CURRICULUM VITAE Paul Gepts Dept. of Plant Sciences ... - Genética

A. Degrees received
CURRICULUM VITAE
Paul Gepts
Dept. of Plant Sciences
Section of Crop & Ecosystem Sciences
University of California
1 Shields Avenue
Davis, CA 95616-8780
Phone: (530) 752-7743 FAX: (530) 752-4361
Email: plgepts@ucdavis.edu
WWW: http://www.plantsciences.ucdavis.edu/gepts/geptslab.htm
1976 MS Agricultural Sciences (Plant Protection) Faculté des Sciences
Agronomiques, Gembloux,
1984 PhD Major: Plant Breeding and Genetics;
Minor: Botany
B. Professional positions held
Belgium
University of Wisconsin, Madison,
Wisconsin, USA
1977-78 Postgraduate researcher, Faculté des Sciences Agronomiques, Gembloux, Belgium
1978-81 Research associate; Centro Internacional de Agricultura Tropical, Cali, Colombia
1981-84 Research assistant; University of Wisconsin, Madison, Wisconsin
1985-87 Visiting postdoctoral research geneticist; University of California, Riverside
1987-90 Assistant Professor; University of California, Davis
1990-95 Associate Professor; University of California, Davis
1995- Professor;University of California, Davis
1997 Visiting professor, Universidad Nacional de Rosario, Argentina
1997-98 Sabbatical; Max-Planck Institute for Plant Breeding Research, Cologne, Germany
1998 Visiting professor; Università degli Studi, Perugia, Italy
1999-2001 Chair, Department of Agronomy and Range Science; University of California,
Davis, California, USA
C. Membership in professional societies
American Society of Agronomy
Crop Science Society of America
American Society for Horticultural Science
Society for Economic Botany
American Association for the Advancement of Science
American Genetics Association
Bean Improvement Cooperative

D. Honors and awards
Fellowship of the Belgian American Educational Foundation, New Haven, Connecticut, USA:
1981-82.
Distinguished Achievement Award, Bean Improvement Cooperative, 1991
Best research paper for 1991, Centro Internacional de Agricultura Tropical, Cali, Colombia (for
1991 Singh SP, Gutiérrez JA, Molina A, Urrea C, Gepts P. Genetic diversity in cultivated
common bean: II. Marker-based analysis of morphological and agronomic traits. Crop Sci
31: 23-29)
Fellow, American Association Advancement of Science, 2001
Fellow, American Society of Agronomy, 2003
Fellow, Crop Science Society of America, 2005
Best paper 2010, Crop Science Society of America Section C8 (Plant Genetic Resources), Kwak
M, Kami J, Gepts P. The putative Mesoamerican domestication center of Phaseolus
vulgaris is located in the Lerma-Santiago Basin of Mexico. Crop Sci 49: 554-563
Gamma Sigma Delta, 2010
E. Other service
Member, Editorial Board, Genetic Resources Crop Evolution, 1991-; Associate editor, American
Journal of Botany, 2005-
Member (1991) and topic manager (1994), USDA SBIR Plant Biology panel
Chair, USDA Phaseolus Crop Germplasm Committee: 1993-1997 and member 1997-
Chair, Plant Genetics Affinity Group, Genetics Graduate Group, UC Davis: 1994-1997
Elected member, Council, American Genetics Association, 2000-2003
Reviewer of grant proposals nationally for USDA NRI (Plant Genome, Weed Biology,
Biotechnology Risk Assessment) and NSF and internationally for Fontagro (research
foundation for Latin America associated with the Inter-American Development Bank),
International Foundation for Science (Sweden), Bureau des Ressources Génétiques and
Institut de Recherches pour le Développement (France), the Ministry of Research and the
Universities of Basilicata and Sienna (Italy), NSERC (Canada), NERC (U.K.), King
Abdul Aziz CITY for Science and Technology (Saudi Arabia), and Comisión Nacional
para el Conocimiento y Uso de la Biodiversidad – CONABIO (Mexico)
Review of manuscripts (2001-2010) for American Journal of Botany, Annals of Botany,
BioScience, BMC Bioinformatics, BMC Genomics, BMC Plant Biology, Cancer
Epidemiology Biomarkers and Prevention, Crop Science, Current Opinion Plant Biology,
Economic Botany, Environmental Biosafety Research, Euphytica, Field Crops Research,
Genetics, Genome, Genetic Resources and Crop Evolution, Journal of Cotton Science,

Journal of Heredity, Journal of the American Society for Horticultural Science, Molecular
Breeding, Molecular Ecology, Phytopathology, Plant Breeding Reviews, Plant Cell
Reports, Plant Genetic Resources, Plant Molecular Biology, Plant Physiology, PLoS One,
Proc. Nat. Acad. Sci. USA, Science, and Theor. Appl. Genet.
Review of book proposals or chapters: Blackwell, CABI, Hancock J (Plant Evolution and the
Origin of Crop Species 2004), University of California Press
Reviewed top graduate programs in agricultural sciences for the Brazilian government (CAPES,
Brasilia) in September 2000.
Reviewed 21 breeding programs for the USDA-ARS (OSQR program) (2003)
External member of doctoral thesis committees: University of Montpellier (France): 2000, 2001,
2004, 2008; University of Paris XI: 2001; U. of Aarhus: 2007; External member, these
d’aggrégation, University of Paris.
Elected member of the steering committee of the Legume Genomics Initiative: 2001-2005
Topical editor, Evolution of Crop Plants for the Encyclopedia of Plant and Crop Science (editor:
R. Goodman): 2002-2004
Nomination of colleagues for awards: Crop Science Society of America: Meyer Award, Fellow
of the Society, International Crop Science Award; Guggenheim Foundation, Fellow;
Institut Universitaire de France.
II. Professional achievements
A. Teaching/Extension (percentage of time: 20%)
a) Courses: He has taught several courses at UC Davis, either as sole instructor or coinstructor.
In these courses, he emphasizes student participation during the lectures and the use of
innovative information technologies in the classroom. Course materials for one of these two
courses can be found on the internet at http://www.plantsciences.ucdavis.edu/
gepts/pb143/pb143.htm. Student give him high marks (4.7/5.0) for the clarity of his presentations
and his organization, preparedness, and availability outside of the classroom. Availability of
course notes or extended outlines is also commented on very favorably. He has been invited to
teach short courses on Plant Genetic Resources Conservation at the National University of
Rosario in Argentina (1997), on Bean Genetic Resources at the University of Perugia (1999), and
on Genetics and Breeding of Beans (for the Bean Genome Sequencing project of CYTED, a
Latin American Science and Technology initiative (2010). Furthermore, he has given guest
lectures in courses at UC Davis and UC Berkeley. He authored a chapter “Ten thousand years of
crop evolution” in the textbook edited by Chrispeels and Sadava on Plants, Genes, and Crop
Biotechnology (2 nd edition, 2003).
b) Faculty advisor: Since 1987, he has been a major professor (including current
students) for 11 MS and 17 PhD students. He has hosted 35 visiting scientists or postdocs. As a

