhiHua Zhou Professor Microbial Metagenomics and Bioenergy Conversion Group 

YongPing Huang Professor Insect Functional Genomics 

Sheng Li Professor Insect Development and Metamorphosis 

ErJun Ling Professor Insect Innate Immunology and Pest Control 

JianHua Shen Professor Molecular Toxicology 

ChengShu Wang Professor Insect Molecular Pathology 

YongZhen Xu Professor Insect RNA Splicing and Development 

WenYing Yin Academician Insect Taxonomy and Systematics 

6 

7

Introduction 


WeiMing Cai Professor Molecular Mechanism of Stress Tolerance of Plants and Space Biology 

JiRong Huang Professor G-protein Signaling and Chloroplast Development 

HuaLing Mi 

YunGang Shen 

Laboratory of Photosynthesis and Environmental Biology 

The Laboratory of Photosynthesis and Environmental Biology was reconstituted from the former two laboratories 

for photosynthesis and environmental biology in 2008. The former photosynthesis laboratory founded by the 

famous Academician Hong-Zhang Yin in 1956 was the first laboratory in this field in China, and had splendid 

achievements. Currently, the laboratory is interested in physiological and molecular mechanisms underlying 

photosynthesis, plant water and stress, gravity and sugar signaling. The long-term mission of the Lab is to provide 

crop breeders with genetic resources and technology to improve yield and food quality. The current director of the 

Lab is Professor Ji-Rong Huang, and chairman of academic board is Academician Yun-Gang Shen. 

The Lab has 38 researchers including two academicians, 8 principal investigators, 28 associate and assistant 

professors, 42 graduate students, and 4 postdoctoral researchers. Professor Ji-Rong Huang was supported by 

the “National Science Fund for Distinguished Young Investigator” in 2010. The Lab has 42 scientific research 

projects (more than RMB 20 million) from the Ministry of Sciences and Technology (973 and 863 programs), 

National Natural Science Foundation of China, and the National Plant Transgenic Program. In the past two 

years, the Lab published 70 papers, 58 of which in SCI journals, applied 7 patents, and made significant and 

substantial progresses on understanding of Rubisco activation, NAD(P)H dehydrogenase and its relationship 

with respiration of chloroplasts and cyclic electron transport, molecular basis of chloroplast development, 

regulation of photosynthetic efficiency, the resistance to abiotic stress; the development of techniques related to 

plant proteomic study, space biology and application of controlled agriculture. In terms of international scientific 

communication, the lab was involved to organize “The 15 th International Conference on Photosynthesis” and “The 

2 nd International Conference on Plant Metabolism”. 

Professor 

Academician 

Regulation of Photosynthetic Electron Transports in the Operation of 

Photosynthetic Apparatus 

Photophosphorylation and Regulation of the Operation of Photosynthetic 

Apparatus 

HuiQiong Zheng Professor Biology and Biotechnology in Microgravity 

National Center of Plant Gene Research (Shanghai) 

The National Center of Plant Gene Research (NCPGRS, Shanghai), a key state project of crop molecular 

breeding and commercialization, was authorized to be launched in 2009, and was formally inaugurated on 

June 25 th , 2011. NCPGRS consists of the well-established scientific research units in Shanghai, Zhejiang and 

Jiangsu, including Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, 

Shanghai Jiaotong University, Fudan University, Zhejiang University, Nanjing Agricultural University, Yangzhou 

University, Chinese National Rice Research Institute, Zhejiang Academy of Agricultural Sciences, Shanghai 

Academy of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, as well as the leading seed 

company Longping High-Tech Industry Group, to format the R & D strategic alliances. The current director of 

NCPGRS is Academician Xiao-Ya Chen and the Chair of Advisory Committee is Academician Zhi-Hong Xu. 

NCPGRS serves national agricultural demand, and focuses on gene discovery and molecular breeding application 

of pest and disease resistance, yield, quality, stress tolerance, and nutrition and water efficiency in the major 

crops such as rice, cotton, wheat and soybean. Several technique platforms will be established, including (1) 

large-scale gene discovering systems; (2) high-throughput gene function analysis and application evaluation; (3) 

crop metabolism and synthetic biology. The major objective of NCPGRS is to establish a world-class integrity 

research center from gene discovery, genetic resource innovation, to crop improvement evaluation. 

National Center for Gene Research, CAS 

In 1992, the National Center for Gene Research (NCGR) was established jointly by the Ministry of Science and 

Technology, the Chinese Academy of Sciences (CAS), and the Shanghai local government to provide a major focus in 

China for mapping and sequencing the rice genome, and genomes of other organisms. Since 1998, NCGR has been a 

member of the International Rice Genome Sequencing Project (IRGSP) to completely sequence the entire rice japonica 

genome. NCGR has been working on the chromosome 4 sequencing in close collaboration with the IRGSP members, 

the Chinese National Human Genome Center at Shanghai, and Institute of Genetics and Developmental Biology of 

CAS. The current director of NCGR is Professor Bin Han. 

NCGR has a staff size of 40, consists of three research groups: sequencing department, large-scale platform and 

bioinformatics department. NCGR has a high-performance DNA sequencing facility with 16 DNA sequencers. There 

are many other types of equipment such as SGI-3800 server, lots of SUN workstations, PCR amplifiers, real-time PCR, 

DNA synthesizers, automatic workstation, fluorescent microscope, ultra centrifuge, incubators, and ultra-low temperature 

freezers. NCGR has also various rice clone resources, including two rice japonica BAC/PAC clone libraries, three rice 

indica BAC/PAC clone libraries, rice indica full-length cDNA library, and some other BAC and cDNA libraries. 

Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions 

is important to world food security. NCGR sequenced 517 rice landraces, constructed a high-density haplotype map of 

rice genome by using a novel data imputation method and also performed genome-wide association studies (GWAS) 

for fourteen agronomic traits in the population of indica subspecies. The loci identified through GWAS explained 

~36% of the phenotypic variance on average. This study thus demonstrates that an integrated approach of secondgeneration 

genome sequencing and GWAS can be used as a powerful complementary strategy to classical bi-parental 

cross mapping for dissecting complex traits in rice, and provides a fundamental resource for rice genetics research and 

breeding. NCGR further developed an analytical framework for haplotype-based de novo assembly of the low-coverage 

sequencing data in rice. This study thus demonstrates that the integrated approach of sequence-based GWAS and 

functional genome annotation has the potential to resolve complex traits to their causal polymorphisms in rice. 

8 

9

Introduction 


Crop Cultivation and Breeding Base 

Experimental and Breeding Base is located at Wushe Modern Agricultural 

Zone, Songjiang District in Shanghai. It includes a biosafety-controlled 

nursery for genetically modified crops and plant trial fields.There is 

an indoor space of 2000 m 2 , equited with complete research and living 

facilities including laboratories, offices, conference room, staff dormitory, 

warehouses, etc. The base was already an experiment and platform for 

functional genomic research and crop breeding. 

2010-2011 PROGRESS 

Core Facility Center 

Taking advantage of the international leading equipments available in 

the institute, SIPPE make every effort on the studies of cell biology, 

metabolism, functional genomics and proteomics. There are many 

facilities including laser scanning confocal microscopes, scanning 

electron microscopes, transmission electron microscope, real-time PCR 

instruments, fluorescence spectrophotometers, HPLC-MS, GC-MS, etc. 

Phytotron 

A phytotron with 4700 m 2 was built on the campus. The environmentally 

controlled area (1650 m 2 ) is divided into 83 units, with rooms equipped 

for full climate control. 

Shanghai Entomological Museum 

The Insect Specimen Gallery in the Shanghai Entomological Museum 

is one of the largest insect museums in China with a broad collection 

of insect specimens. The collection is composed of over 1,000,000 

specimens from across the country, including 400,000 soil animals (over 

1,000 types of insects). This collection provides valuable resources for 

studying the insect fauna of China. 

10 

11

2010-2011 Progress 研究所介绍 

2010-2011 SIPPE SIPPE REPORT Report 

Highlights of Achivements 

In 2010 and 2011, scientists of SIPPE made great contributions in many research fields, and published 161 

papers in leading scientific journals including Nature Genetics, Science, PNAS, PLoS Genetics, Genome 

Research, Plant Cell, ect. Sixty patents were applied, twenty-three inventions have been granted, including one 

from South Africa. A new variety of sweet potato “Taizhong No.9” was examined and approved by Crop Variety 

Authorization Committee of Shandong Province (No. 2010041). 

The achievements in the following fields: 

Crop Functional Genomics 

Analysis of Rice Functional Genomics Based on High-Throughput Sequencing Technology 

Research on Genes Controlling Important Agronomic Traits 

Molecular Mechanisms Underlying Important Processes in Plant Physiology 

Plant Hormone and Signal Transduction 

Plant Development 

Study of Plant Cell Biology 

Plant Metabolic Regulation and Biotechnology 

Mineral Nutrition and Metabolism in Plants 

Analysis of Rice Functional Genomics Based on High-Throughput 

Analysis of Rice Functional Genomics Based on High-Throughput 

Sequencing Technology 

Rice (Oryza sativa L) is an economically important crop that accounts for ~20% of the world’s caloric 

intake. To be grown successfully under a variety of climatic conditions across the globe, breeders maintain 

rice at high genetic diversity. Second-generation sequencing technologies have enabled resequencing of a 

large number of genomes and have provided the possibility of high-throughput genotyping and large-scale 

genetic variation surveys. Identification of allelic variations underpinning the phenotypic diversity 

observed in rice will have enormous practical implications in rice breeding. 

Professor Bin Han’s group sequenced 517 rice landraces and constructed a high-density haplotype map of 

rice genome by using a novel data imputation method. They performed genome-wide association studies 

(GWAS) for fourteen agronomic traits in the population of indica subspecies. The loci identified through 

GWAS explained ~36% of the phenotypic variance on average. The peak signals at six loci tied closely to 

the previously identified genes. This study thus demonstrates that an integrated approach of 

second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to 

classical bi-parental cross mapping for dissecting complex traits in rice, and provides a fundamental 

resource for rice genetics research and breeding (Nature Genetics, 2010). 

Their group further extended the sample to 950 world-wide rice varieties, and constructed a high-density 

haplotype map by the imputation method. They identified a total of 32 new loci associated with flowering 

time and ten grain-related traits, indicating that the larger sample dramatically lifted the power of GWAS in 

rice. They developed an analytical framework for haplotype-based de novo assembly of the low-coverage 

sequencing data in rice. This study thus demonstrates that the integrated approach of sequence-based 

GWAS and functional genome annotation has the potential to resolve complex traits to their causal 

polymorphisms in rice (Nature Genetics, 2011). 

Biomass and Bioenergy Plants 

Insect Developmental and Evolutionary Biology 

Comparative Genomics of Insect Pathogenic Fungi 

Insect Development and Evolutionary Biology 

Synthetic Biology 

Systems and Synthetic Biology of Microbial Metabolism 

Microbial Industrial Biotechnology 

Genome analysis of low-coverage sequencing of rice varieties 

Genetic diversity of rice germplasm 

1 

12 

13

2010-2011 Progress SIPPE REPORT 



During 2010 to 2011, the institute made great progress in discovery, innovation and application of genetic 

resources that control important agronomic traits in crops such as rice. 

Rice productivity is highly associated with its architectural pattern, including plant height, which is mainly 

attributable to stem internode elongation. The uppermost internode is of particular importance for rice 

productivity, since the elongation of the uppermost internode promotes panicle emergence and subsequent 

grain filling. Professor ZuHua He’s group has been devoted to dissecting the rice internode development 

and identified Eui gene which controls rice uppermost internode 

elongation by modulation of the bioactive GA levels. Thereafter they 

find that a new gene BUI1, which encodes the class II formin FH5. 

Mutation of BUI1 results in severely disruption of the actin 

cytoskeleton and consequently inhibition of cell expansion. They 

found that BUI1 could efficiently promote actin filament assembly 

and actin bundling. Thus, their study identified a rice formin protein 

BUI1 that regulates de novo actin nucleation and spatial organization 

of the actin filaments, which are important for proper cell expansion 

and rice morphogenesis. The identification of BUI1 also reveals a 

new regulatory mechanism underlying the development of rice 

internodes (Plant Cell, 2011). 

Domestication has played important roles in crop breeding. Many important agronomic trait-related genes 

are subjected to domestication. Previous study in Zuhua He’s lab has demonstrated that GIF1 encodes a 

cell-wall invertase required for grain filling. Sequence analysis of GIF1 region revealed significant 

domestication signatures in its promoter, which restricted GIF1 expression specifically to the ovular trace. 

Their further study identified another cell-wall invertase gene OsCIN1. GIF1 and OsCIN1 constitute a pair 

of duplicate genes with differentiated expression and function through independent selection (BMC Evol 

Biol, 2010). Using a genetic population constructed by a cross between O. rufipogon W1943 (black hull) 

and O. sativa indica cv Guangluai 4 (straw-white hull), Professor Bin Han’s group cloned Bh4, an a amino 

acid transporter protein, which plays a critical role in controlling seed hull color during grain ripening. Bh4 

sequence alignment revealed a significant reduction in nucleotide diversity in rice cultivars probably due to 

artificial selection, suggesting that straw-white hull was selected as an important visual phenotype of 

nonshattered grains during rice domestication (Plant Physiol, 2011). 

As the predominant component of milled rice, the physicochemical properties of starch determine the 

eating, cooking, and milling qualities of rice. To systemically identify the genes that regulate rice starch 

biosynthesis, Professor HongWei Xue’s group performed gene co-expression analysis to identify candidate 

regulators for starch biosynthesis. They isolated 61 

transcription factors predicted to be involved in starch 

synthesis, including Rice Starch Regulator1 (RSR1). 

Mutation of RSR1 results in increased amylose 

content, altered fine structure of amylopectin, and 

decreased gelatinization temperature. The results 

demonstrate the potential of co-expression analysis 

for studying rice starch biosynthesis and the 

regulation of a complex metabolic pathway, and 

provide informative clue to facilitate the improvement 

of rice quality and nutrition (Plant Physiol, 2010). 

WT 

rsr1 



Plant hormones play crucial regulatory roles in plant growth and development. Studies of the 

corresponding functional mechanism are significant and helpful to understand how plants grow and 

develop, and contribute to the agricultural development. With the technological development of genetics 

and molecular biology, some important progresses on the molecular mechanism of plant hormones have 

been gained. However, the metabolism of different hormones, the signaling transduction pathway, 

functional mechanism, and interactions between different hormones or with other signaling pathways, need 

further studies. 

GA is crucial for multiple aspects of plant growth and development. Prof. HongWei Xue’s group identified 

a rice T-DNA insertion mutant earlier flowering1 (el1), which is deficient in a casein kinase I that plays 

critical roles in both plants and animals. el1 had an enhanced GA response including the elongated second 

leaf sheaths and α-amylase activities. Transcription of GA biosynthesis-related genes was reduced in el1, 

which is consistent with the stimulated GA signaling. 

No. of flowering plants 

16 

14 

12 

10 

8 

6 

4 

2 

0 

WT 

WT 

el1 

el1 

60~62 63~65 66~68 69~71 72~74 

Heading time (days) 

WT 

el1 

WT 

el1 

Biochemical characterization showed that EL1 

specifically phosphorylates rice DELLA protein 

SLR1, a key negative regulator of GA signaling, 

providing a direct evidence for SLR1 

phosphorylation. The severe dwarf phenotype and 

suppressed GA signaling by SLR1 overexpression 

was significantly reduced by EL1 deficiency, 

indicating the negative effect of SLR1 on GA 

signaling requires the EL1 function. Further studies 

revealed that the phosphorylation of SLR1 is 

important for maintaining its activity and stability, 

which provided important clues of casein kinase I 

effects in regulation of GA signaling and plant 

development (EMBO J, 2010). 

Rice ABI5-like1 (ABL1) encodes a bZIP transcription factor and participates in the stress responses by 

regulating the expression of a series of ABRE-containing WRKY family genes. Expression of rice ABL1 

could be significantly enhanced by hormones ABA and IAA, and the abl1 mutant is hypersensitive to 

exogenous IAA. These shed informative lights on the interaction of ABA-auxin signaling (Plant Physiol, 

2010). 

Key enzyme of Arabidopsis phosphatidylinositol signaling, 

PIP5K2, and its product, PtdIns(4,5)P2, is disclosed to 

regulate the lateral root formation and root gravity response 

through modulating auxin accumulation and polar auxin 

transport by enhancing the vesicular trafficking and cycling 

of PIN proteins(Cell Research, 2011). 

Dr. Sheng Teng and other researchers disclosed that eight 

fructose-sensing quantitative trait loci (QTLs) (FSQ1–8) 

existed in Arabidopsis fructose-specific signaling pathway. 

FSQ6-associated fructose-signaling pathway functions 

independently of the hexokinase1 glucose sensor and its 

downstream signaling interacts with abscisic acid (ABA) - 

and ethylene-signaling pathways (PNAS, 2011). 

14 

15






Leaves are the plant organs for photosynthesis, through which the free carbon dioxide isassimilated. The 

molecular regulatory mechanism of leaf development is therefore of significance. Researches in this field 

have been advanced substantially by several groups during 2010-2011. 

Arabidopsis AS1 and AS2 are important genes in specifying leaf adaxial identity, and ribosome and 26S 

proteasome, which are the essential proteins for living organisms, are also involved in leaf polarity 

establishment. The characterization of a novel as2 enhancer mutant ae7, which exhibits developmental 

defects in the leaf adaxial side, partly answered how Ribosome and 26S proteasomegenes regulate leaf 

polarity. The ae7 leaves contained the reduced cell number with the enlarged cell size, indicating that AE7 

is required for cell proliferation.The AE7 gene is expressed in a spotted pattern in plant tissues, similar to 

some cell-cycle marker genes, further support the notion that the basic function of AE7 may be involved in 

cell division. 

Both double mutants, combine as1 (or as2) with Elongator and grf mutants, showed the enhanced defects 

in the leaf adaxial-abaxial axis. These results indicate that defective cell division could generally affect leaf 

adaxial-abaxial polarity. It was proposed that the newly initiated leaf primordium is an abaxialized 

structure, and differentiation toan abaxial identityisthe default pattern in the absence of actionsof the 

adaxially-promoting factors. Hence, because the adaxially featured cells initiate and accumulate later than 

the abaxially featured cells, for the final balanced adaxial and abaxial domains in mature leaves, the 

adaxial cells must proliferate more rapidly than the abaxial cells at certain leaf developmental stages. 

Although all leaf cells in both adaxial and abaxial domains are affected in the cell proliferation defective 

mutants, the adaxial domain must suffer more severely than the abaxial one (Plant J, 2010, 2011). 

The production and distribution of plant trichomes is temporally and spatially regulated. After entering into 

the flowering stage, Arabidopsis thaliana plants have progressively reduced numbers of trichomes on the 

inflorescence stem, and the floral organs are nearly glabrous. SQUAMOSA PROMOTER BINDING 

PROTEIN LIKE (SPL) genes, which define an endogenous flowering pathway and are targeted by 

microRNA 156 (miR156), temporally control the trichome distribution during flowering. During plant 

development, the increase in SPL transcript levels is coordinated with the gradual loss of trichome cells on 

the stem. The MYB transcription factor genes 

TRICHOMELESS1 (TCL1) and TRIPTYCHON (TRY) are 

negative regulators of trichome development. Prof. XiaoYa 

Chen’s group showed that SPL9 directly activates TCL1 and 

TRY expression through binding to their promoters and that 

this activation is independent of GLABROUS1 (GL1). The 

phytohormones cytokinin and gibberellin were reported to 

induce trichome formation on the stem and inflorescence via 

the C2H2 transcription factors GIS, GIS2, and ZFP8, which 

promote GL1 expression. The GIS-dependent pathway does 

not affect the regulation of TCL1 and TRY by miR156-targeted 

SPLs, represented by SPL9. These results demonstrate that the miR156-regulated SPLs establish a direct 

link between developmental programming and trichome distribution (Plant Cell, 2011). 

Plant Cell Biology 

Studies of Plant Cell Biology 

The basic unit of packaging of chromatin is the nucleosome. Its core domain is a compact histone octamer 

which contains two molecules of each core histones H2A, H2B, H3 and H4. In addition to the canonical 

histones, there exist diverse variants of histones through addition, deletion or substitution of specific amino 

acid residues. The incorporation of histone variants into nucleosomes produces various forms of 

nucleosomes with divergent structures and functions, which play important roles in epigenetics and 

regulation of genome functions. The family of histone H3 includes the canonical histone H3.1, variant 

H3.3 and centromere-specific CenH3, which are highly conservative from fly to human and plant. Plant 

H3.3 differs in four amino acid residues from H3.1, these are residue 31 (with Thr in H3.3 instead of Gly 

in H3.1) and 41 (with Tyr in H3.3 instead of Phe in H3.1) in the N-terminal tail and residues 87 (with His 

in H3.3 instead of Cys in H3.1) and 90 (with Leu in H3.3 instead of Gly in H3.1) in the histone folding 

domain (HFD). By live-cell imaging, it was found that H3.1-GFP is mainly loaded into heterchromatin, 

while H3.3 is incorporated into euchromatin and highly enriched in rDNA arrays. Having investigated the 

dynamic loading or unloading of Arabidopsis histone H3.1, H3.3 and their mutated proteins into 

nucleoluar rDNA, Prof. YuDa Fang’s group revealed that amino acid residue 87, and to some extent 

residue 90, of Arabidopsis histone H3.3 is critical for its deposition into rDNA arrays. When RNA 

polymerase I directed nucleolar transcription is inhibited, wild type H3.3 and H3.3 containing mutations at 

residues 87 and 90, but not H3.3 containing mutations at residues 31 and 41, is depleted from the rDNA 

arrays. Based on these results, they put forward a model in which amino acids 87 and 90 in the core 

domain of H3.3 guide nucleosome assembly, while amino acids 31 and 41 in the N-terminal tail of 

Arabidopsis H3.3 guide nucleosome disassembly in nucleolar rDNA. As histone variant H3.3 is highly 

conserved in various organisms, the result may have broad biological significance (PNAS, 2011). 