group, these students and scientists are active represent countries on five continents. They are
active as faculty, research scientists, or research leaders in the US and abroad (Argentina, Brazil,
Chile, Colombia, Costa Rica, France, Italy, Korea, Mexico, Senegal, Spain, Tanzania,
andVenezuela). Currently, he is faculty advisor and chair of the admissions committee for the
International Agricultural Development Graduate Group. He has chaired the Admissions
Committees of the Genetics Graduate Group and was a member of the Admissions Committee of
the Agroecology group. He has also mentored three high school students as interns in his
laboratory.
c) Extension or outreach: As a member of the Food Legumes Workgroup of the
University of California Division of Agriculture and Natural Resources, I attend the meetings and
field days of the workgroup. I usually provide updates on more basic aspects of bean genetics and
breeding. I also respond to questions of the media regarding plant breeding, crop evolution,
biodiversity or environmental topics associated with the release of transgenics to general
audiences, such as Monterey County, CA, and the Culinary Institute of America (1999-2000),
Guardian (2001), Science (2001, 2009), KOVR-13 (2002), San Francisco Chronicle and
Australian Broadcasting Corporation (2002), Nature (2002, 2003, 2009)), Sacramento Bee (2003,
2004), Canadian Broadcasting Corporation (2006), Self Magazine (2006), San Francisco
Magazine (2007), National Geographic (2009), Brownfield Ag News for America (2009), and
the Nation (2010).
B. Research (percentage of time: 60%)
His main academic interest lies in the study of crop evolution and its applications to
genetic diversity conservation and breeding. He has focused primarily on a single group of crops,
namely Phaseolus-Vigna beans given their importance in California crop rotations and
internationally. This has provided his research program with the continuity and opportunity to
conduct in depth studies on these crops. Some of the accomplishments during his research career
include:
a) Elucidation of the domestication pattern in several Phaseolus species, including common,
lima, and tepary beans. Using biochemical markers such as seed proteins, allozymes,
RFLPs, and SSRs, he was able to identify specific locations of domestication for these
species in Latin America. In common bean, in particular, the information that this species
resulted from two independent domestication leading to two major geographic gene pools
and six different ecomorphogeographic races has greatly influenced bean breeding
because it has allowed bean breeders to select parents more efficiently based on the
evolutionary origin of the parents. Similar gene pools exist in rice and chickpea.
However, in these crops the actual domestication pattern has not yet been elucidated.
b) Identification of the wild progenitor of common bean in Ecuador and northern Peru.
Using information from DNA sequences, he was able to identify the wild progenitor from
which all wild beans originated pre-domestication among recently discovered wild beans
in these countries. The significance of this finding for bean germplasm conservation and
utilization is that both major gene pools of beans (Mesoamerican and Andean) are
derived from the same source and both deserve to be conserved as they are likely to
contain different genes, e.g., different genes for disease resistance.

c) Documentation of the loss of diversity during and after domestication. Molecular and
biochemical markers have been used to follow the fate of genetic diversity during the
evolution of beans from their center of origin up until today. This research has identified
a sharp reduction in genetic diversity, including among commercial classes of common
bean in the U.S. These findings strongly suggest that the cultivated gene pool should be
broadened and has led to increased emphasis on exotic germplasm (both landraces and
wild beans) in breeding programs.
d) Genetic basis of coevolution between host and pathogens in beans. Molecular analyses
conducted by his team have shown that some pathogens show the same organization as
their bean host in two major geographic gene pools. Each host gene pools includes
resistance against different strains. The molecular basis for this coevolution resides in
disease resistance gene clusters that preexisted the separation of the gene pool. Upon
divergence of the gene pools, different genes were recruited to confer resistance against
the respective strains in the different geographic areas.
e) Gene flow in common bean and cowpea, predominantly self-pollinated species. As an
important evolutionary factor, gene flow can affect the level and distribution of genetic
diversity in species The upshot of his research on gene flow in common bean and cowpea,
is that outcrossing is an important force affecting the distribution of genetic diversity both
among populations and within the genome, although both species are considered to be
predominantly self-pollinating. Gene flow takes place predominantly from domesticated
to wild types and is of such magnitude that it may be displacing genetic diversity of wild
types (“swamping out”).
f) Isolation of genes for domestication: In one of his recent areas of interest, he has turned
his attention to the isolation of domestication genes. In the first well-studied case, the
gene for determinacy, a component of some bush growth habits, has been isolated.
Diversity analysis of this gene shows that farmers have performed multiple selection for
the determinacy phenotype. Similar studies are now conducted with two other
domestication genes.
g) Role of farmer-based selection in determining genetic diversity: One of the themes
addressed throughout his research is the role of farmers in shaping domestication and the
level of genetic diversity. For example, unlike many other crops, Phaseolus has resulted
from multiple domestications (no less than 5 species and 7 domestications). In addition,
he has shown how farmers can obviate the domestication bottleneck by stimulating gene
flow among farmer varieties, wild populations, and improved varieties. His current
research investigates how farmers select their seedstocks for fields in different
environments.
h) Bean genomics. He has played a significant role in developing genetic and genomic tools
that benefit the bean research community. He developed the core mapping population
(BAT93 x Jalo EEP55), which is used in the US, Latin America, and Europe for mapping
studies. He has developed four Bacterial Artificial Chromosome (BAC) libraries along a
phylogenetic pathway in order to study the structural evolution of complex loci
controlling agronomic traits such as pest and disease resistance. Most recently, he has
been involved in the development of a genetic and genomic database for Phaseolus,
PhaseolusGenes (http://phaseolusgenes.bioinformatics.ucdavis.edu/search/). This
database represents a tool to facilitate basic genetic studies and application of the bean
whole-genome sequences being determined to bean breeding.

i) Bean breeding: Since January 2012, he is responsible for the UC Davis bean breeding
program, with funding from the California Dry Bean Advisory Board. The main focus of
the program is to develop public varieties for the California bean industries, primarily
lima bean, garbanzos, and common bean.
C. Service (percentage time: 10%)
He was chair of the Plant Genetics Affinity Group at UC Davis from 1993-1997 and in this
capacity has led a review of the qualifying examination and the MS in Genetics guidelines. He
was also chair of the Plant Breeding and Biodiversity Focus Group at UC Davis from 2000-2006.
He was chair of the Phaseolus Crop Germplasm Committee. Under his guidance, studies have
been initiated to establish a core collection of the 11,000+ Phaseolus collection. He also led the
development of a “State of the Phaseolus germplasm” report (http://www.arsgrin.gov/npgs/cgc_reports/phascgc.htm).
D. Leadership (percentage of time: 10%)
He led the successful re-write to obtain a five-year extension of the USDA Regional W150
project on beans (1995-2000). Although this project is a regional project, participants come from
other regions as well, making it a challenge to coordinate such a large body of scientists.
He has also been Principal Investigator or Associate Director of a Bean/Cowpea CRSP (1991-
1995) and McKnight grant (1996-2002), respectively, both of which were large, multi-institution
grants, involved in research and education in Malawi and Mexico, respectively.
From 1999-2001, he was chair of the Department of Agronomy and Range Science at UC Davis.
He focused on improving the intellectual excellence of the department (support of seminar
series), promoting the improvement of department facilities (he obtained a ~ $ 250,000 grant to
upgrade farm facilities), and emphasized the development of information technology (department
network, online purchasing system)
He is currently the lead scientist for a large, multi-country project funded by the Kirkhouse Trust
of the U.K., devoted to introducing marker-assisted selection in bean breeding programs in East
Africa (currently Kenya, Tanzania, Uganda, with potential additions in Ethiopia, Rwanda, and
Zambia).
He has been the main organizer of three scientific meetings: 1) Bean Improvement Cooperative
biennial meeting in October 2003 in Sacramento, CA; 2) Plannning of legume genomics research
(funded by USDA and NSF), in December 2004 in Santa Fe, NM; and 3) Harlan II international
symposium on Biodiversity in Agriculture: Domestication, Evolution, & Sustainability, in
September 2008 in Davis, CA (a proceedings book has been submitted to Cambridge University
Press).

III. Professional publications
A. Number of publications
a) Books edited: 2
b) Book chapters, Proceedings, (last 10 years): 20
c) Technical papers, refereed (last 10 years): 44
e) Invited lectures, seminars, or symposia presentations (last 10 years): 40 nationally, 23
internationally
B. Most significant publications
2009 Kwak M, Kami J, Gepts P. The putative Mesoamerican domestication center of Phaseolus
vulgaris is located in the Lerma-Santiago Basin of Mexico. Crop Sci 49: 554-563.
2008 Pasquet R, Peltier A, Hufford M, Oudin E, Saulnier J, Paul L, Knudsen J, Herren H, Gepts
P. Long-distance pollen flow assessment through evaluation of pollinator foraging range
suggests transgene escape distances. Proc Nat Acad Sci USA 105:13456-13461 doi:
10.1073/pnas.0806040105
2008 Marvier M, Carrière Y, Ellstrand N, Gepts P, Kareiva P, Rosi-Marshall E, Tabaschnik BE,
Wolfenbarger LL Harvesting data from genetically engineered crops. Science 320:452-453
2008 Kwak M, Velasco D, Gepts P. Mapping homologous sequences for determinacy and
photoperiod sensitivity in common bean (Phaseolus vulgaris). J Hered 99: 283-291
doi:10.1093/jhered/esn005
2008 Gepts P, Aragão F, de Barros E, Blair MW, Brondani R, Broughton W, Galasso I,
Hernández G, Kami J, Lariguet P, McClean P, Melotto M, Miklas P, Pauls P., Pedrosa-
Harand A, Porch T, Sánchez F, Sparvoli F, Yu K. Genomics of Phaseolus beans, a major
source of dietary protein and micronutrients in the tropics. In: Moore P, Ming R (eds),
Genomics of Tropical Crop Plants, Springer: pp. 113-143
2006 Kami J, Poncet V, Geffroy V, Gepts P. Development of four phylogenetically-arrayed
BAC libraries and sequence of the APA locus in Phaseolus vulgaris. Theor Appl Genet
112: 987 - 998. DOI: 10.1007/s00122-005-0201-2
2005 Papa R, Acosta J, Delgado-Salinas A, Gepts P. A genome-wide analysis of differentiation
between wild and domesticated Phaseolus vulgaris from Mesoamerica. Theor Appl Genet
111: 1147-1158. DOI 10.1007/s00122-005-0045-9
2003 Papa R, Gepts P. Asymmetry of gene flow and differential geographical structure of
molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from
Mesoamerica. Theor Appl Genet (2003) 106:239-250

2002 Gepts, P (November 2002) Evolution during domestication. In: Encyclopedia of Life
Sciences. London: Nature Publishing Group. [doi: 10.1038/npg.els.0003071]
2002 Gepts P. Ten thousand years of crop evolution. In: M. Chrispeels and D. Sadava (eds.),
Plants, Genes, and Crop Biotechnology (2nd ed.). Bartlett and Jones, Sudbury, MA;
Chapter 13: pp. 328- 359
2002 Gepts P. A comparison between crop domestication, classical plant breeding, and genetic
engineering. Crop Sci. 42: 1780-1790.
2000 Geffroy V, Sévignac M, De Oliveira JCF, Fouilloux G, Skroch P, Thoquet P, Gepts P,
Langin T, and Dron M. 2000. Inheritance of partial resistance against Colletotrichum
lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with
genes involved in specific resistance. Mol. Plant-Microbe Inter. 13: 287-296.
1998 Freyre R, Skroch P, Geffroy V, Adam-Blondon A-F, Shirmohamadali A, Johnson W,
Llaca V, Nodari R, Pereira P, Tsai S-M, TohmeJ, Dron M, Nienhuis J, Vallejos CE, Gepts
P. Towards an integrated linkage map of common bean. 4. Development of a core map
andalignment of RFLP maps. Theor Appl Genet 97: 847-856.
1996 Koinange EMK, Singh SP, and Gepts P. Genetic control of the domestication syndrome in
common-bean. Crop Sci. 36: 1037-145.
1995 Gepts P. Genetic markers and core collections. In: Hodgkin T, Brown AHD, van Hintum
ThJL, Morales EAV (eds), Core collections of plant genetic resources. Wiley, New York:
pp. 127-146
1995 Kami J, Becerra Velásquez V, Debouck DG, Gepts P. Identification of presumed ancestral
DNA sequences of phaseolin in Phaseolus vulgaris. Proc Nat Acad Sci 92: 1101-1104.
1991 Singh SP, Gepts P, Debouck DG. Races of common bean (Phaseolus vulgaris L.,
Fabaceae). Econ Bot 45: 379-396.
1986 Gepts P, Osborn TC, Rashka K, Bliss FA. Phaseolin-protein variability in wild forms and
landraces of the common bean (Phaseolus vulgaris): evidence for multiple centers of
domestication. Econ Bot 40: 451-468.
1985 Gepts P, Bliss FA. F1 hybrid weakness in the common bean: differential geographic origin
suggests two gene pools in cultivated bean germplasm. J Hered 76: 447-450.
C. All Publications
1. 1977 Gepts, P., Angarita, A., Kummert, J. Labeling of the replicative forms of three
Tymoviruses. Parasitica 33: 95-102.
2. 1977 Kummert, J., Gepts, P., Angarita-Zerda, A. Comparison between the RNAs of three
Tymoviruses as studied by competitive molecular hybridization. Parasitica 33: 147-54.

3. 1978 Meeus, P., Fraselle, J., Gepts, P., Froidmont, F. Essais de lutte chimique contre la
rynchosporiose (Rynchosporium secalis (Oud.) Davis) de l'escourgeon. Parasitica 34 35-48.
4. 1980 Gepts, P. Variability from interspecific hybridisations. In: Bean Program 1979 Annual
Report, CIAT, Cali, Colombia: pp. 28-34. (not refereed)
5. 1980 Hidalgo, R., Song, L., Gepts, P. Diversidad genética de la especies cultivadas de
Phaseolus. Autotutorial unit, CIAT, Cali, Colombia: 52p. (not refereed)
6. 1981 Gepts, P. Variability from interspecific hybridisations. In: Bean Program 1980 Annual
Report, CIAT, Cali, Colombia: pp. 30-32. (not refereed)
7. 1981 Gepts, P. Hibridaciones interespecíficas para el mejoramiento de Phaseolus vulgaris L.
CIAT, Cali, Colombia, Serie SE-10-81: 17p. (not refereed)
8. 1982 Gepts, P. Variability from interspecific hybridisations. In: Bean Program 1981 Annual
Report, CIAT, Cali, Colombia: pp. 66-70. (not refereed)
9. 1982 Fernandez, F., Gepts, P., Lopez, M. Etapas de desarrollo de la planta de frijol común.
Autotutorial unit, CIAT, Cali, Colombia: 26p. (not refereed)
10. 1984 Gepts, P., Bliss, F.A. Enhanced available methionine concentration associated with
higher phaseolin levels in common bean seeds. Theor. Appl. Genet. 69: 47-53.
11. 1985 Gepts, P., Bliss, F.A. F1 hybrid weakness in the common bean: differential geographic
origin suggests two gene pools in cultivated common bean germplasm. J. Heredity 76: 447-
450.
12. 1986 Gepts, P., Bliss, F.A. Phaseolin variability among wild and cultivated common beans
from Colombia. Econ. Bot. 40: 469-478.
13. 1986 Gepts, P., Osborn, T.C., Rashka, K., Bliss, F.A. Electrophoretic analysis of phaseolin
protein variability in wild forms and landraces of the common bean, Phaseolus vulgaris :
Evidence for multiple centers of domestication. Econ. Bot. 40: 451-468.
14. 1986 Osborn, T.C., Blake, T.K., Gepts, P., Bliss, F.A. Bean arcelin protein. II. Genetic
variation, inheritance, and linkage relationships in common bean. Theor. Appl. Genet. 71:
847-851.
15. 1987 Gepts, P. Wild ancestors of crop plants - A neglected resource. J. Washington Acad.
Sci. 4
16. 1987 Gepts, P. Characterizing plant phenology: growth and development scales. In: K.
Wisiol and J.D. Hesketh (eds.), Plant growth modeling for resource management, 2 vols.,
CRC Press, Boca Raton, Florida, USA, Vol. 2: pp. 4-24.
17. 1988 Gepts, P., Kmiecik, K., Pereira, P., and Bliss, F.A. Dissemination pathways of
common bean (Phaseolus vulgaris, Fabaceae) deduced from phaseolin electrophoretic
variability. I. The Americas. Econ. Bot. 42: 73-85.
18. 1988 Gepts, P., and Bliss, F.A. Dissemination of common bean (Phaseolus vulgaris,
Fabaceae) deduced from phaseolin electrophoretic variability. II. Europe and Africa. Econ.
Bot. 42: 86-104.
19. 1988 Gepts, P. Phaseolin as an evolutionary marker. In: P. Gepts (ed.), Genetic Resources of
Phaseolus beans, Kluwer, the Netherlands: pp. 215-241.
20. 1988 Gepts, P. A Middle American and an Andean common bean gene pool. In: P. Gepts
(ed.), Genetic Resources of Phaseolus beans, Kluwer, the Netherlands: pp. 375-390.
21. 1988 Delgado Salinas, A., Bonet, A., Gepts, P. The wild relative of Phaseolus vulgaris in
Middle America. In: P. Gepts (ed.), Genetic Resources of Phaseolus beans, Kluwer, the
Netherlands: pp. 163-184.