In the studies on plant germ cells, Prof. WeiHua Tang’s group profiled laser-captured rice pollen mother 

cells by microarrays, and found that 59% of genes express in pollen mother cells (PMCs). Among these 

genes expressed in PMCs, 127 genes are not expressed in tricellular pollen or seedling (Plant Physiol, 

2010). In an invited review article in Semin Cell Dev Bio 

(2011), Prof. ZhenBiao Yang’s group updated the recent 

studies on pollen tip growth from aspects of the structure and 

signal regulation system, and summarized the mechanisms of 

regulating the rapid growth of pollen tip by integrating 

cellular and ex-cellular signals and coordinating membrane 

dynamics and recombination of cell wall in a manner of 

self-organization. In another study, Prof. HuiQiong Zheng’s 

group has investigated the structural events associated with 

vacuole biogenesis in root tip cells of tobacco seedlings 

preserved by high-pressure freezing and freeze-substitution 

techniques, and demonstrated that the lytic vacuoles (LVs) of 

root tip cells are derived from protein storage vacuoles (PSVs) by cell type-specific sets of transformation 

events (Plant Physiol, 2011). 

16 

5 

17


植物生理生态研究所年报 


Mineral Nutrition and Metabolism in in Plants 

Mineral nutrition and metabolism are essential processes that determine growth and economical output of 

plants,which enable plants to provide massive biomass and energy to plants themselves and also the 

secondary consumers in the food chain. Substantial progresses in this field have been obtained by serveral 

groups during 2010-2011. 

Nitrogen is one of the most studied macronutrients. Nitrate represents the major nitrogen source for most 

terrestrial plants, functioning as mineral 

nutrient as well as an important signal 

molecule to regulate plant development. 

Once taken up into plant roots, nitrate is 

subjected to long-distance transport to 

aerial parts, where nitrate assimilation 

and photosynthesis are directly coupled 

in chloroplast, and conferring plants 

increased energy efficiency than root 

assimilation. However, environmental 

stresses including low temperature, dim 

light, high salt and heavy metals tend to 

retain proportionally more nitrate in 

roots. How this happens and if it is of 

physiological improtance remain largely 

to be addressed, and Prof. JiMing Gong’s group contributes substantially to a better understanding of these 

questions by functional characterizing a nitrate transporter gene NRT1.8 (Plant Cell, 2010). NRT1.8 is the 

only one gene in nitrate assimilation pathway which is strongly responsive to Cd 2+ stress. Physiological 

analyses showed that NRT1.8 is a pH-dependent nitrate uptake transporter, and it functions primarily to 

transport nitrate across plasma membrane into xylem 

parenchyma cells, thus unloading nitrate from xylem sap 

and mediating nitrate long-distance transport from roots 

to shoots. Under Cd 2+ stress, NRT1.8 expression is 

upregulated and helps to retain more nitrates in roots, and 

consequently mediates the nitrate distribution between 

roots and shoots. In the loss-of-function mutant nrt1.8-1, 

nitrate redistribution under Cd 2+ stress was disrupted and 

plants showed increased sensitivity to Cd 2+ . These results 

reveal that nitrate reallocation into roots is actively 

regulated by NRT1.8 and plays an essential role in stress 

tolerance, rather than a passive consequence of inhibited 

transpiration rate as previously proposed. 

In addition, Prof. HongWei Xue’s group revealed that 

KASI is an essential regulator in the interaction between 

de novo fatty acid biosynthesis and chloroplast 

development (Plant Cell, 2010). Prof. JiRong Huang’s 

group discovered that GDPD1 plays an essential role in 

plant tolerance to environmental Pi deficiency (Plant J, 

2011). 



The institute focuses on the key biological questions and biotechnologies of starch and fiber-based 

bioenergy plants by exploring the molecular mechanism of biomass biosynthesis, verifying gene functions, 

and enhancing germplasm. 

Cassava (Manihot esculenta Crantz) and 

sweet potato (Ipomoea batatas [L.] Lam.) 

are important starchy root crops for 

bioenergy development. The development 

of novel germplasms with high yield and 

starch content and improving capacity of 

resistance to various stresses could 

promote their industrialization. In order to 

further increase yield, analysis of storage root formation and developmental mechanism is of importance. 

Using the microarray technology, thousands of differential expressed genes related to storage root 

development was analyzed. Metabolic pathways, such as glycolysis/gluconeogenesis, starch and sucrose 

metabolism etc., were actively regulated during the biological process. Based on the structural scenario and 

carbon flux, the first molecular model for the development of starchy storage root in cassava was 

suggested. These studies should not only facilitate our understanding of the storage root formation, but also 

explore a number of genes of interest for genetic improvement of cassava and sweet potato. 

Wild-type Transgenic 

Starch quality, an important agronomic trait of root crops, 

determines the conversion efficiency from biomass to 

bioenergy and the potency of novel bioproducts. Using the 

constitutive or vascular-specific promoters, expression of the 

amylase biosynthetic gene GBSSI was silenced in transgenic 

cassava, leading to the development of various waxy plants 

with amylopectin up to 98%. The alternation of starch 

property was further verified by different physico-chemical 

characterizations, including structural, viscosity and 

thermodynamics analyses. The well performance of these 

transgenic plant lines in the field trial also indicates a great 

potential of these waxy cassava for providing new materials 

in industrial applications (Biotech & Bioen, 2011). 

Significant progress has also been made in sweet potato 

traditional breeding, collaborated with Tai’an Academy of Agricultural Sciences. “TaiZhong No.9”, a 

recently released variety approved by the Crop Variety Authorization Committee of Shandong Province 

(No. 2010041), is a high-starch cultivar suitable for cultivation in Shandong and other Huanghuai regions. 

The cultivar has been planted for more than 100,000 hectares to promote local development, which 

significantly supports the development of bioenergy plants and regional agricultural economy. 

For woody plants, Prof. LaiGeng Li’s group identified a number of important new plasma membrane 

proteins which are closely associated with regulating secondary vascular differentiation in poplar. A 

functional study of rice 4-coumarate: CoA ligase (4CL, EC 6.2.1.12), a key enzyme involved in 

monolignol biosynthesis, revealed that different biosynthetic pathways might exist in dicotyledons and 

monocotyledons. This study showed a cooperated evolution of plants and lignin biosynthesis (Plant 

Physiol, 2011). 

18 

19 

6


Comparative Genomics of Insect Pathogenic Fungi 

There are about one thousand fungal species that can infect and kill insects. The species like Metarhizium 

spp. and Beauveria spp. have been developed as promising insect biocontrol agents while the Cordyceps 

species like C. militaris and C. sinensis are traditional Chinese medicines. Before our studies, the genome 

information of these fungi is unknown. 

Prof. ChengShu Wang’s group is focusing on the 

functional genomics and comparative genomics 

studies of insect pathogenic fungi. They initiated and 

finished the genome studies of Metarhizium robertsii, 

M. acridum and Cordyceps militaris. Comparative 

genomics study of the generalist species M. robertsii 

and acridid-specific M. acridum indicated that the 

genus Metarhizium may have evolved from plant 

endophytes or pathogens. Both M. robertsii and M. 

acridum have a strikingly larger proportion of genes 

encoding proteases, chitinases and lipases than other 

sequenced fungi to target insect cuticles. Relative to 

M. acridum, M. robertsii has acquired many 

additional genes for these and other functions that 

may facilitate its ability to adapt to heterogenous environments such as plant root surfaces and multiple 

insect hosts. Unlike M. acridum, M. robertsii has lost the repeat-induced point mutation genomic defense 

system and this loss may have facilitated lineage specific gene duplications and increased niche 

adaptability. RNA-seq transcriptional analysis of both fungi during early infection processes provided 

further insights into the genes and pathways involved in infectivity and specificity. Of particular note, M. 

acridum but not M. robertsii transcribed different G-protein coupled receptors on host but not non-host 

cuticles, thus the fine-tuning mechanisms in association with insect host species (PLoS Genetics, 2011). 

Further genome study of the model species of C. militaris 

found that different species in the Cordyceps/Metarhizium 

genera have evolved into insect pathogens independently of 

each other. The lineage leading to Cordyceps spp. diverged 

130 million year before Metarhizium. However, their 

similar gene family expansions suggest a convergent 

evolution. Consistent with its long track record of safe 

usage as a medicine, the Cordyceps genome does not 

contain genes for known human mycotoxins. C. militaris is 

sexually heterothallic but, very unusually, fruiting can occur 

without an opposite mating-type partner. High throughput 

transcriptional profiling indicated that the fruiting of C. 

militaris involved induction of MAPK pathway and the 

PKA pathway is not activated. As well as providing fundamental new information on the evolution of 

insect pathogens, their studies will facilitate the identification of genes involved in fungal virulence, 

development, sexuality and the biosynthesis of secondary metabolites (Genome Biology, 2011). 

Insect Development and Evolutionary Biology 

Animal cells require extrinsic cues for growth, proliferation and survival. The propagation of Drosophila 

imaginal disc cells in vitro, for example, requires the 

supplementation of fly extract, the composition of which 

remains largely undefined. Prof. Sheng Li’s group reported the 

biochemical purification of iron-loaded ferritin as an active 

ingredient of fly extract that is required for promoting the 

growth of Cl8 imaginal disc cells. They concluded that 

iron-loaded ferritin is an essential mitogen for cell proliferation 

and postembryonic development in Drosophila through 

maintaining iron homeostasis and antagonizing starvation 

response (Cell Research, 2010). 

Sericulture has been greatly advanced by applying hybrid breeding techniques to the domesticated 

silkworm, Bombyx mori, but has reached a plateau during the last decades. For the first time, they report 

improved silk yield in a GAL4/UAS transgenic silkworm. Overexpression of the Ras1 CA oncogene 

specifically in the posterior silk gland improved fibroin production and silk yield 60%, while increasing 

food consumption only 20%. Ras activation by Ras1 CA overexpression in the posterior silk gland enhanced 

phosphorylation levels of Ras downstream effector proteins, up-regulated fibroin mRNA levels, increased 

total DNA content, and stimulated endoreplication. Moreover, Ras1 activation increased cell and nuclei 

sizes, enriched subcellular organelles related to protein synthesis, and stimulated ribosome biogenesis for 

mRNA translation (Cell Research, 2011). 

Insects exhibit the richest diversity of all animals, and the rapid evolution of their phenotypic patterns 

suggests strong selective forces that promote and maintain variation. The pigmentation of insects has 

served as an excellent model for the study of morphological trait evolution and developmental biology. 

The melanism (mln) mutant of the silkworm Bombyx mori is notable for its strong black coloration, 

phenotypic differences between larval and adult stages, and its widespread use in strain selection. Prof. 

YongPing Huang’s group reported the genetic and molecular bases for the formation of the mln 

morphological trait. Fine mapping revealed that an arylalkylamine N-acetyltransferase (AANAT) gene 

co-segregates with the black coloration patterns. 

Coding sequence variations and expression 

profiles of AANAT are also associated with the 

melanic phenotypes. An enzymatic assay 

demonstrated the absolute loss of AANAT 

activity in the mutant proteins. They also 

performed RNA interference of AANAT in 

wild-type pupae and observed a significant 

proportion of adults with ectopic black coloration. 

AANAT is also involved in a parallel melanin 

synthesis pathway in which ebony plays a role, 

whereas no pigmentation defect has been 

reported in the Drosophila model or in other 

insects to date. The mln mutation might be the first characterized mutant phenotype of insects with 

AANAT, and this result contributes to our understanding of dopamine metabolism and melanin pattern 

polymorphisms (Development, 2010). 

20 

21


Systems and and Synthetic Biology of Microbial Metabolism 

Delineatig microbial metabolic network and regulatory mechnisms based on functional genomic and 

comparative genomic techniques has been an important theme of Laboratory of Synthetic Biology 

(LSynB). Recently great progress has been made by Prof. GuoPing Zhao’s group in deciphering the global 

regulatory role of post-translational modification in microbial metabolism. 

Lysine acetylation regulates many eukaryotic cellular processes, but its function in prokaryotes is largely 

unknown. Aiming to answer whether acetylation is a conserved universal modification of metabolic 

enzymes, the groups from Prof. Zhao and Prof. Chen Yang demonstrated that central metabolism enzymes 

in Salmonella were acetylated extensively and differentially in response to different carbon sources, 

concomitantly with changes in cell growth and metabolic fluxes, by integrating the MS and 13 C-based 

metabolic flux analysis techniques. They found almost 200 acetylated proteins in S. enterica., almost every 

intermediary metabolic enzyme was acetylated. For example, the relative activities of key enzymes 

controlling the direction of glycolysis versus gluconeogenesis and the branching between citrate cycle and 

glyoxylate bypass were all regulated by acetylation. This modulation is mainly controlled by a pair of 

protein acetyltransferase (Pat) and NAD + -dependent deacetylase (CobB), whose expressions are 

coordinated with growth status. Reversible acetylation of metabolic enzymes ensures that cells respond 

environmental changes via promptly sensing cellular energy status and flexibly altering reaction rates or 

directions. The identification of extensively acetylated metabolic enzymes in both prokaryotes and human 

indicate that reversible lysine acetylation may represent an evolutionarily conserved mechanism of 

metabolic regulation in both eukaryotes and prokaryotes. (Science, 2010) 

In addition, Prof. Zhao’s group has sequenced the whole genome of Amycolatopsis mediterranei, an 

industrial microorganism for rifamycin production, and delineated the metabolic network related to the 

secondary antibiotic synthesis. Prof. WeiHong Jiang’s group has elucidated the molecular mechanism of a 

two-component regulatory system involved in antibiotic biosynthesis in Streptomyces coelicolor. Prof. 

Yang’s group combined a comparative genomic reconstruction of arabinose utilization regulons in nine 

Clostridium species with the detailed experimental characterization of arabinose pathways and regulatory 

mechanisms in Clostridium acetobutylicum. 

Industrial Microbial Industrial Biotechnology Biotechnology Research 

Clostridium acetobutylicum is an important industrial butanol-producing bacterium. Genetic modification 

of C. acetobutylicum, through metabolic engineering and synthetic biology method, for efficient butanol 

production from hydrolysates of different lignocellulosic materials (e.g. corn stover) and higher butanol 

selectivity has attracted increasing interests. The bio-butanol research group performed a series of research 

around these two aspects with a focus on: studying genetic, physiological and biochemical characteristics 

of C. acetobutylicum, developing new genetic tools, constructing engineered C. acetobutylicum strains 

with improved performance. 

C. acetobutylicum EA 2018 is a patent strain (patent number CN 1143677A) with high butanol-producing 

ability, which was previously obtained through butanol resistance screening by the bio-butanol research 

group. This Clostridium strain exhibits improved fermentative performance than the C. acetobutylicum 

model strain ATCC 824, such as higher butanol ratio, non-sporulation and enhancement of xylose 

utilization. Through cooperation with Chinese National Human Genome Center, the bio-butanol research 

group performed intensive molecular-level studies on this strain by using genome sequencing, comparative 

genomic and transcriptomic analysis, thus discovering and confirming molecular mechanisms underlying 

EA2018’s excellent characteristics. 

C. acetobutylicum normally produces, besides 60%-70% butanol, 20%-30% acetone and 10% ethanol as 

low-value byproducts among the fermentation products. 

Reconstruction and optimization of butanol-synthetic 

pathway in C. acetobutylicum is expected to decrease 

acetone and ethanol formation, and simultaneously, enhance 

butanol ratio without impacting solvents yield, thus 

increasing economical viability for bio-butanol production. 

The bio-butanol research group blocked the acetone 

formation by knockout of acetoacetate decarboxylase gene, 

which located in acetone-synthetic pathway, and then, by the 

following chemical mutagenesis, screening and fermentation 

conditions optimization, further increased the butanol ratio to 

over 85% among the total solvent products. 

Lignocellulose is the most abundant renewable resource in nature. However, C. acetobutylicum is not able 

to efficiently co-utilize mixed sugars in lignocellulosic hydrolysates because of the catabolite repression 

glucose exerts on pentose (xylose and arabinose) 

metabolism. The bio-butanol research group discovered 

Promoter 1 

Gene1 

gene2 

and identified genes responsible for key enzymes, 

gene3 

Promoter 2 

gene4 

xylose transporters and regulators involved in xylose 

gene5 

Titer (g/L) 

gene6 

Xylose pathway genes 

Butanol 

pathway through comparative transcriptomic analysis 

Xylose 

overexpression 

Arabinose Clostridium 

Acetone 

and genetic and biochemical analysis. On this basis, 

Ethanol 

they attenuated glucose phosphoenolpyruvate 

Glucose 

Time 

X 

dependent phosphotransferase system (PTS), 

confirmed and eliminated xylose pathway bottlenecks, 

X 

and gained Clostridium strains capable of efficiently 

Glucose PTS attenuation 

co-fermenting the mixture of glucose, xylose and 

arabinose, thus overcoming a technical bottleneck in 

the lignocellulose based butanol production. 

22 

23



Project Name Description Director 

Mechanisms of Plant Immunity and Practice of Molecular Design 

for Crop Disease Resistance /2011CB100700 

Molecular Regulatory Mechanisms of Endosperm Development 

and Accumulation of Storage Substances in Higher Plants 

/2012CB944800 

Artificial Biology Devices with Special Functions: Designing, 

Construction and Assembly /2012CB721100 

The System and Synthetic Biology Research of Microbial 

Metabolism/31121001 

G-protein Signaling in Plants / 30925005 

Projects 

There has been a steady increase in our research grants from both national and CAS programs.The funds of 

annual new scientific contracts reached RMB 100 million. Among the new scienfic programs, 64 were funded by 

the National Nature Science Foundation of China (NSFC), 3 programs and 13 sub-projects by the National Basic 

Reasearch Program, 8 by scientifc & technological programs of Shanghai. SIPPE also obstained 8 Innovation 

Direction Programs and 2 Province-Institutes Cooperation Programs from CAS, got 9 Competent Young Talents 

Program and a Chief Scientist Program from SIBS. The capacity of SIPPE on organization and commitment of 

importment national research tasks has been continually strengthened. 

973 Project ZuHua He 

973 Project HongWei Xue 

973 Project GuoPing Zhao 

Foundation for Creative 

Research Groups of NSFC 

Distinguished Young 

Investigator Foundation 

Distinguished Young 

Investigator Foundation 

GuoPing Zhao 

JiRong Huang 

Mechanisms of Insects Abnormal Development by the Coregulation 

of Juvenile Hormone and Molting Hormone 

ShengLi 

Silkworm as the Model for Researching Target Genes of 

YongPing 

Key project of NSFC 

Lepidopteran Pest Management /31030060 

Huang 

Mechanism of Fast-growing Fiber Ttimber Cultivating /31130012 Key project of NSFC LaiGengLi 

Mechanism of Rice Hybird Reproductive Isolation /31130071 Key project of NSFC HongXuan Lin 

Studies on the Function of Phosphatidylinositol(PI) Signaling Pathway in 

Regulation of Plant Growth and Development /31130060 

Key project of NSFC 


HongWei Xue 

Research Team Construction 

As usual, SIPPE pays a great attention to recruit the outstanding scientists. SIPPE takes a series of 

measures As usual, SIPPE to ensure pays the a great success attention of talents to recruit recruitment the outstanding subsequent scientists. SIPPE training. takes By a providing series of 

comprehensive measures to ensure facilities, the success the Institute of talents tries recruitment to ensure the and new subsequent PI focusing training. on their By providing own research comprehensive works. The 

Institute facilities, maintains SIPPE tries its to suitable ensure the systems new PIs and focusing culture on atmosphere their own to research inspire works. their SIPPE innovative maintains research its 

enthusiasms. 

suitable systems and culture atmosphere to inspire their innovative research enthusiasms. 

In the past two years, 125 staff including 7 principle investigators joined SIPPE. Of these, the remarkable 

achievements included that one PI won the national “Top One-Thousand-Talents Program” award and one 

for the “One-Thousand-Young-Talents Program” fund. In addition, one was elected as the member of 

Academy of Sciences of Developing Countries, one won the HLHL prize, two won the “National 

Outstanding Young Investigator Fund”, etc. 