22. 1988 Schinkel, C., and Gepts, P. Phaseolin diversity in the tepary bean, Phaseolus
acutifolius A. Gray. Plant Breeding 101: 292-301.
23. 1989 Gepts, P. and M.T. Clegg. Genetic diversity in pearl millet (Pennisetum glaucum (L.)
R. Br.) at the DNA sequence level. J. Hered. 80: 203-208.
24. 1989 Schinkel, C., Gepts, P. Allozyme variability in the tepary bean, Phaseolus acutifolius
A. Gray. Plant Breeding 102: 182-195.
25. 1989 Gepts, P. Bean. McGraw-Hill 1990 Yearbook of Science and Technology: pp. 38-39
(not refereed)
26. 1989 Gepts, P. Genetic diversity of seed storage proteins in plants, pp. 64-82. In: A.H.D.
Brown, M.T. Clegg, A.L. Kahler, and B.S. Weir (eds.), Population Genetics and Germplasm
Resources in Crop Improvement. Sinauer, Sunderland, MA.
27. 1989 Koenig, R., Gepts, P. Segregation and linkage of genes for seed proteins, isozymes,
and morphological traits in common bean (Phaseolus vulgaris). J. Heredity 80: 455-459.
28. 1989 Koenig, R., Gepts, P. Allozyme diversity in wild Phaseolus vulgaris: further evidence
for two major centers of genetic diversity. Theor. Appl. Genet. 78: 809-817
29. 1989 Gepts, P. Diversidad genética y domesticación en el género Phaseolus, y sus
implicaciones, pp. 379-396. In: Progreso en la investigación y producción del frijol común
(Phaseolus vulgaris L.). Centro Internacional de Agricultura Tropical, Cali, Colombia. (Not
refereed)
30. 1989 Singh, S.P., Debouck, D.G., Gepts, P. Races of common bean, Phaseolus vulgaris L.
In S. Beebe (ed.), Current topics in breeding of coommon bean. Working Document No. 47,
Bean Program, Centro Internacional de Agricultura Tropical, Cali, Colombia: pp. 75-89.
(Not refereed)
31. 1990 Koenig, R. Singh, S.P., Gepts, P. Novel phaseolin types in wild and cultivated
common bean (Phaseolus vulgaris, Fabaceae). Econ. Bot. 44: 50-60.
32. 1990 Gepts, P. Biochemical evidence bearing on the domestication of Phaseolus (Fabaceae)
beans. Econ. Bot. 44 (3S): 28-38.
33. 1991 Gepts, P., Debouck, D.G. Origin, domestication, and evolution of the common bean,
Phaseolus vulgaris, pp. 7-53. In: O. Voysest and A. Van Schoonhoven, eds., Common
beans: research for crop improvement, CIAT, Cali, Colombia.
34. 1991 Singh, S.P., Nodari, R. Gepts, P. Genetic diversity in cultivated Phaseolus vulgaris. I.
Allozymes. Crop Sci. 31: 19-23.
35. 1991 Singh, S.P., Gutiérrez, J.A., Molina, A., Urrea, C., Gepts, P. Genetic diversity in
cultivated Phaseolus vulgaris. II. Marker-based analysis of morpho-agronomic diversity.
Crop Sci. 31: 23-29.
36. 1991 Garrido, B., Nodari, R., Debouck, D.G., Gepts, P. Uni-2, a dominant mutation
affecting leaf development in Phaseolus vulgaris. J. Hered. 82: 181-183.
37. 1991 Singh, S.P., Gepts, P, Debouck, D.G. Races of common bean, (Phaseolus vulgaris,
Fabaceae). Econ. Bot. 45: 379-396.
38. 1991 Gepts P. Book review on Tissue culture in leguminous and oilseed crops, edited by
Y.P.S. Bajaj. Springer. Trends Biotech.
39. 1992 Koinange, E.M.K., Gepts, P. Hybrid weakness in wild Phaseolus vulgaris L. J.
Hered.83:135-139
40. 1992 Stockton T, Sonnante G, Gepts P. Detection of minisatellite sequences in Phaseolus
vulgaris. Plant Molec. Biol Rept. 10:47-59

41. 1992 Nodari, R.O., Koinange, E.M.K., Kelly, J.D., Gepts, P. Towards an integrated linkage
map of common bean. I. Development of genomic DNA probes and levels of restriction
fragment length polymorphism. Theor. Appl. Genet. 84: 186-192
42. 1992 Gepts P, Llaca V, Nodari RO, Panella L. Analysis of seed proteins, isozymes, and
RFLPs for genetic and evolutionary studies in Phaseolus. In: Linskens HF, Jackson JF (eds),
Seed analysis, Modern Methods of Plant Analysis, Vol. 14. Springer, Berlin: pp. 63-93.
43. 1992 Panella L, Gepts P. Genetic relationships within Vigna unguiculata (L.) Walp. based
on isozyme analyses. Genet. Res. Crop Evol. 39:71-88.
44. 1993 Nodari RO, Tsai SM, Gilbertson RL, Gepts P. Towards an integrated linkage map of
common bean. 2. Development of an RFLP-based linkage map. Theor. Appl. Genet. 85:
513-520
45. 1993 Gepts P. Linkage map of common bean (Phaseolus vulgaris L.). In: O'Brien SJ (ed),
Genetic Maps, 6th edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY,
pp. 6.101-6.109
46. 1993 Nodari RO, Tsai SM, Guzm

59. 1995 Paredes OM, Gepts P. Extensive introgression of Middle American germplasm into
Chilean common bean cultivars. Genet. Res. Crop Evol. 42: 29-41
60.1995 Kami J, Becerra Velásquez V, Debouck DG, Gepts P. Identification of the presumed
ancestral DNA sequences of phaseolin in Phaseolus vulgaris. Proc. Nat. Acad. Sci. 92:
1101-1104
61. 1995 Paredes OM, Gepts P. Segregation and recombination in inter-gene pool crosses of
Phaseolus vulgaris L. J. Hered. 86: 98-106
62. 1995 Gepts P. Genetic markers and core collections. In: Brown AHD, van Hintum T,
Hodgkin T, Morales EAV (eds.), Core collections: improving the management and use of
plant germplasm collections. Wiley, NY: pp. 127-146.
63. 1995 Singh SP, Molina A, Gepts P. Potential of wild common bean for seed yield
improvement of cultivars in the tropics. Can. J. Plant Sci. 75: 807-813
64. 1996 Freyre R, Ríos R, Guzmán L, Debouck DG, Gepts P. Ecogeographic distribution of
Phaseolus spp. (Fabaceae) in Bolivia. Econ. Bot. 50: 195-215
65. 1996 Koinange EMK, Singh SP, Gepts P. Genetic Control of the domestication syndrome in
common-bean. Crop Sci. 36, 1037-145
66. 1996 Johnson WC, Menéndez C, Nodari R, Koinange EMK, Magnusson S, Singh SP, Gepts
P. 1996. Association of a seed weight factor with the phaseolin seed storage protein locus
across genotypes, environments, and genomes in Phaseolus-Vigna spp.: Sax (1923)
revisited. J. Quant. Trait Loci, Volume 2, Article 5.
http://probe.nalusda.gov:8000/otherdocs/jqtl.
67. 1996 Gepts P, Freyre RO. The use of biochemical and molecular markers in elucidating the
origin and evolution of Phaseolus beans. In: D. Grattapaglia and M. Ferreira (eds.),
Molecular markers in biodiversity, genetics and breeding of plants - current techniques and
their applications, EMBRAPA-CENARGEN, Brasilia
68. 1996 Llaca V, Gepts P. Pulsed field gel electrophoresis analysis of the phaseolin locus
region in Phaseolus vulgaris. Genome 39, 722-729
69. 1996 Gepts P. Origin and evolution of cultivated Phaseolus species. In: Pickersgill B, Lock
JM (eds.) Advances in Legume Systematics, Vol 8, Legumes of economic importance. The
Royal Botanic Gardens, Kew, UK: pp. 65-74
70. 1997 Johnson WC, Guzmán P, Mandala D, Mkandawire ABC, Temple S, Gilbertson RL,
and Gepts P. Molecular tagging of the bc-3 gene for introgression into Andean common
bean. Crop Sci. 37: 248-254
71. 1997 Menéndez CM, Hall AE, Gepts P. A genetic linkage map of cowpea (Vigna
unguiculata) developed from a cross between two inbred, domesticated lines. Theor. Appl.
Genet. 95:1210-1217
72. 1998 Geffroy V, Creusot F, Falquet J, Sévignac M, Adam-Blondon A-F, Gepts P, Dron M.
A family of LRR sequences at the Co-2 locus for anthracnose resistance in Phaseolus
vulgaris and its potential use in marker-assisted selection. Theor. Appl. Genet. 96: 494-502
73. 1998 Gepts P. Origin and evolution of common bean: past events and recent trends.
HortScience 33: 1124-1130
74. 1998 Freyre R, Skroch P, Geffroy V, Adam-Blondon A-F, Shirmohamadali A, Johnson W,
Llaca V, Nodari R, Pereira P, Tsai S-M, Tohme J, Dron M, Nienhuis J, Vallejos CE, Gepts
P. Towards an integrated linkage map of common bean. 4. Development of a core map and
alignment of RFLP maps. Theor Appl Genet 97: 847-856.

75. 1998 Gepts P. What can molecular markers tell us about the process of domestication in
common bean? In: Damania A, Valkoun J, Willcox G, Qualset, CO (eds.), Proc. Symp. on
the Origins of agriculture and the domestication of crop plants, May 10-14, 1997, Aleppo,
Syria: pp. 198-209
76. 1998 Tsai SM, Nodari RO, Moon DH, Camargo LEA, Vencovsky R, Gepts P. QTL
mapping for nodule number and common bacterial blight in Phaseolus vulgaris L. Plant Soil
204:135-145.
77. 1999 Johnson WC, Gepts P. Segregation for performance in recombinant inbred populations
resulting from inter-gene pool crosses of common bean (Phaseolus vulgaris L.) . Euphytica
106: 45-56
78. 1999 Geffroy, V., D. Sicard, J. de Oliveira, M. Sévignac, S. Cohen, P. Gepts, C. Neema, and
M. Dron, 1999. Identification of an ancestral resistance gene cluster involved in the
coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum
lindemuthianum. Mol. Plant-Micr. Inter. 12: 774-784.
79. 1999 Gepts P. A phylogenetic and genomic analysis of crop germplasm: a necessary
condition for its rational conservation and use. In. J. P. Gustafson (ed.), Proc. Stadler
Genetics Symposium, June 8-10, 1998, Columbia, MO. Plenum, pp. 163-181.
80. 1999 Gepts P, Papa R, González Mejía A, Acosta Gallegos J, Delgado Salinas A. Human
effects on Phaseolus vulgaris adaptation before, during and after domestication. In: L. Van
Raamsdonk (ed), Proc. VIIth IOPB Symposium, Evolution in Man-Made Habitats,
Amsterdam August 11-15 1998, pp. 161-181.
81. 1999 Pasquet, R., Schwedes S, Gepts P. Isozyme diversity in Bambara groundnut. Crop Sci.
39: 1228-1236.
82. 1999 Gepts P. Development of an integrated linkage map. In: Singh SP (ed) Common bean
improvement for the twenty-first century. Kluwer, Dordrecht: pp. 53-91, pp. 389-400.
83. 1999 Gepts P, Papa R, Coulibaly S, González Mejía A, Pasquet R. 1999. Wild legume
diversity and domestication - insights from molecular methods. In: D. Vaughan (ed.), Wild
legumes, Proc. 7th MAFF International Workshop on Genetic Resources. National Institute
of Agrobiological Resources, Tsukuba, Japan: pp. 19-31
84. 2000 Geffroy V, Sévignac M, De Oliveira JCF, Fouilloux G, Skroch P, Thoquet P, Gepts
P, Langin T, and Dron M. 2000. Inheritance of partial resistance against Colletotrichum
lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with
genes involved in specific resistance. Mol. Plant-Microbe Inter. 13: 287-296.
85. 2000 Yu K, Park SJ, Poysa V, Gepts P. Integration of simple sequence repeat (SSR)
markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). J Hered 91:
429-434.
86. 2000 Gepts P. A phylogenetic and genomic analysis of crop germplasm: a necessary
condition for its rational conservation and use. In: J. P. Gustafson (ed.), Proc. Stadler
Genetics Symposium, June 8-10, 1998, Columbia, MO. Plenum, pp. 163-181.
87. 2000 Gepts P. Review of CD-ROM Legume (Fabaceae) Fruits and Seeds. Hortscience, 35:
1185-1186.
88. 2001 Spillane C, Gepts P. Evolutionary and genetic perspectives on the dynamics of crop
gene pools. In: Cooper HD, Spillane C, Hodgkin T (eds), Broadening the genetic base of
crop production. CABI, Wallingford, Oxon, UK: pp. 25-70.

89. 2001 Miklas PE, Johnson WC, Delorme R, Gepts P. 2001. Identification of QTL
conditioning physiological resistance and avoidance to white mold in dry bean G 122 (PI
163120). Crop Sci. 41:309-315
90. 2001 Gepts P. Origins of plant agriculture and major crop plants. In: Encyclopedia of Life-
Supporting Systems, pp. 629-637
91. 2002 Gepts P. Phaseolus vulgaris (Beans). Encyclopedia of Genetics, pp. 1444-1445
92. 2002 Johnson WC, Gepts P. The role of epistasis in a wide cross of common bean
(Phaseolus vulgaris L.), Euphytica 125: 69-79
93. 2002 Coulibaly S, Pasquet RS, Papa R, Gepts P. AFLP Analysis of the phenetic organization
and genetic diversity of Vigna unguiculata L. Walp. reveals extensive gene flow between
wild and domesticated types. Theor. Appl. Genet. 104: 358-366
94. 2002 Ouédraogo JT, Gowda B, Jean M, Gepts P, Timko MP, Belzile FJ. Construction of an
improved genetic linkage map of cowpea (Vigna unguiculata L.) combining AFLP, RFLP
and RAPD markers. Génome 45: 175-188
95. 2002 McClean PE, Lee R, Otto C, Gepts P, Bassett MJ. Molecular and phenotypic mapping
of genes controlling seed coat pattern and color in common bean (Phaseolus vulgaris L.) . J.
Hered 93: 148-152
96. 2002 Gepts P. A comparison between crop domestication, classical plant breeding, and
genetic engineering. Crop Sci.42: 1780- 1790.
97. 2002 Gepts P, Papa R. Evolution during domestication. Encyclopedia of Life Sciences, In:
Encyclopedia of Life Sciences. London: Nature Publishing Group. [doi:
10.1038/npg.els.0003071]
98. 2002 Lee SC, Gepts PL, Whitaker JR. Protein structures of common bean (Phaseolus
vulgaris) alpha-amylase inhibitors. J. Agric. & Food Chem. 50: 6618-6627.
99. 2003 Gepts P. Ten thousand years of crop evolution. In: M. Chrispeels and D. Sadava (eds.),
Plants, Genes, and Crop Biotechnology (2 nd ed.). Bartlett and Jones, Sudbury, MA: Chapter
13: pp. 328-359
100. 2003 Papa R, Gepts P. Asymmetry of gene flow and differential geographical structure of
molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from
Mesoamerica. Theor. Appl. Genet. 106:239–250.
101. 2003 Broughton WJ, Hernández G, Blair M, Beebe S, Gepts P, Vanderleyden J. Beans
(Phaseolus spp.) - Model food legumes. Plant Soil 252: 55-128.
102. 2003 Gepts P, Papa R. Possible effects of (trans)gene flow from crops on the genetic
diversity from landraces and wild relatives. Env Biosafety Res 2: 89-103.
103. 2003 Kelly JD, Gepts P, Miklas PN, and Coyne DP. Tagging and mapping of genes and
QTL and molecular marker-assisted selection for traits of economic importance in bean and
cowpea. Field Crops Res. 82, 135–154.
*104. 2004 Gepts P. Crop domestication as a long-term selection experiment. Plant Breed. Rev
24 (part 2): 1-44
105. 2004 Sylla F, Pasquet R, Gepts P. Genetic diversity of Vigna unguiculata as assessed by
RAPDs. Genet. Res. Crop Evol. 51: 539-550.
106. 2004 Gepts P. Topical editor, Crop domestication. Encyclopedia of Plant and Crop
Science, R. Goodman, General Editor. Dekker,
http://www.dekker.com/servlet/product/productid/E-EPCS/sub?n=t