Academician Prof. Guo-Ping Prof. Guo-Ping Zhao was Zhao elected was the Elected Member as of Academy the Member of Sciences of 

Academy of Sciences of Developing of Developing Countries Countries 

Dr. Guo-Ping Zhao was elected as the Member of Chinese Academy of Sciences (CAS) in 

2005 and the Member of the Academy of Sciences of Developing Countries (TWAS) in 

2011. He is the chairmen of academic committee in SIPPE, the Director of the Key 

Laboratory of Synthetic Biology, the chief scientists of MOST’s 973 program and the 

NSFC innovative research team. His lab is engaged in exploring the metabolism and 

physiological regulation of microbes, establishing the research system of synthetic biology 

by the combination of genomics, molecular genetics, proteomics and protein structural 

biology. More than 200 papers have been published by Prof. Zhao in the leading scientific journals 

including Nature, Science, PNAS, Genome Res, J Biol Chem, J Bacteriol, etc. He was also awarded the 

second prize of National Natural Science, the second prize of National Science and Technology Progress, 

HLHL award in Science and Technology and the first prize of Shanghai Natural Science. 

Academician Prof. Hong-Xuan Lin Won the HLHL Award 

Academician Prof. Hong-Xuan Lin Won the HLHL Award 

Dr. Hong-Xuan Lin joined SIPPE as a principle investigator in March, 2001. Eight years 

later, he was elected as the Member of Chinese Academy of Sciences in 2009. His group is 

studying the molecular mechanism of important and complicated agronomic traits and has 

made big progresses in the genetic mechanisms of rice yielding and abiotic stress, including 

salt resistance and drought tolerance. His lab cloned and functionally studied several key 

genes that regulate abiotic stress and yielding in rice. The discoveries made by Prof. Lin 

contribute to our understanding of molecular mechanisms of agronomic traits. Meanwhile, 

the important genes he found with independent intellectual properties were licensed for use for the crop 

molecular breeding. 

Distribution of New Grants (2010-2011) 

24 

2010-2011 New Contracted Funding Structure 

25


Promote the Construction of “Shanghai Center for Plant Stress 

Promote the Construction of Biology, “Shanghai CAS” Center for Plant Stress Biology, 

CAS” 

Outstanding Young Investigator from NSFC 

Following the scientific and technological development strategy, SIPPE 

explores the new mechanism for recruiting talented people. In 2010, Dr. 

Hong-Wei Xue, the director of SIPPE, and Dr. Xiao-Ya Chen, the director of 

SIBS wrote the letter together to sincerely invite Dr. Jian-Kang Zhu to return 

home from abroad to conduct research work in Shanghai. SIPPE and SIBS 

worked together to help Prof. Zhu successfully applied and won the support of 

“the One-Thousand-Outstanding-Talents Program”. In 2011, Prof. Jian-Kang 

Zhu started to set up the laboratory of plant stress biology at SIPPE. SIPPE will 

continue to help the construction of “Shanghai Center for Plant Stress Biology” in the future. 

Professor Jian-Kang Zhu received his Ph. D in plant physiology from the Purdue University in 1993 and 

became a professor in the Department of Plant Biology, University of Arizona in 2000. He has previously 

worked as the Director of the Institute for Integrative Genome Biology at University of California, 

Riverside, the Director of the Plant Stress Genomic and Technology Research Center, the Professor of 

Molecular Biology and Plant Physiology at KAUST, and the Jane S. Johnson Professor of Plant Biology at 

UC Riverside. From 2010 he serves as the distinguished professor in the Department of Horticulture and 

Landscape, Purdue University. He focuses on the research of abiotic stress biology, and has made 

tremendous contribution in the field of plant tolerance against salt, drought and cold. He has published 

more than 200 articles in top journals including Cell, Nature, Science, etc. , and has been recognized as 

the most cited plant scientist in the United States. In 2002, Professor JianKang Zhu was recognized as the 

Researcher of the Year in the College of Agriculture and Life Sciences at the University of Arizona and 

received the Charles Albert Shull Award from the American Society of Plant Biologists. In 2010, he was 

elected as the member of National Academy of Science (NAS) in USA. He is the third NAS member who 

finished his bachelor study in China mainland. 

Professor Ji-Rong Huang (2010) 

G-protein Signaling and 

Chloroplast Development 

One-Thousand-Young-Tanlents supported by the Central 

Organisation Department 

Professor Jia-Wei Wang (2011) 

Plant Small Regulatory RNAs 

One-Hundred-Talents supported by the Chinese Academy of Science 

Professor Han Xiao (2010) 

Fruit Developmental Biology 

Professor Yu-Da Fang (2010) 

Cell Biology of Plant 

Genome and Epigenome 

Professor Sheng Li (2010) 

Insect Development and 

Metamorphosis 

Professor Er-Jun Ling (2010) 

Insect Innate Immunology 

and Pest Control 

Professor Xuan Li (2010) 

Bioinformatics Research 

Professor Yong-Fei Wang (2011) 

Ion Channel and Signal 

Transduction in Plant Cells 

Professor Yang Zhao (2011) 

Chemical Genetics 

26 

27

2010-2011 Progress 


Cooperation and Extension 

SIPPE stays active in the international academic exchanges in 2010 and 2011, co-organized "The 2nd 

International Conference on Plant Metabolism" and other five influential international conferences. There 

were 169 overseas visits of our scientists and staff and 70 incoming visits of foreign scientists to our institute, 

including Dr. Dale Sanders, the 

director of John Innes Centre and the 

senior editor of Nature, Dr. Magdalena 

Skipper. The institute obtained two 

projects co-funded by the national 

natural science foundation (NSFC) 

and Dutch Organization for Scientific 

Research (NWO). 

APPENDIX 

The Huzhou biotechnology center, SIBS, constantly increased investment on equipments and had the productive 

capacity from test tubes to 2 tons fermentation tanks, those equipments could satisfy not only industrial technology 

research and development but also commercial production demand. In 2011, the center signed 7 new technology 

contracts, amount to RMB 4.3 million and put two new projects into operation. The Huzhou modern agricultural 

biotechnology innovation center, SIBS, signed 9 technology development contracts with Coca-Cola beverage (Shanghai) 

Co., Ltd., and involved in 8 projects from national and provincial sources. At present, these projects are progressing well. 

It is expected that after the transformation in 2012-2013, these projects would bring RMB 40 million for enterprise. The 

joint research centre of Zhejiang Academy of Agricultural Science and SIPPE was established in 2007, this centre made 

significant achievements in 2011 after several years’ collaboration. Both parties co-applied for the the National Plant 

Transgenic Program and also are applying for a prize of national Science from Shanghai. 

Through deepening cooperation with enterprise, the institute dramatically promotes transformation of the 

scientific research achievements. The project "Genetic Engineering and Industrialization Demonstration of 

Butanol Production Strains" cooperated with Songyuan Laihe chemicals Co., Ltd was supported by CAS- 

JiLin province foundation, and would achieve new production value RMB 80 million after the industrialization 

in 2012. The cooperation with ChangChun DaCheng fermentation technology development Co., Ltd, would 

increase the production of lysine to about 5000 tons, and bring direct economic benefits of RMB 75 million. 

The new sweet potato varieties "ThaiZhong No.9”, collaborated with the Institute of TaiAn Agricultural science 

research, was approved by Crop 

Variety Authorization Committee of 

Shandong Province (No. 2010041) 

and produced economic benefits of 

RMB 56.3 million. 

28 

29

Appendix 



Publication 

Publication 


1. Aileni M, Abbagani S, Zhang P*. (2011). Highly efficient production of transgenic Scoparia dulcis L. mediated by 

Agrobacterium tumefaciens: plant regeneration via shoot organogenesis. Plant Biotechnol Rep 5: 147-156. 

2. Bi HP, Aileni M, Zhang P*. (2010). Evaluation of cassava varieties for cassava mosaic disease resistance jointly by 

agro-inoculation screening and molecular markers. Afr J Plant Sci 4: 330-338. 

3. Bu Y, Yin WY*. (2010). The Protura from Liupan Mountain, northwest China. Acta Zootaxonomica Sinica 35: 

278-286. 

4. Bu Y, Yin WY*. (2010). Two new species of the genus Kenyentulus Tuxen, 1981 from Shaanxi Province, Northwest 

China (Protura: Berberentulidae). Acta Zoologica Cracoviensia 53B: 65-71. 

5. Chen AM, Wang YB, Sun J, Yu AY, Luo L, Yu GQ, Zhu JB, Wang YZ*. (2010). Identification of a TRAP transporter 

for malonate transport and its expression regulated by GtrA from Sinorhizobium meliloti. Res Microbiol 161: 556-564. 

6. Chen F, Gao MJ, Miao YS, Yuan YX, Wang MY, Li Q, Mao BZ, Jiang LW, He ZH*. (2010). Plasma membrane 

localization and potential endocytosis of constitutively expressed XA21 proteins in transgenic rice. Mol Plant 3: 

917-926. 

7. Chen FF, Lin L, Wang L, Tan Y, Zhou HX, Wang YG, Wang Y* and WQ He*. (2011). Distribution and diversity of 

glycosylated natural product genes in marine bacteria genomes. Appl Microbiol Biotechnol. 90: 1347-1359. 

8. Chen HY, Ying L, Jin J, Li Q, Cai WM*. (2010). Determining the transcriptional regulation pattern of PgTIP1 in 

transgenic Arabidopsis thaliana by constructing gene coexpression networks. Adv Bio Biotech 1: 384-390. 

9. Chen J, Wang P, Mi HL, Chen GY*, Xu DQ. (2010). Reversible association of ribulose-1, 5-bisphosphate 

carboxylase/oxygenase activase with the thylakoid membrane depends upon the ATP level and pH in rice without heat 

stress. J Exp Bot 61: 2930-2950. 

10. Chen WH and Qin ZJ*. (2011). Development of a gene cloning system in a fast-growing and moderately thermophilic 

Streptomyces species and heterologous expression of Streptomyces antibiotic biosynthetic gene clusters. BMC Microbiol. 

11: 243. 

11. Cheng YX, Zhou WB, El Sheery NI, Peters C, Li MY, Wang XM, Huang JR*. (2011). Characterization of the 

Arabidopsis glycerophosphodiester phosphodiesterase (GDPD) family reveals a role of the plastid-localized AtGDPD1 

in maintaining cellular phosphate homeostasis under phosphate starvation. Plant J 66: 781-795. 

12. Dai C, Xue HW*. (2010). Rice EARLY FLOWERING1, a CKI, phosphorylates DELLA protein SLR1 to negatively 

regulate GA signaling. EMBO J 29: 1916-1927. 

13. Dallai R, Mercati D, Bu Y, Yin WY*. (2010). Spermatogenesis and sperm structure of Acerella muscorum, (Ionescu, 

1930) (Hexapoda, Protura). Tissue and Cell 42: 97-104. 

14. Fang X, Yang CQ, Wei YK, Ma QX, Yang L, Chen XY*. (2011). Genomics grand for diversified plant secondary 

metabolites. Plant Diversity and Resources 33: 53-64. 

15. Fang YD, Spector DL. (2010). “Live Cell Imaging of Plants,” in Live Cell Imaging: A Laboratory Manual, 2th ed., 

Robert D. Goldman, Jason R. Swedlow, David L. Spector, Eds. New York: Cold Spring Harbor Laboratory Press 

pp.371-386. 

16. Fu FF, Xue HW*. (2010). Co-expression Analysis Identifies Rice Starch Regulator1 (RSR1), a rice AP2/EREBP family 

transcription factor, as a novel rice starch biosynthesis regulator. Plant Physiol 154: 927-938. 

17. Gao LL, Xue HW*. (2011). Global analysis of expression profiles of rice receptor-like kinase genes. Mol Plant 

doi:10.1093/mp/ssr062. 

18. Gao Q, Jin K, Ying SH, Zhang Y, Xiao G, Shang Y, Duan Z, Hu X, Xie XQ, Zhou G, Peng G, Luo Z, Huang W, Wang 

B, Fang W, Wang S, Zhong Y, Ma LJ, St Leger RJ, Zhao GP, Pei Y, Feng MG, Xia Y, Wang C*. (2011).Genome 

sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. 

acridum. PLoS Genet. 7: e1001264. 

19. Geng AL, He YL, Qian CL, Yan X, Zhou ZH*. (2010). Effect of key factors on hydrogen production from cellulose in a 

co-culture of Clostridium thermocellum and C. thermopalmarium. Bioresource Technol 101: 4029-4033. 

20. Gruntenko NЕ, Wen D, Karpova EK, Adonyeva NV, Liu Y, He Q, Faddeeva NV, Fomin AS, Li S*, Rauschenbach IY. 

(2010). Altered juvenile hormone metabolism, reproduction and stress resistance in Drosophila adults with genetic 

ablation of the corpus allatum cells. Insect Biochem Mol Biol 40: 891-897. 

21. Gu XL, Wang H, Huang H, Cui XF*. (2011). SPT6L encoding a putative WG/GW-repeat protein regulates apical-basal 

polarity of embryo in Arabidopsis. Mol Plant doi:10.1093/mp/ssr073. 

22. Gu Y, Ding Y, Ren C, Sun Z, Dmitry AR, Zhang WW, Yang S, Yang C*, Jiang WH*. (2010). Reconstruction of 

xylose utilization pathway and regulons in Firmicutes. BMC Genomics 11: 255-268. 



23. Gui JS, Shen JH, Li LG*. (2011). Functional characterization of evolutionarily divergent 4-coumarate: CoA ligases in 

rice. Plant Physiol 157: 574-586. 

24. Hao P, Zheng HJ, Yu Y, Ding GH, Gu WY, Chen ST, Yu ZH, Ren SX, Oda M, Konno T, Wang SY, Li X*, Ji ZS* and 

Zhao GP*. (2011). Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp. bulgaricus 

Reveal Its Genetic Basis for Industrial Yogurt Production. PLoS ONE. 6(1): e15964. 

25. Hao W, Lin HX*. (2010). Toward understanding genetic mechanisms of complex traits in rice. J Genet Genomics 37: 

1-14. 

26. He ZQ, Li K, Fang Y, Liu XW*. (2010). A taxonomic study of the genus Amusurgus Brunner von Wattenwyl from 

China (Orthoptera, Gryllidae, Trigonidiinae). Zootaxa 2423: 55-62. 

27. Horvath B, Peralta P, Peszlen I, Divos F, Kasal B, Li L*. (2010). Elastic modulus of transgenic aspen. Wood Research 

55: 1-10. 

28. Horvath B, Peszlen I, Peralta P, Horvath L, Kasal B, Li L*. (2010). Elastic modulus determination of transgenic aspen 

trees using a dynamic mechanical analyzer in static bending mode. Forest Products J 60: 296-300. 

29. Horvath B, Peszlen I, Peralta P, Kasal B, Li L*. (2010). Effect of lignin genetic modification on wood anatomy of aspen 

trees. IAWA J 31: 29-38. 

30. Hou S, Li LG*. (2011). Rapid characterization of woody biomass digestibility and chemical composition using 

near-infrared spectroscopy. J Integr Plant Biol 53: 166-175. 

31. Hu SY, Chen J, Yang ZY, Shao LJ, Bai H, Luo JL, Jiang WH, Yang YL*. (2010). Coupled bioconversion for 

preparation of N-acetyl-Dneuraminic acid using immobilized N-acetyl-D-glucosamine-2-epimerase and 

N-acetyl-Dneuraminic acid lyase. Appl Microbio Biotechnol 85: 1383-1391. 

32. Hu SY, Zheng HJ, Gu Y, Zhao JB, Zhang WW, Yang YL, Wang SY, Zhao GP, Yang S*, Jiang WH*. (2011). 

Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and 

xylose utilization in Clostridium acetobutylicum EA 2018. BMC Genomics 12: 93. 

33. Huang CW, Potapov M, Gao Y*. (2010). Taxonomy of the Proisotoma complex. III. A revision of the genus Narynia 

(Collembola: Isotomidae) with a description of a new species from China. Zootaxa 2410: 45-52. 

34. Huang W, Bi T, Sun W*. (2010). Comparative analysis of panicle proteomes of two upland rice varieties upon 

hyper-osmotic stress. Front Biol 5: 546-555. 

35. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang 

L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q, Li J, 

Han B*. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genet 42: 961-967. 

36. Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, Li W, Guo Y, Deng L, Zhu C, Fan D, Lu Y, Weng Q, Liu K, Zhou T, 

Jing Y, Si L, Dong G, Huang T, Lu T, Feng Q, Qian Q, Li J, Han B*. (2011). Genome-wide association study of 

flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32-39. 

37. Huang Y, Zong WM, Yang X, Wang RF, Hemme CL, Zhou JZ, Zhou ZH*. (2010) Succession of the bacterial 

community and dynamics of hydrogen producers in a hydrogen-producing bioreactor. Appl Environ Microbiol 76: 

3387-3390. 

38. Huang, J., Tian, L., Abdou, M., Wen, D., Wang, Y., Li, S.*, Wang, J. (2011). DPP-mediated TGF-β signaling regulates 

juvenile hormone biosynthesis by upregulating expression of JH acid methyltransferase. Development. 138:2283-91. 

39. Hwang JU, Wu G, Yan A, Lee YJ, Grierson CS, Yang ZB*. (2010). Pollen-tube tip growth requires a balance of lateral 

propagation and global inhibition of Rho-family GTPase activity. J Cell Sci 123: 340-350. 

40. Khalid KA, Teixeira da Silva JA, Cai WM*. (2010). Water deficit and polyethylene glycol 6000 affects morphological 

and biochemical characters of Pelargonium odoratissimum (L.). Scientia Horticulturae 125: 159-166. 

41. Li J, Zhao LJ, Zhao M, Yang YL, Zhang WW, Yang S*. (2010). Screening and characterization of butanol tolerant 

microorganisms. Lett Appl Microbiol 50: 373-379. 

42. Li JY, Gong JM*. (2010). Nitrate signal sensing and transduction in higher plants. J Plant Physiol 47: 111-118. 

43. Li JY, Fu YL, Pike SM, Bao J, Tian W, Zhang Y, Chen CZ, Zhang Y, Li HM, Huang J, Li LG, Schroeder JI, Gassmann 

W, Gong JM*. (2010). The Arabidopsis nitrate transporter NRT1.8 functions in nitrate removal from the xylem sap and 

mediates cadmium tolerance. Plant Cell 22: 1633-1646. 

44. Li K, He ZQ, Liu XW*. (2010). A taxonomic study of the genus Metiochodes Chopard from China (Orthoptera, 

Gryllidae, Trigonidiinae). Zootaxa 2506: 43-50. 

45. Li K, He ZQ, Liu XW*. (2010). Four new species of Nemobiinae from China (Orthoptera, Gryllidae, Nemobiinae). 

Zootaxa 2540: 59-64. 

46. Li L, Shi ZY, Li L, Shen GZ, Wang XQ, An LS, Zhang JL*. (2010). Over-expression of ACL1 (abaxially curled leaf) 

increased bulliform cells and induced abaxial curling of leaf blade in rice. Mol Plant 3: 807-817. 

47. Li P, Julia JW, Shi XL, Zhang HL, Johannes H, Sjef CS, and Teng S*. (2011). Fructose sensitivity is suppressed in 

Arabidopsis by the transcription factor ANAC089 lacking the membrane-bound domain. Proc Natl Acad Sci U S A. 

108:3436-41. 

30 

1 

2 

31

Appendix 






48. Li S*. (2010). Identification of iron-loaded ferritin as an essential mitogen for cell proliferation and postembryonic 

development in Drosophila. Cell Res. 20: 1148-1157. 

49. Li TX, Zhang Y, Liu H, Wu YT, Zhang HX*. (2010). Stable expression of Arabidopsis vacuolar Na + /H + antiporter gene 

AtNHX1, and its salt tolerance in the transgenic soybean for over six generations. Chinese Sci Bull 55: 1127-1134. 

50. Li W, Zhong SH, Li GJ, Li Q, Mao BZ, Deng YW, Zhang HJ, Zeng LJ, Song FM, He ZH*. (2011). Rice RING protein 

OsBBI1 with E3 ligase activity confers broad-spectrum resistance against Magnaporthe oryzae by modifying the cell 

wall defence. Cell Res 21: 835-848. 

51. Li XF, Liu T, Wu YQ, Zhao GP, Zhou ZH*. (2010). Derepressive effect of NH 4 + on hydrogen production by deleting 

the glnA1 gene in Rhodobacter sphaeroides. Biotechnol and Bioen 106: 564-572. 

52. Lin GF, Du H, Chen JG, Lu HC, Guo WC, Golka K, Shen JH*. (2010). Association of XPD/ERCC2 G 23591 A and 

A 35931 C polymorphisms with skin lesion prevalence in a multiethnic, arseniasis-hyperendemic village exposed to indoor 

combustion of high arsenic coal. Arch Toxicol 84: 17-24. 

53. Lin GF, Meng H, Du H, Lu HC, Zhou YS, Chen JG, Golka K, Lu JC, Shen JH*. (2010). Factors impacting on the 

excess arseniasis prevalence due to indoor combustion of high arsenic coal in a hyperendemic village. Int Arch Occup 

Environ Health 83: 433-440. 