107. 2004 Papa R, Gepts P. Gene flow between crops and their wild progenitors. In:
Encyclopedia of Plant and Crop Science, R. Goodman, General Editor. Dekker,
http://www.dekker.com/servlet/product/DOI/101081EEPCS120017095
108. 2004 Poncet V, Robert T, Sarr A, Gepts P. Qualitative trait location analyses of the
domestication syndrome and domestication process. In: Encyclopedia of Plant and Crop
Science, R. Goodman, General Editor. Dekker,
http://www.dekker.com/servlet/product/DOI/101081EEPCS120017088
109. 2004 Pallottini L, Garcia E, Kami J, Barcaccia G, P. Gepts P. The genetic anatomy of a
patented yellow bean. Crop Sci. 44, 968-977.
110. 2004 Gepts P. Who owns biodiversity and how should the owners be compensated? Plant
Physiol.134: 1295–1307.
111. 2004 Seo Y.-S., Gepts P, Gilbertson RL. Genetics of resistance to the geminivirus, Bean
dwarf mosaic virus, and the role of the hypersensitive response in common bean. Theor
Appl Genet 108: 786-793.
112. 2004 Snow AA, Andow DA, Gepts P, Hallerman EM, Power A, Tiedje JM, Wolfenbarger
LL. Genetically engineered organisms and the environment: Current status and
recommendations. Ecological Society of America (ESA) Position Paper Submitted to the
ESA Governing Board November 21, 2003. Accepted by the ESA Governing Board
February 26, 2004. http://www.esa.org/pao/esaPositions/Papers/geo_position.htm Also
published in Ecol. Applic. 15: 377–404 (2005).
113. 2004 Papa R, Gepts P. Asymmetric gene flow and introgression between domesticated and
wild populations. In: H.C.M. den Nijs, D. Bartsch, J. Sweet (eds.), Introgression from
Genetically Modified Plants into Wild Relatives, Proc. Conf. on Genetically Modified Plants
into Wild Relatives and its Consequences, 21-24 January, 2003, Amsterdam. CABI,
Wallingford, Oxfordshire, UK
114. 2004 Mkandawire ABC, Mabagala RB, Guzman P, Gepts P, Gilbertson RL. Genetic
diversity and pathogenic variation of common blight bacteria (Xanthomonas campestris pv.
phaseoli and X. campestris pv. phaseoli var. fuscans) suggests pathogen coevolution with
the common bean. Phytopathology 94: 593-603.
115. 2004 McClean P, Gepts P, Kami J. Genomics and genetic diversity in common bean. In:
Wilson RF, Stalker HT, Brummer EC (eds.), Legume crop genomics. AOCS Press,
Champaign, IL: pp. 60-82.
116. 2004 Berthaud J, Gepts P. Assessment of effects on genetic diversity. In: Maize and
biodiversity: the effects of transgenic maize in Mexico. Part of a background volume to a
Report from the North American Commission on Environmental Cooperation (CEC).
http://www.cec.org/files/PDF//Maize-Biodiversity-Chapter3_en.pdf
117. 2004 Andow, D.A., H. Daniell, P. Gepts, K.R. Lamkey, E. Nafziger, and D. Strayer. A
growing concern: Protecting the food supply in an era of pharmaceutical and industrial
crops. Union of Concerned Scientists, Cambridge, MA.
118. 2005 González-Mejía A, Wong A, Delgado-Salinas A, Gepts P. Assessment of Inter
Simple Sequence Repeat Markers to differentiate sympatric wild and domesticated
populations of common bean (Phaseolus vulgaris L.). Crop Sci 45:606–615.
119. 2005 Gepts P. Introduction of transgenic crops in centers of origin and domestication. In:
Daniel Lee Kleinman, Abby J. Kinchy, and Jo Handelsman, eds. Controversies in Science &
Technology: From Maize to Menopause. Madison, WI: The University of Wisconsin Press.

120. 2005 Gepts P, Beavis WD, Brummer EC, Shoemaker RC, Stalker HT, Weeden NF, Young
ND. Legumes as a model plant family. Genomics for food and feed. Report of the Crosslegume
Advances Through Genomics conference. Plant Phys 137: 1228-1235.
121. 2005 Zizumbo-Villarreal D, Colunga-GarcíaMarín P, Payró de la Cruz E, Delgado-Valerio
P, Gepts P. Population structure and evolutionary dynamics of wild–weedy–domesticated
complexes of common bean in a Mesoamerican region. Crop Sci 45:1073-1083.
122. 2005 Papa R, Acosta J, Delgado-Salinas A, Gepts P. A genome-wide analysis of
differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica. Theor
Appl Genet 111: 1147-1158. DOI 10.1007/s00122-005-0045-9
123. 2005 Payró de la Cruz E, Gepts P, Colunga García-Marín P, Zizumbo Villareal D. Spatial
distribution of genetic diversity in wild populations of Phaseolus vulgaris L. from
Guanajuato and Michoacán, México. Genet Res Crop Evol. 52: 589–599.
124. 2005 Cleveland DA, Soleri D, Aragón Cuevas F, Crossa J, Gepts P. Detecting (trans)gene
flow to landraces in centers of crop origin: lessons from the case of maize in Mexico.
Environmental Biosafety Research 4: 197–208
125. 2005 Gepts P. Plant and animal domestication as human-made evolution. In: Cracraft J and
Bybee RW (eds), Evolutionary science and society: educating a new generation. Proceedings
of the BSCS, AIBS Symposium November 2004, NABT Convention, Chicago, IL.
Published by BSCS, Colroado Springs, CO: pp. 180-186
126. 2006 Kami J, Poncet V, Geffroy V, Gepts P. Development of four phylogenetically-
arrayed BAC libraries and sequence of the APA locus in Phaseolus vulgaris. Theor Appl
Genet 112: 987 - 998.
127. 2006 Martínez-Castillo J, Zizumbo-Villarreal J, Gepts P, Delgado-Valerio P, and Colunga-
GarcíaMarín P. Structure and genetic diversity of wild populations of Lima bean (Phaseolus
lunatus L.) from the Yucatan peninsula, Mexico. Crop Sci 2006 46: 1071-1080
doi:10.2135/cropsci2005.05-0081.
128. 2006 Gepts P, Hancock J. The future of plant breeding. Crop Science 46: 1630-1634 DOI:
10.2135/cropsci2005-12-0497op.
129. 2006 Gepts P. Plant genetic resources conservation and utilization: the accomplishments
and future of a societal insurance policy. Crop Science 46:2278–2292.
DOI:10.2135/cropsci2006.03.0169gas
130. 2006 Feleke, Y., Pasquet R.S., Gepts P. Development of PCR-based chloroplast DNA
markers that characterize domesticated cowpea (Vigna unguiculata ssp. unguiculata var.
unguiculata) and highlight its crop-weed complex. Plant Systematics and Evolution, in
press. DOI 10.1007/s00606-006-0475-0
131. 2007 Martínez-Castillo J, Zizumbo-Villareal D, Gepts P, Colunga-García-Marín P. Gene
flow and genetic structure in the wild–weedy–domesticated complex of Phaseolus lunatus
L. in its Mesoamerican center of domestication and diversity. Crop Sci. 47:58–66
132. 2007 Chambers KJ, Brush SB, Grote MN, Gepts P. Describing maize (Zea mays L.)
landrace persistence in the Bajío of Mexico: a survey of 1940s and 1950s collection
locations. Econ Bot 60: 61:60-72.
133. 2007 Papa R, Bellucci E, Rossi M, Leonardi S, Rau D, Gepts P, Nanni L, Attene G.
Tagging the signatures of domestication in common bean (Phaseolus vulgaris L.). Annals of
Botany100: 1039-1051; doi:10.1093/aob/mcm151

134. 2007 Acosta-Gallegos JA, Kelly JD, Gepts P. Pre-breeding and genetic diversity in common
bean (Phaseolus vulgaris). Proc. International Plant Breeding Symposium, Ciudad de
México. Crop Sci 47(S3): S44–S59
135. 2007 Mattos Grisi MC de, Vianello Brondani RP, Gepts P, Blair MW, Arraes Pereira P.
Genetic mapping of a new set of microsatellite markers in a reference common bean
(Phaseolus vulgaris) population BAT93 x Jalo EEP558. Genet Molec Res 6: 691-706.
136. 2008 Gepts P. Tropical Environments, Biodiversity, and the Origin of Crops. In: Moore PH,
Ming R (eds.), Genomics of Tropical Crop Plants. Springer, Berlin. Pp. 1-20.
137. 2008 Gepts P, Aragão F, de Barros E, Blair, MW, Brondani R, Broughton WJ, Galasso I,
Hernández G, Kami J, Lariguet P, McClean P, Melotto M, Miklas P, Pauls P, Pedrosa-
Harand A, Porch T, Sánchez F, Sparvoli F and Yu K. Genomics of Phaseolus beans, a major
source of dietary protein and micronutrients in the Tropics. In: Moore PH, and Ming R
(Eds), Genomics of Tropical Crop Plants. Springer, Berlin, pp. 113-143.
138. 2008 Kwak M, Velasco D, Gepts P. Mapping homologous sequences for determinacy and
photoperiod sensitivity in common bean (Phaseolus vulgaris). J Hered 99: 283-291
doi:10.1093/jhered/esn005
139. 2008 Marvier M, Carrière Y, Ellstrand N, Gepts P, Kareiva P, Rosi-Marshall E, Tabaschnik
BE, Wolfenbarger LL Harvesting data from genetically engineered crops. Science 320:452-
453
140. 2008 McClean PE, Lavin M, Gepts P, and Jackson SA. Phaseolus vulgaris L.: A diploid
model for soybean. In: Stacey G (ed), Genomics of Soybean. Springer Science+Business
Media, LLC, New York (in press).
141. 2009 Pasquet R, Peltier A, Hufford M, Oudin E, Saulnier J, Paul L, Knudsen J, Herren H,
Gepts P. Long-distance pollen flow assessment through evaluation of pollinator foraging
range suggests transgene escape distances. Proc Nat Acad Sci USA 105:13456-13461 doi:
10.1073/pnas.0806040105
142. 2009 Kwak M, Kami J, Gepts P. The putative Mesoamerican domestication center of
Phaseolus vulgaris is located in the Lerma-Santiago Basin of Mexico. Crop Sci 49: 554-
563.
143. 2009 Piñeyro-Nelson A, van Heerwaarden J, Perales H, Serratos J, Rangel A, Hufford, M,
Gepts P, Garay-Arroyo A, Rivera-Bustamante R, Alvarez-Buylla E. Transgenes in Mexican
maize: molecular evidence and methodological considerations for GMO detection in
landrace populations. Molec Ecol 18, 750–761. doi: 10.1111/j.1365-294X.2008.03993.x
144. 2009 Pedrosa-Harand A, Kami J, Gepts P, Geffroy V, Schweizer D. Cytogenetic mapping
of common bean chromosomes reveals a less compartmentalized small-genome plant
species. Chromosoma 17: 405-417. DOI: 10.1007/s10577-009-9031-4
145. 2009 Dyer GA, Serratos-Hernández JA, Perales HR, Gepts P, Piñeyro-Nelson A, Chávez A,
Salinas-Arreortua N, Yúnez-Naude A, Taylor JE, and Alvarez-Buylla ER. Dispersal of
transgenes through maize seed systems in Mexico. PloS One 4(5): e5734.
doi:10.1371/journal.pone.0005734
146. 2009 Piñeyro-Nelson A, van Heerwaarden J, Perales H, Serratos J, Rangel A, Hufford M,
Gepts P, Garay-Arroyo A, Rivera-Bustamante R, Alvarez-Buylla E. Resolution of the
Mexican transgene detection controversy: error sources and scientific practice in commercial
and ecological contexts. 18: 4145-4150

147. 2010 Hanai LR, Santini L, Aranha Camargo LE, Fungaro MEP, Gepts P, Tsai S, Vieira
MLC. Extension of the core map of common bean with EST-SSR, RGA, AFLP, and
putative functional markers. Molec Breed 25:25-45
148. 2010 Fonsêca A, Ferreira J, dos Santos TR, Mosiolek M, Bellucci E, Kami J, Gepts P,
Geffroy V, Schweizer D, dos Santos KG, Pedrosa-Harand A. Cytogenetic map of common
bean (Phaseolus vulgaris L.). Chromosome Research 18:487-502
149. 2010 Burle M, Fonseca J, Kami J, Gepts P. Microsatellite diversity and genetic structure
among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of
diversity. Theor Appl Genet, in press
150. 2010 Kraft KH, Luna-Ruíz JJ, Gepts P. Different seed selection and conservation practices
for fresh market and dried chile farmers in Aguascalientes, Mexico. Econ Bot, in press.
151. 2010 Gepts P. Du berceau à l’assiette, le genre Phaseolus. In: Debarle G, Jacobsohn A
(eds), Du fayot au mangetout, l’histoire du haricot sans en perdre le fil. Rouergue, Rodez.
(Not peer-reviewed)
152. 2011 Hufford MB, Gepts P, Ross-Ibarra J. Influence of cryptic population structure on
observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis).
Molec Ecol 20: 2796-2811. DOI: 10.1111/j.1365-294X.2010.04924.x
153. 2011 Gonçalves-Vidigal MC, Cruz AS, Garcia A, Kami J, Vidigal Filho PS, Sousa LL,
McClean P, Gepts P, Pastor-Corrales PA. Linkage mapping of the Phg-1 and Co-14 genes
for resistance to angular leaf spot and anthracnose in the common bean cultivar AND 277.
Theor Appl Genet 122:893–903. DOI 10.1007/s00122-010-1496-1
154. 2011 Alo F, Furman BJ, Akhunov E, Dvorak J, Gepts P. Leveraging genomic resources of
model species for the assessment of phylogeny in wild and domesticated lentil. J Hered 102:
315-329. DOI: 10.1093/jhered/esr015
155. 2011 Nzungize J, Gepts P, Buruchara R, Male A, Ragama P, Busogoro JP, Baudoin JP.
Introgression of Pythium root rot resistance gene into Rwandan susceptible common bean
cultivars. African Journal of Plant Science 5: 193-200.
156. 2011 Nzungize J, Gepts P, Buruchara R, Buah S, Ragama P, Busogoro JP, Baudoin JP.
Pathogenic and molecular characterization of Pythium species inducing root rot symptoms
of common bean in Rwanda. African J Microbiol Res 5: 1169-1181.
157. 2011 Miklas PN, Fourie D, Trapp J, Larsen RC, Chavarro C, Blair MW, Gepts P. Genetic
characterization and molecular mapping Pse-2 gene for resistance to halo blight in common
bean. Crop Sci 51: 2439-2448. doi: 10.2135/cropsci2011.01.0046
158. 2011 Burle ML, Fonseca JR, Peloso MJ, Melo LC, Temple SR, Gepts P. Integrating
phenotypic evaluations with a molecular diversity assessment of a Brazilian collection of
common bean (Phaseolus vulgaris L.) landraces. Crop Sci 51: 2668-2680. doi:
10.2135/cropsci2010.12.0710
159. 2011 Nanni, L., Bitocchi, E., Bellucci, E., Rossi, M., Rau, D., Attene, G., Gepts, P., Papa,
R. Nucleotide diversity of a genomic sequence similar to SHATTERPROOF (PvSHP1) in
domesticated and wild common bean (Phaseolus vulgaris L.). Theor. Appl. Genet. 123:
1341-1357. DOI: 10.1007/s00122-011-1671-z
160. 2012 Gepts P, Famula TR, Bettinger RL, Brush SB, Damania AB, McGuire PE, Qualset CO
(eds) (2012) Biodiversity in agriculture: domestication, evolution, and sustainability.
Cambridge University Press, Cambridge, U.K. ISBN (hardback) 978-0-521-76459-9; ISBN
(paperback) 978-0-521-17087-1