54. Liu H, Tang RJ, Zhang Y, Wang CT, Lv QD, Gao XS, Li WB, Zhang HX*. (2010). AtNHX3 is a vacuolar K + /H + 

antiporter required for low-potassium tolerance in Arabidopsis thaliana. Plant Cell Environ 33: 1989-1999. 

55. Liu J, Zheng QJ, Ma QX, Gadidasu KK, Zhang P*. (2011). Cassava genetic transformation and its application in 

breeding. J Integr Plant Biol 53: 552-569. 

56. Liu Q, Shi LL, Fang YD*. (2011). Dicing Bodies. Plant Physiol doi:10.1104/pp.111.186734. 

57. Liu Q, Xu C, Wen CK*. (2010). Genetic and transformation studies reveal negative regulation of ERS1 ethylene 

receptor signaling in Arabidopsis. BMC Plant Biol 10: 60-73. 

58. Liu T, Li XF, Zhou ZH*. (2010). Improvement of hydrogen yield by hupr gene knock-out and nifa gene overexpression 

in Rhodobacter sphaeroides 6016. Int J. Hydrogen Energy. 35: 9603-9610. 

59. Liu W, Luo L, Sun J, Cao LP, Yu GQ, Zhu JB, Wang YZ*. (2010). Characterization and expression analysis of 

Medicago truncatula ROP GTPase family during the early stage of symbiosis. J Integr Plant Biol 52: 639-652. 

60. Liu Y, Zhou S, Ma L, Tian L, Wang S, Sheng Z, Jiang R-J, Bendena WG, Li S*. (2010). Transcriptional regulation of 

the insulin signaling pathway genes by starvation and 20-hydroxyecdysone in the Bombyx fat body. J Insect Physiol 56: 

1436-1444. 

61. Liu ZY, Jia LG, Mao YF, He YK*. (2010). Classification and quantification of leaf curvature. J Exp Bot 61: 2757-2767. 

62. Liu ZY, Jia LG, Wang H, He YK*. (2011). HYL1 regulates the balance between adaxial and abaxial identity for leaf 

flattening via miRNA-mediated pathways. J Exp Bot 62: 4367-4381. 

63. Long YH, Xie L, Liu N, Yan X, Fan MZ, Wang Q*. (2010). Comparison of gut-associated and nest-associated 

microbial communities of a fungus-growing termite (Odontotermes yunnanensis). Insect science 17: 265-276. 

64. Lu LD, Sun Q, Fan XY, Zhong Y, Yao YF*, Zhao GP*. (2010). Mycobacterial MazG is a novel NTP 

pyrophosphohydrolase involved in oxidative stress response. J Biol Chem 285: 28076-28085. 

65. Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Li W, Huang X, Han B*. (2010). Function 

annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res 20: 1238-1249. 

66. Lu YH, He JM, Zhu H, Yu ZY, Wang R, Chen YL, Dang FJ, Zhang WW, Yang S, and Jiang WH*. (2011). An Orphan 

Histidine Kinase, OhkA, Regulates Both Secondary Metabolism and Morphological Differentiation in Streptomyces 

coelicolor. J. Bacteriol. 193: 3020-3032. 

67. Lu ZQ, Xie PF, Qin ZJ*. (2010). Promotion of markerless deletion of the actinorhodin biosynthetic gene cluster in 

Streptomyces coelicolor. Acta Biochimica et Biophysica Sinica 42: 717-721. 

68. Ma L, Xu HF, Zhu JQ, Ma SY, Liu Y, Jiang RJ, Xia QY and Li S*. (2011). Ras1 CA overexpression in the posterior silk 

gland improves silk yield. Cell Res. 21:934-43. 

69. Ma L, Jun Z, Zou G, Wang CS, Zhou ZH*. (2011). Improvement of cellulase activity in Trichoderma reesei by 

heterologous expression of a beta-glucosidase gene from Penicillium decumbens. Enzyme Microb. Technol. 49: 

366-371. 

70. Mao YB, Tao XY, Xue XY, Wang LJ, Chen XY*. (2011). Cotton plants expressing CYP6AE14 double-stranded RNA 

show enhanced resistance to bollworms. Transgenic Res 20: 665-673. 

71. Mei Y, Jia WJ, Chu YJ, Xue HW*. (2011). Arabidopsis PIPK2 is involved in root gravitropism through regulating auxin 

polar transport by affecting the cycling of PIN proteins. Cell Res doi:10.1038/cr.2011. 

72. Peng Z, Lu T, Li L, Liu X, Gao Z, Hu T, Yang X, Feng Q, Guan J, Weng Q, Fan D, Zhu C, Lu Y, Han B*, Jiang Z*. 

(2010). Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA 

sequences. BMC Plant Biol 10: 116. 

73. Potapov MB, Bu Y, Huang CW, Gao Y, Luan YX*. (2010). Generic switch-over during ontogenesis in 

Dimorphacanthella gen. n. (Collembola, Isotomidae) with barcoding evidence. Zookeys 73: 13-23. 

74. Qin Y, Yang ZB*. (2011). Rapid tip growth: Insights from pollen tubes. Semin Cell Dev Biol 22: 816-824. 

75. Rao XJ*, Ling EJ*, Yu XQ. (2010) The role of lysozyme in the prophenoloxidase activation system of Manduca sexta: 

An in vitro approach. Dev & Comp Immunol 34: 264-271. 

76. Ren C, Gu Y, Hu SY, Wu Y, Wang P, Yang YL, Yang C, Yang S*, Jiang WH*. (2010). Identification and inactivation 

of pleiotropic regulator CcpA to eliminate glucose repression of xylose utilization in Clostridium acetobutylicum. Metab 

Eng 12: 446-454. 

77. Shangguan XX, Yu N, Wang LJ, Chen XY*. (2010). Recent advances in molecular biology research on cotton fiber 

development. Cotton, Biotechnology in Agriculture and Forestry 65: 161-175. 

78. Shi LL, Fang YD*. (2011). Histone variants: making structurally and functionally divergent nucleosomes and linkers in 

chromatin. Front Biol 6: 93-101. 

79. Shi LL, Wang J, Hong F, Spector DL, Fang YD*. (2011). Four amino acids guide the assembly or disassembly of 

Arabidopsis histone H3.3-containing nucleosomes. P Natl Acad Sci USA 108: 10574-10578. 

80. Shi QM, Yang X, Song L, Xue HW*. (2011). Arabidopsis MSBP1 is activated by HY5 and HYH and is involved in 

photomorphogenesis and brassinosteroid sensitivity regulation. Mol Plant 4: 1092-1104. 

81. Song DL, Shen JH, Li L*. (2010) Characterization of cellulose synthase complexes in Populus xylem differentiation. 

New Phytologist 187: 777-790. 

82. Song DL, Xi W, Shen JH, Bi T, Li LG*. (2011). Characterization of the plasma membrane proteins and receptor-like 

kinases associated with secondary vascular differentiation in poplar. Plant Mol Biol 76: 97-115. 

83. Sun CB, Du XM, He YK*. (2010). A novel method for constructing pathogen-regulated small RNA cDNA library. 

Biochem Bioph Res Co 397: 532-536. 

84. Sun Q, Xiao W, Xin D, Shi JP, Yan X, Zhou ZH*. (2010). Statistical optimization of process parameters on 

biohydrogen production from sucrose by co-culture of Clostridium acidisoli sp. Nov and Rhodobacter sphaeroides. Int J. 

Hydrogen Energy. 35: 4076-4084. 

85. Tang RJ, Liu H, Bao Y, Lv QD, Yang L, Zhang HX*. (2010). The woody plant poplar has a functionally conserved 

salt overly sensitive pathway in response to salinity stress. Plant Mol Biol 74: 367-380. 

86. Tang X, Zhang ZY, Zhang WJ, Zhao XM, Li X, Zhang D, Liu QQ, Tang WH*. (2010). Global gene profiling of 

laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis. Plant 

Physiol 154: 1855-1870. 

87. Tao YZ, Liu D, Yan X, Zhou ZH, Jeong KL, and Yang C*. (2011). Network identification and flux quantification of 

glucose metabolism in Rhodobacter sphaeroides under photoheterotrophic H 2 -producing conditions. J. Bacteriol. 

Accepted. 

88. Tian L, Guo E, Diao Y, Wang S, Liu S, Cao Y, Jiang R-J, Ling E, Li S*. (2010). Developmental regulation of 

glycolysis by 20-hydroxyecdysone and juvenile hormone in fat body tissues of the silkworm, Bombyx mori. J Mol Cell 

Biol 2: 255-263. 

89. Tian L, Guo E, Diao Y, Zhou S, Peng Q, Cao Y, Ling E, Li S*. (2010). Genome-wide regulation of innate immunity by 

juvenile hormone and 20-hydroxyecdysone in the Bombyx fat body. BMC Genomics 11: 549. 

90. Wang CL, Wang ZX, Ling QZ, Kariuki MM, Kiguchi K, Ling EJ*. (2010). Physiological functions of hemocytes 

newly emerged from the cultured hematopoietic organs in the silkworm, Bombyx mori. Insect Science 17: 7-20. 

91. Wang CT, Liu H, Gao XS, Zhang HX*. (2010). Overexpression of G10H and ORCA3 in the hairy roots of 

Catharanthus roseus improves catharanthine production of Catharanthus roseus improves catharanthine production. 

Plant Cell Rep 29: 887-894. 

92. Wang ET, Xu X, Zhang L, Zhang H, Lin L, Wang Q, Li Q, Ge S, Lu BR, Wang W, He ZH*. (2010). Duplication and 

independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC 

Evol Biol 10: 108-120. 

93. Wang HH, Wang CT, Liu H, Tang RJ, Zhang HX*. (2011). An efficient Agrobacterium-mediated transformation and 

regeneration system for leaf explants of two elite aspen hybrid clones Populus alba × P. Berolinensis and Populus 

Davidiana×P. Bolleana. Plant Cell Rep 30: 2037-2044. 

94. Wang J, Gao XY, Shi XY, Zhang JL, Shi ZY*. (2010). Over expression of ta-siR2141 in rice resulted in adaxialization 

and disturbed vascular bundle development. J Exp Bot 61: 1885-1895. 

95. Wang J, Wang Y, Luo D*. (2011). LjCYC genes constitute floral dorsoventral asymmetry in Lotus japonicus. J Integr 

Plant Biol 52: 959-970. 

96. Wang K, Xiang XH, He F, Lin LB, Zhang R, Ping XJ, Han JS, Guo N, Zhang QH, Cui CL, Zhao GP*. (2010). 

Transcriptome profiling analysis reveals region-distinctive changes of gene expression in the CNS in response to 

different moderate restraint stress. J Neurochem 113: 1436-1446. 

32 

3 

4 

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Appendix 






97. Wang L, Gu XL, Xu DY, Wang W, Wang H, Zeng MH, ZhaoY, Huang H, Cui XF*. (2010). miR396-targeted AtGRF 

transcription factors are required for coordination of cell division and differentiation during leaf development in 

Arabidopsis. J Exp Bot 62: 761-773. 

98. Wang L, Li XR, Lian H, Ni DA, He YK, Chen XY, Ruan YL*. (2010). Evidence that high activity of vacuolar 

invertase is required for cotton fiber and Arabidopsis root elongation through osmotic dependent and independent 

pathway, respectively. Plant Physiol 154: 744-756. 

99. Wang L, Yu X, Wang H, Lu YZ, de Ruiter M, Prins M, He YK*. (2011). A novel class of heat-responsive small RNAs 

derived from the chloroplast genome of Chinese cabbage (Brassica rapa). BMC Genomics 12: 289-302. 

100. Wang QJ, Zhang YK, Yang C, Xiong H, Lin Y, Yao J, Li H, Xie L, Zhao W, Yao YF, Ning ZB, Zeng R, Xiong Y, 

Guan KL, Zhao SM and Zhao GP*. (2010). Acetylation of metabolic enzymes coordinates carbon source utilization 

and metabolic flux. Science. 327: 1004-1007. 

101. Wang S, Liu S, Liu H, Wang J, Zhou S, Liu Y, Jiang R-J, Bendena WG, Li S*. (2010). The insect steroid hormone 

20-hydroxyecdysone reduces food consumption resulting in fat body lipolysis during molting and pupation. J Mol Cell 

Biol 2: 128-138. 

102. Wang W, Xu B, Wang H, Li JQ, Huang H, Xu L*. (2010). YUCCA genes are expressed in response to leaf 

adaxial-abaxial juxtaposition and are required for leaf margin development. Plant Physiol 157: 1805-1819. 

103. Wang Y, Xu J, Shen J, Luo Y, Scheu S, Ke X*. (2010). Tillage, residue burning and crop rotation alter soil fungal 

community and water-stable aggregation in arable fields. Soil & Tillage Research 107: 71-79. 

104. Wang YW, Xu J, Chen AM, Wang YZ, Zhu JB, Yu GQ, Xu L, Luo L*.(2010). GGDEF and EAL proteins play 

different roles in the control of Sinorhizobium meliloti growth, motility, exopolysaccharide production, and competitive 

nodulation on host alfalfa. Acta Bioch Bioph Sin 42: 410-417. 

105. Wei JL, Xu M, Zhang DB*, Mi HL*. (2010). The role of carotenoid isomerase in maintenance of photosynthetic 

oxygen evolution in rice plant. Acta Biochim Biophys Sin 42: 457-463. 

106. Wei N, Tan C, Qi B, Zhang Y, Xu G, Zheng HQ*. (2010). Changes in gravitational forces induce the modification of 

Arabidopsis thaliana silique pedicel positioning. J Exp Bot 61: 3874-3884. 

107. Wei WQ, Liu FQ, Liu L, Li ZF, Zhang XY, Jiang F, Shi Q, Zhou XY, Sheng WQ, Cai SJ, Li X*, Xu Y*, Nan P*. 

(2011). Distinct mutations in MLH1 and MSH2 genes in hereditary non-polyposis colorectal cancer (HNPCC) families 

from China. BMB Rep. 44: 317-322. 

108. Shao W, Kim HS, Cao Y, Xu YZ*, and Query CC*. (2012). A U1–U2 snRNP interaction network during intron 

definition. Mol Cell Biol. 32:470-8. 

109. Weng L, Tian Z, Feng X, Li X, Xu S, Hu X, Luo D*, Yang J*. (2011). Petal development in Lotus japonicus. J Integr 

Plant Biol 53: 770-782. 

110. Wu GZ, Xue HW*. (2010). Arabidopsis β-ketoacyl-[acyl carrier protein] synthase I (KASI) is crucial for fatty acid 

synthesis and plays a role in chloroplast division and embryo development. Plant Cell 22: 3726-3744. 

111. Wu S, Zhang XF, Chen XM, Cao PS, Ling EJ*. (2010). BmToll9, an Arthropods conservative Toll, is probably 

involved in the local gut immune response in the silkworm, Bombyx mori. Dev & Comp Immunol 34: 93-96. 

112. Wu S, Zhang XF, He YQ, Shuai JB, Chen XM, Ling EJ*. (2010) Expression of antimicrobial peptide genes in Bombyx 

mori gut modulated by oral bacterial infection and development. Dev & Comp Immunol 34: 1191-1198. 

113. Wu WJ, Elsheery N, Wei Q, Zhang LG, Huang JR*. (2011). Defective etioplasts observed in variegation mutants may 

reveal the light-independent regulation of white/yellow sectors of Arabidopsis leaves. J Integr Plant Biol 53: 846-857. 

114. Wu Y, Zheng F, Ma W, Han Z, Gu Q, Shen Y, Mi HL*. (2011). Regulation of NAD(P)H dehydrogenase-dependent 

cyclic electron transport around photosystem I by NaHSO3 at low concentrations in tobacco chloroplasts. Plant Cell 

Physiol 52: 1734-1743. 

115. Xiao H, Gu Y, Ning YY, Yang YL, Wilfrid JM, Yang S*, and Jiang WH*. (2011). Confirmation and Elimination of 

Xylose Metabolism Bottlenecks in Glucose Phosphoenolpyruvate-Dependent Phosphotransferase System-Deficient 

Clostridium acetobutylicum for Simultaneous Utilization of Glucose, Xylose, and Arabinose. Appl Environ Microbiol. 

77: 7886-7895. 

116. Xiong CH, Xia YL, Zheng P, Shi SH, Wang CS*. (2010). Developmental stage-specific gene expression profiling for a 

medicinal fungus Cordyceps militaris. Mycology 1: 25-66. 

117. Xu DY, Huang WH, Li Y, Wang H, Huang H, Cui XF*. (2011). Elongator complex is critical for cell cycle progression 

and leaf patterning in Arabidopsis. Plant J doi:10.1111/j.1365-313X.2011.04831.x. 

118. Xu J, Aileni M, Abbagani S, Zhang P*. (2010). A reliable and efficient method for total RNA isolation from various 

members of spurge family (Euphorbiaceae). Phytochem Anal 21: 395-398. 

119. Xu J, Zhao Q, Du P, Xu C, Wang B, Feng Q, Liu Q, Tang S, Gu M, Han B*, Liang G*. (2010). Developing high 

throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice 

(Oryza sativa L.). BMC Genomics 11: 656. 

120. Xu T, Ping J, Yu Y, Yu FD, Yu YT, Hao P*, Li X*. (2010). Revealing parasite influence in metabolic pathways in 

Apicomplexa infected patients. BMC Bioinformatics 11(Suppl 11): S13. 

121. Yan J, Cai XF, Luo JH, Sato S, Jiang QY, Yang J, Cao XL, Hu XH, Tabata S, Gresshoff PM, Luo D*. (2010). The 

REDUCED LEAFLET genes encode key components of the trans-acting small interfering rna pathway and regulate 

compound leaf and flower development in Lotus japonicus. Plant Physiol 152: 797-807. 

122. Yang CQ, Lu S, Mao YB, Wang LJ, Chen XY*. (2010). Characterization of two NADPH: Cytochrome P450 

reductases from cotton (Gossypium hirsutum). Phytochemistry 71: 27-35. 

123. Yang J, An D, Zhang P*. (2011). Expression profiling of cassava storage roots reveals an active process of 

glycolysis/gluconeogenesis. J Integr Plant Biol 53: 193-211. 

124. Yang J, Bi HP, Fan WJ, Zhang M, Wang HX, Zhang P*. (2011). Efficient embryogenic suspension culturing and rapid 

transformation of a range of elite genotypes of sweet potato (Ipomoea batatas [L.] Lam.). Plant Sci 181: 701-711. 

125. Yang JW, Xu J, Chen XY, Zhang YX, Jiang XC, Guo XK, Zhao GP*. (2010). Decrease of plasma platelet-activating 

factor acetylhydrolase activity in lipopolysaccharide induced mongolian gerbil sepsis model. PLoS ONE 5(2): e9190. 

126. Yang WB, Ren SL, Zhang XM, Gao MJ, Ye SH, Qi YB, Zheng YY, Zeng LJ, Li Q, Huang SJ, He ZH*. (2011). 

UPPERMOST INTERNODE1 encodes a class II formin FH5 crucial for actin organization and rice development. Plant 

Cell 23: 661-680. 

127. Yang X, Yang YN, Xue LJ, Zou MJ, Liu JJ, Chen F, Xue HW*. (2011). Rice ABI5-like1 regulates ABA and auxin 

responses by affecting the expression of ABRE-containing genes. Plant Physiol 156: 1397-1409. 

128. Zhong Yi, Chang Xiao, Cao Xingjun, Zhang Yan, Zheng Huajun, Zhu Yongzhang, Cai Chengsong, Cui Zelin, Zhang 

Yunyi, Li Yuanyuan, Zhao Guoping, Wang Shengyue*, Li Yixue*, Zeng Rong*, Li Xuan*, Guo Xiaokui* .(2011). 

Comparative Proteogenomic Analysis of the Leptospira interrogans Virulence Attenuated Strain IPAV against the 

Pathogenic Strain 56601. Cell Res. 21:1210-1229. 

129. Yao HY, Xue HW*. (2011). Invited review: Signals and mechanisms affecting vesicular trafficking during root 

growth. Curr Opin Plant Biol 14: 1-9. 

130. Yu N, Cai WJ, Wang SC, Shan CM, Wang LJ, Chen XY*. (2010). Temporal control of trichome distribution by 

miR156-targeted SPL genes in Arabidopsis thaliana. Plant Cell 22: 2322-2335. 

131. Yu X, Wang H , Lu YZ, de Ruiter M, Cariaso M, Prins M, van Tunen A, He YK*. (2011). Identification of conserved 

and novel miRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot doi:10.1093/jxb/err337. 

132. Yu Y, Xu T, Yu YT, Hao P*, Li X*. (2010). Association of tissue lineage and gene expression: conservatively and 

differentially expressed genes define common and special functions of tissues. BMC Bioinformatics 11(Suppl 11): S1. 

133. Yuan ZH, Luo DX, Li G, Yao XZ, Wang H, Zeng MH, Huang H, Cui XF*. (2010). Characterization of the AE7 gene 

in Arabidopsis suggests that normal cell proliferation is essential for leaf polarity establishment. Plant J 64: 331-342. 

134. Wang YB, Zhang H, Li H, Miao XX*. Second-Generation Sequencing Supply an Effective Way to Screen RNAi 

Targets in Large Scale for Potential Application in Pest Insect Control. PLoS One. 2011 6: e18644. 

135. Zang AP, Xue XJ, Neill S, Cai WM*. (2010). Overexpression of OsRAN2 in rice and Arabidopsis renders transgenic 

plants hypersensitive to salinity and osmotic stress. J Exp Bot 61: 777-789. 

136. Zhang DL, Zhu FY, Fan WC, Tao RZ, Yu H, Yang YL, Jiang WH, Yang S*. (2011). Gradually accumulating 

beneficial mutations to improve the thermostability of N-carbamoyl-D: -amino acid amidohydrolase by step-wise 

evolution. Appl Microbiol Biotechnol. 90: 1361-1371. 

137. Zhan S, Guo QH, Li MH, Li MW, Li JY, Miao XX, Huang YP*. (2010). Deletion of an N-acetyltransferase gene of 

silkworm confers the new black pattern in insects. Development 137: 4083-4090. 

138. Zhang J, Wei YJ, Xiao W, Zhou ZH, Yan X*. (2011). Performance and spatial community succession of an anaerobic 

baffled reactor treating acetone–butanol–ethanol fermentation wastewater. Bioresour Technol. 102: 7407–7414. 

139. Zhang L, Wang L, Wang J, Ou XJ, Zhao GP*, Ding XM*. (2010). DNA cleavage is independent of synapsis during 

Streptomyces phage BT1 integrase-mediated site-specific recombination. J Mol Cell Biol 2: 264-275. 

140. Zhang M, Li G., Huang W, Bi T, Tang Z, Su W, Sun W*. (2010). Proteomic study of Carissa spinarum in response to 

combined heat and drought stress. Proteomics 10: 3117-3129. 

141. Zhang M, Lü S, Li G, Mao Z, Yu X, Sun W, Tang Z, Long M*, Su W*. (2010). Identification of a residue in helix 2 of 

rice plasma membrane intrinsic proteins that influences water permeability. J Biol Chem 285: 41982-4199. 

142. Zhang P*, Wang WQ, Zhang GL, Kaminek M, Dobrev P, Xu J, Gruissem W. (2010). Senescence-inducible expression 

of isopentenyl transferase extends leaf life, increases drought stress resistance and alters cytokinin metabolism in 

cassava. J Integr Plant Biol 52: 653-669. 

143. Zhang R, Peng SY, Qin ZJ. (2010). Two Internal Origins of Replication on Streptomyces Linear Plasmid pFRL1. 

Applied and Environmental Microbiology 76: 5676-5683. 

144. Zhang W, Hu WL, Wen CK*. (2010). Ethylene preparation and its application to physiological experiments. Plant 

Signal Behav 5: 453-457. 

34 

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145. Zhang W, Wen CK*. (2010). Preparation of ethylene gas and comparison of ethylene responses induced by ethylene, 

ACC, and ethephon. Plant Physiol Bioch 48: 45-53. 

146. Zhang YY, Zhang BC, Yan DW, Dong WX, Yang WB, Li Q, Zeng LJ, Wang JJ, Wang LY, Hicks LM, He ZH*. 

(2011). Two Arabidopsis cytochrome P450 monooxygenases CYP714A1 and CYP714A2 function redundantly in plant 

development through gibberellin deactivation. Plant J 67: 342-353. 

147. Zhang ZZ, Wang H, Luo DX, Zeng MH, Huang H, Cui XF*. (2010). Convergence of the 26S proteasome and the 

REVOLUTA pathways in regulating inflorescence and floral meristem functions in Arabidopsis. J Exp Bot 62: 359-369. 

148. Zhao Q, Huang X, Lin Z, Han B*. (2010). SEG-Map: A novel software for genotype calling and genetic map 

construction from next-generation sequencing. Rice 3: 98-102. 

149. Zhao SQ, Hu J, Guo LB, Qian Q, Xue HW*. (2010). Rice leaf inclination 2 (LC2), a VIN3-like protein, regulates leaf 

angle through modulating cell division of the collar. Cell Res 20: 935-947. 

150. Zhao SS, Dufour D, Sánchez T, Ceballos H, Zhang P*. (2011). Development of waxy cassava with different biological 

and physico-chemical characteristics of starches for industrial applications. Biotechnol Bioeng 108: 1925-1935. 

151. Zhao W, Zhong Y, Yuan H, Wang J, Zheng HJ, Wang Y, Cen XF, Xu F, Bai J, Han XB, Lu G, Zhu YQ, Shao ZH, Yan 

H, Li C, Peng NQ, Zhang ZL, Zhang YY, Lin W, Fan Y, Qin ZJ, Hu YF, Zhu BL, Wang SY*, Ding XM*, Zhao GP*. 

(2010). Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its 

genetic characteristics in phylogeny and metabolism. Cell Research 20: 1096-1108. 

152. Zhao XL, Shi ZY, Peng LT, Shen GZ, Zhang JL*. (2011). An atypical HLH protein OsLF protein participates in 

regulating flowering time through interacting with OsPIL13 and OsPIL15 in rice. New Biotech 28: 788-797. 

153. Zheng HQ*, L. Andrew S. (2011). L Andrew Staehelin. Protein storage vacuoles are transformed into lytic vacuoles in 

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154. Zheng P, Xia YL, Xiao GH, Xiong CH, Hu X, Zhang SW, Zheng HJ, Huang Y, Zhou Y, Wang SY, Zhao GP, Liu XZ, 

Raymond J SL and Wang CS*. (2011). Genome sequence of the insect pathogenic fungus Cordyceps militaris, a 

valued traditional Chinese medicine. Genome Biol. 12(11):R116. 

155. Zhong L, Cheng QX, Tian XL, Zhao LiQ, Qin ZJ*. (2010). Characterization of the Replication, Transfer and 

Plasmid/Lytic Phage Cycle of the Streptomyces Plasmid-Phage pZL12. Journal of Bacteriology 192: 3747-3754. 

156. Zhou B, Yang XN, Jiang JH, Wang YB, Li MH, Li MW, Miao XX, Huang YP*. (2010). Silkworm (Bombyx mori) 

BmLid is a more prevalent histone lysine demethylase than its homologues in drosophila and mammals. Cell Research 

20: 1079-1082. 

157. Zhou M*, Bi WX, Liu XW. (2010). The genus Conocephalus (Orthoptera, Tettigonioidea) in China. Zootaxa 2527: 

49-60. 

158. Zhou S, Zhou Q, Liu Y, Wang S, Wen D, He Q, Wang W, Bendena WG, Li S*. (2010). Two Tor genes in the silkworm, 

Bombyx mori. Insect Mol Biol 19: 727-735. 

159. Sun ZT, Ning YY, Liu LX, Liu YM, Sun BB, Jiang WH, Yang C, Yang S*. (2011). Metabolic engineering of the 

L-phenylalanine pathway in Escherichia coli for the production of S- or R-mandelic acid. Microb Cell Fact. 13: 10-71. 

160. Zhu L, Tao RS, Wang Y, Jiang Y, Lin X, Yang YL, Zheng HB, Jiang WH, Yang S*. (2011). Removal of L: -alanine 

from the production of L: -2-aminobutyric acid by introduction of alanine racemase and D: -amino acid oxidase. Appl 

Microbiol Biotechnol. 90:903-910. 

161. Zhu Q, Zhang JT, Gao XS, Tong JH, Xiao LT, Li WB, Zhang HX*. (2010). The Arabidopsis AP2/ERF transcription 

factor R AP2.6 participates in ABA, salt and osmotic stress responses. Gene 457:1-12 

2010-2011 Major Event 

Year 2010 

1.19 The Advisory Committee of "Molecular Mechanism of Plant 

Hormone", funded by Key Project of Major Resarch Plan from NSFC, 

visited SIPPE twice in January. 

2.7 A Forum for "Mechanism of Plant Immunity and Crop Productivity" 

was held in Shanghai Institute of Advanced Studies. 

4.8 The International Partner Creative Research Group of "Metabolic 

Basis of Crop Yield" sponsored by SIPPE passed through the evaluation 

organized by Chinese Academy of Science, CAS. 

4.20 A new variety of sweet potato "Taizhong No.9" was examined and 

approved by Crop Variety Authorization Committee of Shandong Province 

(No. 2010041). 

5.16 The Unveiling Ceremony for Key Laboratory of Insect 

Developmental and Evolutionary Biology was held in the institute. 

5.19 National Center of Plant Gene Research (Shanghai) was launched 

in Shanghai. 

6.18 The annual impact factor of Molecular Plant which is sponsored by 

SIPPE and Chinese Society of Plant Biology reached 2.784 in 2009. 

7.7 Shanghai Entomological Museum was awarded the title of "National 

Science Education Base”. 

9.6 The Agricultural Biotechnology Department of DuPont Pioneer Hi- 

Bred International Corporation visited SIPPE. 

9.26 The 1 st Synthetic Microbiology Symposium organized by SIPPE 

was held in Shanghai. 

9.30 Dr. Julian I. Schroeder visited SIPPE and gave a lecture.On behalf 

of Chinese Academy of Science, Dr. HongWei Xue, the director of SIPPE, 

honored him as the distinguished research fellow of Foreign Experts. 

10.21 Dr. Pamela F. Colosimo, deputy chief editor of Nature Genetics, 

visited SIPPE. 

10.25 Dr. HongWei Xue, together with a delegation from SIPPE visited 

South China Botanical Garden by their invitation. 

36 

7 

37

2011 period 

ject "Mechanisms of plant immunity and practice of molecular design for crop disease 

ed by SIPPE was launched 

Appendix 

in Shanghai. 


Year 2011 

ation office of SIPPE was awarded the 2009-2010 National Advanced Women Collective 

ence and Technology System 

2.26 The 973 program "Mechanisms of Plant Immunity and Practice 

of Molecular Design for Crop Disease Resistance" hosted by SIPPE was 

launched in Shanghai. 

3.8 The executive office of SIPPE was awarded the 2009-2010 

Advanced Women Collective of Shanghai Science and Technology 

cience visited SIPPE twice on 17th and 29th March. 

System. 

3.17 Bayer Crop Science visited SIPPE twice on 17th and 29th March. 

5.3 Dr. XiuLing Cai, associate professor of SIPPE, won the third prize 

of Shanghai Technological Invention Award for her research of "Screening 

Methods for Low Amylose Content of Rice Seeds". 

Cai, associate professor of SIPPE, won the third prize 5.5 of Dr. Shanghai XuHong Technological Qian, president of East China University of Science 

for her research of "Screening methods for low amylose content of rice seeds". 

and Technology, with a delegation from Shanghai Key Laboratory of 

ian, director of East China University of Science and Technology, with a delegation 

Key Laboratory of Chemical Biology, visited the Chemical Key Laboratory Biology, visited of Insect the Key Laboratory of Insect Developmental and 

and Evolutionary Biology, CAS. 

Evolutionary Biology, CAS. 

n, the president of SIBS and Dr.HongWei Xue, the director of SIPPE, with a delegation 

ey Laboratory of Plant Molecular Genetics, National Center of Plant Gene Research 

5.6 Dr. XiaoYa Chen, the president of SIBS and Dr. HongWei Xue, the 

director of SIPPE, with a delegation from National Key Laboratory of Plant 

Molecular Genetics, National Center of Plant Gene Research (Shanghai) 

and Office of Projects Management visited Yangzhou University to carry 

out academic exchanges in rice genetics and breeding. 

5.10 The Strategy Symposium of Key Laboratory of Insect 

Developmental and Evolutionary Biology 2011 were held in SIPPE. 

5.26 The Development Strategy Seminar 

and Annual Academic Meeting of SIPPE was 

held in Fuyang, Zhejiang province. More than 

180 staff including the leading group, members 

of the academic committee, PIs, research and 

administrative personnel, as well as postdoctors 

and graduate students attended the meeting. 

6.9 Dr. Dale Sanders, the director of John Innes Centre, visited SIPPE 

and gave a lecture on"Cations in Plants: Losing Them and Using Them". 

6.24 The opening ceremony of National Center of Plant Gene Research 

(Shanghai) was held in SIPPE. 

6.30 “The 2 nd International Conference on Plant Metabolism” organized 

by SIPPE was held in Qingdao. 

7.2 “The 3 rd International Symposium on Insect Physiology, Biochemistry 

and Molecular Biology” was held in Shanghai by the organization of Key 

Laboratory of Insect Developmental and Evolutionary Biology, CAS. 

7.7 According to the annual journal citation report published by ISI in 

2010, the impact factor of Molecular Plant reached 4.296. For the first time, 

MP ranked in the top 8%, and first in plant science journals of Asia. 

7.21 In the evaluation of State Key Laboratories by the Ministry of 

Science and Technology, National Key Laboratory of Plant Molecular 

Genetics was ranked “Excellent". 

8.31 The opening ceremony for new graduate 

student was held in the institute. 

9.29 Dr. JiaYang Li, the associate president of 

Chinese Academy of Sciecnes, attended the midterm 

assessment of the leading group in SIPPE. Dr. 

HongWei Xue, the director of SIPPE, on behalf of the 

leading group, made the summing-up report for all the 

attendee. The leading group of SIPPE that assumed 

office in 2008 December faced the frontiers of life sciences and focused on 

the national strategy need of agriculture, environment and resource. All the 

members of the leading group united and cooperated to make an efficient 

exploration in the key developmental areas of SIPPE. The great efforts 

made by the leading group made brilliant achievements. 

38 

39

Appendix 


Representative Publications 

10.12 The “Enabling Technology for Synthetic-Six- 

Academy Synthetic Biology Symposium II” was held in 

Shanghai Institute of Biological Science. 

10.15 The 973 program "Study on Crop Nutrient 

Metabolism and Its Regulation Mechanism" organized by 

SIPPE was completed and passed the evaluation in Beijing. 

10.18 The celebration of the 65 years anniversary of academician 

Wenying Yin engaged in research and her 90 th birthday was held in SIPPE. 

11.1 During the launch of "Shenzhou-8", Dr. HongWei Xue, director of 

SIPPE and the designers of biotechnology system in space life sciences, 

with a delegation, visited the launch site and guided the preparation work. 

11.3 Mr.JingDun Jia, the director of China Rural Technology Development 

Center from Ministry of Science and Technology, visited SIPPE. 

11.15 Dr. Katharine Barnes, the chief editor of Nature Protocols, visited 

SIPPE. 

11.21 Dr. HongWen Huang, the head of South China Botanical Garden, 

with a delegation visited SIPPE. The academic exchanges activity is 

helpful to further expand and deepen the bilateral strategic and cooperative 

partnership. 

11.24The Creative Research group of “System and Synthetic Biology 

Research of Microbial Metabolism”funded by NSFC held a kick-off 

meeting in SIPPE. 

11.28The Annual Academic Meeting 2011 of the CAS National Key 

Laboratory of Plant Molecular Genetics was held in SIPPE. 

11.30 Dr. Magdalena Skipper, the chief editor of Nature, visited SIPPE. 

12.15 Dr. GuoPing Zhao was elected as the academician of the 

Academy of Sciences of Developing Country. 

12.18 The 973 program "Artifical Biology Devices with Special 

Functions: Designing, Construction and Assembly" hosted by SIPPE was 

launched in Shanghai. 

© 2010 Nature America, Inc. All rights reserved. 

Genome-wide association studies of 14 agronomic traits 

in rice landraces 

Xuehui Huang 1,2,10 , Xinghua Wei 3,10 , Tao Sang 4,10 , Qiang Zhao 1,2,10 , Qi Feng 1,10 , Yan Zhao 1 , Canyang Li 1 , 

Chuanrang Zhu 1 , Tingting Lu 1 , Zhiwu Zhang 5 , Meng Li 5,6 , Danlin Fan 1 , Yunli Guo 1 , Ahong Wang 1 , Lu Wang 1 , 

Liuwei Deng 1 , Wenjun Li 1 , Yiqi Lu 1 , Qijun Weng 1 , Kunyan Liu 1 , Tao Huang 1 , Taoying Zhou 1 , Yufeng Jing 1 , 

Wei Li 1 , Zhang Lin 1 , Edward S Buckler 5,7 , Qian Qian 3 , Qi-Fa Zhang 8 , Jiayang Li 9 & Bin Han 1,2 

Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is 

important to world food security. Here we have identified ~3.6 million SNPs by sequencing 517 rice landraces and constructed 

a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association 

studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS 

explained ~36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified 

genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach 

integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical 

biparental cross-mapping for dissecting complex traits in rice. 

Rice (Oryza sativa L.) is a staple food for more than half of the 

world population. Rice landraces have evolved from their wild progenitor 

under natural and human selection, leading to the maintenance 

of high genetic diversity 1,2 . These cultivated varieties also 

have a high capacity to tolerate biotic and abiotic stress, resulting 

in highly stable yields and an intermediate yield under a low-input 

agricultural system. Identifying the genetic basis of these diverse 

varieties will provide important insights for breeding elite varieties 

for sustainable agriculture. 

GWAS have emerged as a powerful approach for identifying 

genes underlying complex diseases at an unprecedented rate 3–6 . 

However, despite their promise, GWAS have largely not been 

applied to the dissection of complex traits in crop plants 7–9 . This 

is due mainly to the lack of effective genotyping techniques for 

plants and the limited resources for developing high-density haplotype 

maps like those seen in other well-developed systems, such 

as the human genome HapMap project 3,4 . Rice is an ideal candidate 

system for the application of GWAS because it is self-fertilizing 

and has a high-quality reference genome sequence 10 and phenotyping 

resources. Such a system should permit the identification of 

high-quality haplotypes necessary to accurately associate molecular 

markers with phenotypes. 

Here we have genotyped rice landraces through direct resequencing 

of their genomes by adopting sequencing-by-synthesis technology, 

which represents a step forward from the oligonucleotide array 

technology widely used for GWAS 11–13 . More than 500 diverse rice 

landraces, representing a large collection of rice accessions, were 

sequenced at approximately onefold genome coverage. The resulting 

data set captures more of the common sequence variation in cultivated 

rice than any other data set to date. Using a highly accurate 

imputation method, we constructed a high-density rice haplotype 

map and performed GWAS for 14 agronomic traits to identify a substantial 

number of loci potentially important for rice production and 

improvement. Some loci were mapped at close to gene resolution, 

indicating that GWAS of rice landraces could provide an effective 

approach for gene identification. 

RESULTS 

Genome sequencing and SNP identification 

From a collection of ~50,000 rice accessions originating in China, 

we have undertaken an effort to build a large sample of morphologically, 

genetically and geographically diverse landraces for genetic 

studies. In this study, a total of 517 landraces were selected and 

comprehensively phenotyped (see Online Methods). We genotyped 

1 National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 

China. 2 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. 3 State Key Laboratory 

of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China. 4 Department of Plant Biology, Michigan State 

University, East Lansing, Michigan, USA. 5 Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA. 6 National Center for Soybean Improvement, 

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China. 7 US Department of 

Agriculture–Agricultural Research Service, Ithaca, New York, USA. 8 National Key Laboratory of Crop Genetic Improvement, National Center for Plant Gene Research 

(Wuhan), Huazhong Agricultural University, Wuhan, China. 9 National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese 

Academy of Sciences, Beijing, China. 10 These authors contributed equally to this work. Correspondence should be addressed to B.H. (bhan@ncgr.ac.cn). 

Received 10 May; accepted 27 September; published online 24 October 2010; doi:10.1038/ng.695 

Articles 

Nature GeNetics VOLUME 42 | NUMBER 11 | NOVEMBER 2010 961 

40 

41

Appendix 


Articles 

Fructose sensitivity is suppressed in Arabidopsis by 

the transcription factor ANAC089 lacking the 

membrane-bound domain 

© 2012 Nature America, Inc. All rights reserved. 

Genome-wide association study of flowering time and grain 

yield traits in a worldwide collection of rice germplasm 

Xuehui Huang 1,2,5 , Yan Zhao 1,2,5 , Xinghua Wei 3,5 , Canyang Li 1 , Ahong Wang 1 , Qiang Zhao 1 , Wenjun Li 1 , 

Yunli Guo 1 , Liuwei Deng 1 , Chuanrang Zhu 1 , Danlin Fan 1 , Yiqi Lu 1 , Qijun Weng 1 , Kunyan Liu 1 , Taoying Zhou 1 , 

Yufeng Jing 1 , Lizhen Si 1 , Guojun Dong 1,3 , Tao Huang 1 , Tingting Lu 1 , Qi Feng 1 , Qian Qian 3 , Jiayang Li 4 & 

Bin Han 1,2 

A high-density haplotype map recently enabled a genome-wide association study (GWAS) in a population of indica subspecies of 

Chinese rice landraces. Here we extend this methodology to a larger and more diverse sample of 950 worldwide rice varieties, 

including the Oryza sativa indica and Oryza sativa japonica subspecies, to perform an additional GWAS. We identified a total of 

32 new loci associated with flowering time and with ten grain-related traits, indicating that the larger sample increased the power 

to detect trait-associated variants using GWAS. To characterize various alleles and complex genetic variation, we developed an 

analytical framework for haplotype-based de novo assembly of the low-coverage sequencing data in rice. We identified candidate 

genes for 18 associated loci through detailed annotation. This study shows that the integrated approach of sequence-based GWAS 

and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice. 

Rice (Oryza sativa L) is an economically important crop that accounts 

for ~20% of the world’s caloric intake. To be grown successfully under 

a variety of climatic conditions across the globe, breeders maintain 

rice at high genetic diversity. Second-generation sequencing technologies 

have enabled resequencing of a large number of genomes 

and have provided the possibility of high-throughput genotyping and 

large-scale genetic variation surveys 1 . Identification of allelic variations 

underpinning the phenotypic diversity observed in rice will have 

enormous practical implications in rice breeding 2 . 

Recently we performed low-coverage sequencing of 517 Chinese 

rice landraces and imputed missing genotypes to construct a haplotype 

map of the rice genome. We then used this map to perform 

GWAS in the indica population in a previous study 3 . However, identifying 

the loci associated with complex traits in rice is challenging. 

This is because (i) O. sativa contains indica and japonica subspecies, 

which can be further divided into several divergent groups with high 

amounts of population differentiation 2,3 , and (ii) there is a low rate 

of linkage disequilibrium (LD) decay in rice 3 . Therefore, the interpretation 

of association signals and the identification of causal genes 

through GWAS requires a full incorporation of population structure 

and detailed follow-up analyses of associated loci for candidate genes 

and causal polymorphisms. 

In this study, we examined 950 worldwide rice cultivars, representing 

a much broader and larger sample than has previously been used. 

We developed a new analytical framework to assemble low-coverage 

sequences of different gene alleles 4 . This approach was then used to 

detect SNPs and complex polymorphisms such as insertions and deletions 

(indels). Using this new method, we were able to project a map 

of genic variation onto the rice genome. This facilitated the discovery 

of functional variation among rice varieties. We collected phenotypic 

data of flowering time (heading date) and grain-related traits and used 

them for a GWAS in the O. sativa indica and japonica subpopulations 

and in the full O. sativa population. The broader sampling greatly 

enhanced the power of the GWAS. In addition to the loci identified 

previously, we identified 32 new loci underlying flowering time and 

ten grain-related traits. In the follow-up analysis of these regions, we 

integrated detailed annotation, expression profiles and genetic variation 

to identify candidate genes and potential causal polymorphisms 

for the grain-related traits. 

RESULTS 

Genetic structure of worldwide rice germplasm 

The germplasm collection used in this study included a previous set 

of 520 Chinese landraces, plus a new set from China and other widespread 

countries (Supplementary Fig. 1). We sequenced the genomes 

of the plants in the new set, which included 100 additional Chinese 

japonica landraces and 330 diverse global cultivars from 33 countries, 

on the Illumina Genome Analyzer IIx to approximately onefold coverage. 

The resulting sequence dataset of 950 rice varieties consisted of 

4.6 billion 73-bp paired-end reads. After aligning these short reads 

1 National Center for Gene Research, National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological 

Sciences, Chinese Academy of Sciences, Shanghai, China. 2 Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute 

of Genomics, Chinese Academy of Sciences, Beijing, China. 3 State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of 

Agricultural Sciences, Hangzhou, China. 4 National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 

Beijing, China. 5 These authors contributed equally to this work. Correspondence should be addressed to B.H. (bhan@ncgr.ac.cn). 

Received 3 June; accepted 2 November; published online 4 December 2011; doi:10.1038/ng.1018 

32 VOLUME 44 | NUMBER 1 | JANUARY 2012 Nature GeNetics 

Ping Li a,1 , Julia J. Wind b,1 , Xiaoliang Shi a , Honglei Zhang a , Johannes Hanson b,c,d , Sjef C. Smeekens b,c , 

and Sheng Teng a,b,c,2 

a Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, The Chinese Academy of Sciences, Shanghai 200032, China; b Department 

of Molecular Plant Physiology, Utrecht University, 3584 CH, Utrecht, The Netherlands; c Centre for BioSystems Genomics, 6700 AB, Wageningen, 

The Netherlands; and d Umeå Plant Science Center (UPSC), Umeå University, 901 87 Umea, Sweden 

Edited by Maarten Koornneef, Max Planck Institute for Plant Breeding Research, Cologne, Germany, and approved January 19, 2011 (received for review 

December 16, 2010) 

In living organisms sugars not only provide energy and carbon 

skeletons but also act as evolutionarily conserved signaling molecules. 

The three major soluble sugars in plants are sucrose, glucose, 

and fructose. Information on plant glucose and sucrose signaling is 

available, but to date no fructose-specific signaling pathway has 

been reported. In this study, sugar repression of seedling development 

was used to study fructose sensitivity in the Landsberg 

erecta (Ler)/Cape Verde Islands (Cvi) recombinant inbred line population, 

and eight fructose-sensing quantitative trait loci (QTLs) 

(FSQ1–8) were mapped. Among them, FSQ6 was confirmed to be 

a fructose-specific QTL by analyzing near-isogenic lines in which Cvi 

genomic fragments were introgressed in the Ler background. These 

results indicate the existence of a fructose-specific signaling pathway 

in Arabidopsis. Further analysis demonstrated that the FSQ6- 

associated fructose-signaling pathway functions independently 

of the hexokinase1 (HXK1) glucose sensor. Remarkably, fructosespecific 

FSQ6 downstream signaling interacts with abscisic acid 

(ABA)- and ethylene-signaling pathways, similar to HXK1-dependent 

glucose signaling. The Cvi allele of FSQ6 acts as a suppressor 

of fructose signaling. The FSQ6 gene was identified using mapbased 

cloning approach, and FSQ6 was shown to encode the transcription 

factor gene Arabidopsis NAC (petunia No apical meristem 

and Arabidopsis transcription activation factor 1, 2 and Cup-shaped 

cotyledon 2) domain containing protein 89 (ANAC089). The Cvi allele 

of FSQ6/ANAC089 is a gain-of-function allele caused by a premature 

stop in the third exon of the gene. The truncated Cvi FSQ6/ 

ANAC089 protein lacks a membrane association domain that is 

present in ANAC089 proteins from other Arabidopsis accessions. 

As a result, Cvi FSQ6/ANAC089 is constitutively active as a transcription 

factor in the nucleus. 

sugar signaling | natural variation | fructose quantitative trait locus | map 

based cloning 

n plants, sugars provide the energy and carbon skeletons needed 

Ifor growth and in addition act as crucial signaling molecules that 

affect growth, development, and response to the (a)biotic environment 

(1–3). Plant cells harbor sugar-sensing and -signaling systems 

that regulate the expression of thousands of genes and control the 

metabolic processes needed for growth (2–4). These sugar-response 

systems are known to interact with other signaling pathways, such 

as those for light, phytohormones, stress, and nutrients (1). 

The neutral sugars sucrose, glucose, and fructose are central to 

metabolism in plants and in other organisms as well. So far, detailed 

information is available only on glucose sensing, and it has 

been shown that the hexokinase 1 (HXK1) enzyme acts as a glucose 

sensor (5, 6). Sucrose-specific signaling also was demonstrated 

because the effect of sucrose cannot be mimicked by 

glucose and/or fructose (7), but so far no information on sucrosesensing 

systems is available. A signaling function for fructose has 

been proposed (8, 9), but no convincing experimental evidence on 

such fructose-specific signaling is available. 

In Arabidopsis early seedling development is arrested by high 

concentrations of exogenous glucose or sucrose. This observation 

has been used in several screens to identify mutants defective in 

sugar sensing or signaling (10, 11). This rapid and convenient 

phenotypic screen allowed the isolation of many mutants with 

altered sugar responses and the subsequent identification of the 

genes involved. In this way the glucose-insensitive (gin) phenotype 

of the hxk1/gin2 mutant (6) was established, and a network of 

HXK1-dependent glucose signaling and abscisic acid (ABA) and 

ethylene biosynthesis and signaling was identified (10–17). 

Fructose is a major soluble monosaccharide in plant. Fructose 

is produced from sucrose by invertases and sucrose synthases. 

Like glucose, fructose can repress the expression of photosynthesis 

genes (18). Most likely, fructose is phosphorylated mainly 

by fructokinases (FRKs), and a member of that gene family is 

present in Arabidopsis. The putative regulatory role of FRK in 

fructose signaling was investigated first in tomato (9, 19). Inhibition 

of the tomato fructokinase 2 (LeFRK2) interferes with 

development of phloem and xylem by impairing callose deposition, 

thus reducing transport of sugars and water (20). In this 

way LeFRK2 affects tomato stem and root growth and the normal 

development of flowers, fruits, and seeds. These experiments 

illustrate the important role of FRK in metabolism, but a signaling 

function for FRKs or for fructose could not be established. 

Here, a fructose-specific signaling pathway is proposed by the 

identification of Arabidopsis quantitative trait loci (QTLs) in the 

Landsberg erecta (Ler)/Cape Verde Islands (Cvi) recombinant 

inbred line (RIL) population that displays altered fructose-specific 

sensitivity. This fructose-signaling pathway is HXK1 independent, 

but, remarkably, the fructose signal feeds into the same downstream 

ABA-signaling pathway as the glucose/HXK signal. The 

Cvi fructose-sensing QTL allele 6 (FSQ6) was cloned by a mapbased 

cloning approach and shown to encode the Arabidopsis 

NAC (petunia No apical meristem and Arabidopsis transcription 

activation factor 1, 2 and Cup-shaped cotyledon 2) domain containing 

protein 89 (ANAC089) gene. Functional analysis indicates 

that the Cvi FSQ6/ANAC089 allele is a gain-of-function allele that 

represses the fructose-induced ABA-signaling pathway. 

Results 

Identification of Fructose-Sensitivity QTLs in the Ler/Cvi RIL 

Population. High concentrations of glucose and sucrose repress 

Arabidopsis seedling development. The identified gin and sugarinsensitive 

(sis) mutants are insensitive to glucose and/or sucrose 

Author contributions: S.T. designed research; P.L., J.J.W., X.S., and H.Z. performed research; 

J.H. and S.C.S. analyzed data; and S.C.S. and S.T. wrote the paper. 

The authors declare no conflict of interest. 

This article is a PNAS Direct Submission. 

1 P.L., and J.J.W. contributed equally to this work. 

2 To whom correspondence should be addressed. E-mail: steng@sippe.ac.cn. 

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. 

1073/pnas.1018665108/-/DCSupplemental. 

3436–3441 | PNAS | February 22, 2011 | vol. 108 | no. 8 www.pnas.org/cgi/doi/10.1073/pnas.1018665108 

42 

43

Appendix 


Four amino acids guide the assembly or disassembly of 

Arabidopsis histone H3.3-containing nucleosomes 

Leilei Shi a,1 , Jing Wang a,1,2 , Fang Hong a , David L. Spector b , and Yuda Fang a,3 

a National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese 

Academy of Sciences, Shanghai 200032, China; and b Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 

Edited* by Steven Henikoff, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved May 17, 2011 (received for review November 30, 2010) 

The histone variant H3.3 and the canonical histone H3.1, which 

differ in only 4- to 5-aa positions, are coexpressed in complex 

multicellular eukaryotes from fly to human and plant. H3.3 is mainly 

associated with active chromatin by replacing H3.1 through chaperones 

such as histone regulator A, death domain associated protein 

DAXX, thalassemia/mental retardation syndrome X-linked homolog 

ATRX, or proto-oncogene protein DEK and plays important roles in 

the germline, epigenetic memory, and reprogramming. However, 

the signals within H3.3 that serve as a guide for its dynamic deposition 

or depletion in plant chromatin are not clear. Here, we show 

that Arabidopsis histone H3.3 differs from H3.1 by 4-aa sites: amino 

acids 31, 41, 87, and 90. Although histone H3.1 is highly enriched in 

chromocenters, H3.3 is present in nucleolar foci in addition to being 

diffusely distributed in the nucleoplasm. We have evaluated the 

function of the 4 aa that differ between H3.1 and H3.3. We show 

that amino acid residue 87, and to some extent residue 90, of 

Arabidopsis histone H3.3 are critical for its deposition into rDNA 

arrays. When RNA polymerase I-directed nucleolar transcription is 

inhibited, wild type H3.3, but not H3.3 containing mutations at residues 

31 and 41, is depleted from the rDNA arrays. Together, our 

results are consistent with a model in which amino acids 87 and 90 

in the core domain of H3.3 guide nucleosome assembly, whereas 

amino acids 31 and 41 in the N-terminal tail of Arabidopsis H3.3 

guide nucleosome disassembly in nucleolar rDNA. 

H3 dynamics | histone code | nucleolar dominance | chromatin remodeling 

he fundamental repeat unit of packaging of eukaryotic ge- 

DNA is predominantly the nucleosome where DNA is 

Tnomic 

wrapped around a histone octamer that contains two molecules 

of each core histone: H2A, H2B, H3, and H4. The four core 

histones share the common histone folding domain (HFD), which 

is composed of three α-helices (α1, α2, and α3) separated by two 

loops (L1 and L2) (1). The N- and C-terminal tails stretch out of 

the nucleosome core and are subject to diverse posttranslational 

modifications (PTMs) including methylation, acetylation, phosphorylation, 

ubiquitination, and poly-ADP ribosylation (2, 3). In 

addition, the incorporation of histone variants into nucleosomes 

has been proposed to provide another mechanism for modifying 

chromatin structure (4). 

In addition to the centromere-specific histone 3 variant (CenH3), 

which can be deposited into the centromeric nucleosomes in tetrameric 

(5, 6) or hexameric states (7), the histone H3 family 

includes another universal histone H3 variant H3.3 (4) or H3.2 in 

alfalfa, a plant histone H3.3 (8). In most animals, histone variant 

H3.3 differs by 4-aa residues from H3.1, which are residue 31 in the 

N-terminal tail and residues 87, 89, and 90 in the HFD near the 

beginning of α2 (1, 9). In contrast to the replication-coupled 

deposition of H3.1 during S-phase mediated by chromatin-assembly 

factor 1 (CAF1) (4), H3.3 in eukaryotes incorporates into nucleosomes 

mostly in a replication-independent manner (9) 

through the histone chaperones, including the histone regulator 

A (HIRA), ATRX, death-associated protein DAXX, and DEK 

(10–17). H3.3 is deposited primarily in promoters, gene regulatory 

sites, and regions with PTMs that are associated with transcribed 

genes (18). H3.3 has been shown to play roles in epigenetic 

reprogramming (19) and memory (20). When the H3.3 gene was 

knocked out in Drosophila melanogaster, flies exhibited sterility, 

and the transcriptional defects were able to be rescued by overexpression 

of H3.1, which shows that H3.3 is not necessary for 

somatic development (21, 22). In addition, H3.3 mutants display 

meiotic defects in chromosome condensation in spermatocytes, 

which is dependent on residues 87, 89, and/or 90 but not on 

methylation of H3.3K4 or phosphorylation of Ser31, suggesting 

a role of H3.3 in the germline (22). 

H3.3 can be displaced dynamically by H3.1 and reloaded at 

the site of transcription in D. melanogaster (23). The nucleosome 

turnover might have functional significance in epigenome maintenance, 

gene regulation, and DNA replication (24). However, 

the signals within H3.3 that serve as a guide for its dynamic deposition 

or depletion in plant chromatin are not clear. Here, we 

have evaluated the function of 4 aa that differ between Arabidopsis 

histone H3.1 and H3.3, and we have identified the specific signals 

within H3.3 that serve as guides for its dynamic deposition into or 

depletion from the H3.3-containing nucleosomes. 

Results and Discussion 

Arabidopsis Histone H3.3 Is Highly Enriched at Nucleolar rDNA Foci 

in Addition to Being Diffusely Distributed in the Nucleoplasm. The 

Arabidopsis genome encodes six H3.3 or H3.3-like genes, including 

histone three related 4(HTR4, At4g40030), HTR5(At4g40040), 

HTR6(At1g13370), HTR8(At5g10980), HTR14(At1g75600), and 

the male gamete-specific HTR10/AtMGH3(At1g19890) (25). To 

investigate the regions in the plant histone H3.3 variant that are 

responsible for guiding its incorporation into and its depletion 

from nucleosomes, we first examined the sequence alignment of 

canonical Arabidopsis histone H3.1(HTR1) and variant H3.3 

(HTR4) proteins and compared them with corresponding sequences 

from other organisms (Fig. 1). The difference between 

histone H3.1 and H3.3 is defined by 4-aa residues at the sites 31 

(Ala vs. Ser), 87 (Ser vs. Ala), 89 (Val vs. Ile), and 90 (Met vs. Gly) 

in Drosophila (26), and an additional site at 96 (Cys vs. Ser) is 

included in humans (27, 28). The difference of 4-aa residues between 

Arabidopsis histone H3.1/HTR1 and H3.3/HTR4 was observed 

at the sites 31 (Ala vs. Thr), 41 (Phe vs. Tyr), 87 (Ser vs. 

His), and 90 (Ala vs. Leu); they lack the amino acid change at 

residue 89 observed in other organisms, but contain an additional 

amino acid difference at residue 41. This plant-specific feature 

is conserved in both dicot and monocot plant species such as rice 

and maize (Figs. S1–S3) (19).The amino acid residues 87 and 90 

are located in the α2-helix of the H3 core domain and residues 

Author contributions: D.L.S. and Y.F. designed research; L.S., J.W., F.H., and Y.F. performed 

research; L.S., J.W., and Y.F. analyzed data; and L.S. and Y.F. wrote the paper. 

The authors declare no conflict of interest. 

*This Direct Submission article had a prearranged editor. 

1 L.S. and J.W. contributed equally to this work. 

2 Present address: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724. 

3 To whom correspondence should be addressed. E-mail: yfang@sippe.ac.cn. 

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. 

1073/pnas.1017882108/-/DCSupplemental. 

REPORTS 

1004 

mammalian cells with CobB deacetylase increased 

ASL activity (Fig. 3H), supporting a direct role of 

acetylation in ASL inactivation. The dual regulation 

of ASL by both amino acids and glucose 

indicates that acetylation may have an important 

role in the coordination of metabolic pathways. 

In the presence of sufficient glucose, amino acid 

catabolism for energy production and gluconeogenesis 

would be inhibited. In the presence of 

abundant amino acids and low glucose, cells would 

switch to using amino acids for energy production 

with enhanced urea cycle activity. Cells may use 

acetylation to coordinate multiple pathways in 

order to achieve these metabolic adaptations 

Phosphoenolpyruvate carboxykinase 1(PEPCK1; 

EC code 4.1.1.32) is a key regulatory enzyme in 

gluconeogenesis (Fig. 1D) (9, 10). Three acetylated 

lysine residues were identified in PEPCK1 by MS 

analysis (Lys 70 , Lys 71 , and Lys 594 ; table S2). Acetylation 

of PEPCK1 was enhanced in cells treated 

with high concentrations of glucose (Fig. 4A) but 

was decreased by addition of amino acids in glucosefree 

medium (Fig. 4B). These results suggest a potential 

mechanism by which cells could regulate 

gluconeogenesis through regulating acetylation 

of PEPCK1 in response to the availability of 

extracellular fuels. 

In searching for an effect of acetylation on the 

regulation of PEPCK1, we noticed that levels of 

endogenous PEPCK1 protein were decreased by 

high glucose (Fig. 4C). Furthermore, treatment 

with TSA and NAM caused a 70% reduction in 

the amount of PEPCK1 protein in both HEK293T 

and Chang liver cells (Fig. 4D). PEPCK1 was stable 

in cells in glucose-free medium but unstable 

in high-glucose medium (Fig. 4E). When cells 

were treated with TSA and NAM, PEPCK1 was 

unstable even in glucose-free medium or in the 

presence of amino acids. These results indicate that 

acetylation may regulate the stability of PEPCK1. 

We replaced the three putative acetylation lysine 

residues by arginine (PEPCK1 3KR ) or glutamine 

(PEPCK1 3KQ ) to abolish or mimic acetylation, 

respectively. The PEPCK1 3KR mutant was more 

stable than the wild type, whereas the PEPCK1 3KQ 

mutant remained unstable (Fig. 4F). Moreover, 

treatment of cells with TSA and NAM failed to 

destabilize the PEPCK1 3KR mutant. 

The importance of lysine acetylation in the 

regulation of chromatin dynamics and gene expression 

is well appreciated. Our study and others 

extend the scope of cell regulation by lysine acetylation 

to an extent comparable to that of other 

major posttranslational modifications such as phosphorylation 

and ubiquitination. We show that most 

intermediate metabolic enzymes are acetylated and 

that acetylation can directly affect the enzyme activity 

or stability. We found that acetylation of 

metabolic enzymes changed in response to the 

alterations of extracellular nutrient availability, providing 

evidence for a physiological role of dynamic 

acetylation in metabolic regulation. The 

mechanism of acetylation in regulating metabolism 

may be conserved during evolution. Many 

metabolic enzymes in Escherichia coli are acetylated, 

although the functional importance of these 

acetylations has not been investigated (11). We 

propose that lysine acetylation is an evolutionarily 

conserved mechanism involved in regulation of 

metabolism in response to nutrient availability 

Acetylation of Metabolic Enzymes 

Coordinates Carbon Source Utilization 

and Metabolic Flux 

Qijun Wang, 1 Yakun Zhang, 2 Chen Yang, 3 Hui Xiong, 1,2 Yan Lin, 4 Jun Yao, 4 Hong Li, 3 Lu Xie, 3 

Wei Zhao, 3 Yufeng Yao, 5 Zhi-Bin Ning, 3 Rong Zeng, 3 Yue Xiong, 4,6 Kun-Liang Guan, 4,7 

Shimin Zhao, 1,4 * Guo-Ping Zhao 1,2,3,8 * 

Lysine acetylation regulates many eukaryotic cellular processes, but its function in prokaryotes is largely 

unknown. We demonstrated that central metabolism enzymes in Salmonella were acetylated extensively 

and differentially in response to different carbon sources, concomitantly with changes in cell growth 

and metabolic flux. The relative activities of key enzymes controlling the direction of glycolysis 

versus gluconeogenesis and the branching between citrate cycle and glyoxylate bypass were all 

regulated by acetylation. This modulation is mainly controlled by a pair of lysine acetyltransferase 

and deacetylase, whose expressions are coordinated with growth status. Reversible acetylation of 

metabolic enzymes ensure that cells respond environmental changes via promptly sensing cellular 

energy status and flexibly altering reaction rates or directions. It represents a metabolic regulatory 

mechanism conserved from bacteria to mammals. 

P 

CORRECTED 21 MAY 2010; SEE LAST PAGE 

rotein lysine acetylation regulates wide 

range of cellular functions in eukaryotes, 

especially transcriptional control in the 

nucleus (1, 2). It also plays an extensive role in 

regulation of metabolic enzymes through various 

mechanisms in human liver (3). In prokaryotes 

such as Salmonella enterica, reversible lysine 

acetylation is known to regulate the activity of 

acetyl–coenzyme A (CoA) synthetase (4). To determine 

how lysine acetylation globally regulates 

19 FEBRUARY 2010 VOL 327 SCIENCE www.sciencemag.org 

and cellular metabolic status. Acetylation may 

play a key role in the coordination of different 

metabolic pathways in response to extracellular 

conditions. 

References and Notes 

1. X. J. Yang, E. Seto, Mol. Cell 31, 449 (2008). 

2. S. C. Kim et al., Mol. Cell 23, 607 (2006). 

3. C. Choudhary et al., Science 325, 834 (2009). 

4. K. Alvares et al., Cancer Res. 54, 2303 (1994). 

5. C. S. Yeh et al., Cancer Lett. 233, 297 (2006). 

6. P. A. Watkins et al., J. Clin. Invest. 83, 771 

(1989). 

7. E. Trevisson et al., Hum. Mutat. 28, 694 (2007). 

8. R. L. Jungas, M. L. Halperin, J. T. Brosnan, Physiol. Rev. 

72, 419 (1992). 

9. H. Lardy, P. E. Hughes, Curr. Top. Cell. Regul. 24, 171 

(1984). 

10. P. She et al., Mol. Cell. Biol. 20, 6508 (2000). 

11. J. Zhang et al., Mol. Cell. Proteomics 8, 215 (2009). 

12. We thank members of Fudan MCB laboratory for their 

valuable inputs throughout this study and S. Jackson for 

reading the manuscript. Supported by the 985 program 

from the Chinese Ministry of Education, state key 

development programs of basic research of China 

(grants 2009CB918401 and 2006CB806700), the 

national high technology research and development 

program of China (grant 2006AA02A308), Chinese 

National Science Foundation grants 30600112 and 

30871255, Shanghai key basic research projects 

(grants 06JC14086, 07PJ14011, 08JC1400900), 

and NIH grants R01GM51586, R01CA108941, and 

R01CA65572 (K.L.G., X.C., and Y.X.). 

Supporting Online Material 

www.sciencemag.org/cgi/content/full/327/5968/1000/DC1 

Materials and Methods 

Figs. S1 to S3 

Tables S1 to S3 

References 

27 July 2009; accepted 7 January 2010 

10.1126/science.1179689 

the metabolism in prokaryotes, we determined the 

overall acetylation status of S. enterica proteins 

under either fermentable glucose-based glycolysis 

or under oxidative citrate-based gluconeogenesis. 

By immunopurification of acetylated peptides with 

antibody to acetyllysine and peptide identification 

1 State Key Laboratory of Genetic Engineering, Department of 

Microbiology, School of Life Sciences and Institute of 

Biomedical Sciences, Fudan University, Shanghai 200032, 

China. 2 MOST-Shanghai Laboratory of Disease and Health 

Genomics, Chinese National Human Genome Center at 

Shanghai, Shanghai 201203, China. 

3 Key Laboratory of 

Synthetic Biology, Bioinformatics Center and Laboratory of 

Systems Biology, Institute of Plant Physiology and Ecology, 

Shanghai Institutes for Biological Sciences, Chinese Academy 

of Sciences, Shanghai 200032, China. 4 Molecular Cell Biology 

Laboratory, Institute of Biomedical Sciences, Fudan University, 

Shanghai 200032, China. 5 Laboratory of Human Bacterial 

Pathogenesis, Department of Medical Microbiology and 

Parasitology, Institute of Medical Sciences, Shanghai Jiao 

Tong University School of Medicine, Shanghai 200025, China. 

6 Department of Biochemistry and Biophysics and Lineberger 

Comprehensive Cancer Center, University of North Carolina at 

Chapel Hill, Chapel Hill, NC 27599, USA. 7 Department of 

Pharmacology and Moores Cancer Center, University of 

California San Diego, La Jolla, CA 92093, USA. 8 Department 

of Microbiology and Li Ka Shing Institute of Health Sciences, 

The Chinese University of Hong Kong, Prince of Wales 

Hospital, Shatin, New Territories, Hong Kong SAR, China. 

*To whom correspondence should be addressed. E-mail: 

zhaosm@fudan.edu.cn (S.Z.); gpzhao@sibs.ac.cn (G.-P.Z.) 

Downloaded from www.sciencemag.org on February 27, 2012 

10574–10578 | PNAS | June 28, 2011 | vol. 108 | no. 26 www.pnas.org/cgi/doi/10.1073/pnas.1017882108 

44 

45

Appendix 


Research 

Downloaded from genome.cshlp.org on September 1, 2010 - Published by Cold Spring Harbor Laboratory Press 

Function annotation of the rice transcriptome 

at single-nucleotide resolution by RNA-seq 

Tingting Lu, 1,4 Guojun Lu, 1,4 Danlin Fan, 1 Chuanrang Zhu, 1 Wei Li, 1 Qiang Zhao, 1,2 

Qi Feng, 1 Yan Zhao, 1 Yunli Guo, 1 Wenjun Li, 1 Xuehui Huang, 1 and Bin Han 1,3,5 

1 National Center for Gene Research & Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese 

Academy of Sciences, Shanghai 200233, China; 2 College of Life Science & Biotechnology, Shanghai Jiaotong University, Shanghai 

200240, China; 3 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China 

The functional complexity of the rice transcriptome is not yet fully elucidated, despite many studies having reported the 

use of DNA microarrays. Next-generation DNA sequencing technologies provide a powerful approach for mapping and 

quantifying the transcriptome, termed RNA sequencing (RNA-seq). In this study, we applied RNA-seq to globally sample 

transcripts of the cultivated rice Oryza sativa indica and japonica subspecies for resolving the whole-genome transcription 

profiles. We identified 15,708 novel transcriptional active regions (nTARs), of which 51.7% have no homolog to public 

protein data and >63% are putative single-exon transcripts, which are highly different from protein-coding genes (

Appendix 


COPLBI-888; NO. OF PAGES 9 

Available online at www.sciencedirect.com 

The Plant Cell, Vol. 22: 1633–1646, May 2010, www.plantcell.org ã 2010 American Society of Plant Biologists 

Signals and mechanisms affecting vesicular trafficking during 

root growth 

Hong-Yan Yao and Hong-Wei Xue 

Vesicular trafficking is mediated by distinct exocytic and 

endocytic routes in eukaryotic cells. These pathways involve 

RAB family proteins, ADP-ribosylation factor, RHO proteins of 

the Ras superfamily, and SNAREs (soluble N-ethylmaleimidesensitive 

factor adaptors). Studies have shown that vesicular 

trafficking plays a crucial role in protein localization and 

movement, signal transduction, and multiple developmental 

processes. Here we summarize the role of vesicular trafficking 

in root and root hair growth and in auxin-mediated root 

development, focusing on the regulation of the polarized 

subcellular distribution of the PIN proteins (auxin efflux 

carriers). 

Address 

National Key Laboratory of Plant Molecular Genetics, Shanghai Institute 

of Plant Physiology and Ecology, Chinese Academy of Sciences, 300, 

Fenglin Road, 200032 Shanghai, China 

Corresponding author: Xue, Hong-Wei (hwxue@sibs.ac.cn) 

Current Opinion in Plant Biology 2011, 14:1–9 

This review comes from a themed issue on 

Cell signalling and gene regulation 

Edited by Sean Cutler and Christa Testerink 

1369-5266/$ – see front matter 

# 2011 Elsevier Ltd. All rights reserved. 

DOI 10.1016/j.pbi.2011.06.009 

Introduction 

Vesicular trafficking maintains cellular homeostasis by 

delivering newly synthesized proteins from the endoplasmic 

reticulum (ER) to the correct destination: for 

example, the trans-Golgi network (TGN), for retrograde 

transport; the plasma membrane (PM), for recycling by 

transport vesicles; or the lysosomes and vacuoles, for 

degradation. Vesicular trafficking is also important in 

maintaining compartment identity and fidelity in eukaryotic 

cells. Furthermore, cell endocytosis and exocytosis 

are dependent on vesicular trafficking. 

Studies in yeast (Saccharomyces cerevisiae), mammals, 

and plants have indicated that regulatory molecules 

are required for efficient and accurate vesicular trafficking 

[1]. Specifically, the successive steps from the ER to 

the Golgi, intra-Golgi, post-Golgi, and endocytic trafficking 

are mediated by five gene families [RAS, RHO, 

RAB/YPT, ADP-ribosylation factor (ARF), and Rasrelated 

nuclear proteins (RAN)] of the Ras superfamily 

and the soluble N-ethylmaleimide-sensitive factor 

adaptor (SNARE) machinery [2,3]. However, no homologue 

of the mammalian RAS has been identified in 

plants, whereas RAB, ARF, RHO and RAN GTPases 

have been well characterized. Only the RAS and RHO 

GTPases are considered to be signaling proteins, 

whereas RAB/YPT and ARF are directly involved in 

the regulation of vesicular trafficking [3], and RAN has 

been implicated in nuclear trafficking [4]. 

The RAB GTPases function in the regulation of vesicle 

formation on donor membranes. These proteins also 

direct vesicles to dock on target membranes [5]. The 

57 Arabidopsis RAB sequences fall into eight clades 

named RAB-A to RAB-H [6]. The RAB11/A and 

RAB2/RABB GTPases members have been implicated 

in the regulation of tip growth through polarized secretion 

of new cell wall components or through control of polar 

recycling events during pollen tube growth [7] (Table 1). 

RAB5/F2 is involved in endocytosis and is important for 

the biosynthetic vacuolar transport pathway [8]. 

ARF GTPases are major regulators of vesicle biogenesis 

[9]. The most studied small GTPase in vesicular trafficking 

in tobacco BY-2 cells is ARF1, which controls the 

assembly of COPI- and AP1, AP3, and AP4/clathrincoated 

vesicles and recruits other proteins to membranes 

[10]. ARF1p controls COPI transport and influences the 

BP-80-mediated transport route to the lytic vacuole in 

tobacco leaf protoplasts [11]. 

ARF-guanine exchange factors (ARF-GEFs) increase 

levels of the active GTP-bound ARF protein, which 

are tethered to the membrane by a myristoylated tail. 

An Arabidopsis GEF called GNOM (also called EMB30 or 

VAN7) was identified as a GBF protein that plays a key 

role during embryo development by regulating the endosomal 

cycling of the auxin efflux carrier PIN1 [12,13] 

(Table 1). 

ARF-GTPase-activating proteins (ARF-GAPs) regenerate 

the inactive, soluble GDP-bound ARF protein by 

stimulating GTP hydrolysis. These ARF-GAPs modulate 

intracellular trafficking from multiple sites, including the 

Golgi, TGN and the endosome in Arabidopsis [14]. Interactions 

of ARF-GAPs with lipids, coat proteins and cargo 

receptors promote the efficient loading of cargo into 

vesicles and remodeling of the actin cytoskeleton [15]. 

www.sciencedirect.com Current Opinion in Plant Biology 2011, 14:1–9 

The Arabidopsis Nitrate Transporter NRT1.8 Functions in 

Nitrate Removal from the Xylem Sap and Mediates 

Cadmium Tolerance C W 

Jian-Yong Li, a,1 Yan-Lei Fu, a,1 Sharon M. Pike, b Juan Bao, a Wang Tian, c Yu Zhang, a Chun-Zhu Chen, a Yi Zhang, a 

Hong-Mei Li, a Jing Huang, a Le-Gong Li, c Julian I. Schroeder, d Walter Gassmann, b and Ji-Ming Gong a,2 

a 

National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for 

Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China 

b 

Division of Plant Sciences, C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, 

Missouri 65211-7310 

c 

College of Life Sciences, Capital Normal University, Beijing 100037, People’s Republic of China 

d 

Division of Biological Sciences and Center for Molecular Genetics, Cell and Developmental Biology Section, University of 

California, San Diego, California 92093-0116 

Long-distance transport of nitrate requires xylem loading and unloading, a successive process that determines nitrate 

distribution and subsequent assimilation efficiency. Here, we report the functional characterization of NRT1.8, a member of 

the nitrate transporter (NRT1) family in Arabidopsis thaliana. NRT1.8 is upregulated by nitrate. Histochemical analysis using 

promoter-b-glucuronidase fusions, as well as in situ hybridization, showed that NRT1.8 is expressed predominantly in xylem 

parenchyma cells within the vasculature. Transient expression of the NRT1.8:enhanced green fluorescent protein fusion in 

onion epidermal cells and Arabidopsis protoplasts indicated that NRT1.8 is plasma membrane localized. Electrophysiological 

and nitrate uptake analyses using Xenopus laevis oocytes showed that NRT1.8 mediates low-affinity nitrate uptake. 

Functional disruption of NRT1.8 significantly increased the nitrate concentration in xylem sap. These data together suggest 

that NRT1.8 functions to remove nitrate from xylem vessels. Interestingly, NRT1.8 was the only nitrate assimilatory pathway 

gene that was strongly upregulated by cadmium (Cd 2+ ) stress in roots, and the nrt1.8-1 mutant showed a nitrate-dependent 

Cd 2+ -sensitive phenotype. Further analyses showed that Cd 2+ stress increases the proportion of nitrate allocated to wildtype 

roots compared with the nrt1.8-1 mutant. These data suggest that NRT1.8-regulated nitrate distribution plays an 

important role in Cd 2+ tolerance. 

INTRODUCTION 

The nitrate assimilation pathway has been extensively studied. It 

consists of several steps, beginning with uptake into roots. 

Nitrate concentrations in soil vary considerably, mainly as a result 

of two microbial processes, mineralization and nitrification, that 

are highly sensitive to environmental conditions (Marschner, 

1995). To cope with highly variable nitrate concentrations in soil, 

plants have developed both a high-affinity transport system 

(HATS) and a low-affinity transport system (LATS) (Glass et al., 

1992; Crawford, 1995; Crawford and Glass, 1998; Forde, 2000). 

When the external nitrate concentration is high (>1 mM), LATS is 

preferentially used. When nitrate availability is limited, HATS is 

1 

These authors contributed equally to this work. 

2 

Address correspondence to jmgong@sibs.ac.cn. 

The author responsible for distribution of materials integral to the 

findings presented in this article in accordance with the policy described 

in the Instructions for Authors (www.plantcell.org) is: Ji-Ming Gong 

( jmgong@sibs.ac.cn). 

C 

Some figures in this article are displayed in color online but in black 

and white in the print edition. 

W 

Online version contains Web-only data. 

www.plantcell.org/cgi/doi/10.1105/tpc.110.075242 

activated and takes over the nitrate uptake process (Glass et al., 

1992; Crawford and Glass, 1998). 

To date, two nitrate transporter gene families, NRT1 and 

NRT2, were identified as responsible for LATS and HATS, 

respectively (Glass et al., 1992; Orsel et al., 2002b; Tsay et al., 

2007). In the Arabidopsis thaliana NRT1 family, the 53 NRT1 

(PTR, peptide transporter) members include both nitrate and 

oligopeptide transporters. Among the characterized nitrate 

transporters, CHLorate resistant 1 (CHL1/NRT1.1) is the most 

studied and represents a major low-affinity uptake mechanism 

for nitrate (Tsay et al., 1993, 2007). Furthermore, CHL1/NRT1.1 

functions as a dual-affinity transporter with regulation by phosphorylation 

(Wang et al., 1998; Liu et al., 1999). The NRT2 family 

consists of seven members in the Arabidopsis genome. NRT2.1 

and NRT2.2 are involved in inducible high-affinity nitrate uptake 

(Cerezo et al., 2001; Li et al., 2007). Though functionally and 

phylogenetically distinct, the nitrate transport functions of both 

NRT1 and NRT2 are believed to be proton dependent (Paulsen 

and Skurray, 1994; Orsel et al., 2002a). 

Once taken up into the root cytoplasm, nitrate is either translocated 

across the tonoplast and stored in the vacuoles, or it is 

reduced to nitrite and then partitioned to plastids where it is 

further assimilated to organic nitrogen (Orsel et al., 2002a). 

Please cite this article in press as: Yao H-Y, Xue H-W. Signals and mechanisms affecting vesicular trafficking during root growth, Curr Opin Plant Biol (2011), doi:10.1016/j.pbi.2011.06.009 

48 

49

Appendix 


The Plant Cell, Vol. 22: 2322–2335, July 2010, www.plantcell.org ã 2010 American Society of Plant Biologists 

The Plant Cell, Vol. 22: 3726–3744, November 2010, www.plantcell.org ã 2010 American Society of Plant Biologists 

Temporal Control of Trichome Distribution by 

MicroRNA156-Targeted SPL Genes in Arabidopsis thaliana W OA 

Nan Yu, a,b,1 Wen-Juan Cai, a,b,1 Shucai Wang, c Chun-Min Shan, a,b Ling-Jian Wang, a and Xiao-Ya Chen a,2 

a 


Biological Sciences, 200032 Shanghai, P.R. China 

b 

Graduate School of Chinese Academy of Sciences, 200032 Shanghai, P.R. China 

c 

Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada 

Arabidopsis b-Ketoacyl-[Acyl Carrier Protein] Synthase I Is 

Crucial for Fatty Acid Synthesis and Plays a Role in 

Chloroplast Division and Embryo Development C W OA 

Guo-Zhang Wu and Hong-Wei Xue 1 


Biological Science, Chinese Academy of Sciences, 200032 Shanghai, China 

The production and distribution of plant trichomes is temporally and spatially regulated. After entering into the flowering 

stage, Arabidopsis thaliana plants have progressively reduced numbers of trichomes on the inflorescence stem, and the 

floral organs are nearly glabrous. We show here that SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes, which 

define an endogenous flowering pathway and are targeted by microRNA 156 (miR156), temporally control the trichome 

distribution during flowering. Plants overexpressing miR156 developed ectopic trichomes on the stem and floral organs. By 

contrast, plants with elevated levels of SPLs produced fewer trichomes. During plant development, the increase in SPL 

transcript levels is coordinated with the gradual loss of trichome cells on the stem. The MYB transcription factor genes 

TRICHOMELESS1 (TCL1) and TRIPTYCHON (TRY) are negative regulators of trichome development. We show that SPL9 

directly activates TCL1 and TRY expression through binding to their promoters and that this activation is independent of 

GLABROUS1 (GL1). The phytohormones cytokinin and gibberellin were reported to induce trichome formation on the stem 

and inflorescence via the C2H2 transcription factors GIS, GIS2, and ZFP8, which promote GL1 expression. We show that the 

GIS-dependent pathway does not affect the regulation of TCL1 and TRY by miR156-targeted SPLs, represented by SPL9. 

These results demonstrate that the miR156-regulated SPLs establish a direct link between developmental programming and 

trichome distribution. 

Lipid metabolism plays a pivotal role in cell structure and in multiple plant developmental processes. b-Ketoacyl-[acyl 

carrier protein] synthase I (KASI) catalyzes the elongation of de novo fatty acid (FA) synthesis. Here, we report the functional 

characterization of KASI in the regulation of chloroplast division and embryo development. Phenotypic observation of an 

Arabidopsis thaliana T-DNA insertion mutant, kasI, revealed multiple morphological defects, including chlorotic (in netted 

patches) and curly leaves, reduced fertility, and semidwarfism. There are only one to five enlarged chloroplasts in the 

mesophyll cells of chlorotic sectors of young kasI rosette leaves, indicating suppressed chloroplast division under KASI 

deficiency. KASI deficiency results in a significant change in the polar lipid composition, which causes the suppressed 

expression of FtsZ and Min system genes, disordered Z-ring placement in the oversized chloroplast, and inhibited 

polymerization of FtsZ protein at mid-site of the chloroplast in kasI. In addition, KASI deficiency results in disrupted embryo 

development before the globular stage and dramatically reduces FA levels (;33.6% of the wild type) in seeds. These results 

demonstrate that de novo FA synthesis is crucial and has pleiotropic effects on plant growth. The polar lipid supply is 

important for chloroplast division and development, revealing a key function of FA synthesis in plastid development. 

INTRODUCTION 

1 


2 

Address correspondence to xychen@sibs.ac.cn. 



in the Instructions for Authors (www.plantcell.org) is: Xiao-Ya Chen 

(xychen@sibs.ac.cn). 

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Open Access articles can be viewed online without a subscription. 


Trichomes are specialized epidermal cells that act as barriers to 

protect plants from herbivores, UV irradiation, and excessive 

transpiration (Johnson, 1975; Mauricio and Rausher, 1997). In 

Arabidopsis thaliana, the distribution of trichomes is spatially and 

temporally regulated. During the early vegetative phase, trichomes 

are evenly distributed on the adaxial side of juvenile 

rosette leaves. As trichome production initiates on the abaxial 

side of leaves, the plant prepares for the transition from the 

vegetative to the reproductive stage (Telfer et al., 1997). After 

entering into the reproductive stage, the number of trichomes 

produced on the main inflorescence stem is gradually reduced. 

Floral organs are nearly glabrous except for a few trichomes 

present on the abaxial surface of sepals. 

Previous studies of Arabidopsis trichome development have 

focused on rosette leaves (Marks, 1997; Hülskamp et al., 1999; 

Larkin et al., 2003; Ishida et al., 2008). A series of genes positively 

regulating trichome initiation and development have been identified, 

including TRANSPARENT TESTA GLABRA1 (TTG1) 

(Galway et al., 1994; Walker et al., 1999; Bouyer et al., 2008), 

GLABRA1 (GL1) (Oppenheimer et al., 1991), GL3, and EN- 

HANCER OF GLABRA3 (EGL3) (Payne et al., 2000; Szymanski 

et al., 2000; Zhang et al., 2003). TTG1, GL1, and GL3+EGL3 

encode a WD40 protein, an R2R3 MYB transcription factor, and 

two basic helix-loop-helix–type transcription factors, respectively, 

and they form a ternary complex that initiates trichome cell 

development by activating GL2, which encodes a homeodomain/leucine 

zipper t ranscription factor (Rerie et al., 1994; 

Masucci et al., 1996; Schiefelbein, 2003; Pesch and Hülskamp, 

2004; Ramsay and Glover, 2005). Another group of genes 

encode the single-repeat R3 MYB factors TRIPTYCHON (TRY), 

CAPRICE (CPC), ENHANCER OF TRY AND CPC1 (ETC1), ETC2, 

ETC3, and TRICHOMELESS1 (TCL1) (Wada et al., 1997; Esch 

et al., 2004; Kirik et al., 2004a, 2004b; Schellmann et al., 2002; 

Simon et al., 2007; Wang et al., 2007). They suppress trichome 

initiation in a redundant manner, although TRY, TCL1, and CPC 

exert a major influence on rosette leaves, inflorescences, and 

roots (root hairs), respectively (Wada et al., 1997; Schnittger 

et al., 1998; 1999; Schellmann et al., 2002; Wang et al., 2007). It 

was suggested that expression of some of the negative regulator 

genes, including TRY, CPC, ETC1, and ETC3, was completely or 

partially dependent on the GL1-GL3-TTG1 protein complex 

(Morohashi et al., 2007), whereas TCL1 and ETC2 were regulated 

by yet unidentified mechanisms (Wang et al., 2008b). The singlerepeat 

MYB proteins can move from the trichome into neighboring 

cells where they compete with GL1 for the binding site of 

INTRODUCTION 

Studies have demonstrated the crucial roles of fatty acids (FAs) in 

plant development, cell signaling, and stress responses. The de 

novo biosynthesis of FAs starts with the formation of the direct 

substrate malonyl-coenzyme A (CoA), which is catalyzed by 

acetyl-CoA carboxylase (Guchhait et al., 1974; Gornicki and 

Haselkorn, 1993). As the initiation enzyme of FA chain elongation, 

b-ketoacyl-[acyl carrier protein] synthase III (KASIII) is responsible 

for the condensation reaction of malonyl-acyl carrier protein 

(ACP) and acetyl-ACP (Jackowski and Rock, 1987; Clough et al., 

1992), and KASI and KASII are the condensing enzymes for the 

elongation of the carbon chain from C4 to C18. KASI has high 

activity when butyryl- to myristyl-ACP (C4:0-C14:0 ACP) is used 

as the substrate to produce hexanoyl- to palmitoyl-ACP (C6:0- 

C16:0 ACP), whereas KASII mainly uses palmitoyl-ACP as the 

substrate to produce stearoyl-ACP (Shimakata and Stumpf, 

1982b). After the condensing reaction, the 3-ketoacyl-ACP is 

reduced at the carbonyl group by 3-ketoacyl-ACP reductase 

(KAR), dehydrated by hydroxyacyl-ACP dehydratase (HAD), and 

completed by enoyl-ACP reductase (ENR; which reduces the 

1 

Address correspondence to hwxue@sibs.ac.cn. 



in the Instructions for Authors (www.plantcell.org) is: Hong-Wei Xue 

(hwxue@sibs.ac.cn). 

C 

Some figures in this article are displayed in color online but in black 

and white in the print edition. 

W 


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trans-2 double bond to form a saturated FA; Mou et al., 2000). 

Subsequently, the mature palmitoyl-ACP and stearoyl-ACP participate 

in eukaryotic or prokaryotic FA processing pathway. 

These 16:0 and 18:0 FAs are involved in multiple biological 

processes, including producing glycerolipids and phospholipids 

that are important in cell signaling, forming very-long-chain fatty 

acids (VLCFAs) for cuticular waxes and plant development or 

being converted to plant hormones, such as jasmonic acid, that 

participate in stress responses (Ohlrogge and Browse, 1995). 

Several Arabidopsis thaliana mutants that are deficient in 

different steps of the FA biosynthesis pathway have been identified, 

and genetic studies have revealed that FAs participated in 

multiple aspects of plant growth (Ohlrogge and Browse, 1995). 

An Arabidopsis mutant that has a deficiency in acyl-ACP thioesterases 

(FATB) shows dramatically reduced eukaryotic lipids 

(lipids species mainly existing outside of the plastid, such as 

phosphatidylcholine [PC] and phosphatidylethanolamine [PE]), 

and fatb seedlings are semidwarf, exhibit altered morphology, 

and produce seeds with low viability (Bonaventure et al., 2003). A 

point mutation in the sixth exon of MOD1, which encodes the 

ENR in Arabidopsis, causes significantly decreased ENR activity, 

defective development of the chloroplast grana, premature 

cell death in mesophyll cells, and reduced fertility (Mou et al., 

2000). The VLCFAs have been demonstrated to participate 

in many aspects of plant growth, development, and stress 

response. Enoyl-CoA reductase has been identified as an important 

enzyme that is involved in the synthesis of all VLCFAs. An 

enoyl-CoA reductase knockout mutant, cer10, exhibits severe 

morphological abnormalities and reduced size of aerial organs, 

demonstrating the important roles of VLCFAs in endocytic 

50 

51

Appendix 


The Plant Cell, Vol. 23: 661–680, February 2011, www.plantcell.org ã 2011 American Society of Plant Biologists 

BENT UPPERMOST INTERNODE1 Encodes the Class II 

Formin FH5 Crucial for Actin Organization and 

Rice Development W OA 

The EMBO Journal (2010) 29, 1916–1927 | & 2010 European Molecular Biology Organization | Some Rights Reserved 0261-4189/10 

www.embojournal.org 

Rice early flowering1, a CKI, phosphorylates 

DELLA protein SLR1 to negatively regulate 

gibberellin signalling 

THE 

EMBO 

JOURNAL 

EMBO 

open 

Weibing Yang, a,1 Sulin Ren, b,1 Xiaoming Zhang, c,1 Mingjun Gao, a Shenghai Ye, c Yongbin Qi, c Yiyan Zheng, b 

Juan Wang, b Longjun Zeng, a Qun Li, a Shanjin Huang, b,2 and Zuhua He a,2,3 

a 

National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 

Shanghai 200032, China 

b 

Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of 

Sciences, Beijing 100093, China 

c 

State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural 

Sciences, Hangzhou 310021, China 

The actin cytoskeleton is an important regulator of cell expansion and morphogenesis in plants. However, the molecular 

mechanisms linking the actin cytoskeleton to these processes remain largely unknown. Here, we report the functional 

analysis of rice (Oryza sativa) FH5/BENT UPPERMOST INTERNODE1 (BUI1), which encodes a formin-type actin nucleation 

factor and affects cell expansion and plant morphogenesis in rice. The bui1 mutant displayed pleiotropic phenotypes, 

including bent uppermost internode, dwarfism, wavy panicle rachis, and enhanced gravitropic response. Cytological 

observation indicated that the growth defects of bui1 were caused mainly by inhibition of cell expansion. Map-based cloning 

revealed that BUI1 encodes the class II formin FH5. FH5 contains a phosphatase tensin-like domain at its amino terminus 

and two highly conserved formin-homology domains, FH1 and FH2. In vitro biochemical analyses indicated that FH5 is 

capable of nucleating actin assembly from free or profilin-bound monomeric actin. FH5 also interacts with the barbed end of 

actin filaments and prevents the addition and loss of actin subunits from the same end. Interestingly, the FH2 domain of FH5 

could bundle actin filaments directly and stabilize actin filaments in vitro. Consistent with these in vitro biochemical 

activities of FH5/BUI1, the amount of filamentous actin decreased, and the longitudinal actin cables almost disappeared 

in bui1 cells. The FH2 or FH1FH2 domains of FH5 could also bind to and bundle microtubules in vitro. Thus, our study 

identified a rice formin protein that regulates de novo actin nucleation and spatial organization of the actin filaments, which 

are important for proper cell expansion and rice morphogenesis. 

INTRODUCTION 

Rice (Oryza sativa) is a major food resource for nearly half of the 

world human population. Rice productivity is highly associated 

with its architectural pattern, including plant height, which is 

attributable mainly to stem internode elongation (Sasaki et al., 

2002; Wang and Li, 2008). The uppermost internode is of 

particular importance for rice productivity, since the elongation 

of the uppermost internode promotes panicle emergence 

(Zhu et al., 2006). The phytohormones gibberellins (GAs) and 

brassinosteroids are the two major factors that affect rice 

internode length by modulating cell expansion (Wang and Li, 

2008). The cytoskeleton, including microtubules and actin 

1 


2 


3 

Address correspondence to zhhe@sibs.ac.cn. 

The authors responsible for distribution of materials integral to the 


in the Instructions for Authors (www.plantcell.org) are: Shanjin Huang 

(sjhuang@ibcas.ac.cn) and Zuhua He (zhhe@sibs.ac.cn). 

W 


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microfilaments, is also essential for plant development and 

morphogenesis by modulation of cell expansion. For example, 

loss of function of DWARF AND GLADIUS LEAF1, which 

encodes an ATPase katanin-like protein in rice, caused disorganization 

of microtubule arrays and inhibited cell elongation, 

resulting in a dwarf phenotype (Komorisono et al., 2005). 

However, the information about the functions of the actin cytoskeleton 

in cell elongation and rice morphogenesis is rather 

limited. 

Pharmacological perturbation of actin organization indicates 

that the actin cytoskeleton is a major regulator of cell elongation 

in Arabidopsis thaliana and other plant species (Baluska et al., 

2001; Collings et al., 2006). Simultaneous downregulation of 

ACTIN2 and ACTIN7 reduced cell elongation in Arabidopsis 

hypocotyls (Kandasamy et al., 2009). Misexpression of actin 

regulatory proteins, such as profilin and actin-depolymerizing 

factors, also perturbs cell elongation (Ramachandran et al., 

2000; Dong et al., 2001; Kandasamy et al., 2009). In addition, 

the actin cytoskeleton plays pivotal roles in polar cell expansion 

and the establishment of cell division planes by governing 

cytoplasmic streaming, organelle movement, and vesicle transport 

(Martin et al., 2001; Staiger and Blanchoin, 2006). However, 

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits 

distribution, and reproduction in any medium, provided the original authorand source are credited. This license does not 

permit commercial exploitation or the creation of derivative works without specific permission. 

Cheng Dai and Hong-Wei Xue* 

National Key Laboratory of Plant Molecular Genetics, Institute of Plant 

Physiology and Ecology, Shanghai Institutes for Biological Sciences, 

Chinese Academy of Sciences, Shanghai, PR China 

The plant hormone gibberellin (GA) is crucial for multiple 

aspects of plant growth and development. To study the 

relevant regulatory mechanisms, we isolated a rice mutant 

earlier flowering1, el1, which is deficient in a casein 

kinase I that has critical roles in both plants and animals. 

el1 had an enhanced GA response, consistent with the 

suppression of EL1 expression by exogenous GA 3 . 

Biochemical characterization showed that EL1 specifically 

phosphorylates the rice DELLA protein SLR1, proving a 

direct evidence for SLR1 phosphorylation. Overexpression 

of SLR1 in wild-type plants caused a severe dwarf phenotype, 

which was significantly suppressed by EL1 deficiency, 

indicating the negative effect of SLR1 on GA 

signalling requires the EL1 function. Further studies 

showed that the phosphorylation of SLR1 is important 

for maintaining its activity and stability, and mutation of 

the candidate phosphorylation site of SLR1 results in the 

altered GA signalling. This study shows EL1 a novel and 

key regulator of the GA response and provided important 

clues on casein kinase I activities in GA signalling and 

plant development. 

The EMBO Journal (2010) 29, 1916–1927. doi:10.1038/ 

emboj.2010.75; Published online 16 April 2010 

Subject Categories: genome stability & dynamics; plant 

biology 

Keywords: casein kinase I; EL1; flowering time; GA 

response; rice 

Introduction 

The switch from vegetative to reproductive growth is a 

critical event in the life cycle of flowering plants and is 

essential for their maximum reproductive success (Bernier, 

1988). In Arabidopsis, a model plant for eudicots, four major 

pathways are involved in the control of flowering time: the 

*Corresponding author. National Key Laboratory of Plant Molecular 

Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese 

Academy of Sciences, 300 Fenglin Road, 200032 Shanghai, PR China. 

Tel.: þ 86 21 54924059; Fax: þ 86 21 54924060; 

E-mail: hwxue@sibs.ac.cn 

Received: 11 February 2010; accepted: 26 March 2010; published 

online: 16 April 2010 

photoperiod, autonomous, vernalization, and gibberellin 

(GA) pathways. In contrast to Arabidopsis, rice is a shortday 

plant. Several rice genes in the photoperiod pathway 

controlling heading date (Hd) (flowering time) have been 

genetically characterized, including Se1 (photoperiod sensitivity 

1; Yokoo et al, 1980; Yamagata et al, 1986), Se3–Se7 

(Yamagata et al, 1986; Poonyarit et al, 1989; Sano, 1992; 

Yokoo and Okuno, 1993), and E1–E3 (Hd 1–3, Tsai, 1995; 

Kinoshita, 1998). Some rice genes encode proteins similar to 

those in the Arabidopsis long-day pathway. Specifically, the 

products of Hd 1, 3a, and 6 are homologous to Arabidopsis 

CO (Yano et al, 2000), FT (FLOWERING LOCUS T, Kojima 

et al, 2002), and a subunit of kinase CK2 (a regulator of 

circadian rhythm and flowering time, Takahashi et al, 2001), 

respectively. In addition, rice phytochromes are also involved 

in the regulation of flowering time in response to day length 

(Izawa et al, 2000). Similar to Arabidopsis, circadian-regulated 

OsGI expression in transgenic rice has striking effects on 

flowering time (Hayama et al, 2003). 

Arabidopsis mutants defective in GA biosynthesis or 

signalling show severe delayed flowering (Moon et al, 2003; 

Yu et al, 2004); however, the role of GA in rice flowering is less 

clear. Biochemical and genetic studies have characterized key 

components, especially DELLA proteins, in the GA signalling 

cascade in both Arabidopsis (Peng et al, 1997; Dill and Sun, 

2001; Lee et al, 2002; Hussain et al, 2005) and rice (Ikeda et al, 

2001). The Arabidopsis DELLA proteins GAI, RGA, and RGL1 

negatively regulate flowering time in the absence of GA 

(Mouradov et al, 2002). Recently, the GA receptor GID1 was 

identified in Arabidopsis (Griffiths et al, 2006; Nakajima et al, 

2006) and rice (Ueguchi-Tanaka et al, 2005), and found 

to interact with DELLA proteins (GAI, RGA, or SLR1) in a 

GA-dependent manner both in vitro and in vivo (Willige et al, 

2007; Ueguchi-Tanaka et al, 2007a, b). The GA–GID1–SLR1 

complex is targeted for ubiquitination by SCF GID2 , an F-box 

protein, and degraded by the ubiquitin-dependent proteasome 

pathway (Sasaki et al, 2003; Gomi et al, 2004; Ueguchi-Tanaka 

et al, 2005, 2007a, b), which in turn results in the activated 

GA response. 

Casein kinase I, a serine/threonine protein kinase, is a 

multifunctional protein kinase detected in most eukaryotic 

cells (Gross and Anderson, 1998). In mammalian cells, there 

are five isoforms of casein kinase I: a, b, g, d, and e (Fish et al, 

1995). They are involved in multiple signalling pathways, 

including vesicular trafficking (Panek et al, 1997; Murakami 

et al, 1999), growth and morphogenesis (Robinson et al, 

1993), circadian rhythm (Kloss et al, 1998; Peters et al, 

1999), DNA-repair (Dhillon and Hoekstra, 1994), and cell 

cycle progression, and cytokinesis (Behrend et al, 2000). 

Previous studies showed that CKI regulates BR signalling 

1916 The EMBO Journal VOL 29 | NO 11 | 2010 & 2010 European Molecular Biology Organization 

52 

53

Appendix 


Committee 

Advisory Committee 

XiaoYa Chen MengMin Hong HongXuan Lin ShanJiong Shen 

YunGang Shen JiaoNai Shi ZhiHong Xu WenYing Yin 

GuoPing Zhao 

Academic Committee 

Chair: GuoPing Zhao 

Vice-Chair: ZuHua He YongPing Huang HongWei Xue ChengShu Wang 

Members: XiaoYa Chen Bin Han YuKe He Hai Huang 

Secretary: LaiGeng Li 

JiRong Huang WeiHong Jiang LaiGeng Li Xuan Li 

HongXuan Lin ZhongJun Qin QiGuang Wen ZhenBiao Yang 

Academic Degree Committee 

Chair: QiGuang Wen 

JiaMin Fang 

Members: WeiMing Cai JiMing Gong FangQing Guo Bin Han 

YuKe He ZuHua He Hai Huang JiRong Huang 

YongPing Huang WeiHong Jiang LaiGeng Li HongXuan Lin 

HuaLing Mi ZhongJun Qin WeiHua Tang ChengShuWang 

HongWei Xue 

Academic Committee of National Key Laboratory of Plant Molecular Genetics 

Chair: ZhiHong Xu 

Vice-Chair: Bin Han 

Hong Ma 

Members: XiaoYa Chen Chong Kong Yan Guo Hongxuan Lin 

YaoGuang Liu Qian Qian LiJia Qu JianMin Wan 

DaoXin Xie HongWei Xue YongBiao Xue zhenBiao Yang 

DaBing Zhang 

Academic Committee of Key Laboratory of Synthetic Biology 

Chair: ShengLi Yang 

Members: ZiXin Deng GuoPing Zhao LuHua Lai Li Huang 

HaiYan Liu JiaRui Wu SiLiang Zhang DaiJie Chen 

Lei Wang ZhiHao Sun YiXue Li Wen Liu 

WeiHong Jiang 

HongWei Xue 

Academic Committee of Key Laboratory of Insect Developmental and Evolutionary 

Biology 

Chair: Le Kang 

Members: KongMing Wu WenYing Yin GuoPing Zhao WenJun Bu 

JiaAn Chen FangQing Guo ZhaoJun Han WeiHua Xu 

XiaoFan Zhao ZhangWu Zhao 

54 

55

Appendix 

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Shanghai PuDong 

International Airport 

Zhaojiabang Road 

Sourth Wanping Road 

Dongan Road 

Xietu Road 

SIPPE 

Fenglin Road 

Lingling Road 

Xiaomuqiao Road 

Sourth Ruijing Road 

Inner Ring Elevated Road

ANNUAL REPORT

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