161. 2012 Gepts P, Bettinger RL, Brush SB, Damania AB, Famula TR, McGuire PE, Qualset CO
The domestication of plants and animals: ten unanswered questions. In: Gepts P, Famula
TR, Bettinger RL, Brush SB, Damania AB, McGuire PE, Qualset CO (eds) Biodiversity in
agriculture: domestication, evolution, and sustainability. Cambridge University Press,
Cambridge, U.K.: pp. 1-8
162. 2012 Repinski S, Kwak M, Gepts P. The common bean growth habit gene PvTFL1y is a
functional homolog of Arabidopsis TFL1. Theor Appl Genet 124: 1539-154. DOI
10.1007/s00122-012-1808-8
163. 2012 Kraft KH, Luna-Ruíz JJ, Gepts P. A new collection of wild populations of Capsicum
in Mexico and the southern United States. Genet Res Crop Evol, published online: DOI:
10.1007/s10722-012-9827-5
164. 2012 Worthington M, Soleri D, Gepts P. Genetic composition and spatial distribution of
farmer-managed Phaseolus bean plantings: an example from a village in Oaxaca, Mexico.
Crop Sci 52: 1721-1735 doi:10.2135/cropsci2011.09.0518
IV. Current and Past Graduate Students, Postdocs and Visiting Scientists
A. MS degree students
1. Rosalie Koenig (USA) -- MS in International Agricultural Development -- Graduated August
1988 -- Thesis: Phaseolin and isozyme diversity in wild Phaseolus vulgaris L. Current
occupation: Organic farmer and leader in the organic movement.
2. Belén Garrido (Spain) -- M.S. in Agronomy -- Graduated June 1990 -- Thesis: Genetics of a
unifoliolate mutant in Phaseolus vulgaris. Current occupation: Bilingual teacher, Berkeley (CA)
School District
3. Viviana Becerra (Chile) -- M.S. in Agronomy -- Graduation: June 1992 -- Thesis: RFLPs in
Phaseolus vulgaris. Current occupation: Investigadora de Biotecnología INIA Quilamapu,
Chillán, Chile
4. Fana Sylla (Senegal) — MS Agronomy -- Graduation: December 1998 -- Thesis: RAPD
diversity in cowpea —. Current occupation: Researcher, Institut Senegalais de Recherche
Agronomique, Dakar, Senegal
5. Asghar Shirmohamadali (Iran) — MS in Genetics – Graduation: December 1998.
6. Timothy Wills (USA) – MS in Horticulture and Agronomy – Graduation: December 2003 –
Current occupation: Tomato Genetic Resources Center
7. Matthew Hufford (USA; started Fall 2002) – MS in International Agricultural Development -
Graduation: Spring 2005. Current occupation: PhD Ecology student, UC Davis
8. Benilda Zamora-Sable (Philippines; started Fall 2002) – MS in International Agricultural
Development. Current occupation: PhD student, U. of Manitoba
9. Sarah Barber (USA; started Fall 2003) – MS in International Agricultural Development
10. Margaret Worthington (USA; started Winter 2008) – MS in International Agricultural
Development - Thesis: Farmers choices and environmental adaptation of Phaseolus bean species
in Oaxaca, Mexico
11. Tamara Miller (USA; started Fall 2012) - MS Horticulture & Agronomy - Thesis: Marker
development for MAS for disease resistance

B. PhD degree students
1. Gisela Arndt (USA) -- Ph.D. in Genetics -- Thesis: Genetics of heat tolerance in common bean
-- Graduation Summer 1991- Current occupation: homemaker
2. Rubens Nodari (Brazil) -- Ph.D. in Genetics ---- Thesis: Mapping of the common bean genome
-- Graduation December 1991 -- Current occupation: Faculty, Universidade Federal de Santa
Catarina, Florianopolis, SC, Brazil and Ministry of the Environment, Federal Government of
Brazil, Brasilia
3. Lee Panella (USA) -- Ph.D. in Genetics -- Thesis: Genetic diversity of cowpea (Vigna
unguiculata) -- Graduation Summer 1992 — Current occupation: Research leader and Geneticist,
USDA-ARS, Colorado State University, Fort Collins, CO
4. Jim Kami (USA) -- Ph.D. in Genetics -- Thesis: Molecular evolution of phaseolin --
Graduation Summer 1992 — Current occupation: Postgraduate researcher, University of
California, Davis, CA
5. Epimaki Koinange (Tanzania) -- Ph.D. in Genetics -- Thesis: Genetics of domestication in
common bean -- Graduation Summer 1992 — Former occupation: Leader, Coffee research,
Ministry of Agriculture, Lyamungu, Tanzania. Deceased.
6. Mario Paredes (Chile) -- Ph.D. in Genetics -- Thesis: Transmission genetics in inter-gene pool
crosses of Phaseolus vulgaris — Graduation Spring 1993. Current occupation: Leader plant
research, INIA, Chile
7. Victor Llaca (Mexico) -- Ph.D. in Genetics -- Thesis: Genetic diversity and molecular
evolution of Phaseolus coccineus — Graduation spring 1994 -- Current occupation: Plant
genome research, Dupont, DE
8. William C. Johnson (USA)-- PhD in Genetics — Thesis: Molecular markers as tools in bean
breeding — Graduation: Summer 1997 – Current occupation: Squash breeder, Seminis,
Woodland, CA
9. Maria Rojas (Costa Rica) — PhD in Plant Biology — Thesis: Host-virus relationships in
common bean — Graduation: Spring 1998 – Current occupation: Research associate, Department
of Plant Pathology, University of California, Davis.
10. Sylvaine Coulibaly (Ivory Coast) — PhD in Genetics — Thesis: Analysis of seed protein
multigene families and AFLP diversity in cowpea – Graduation Spring 1999 – Current
occupation: Plant breeder, Nunhems Co., CA
11. Margarita Mauro (Mexico; started Winter 1997, Graduate Spring 2003) — PhD in Genetics
— Thesis: Introgression of yield genes from wild beans. Postdoc, USDA-ARD, Miami, FL
12. Julianno Sambatti (Brazil; started Fall 1998; graduate Spring 2004) – PhD in Ecology –
Thesis: Ecological genetics of wild Helianthus species. Postdoc, University of British Columbia
13. Myounghai Kwak (South Korea; Fall 2002-Winter 2008; postdoc, Seoul National University)
– PhD in Genetics – Thesis: Identification of the genes underlying the determinacy trait in
common bean and effect on linkage disequilibrium.
14. Marilia Lobo Burle (Brazil; started Fall 2003) – PhD in Ecology – Thesis: Molecular,
phenotypic, and adaptational diversity in Brazilian beans
15. Matthew Hufford (USA; started Fall 2004) – PhD in Ecology - Thesis: Dynamics of wild
populations of maize in Mesoamerica – Graduation December 2009 - Current occupation:
Postdoc, UC Davis

16. Kraig Kraft (USA; started Fall 2004) - PhD Ecology - Thesis: Evolutionary dynamics of
pepper landraces and wild populations. Graduation: September 2009 – Current occupation: Selfemployed,
Nicaragua
17. Shelby Repinski (USA: started Winter 2007; graduated Winter 2012) - PhD Genetics -
Thesis: Expression of genes for determinate growth habit in common bean – Current occupation:
Postdoc, University of Wisconsin Madison
C. Visiting students and scientists and postdoctoral fellows:
1. Giambatista Polignano, Istituto di Germoplasma, Bari, Italy: July 20-September 20, 1989
2. James Kelly, Dept. of Crop and Soil Science, Michigan State University, East Lansing, MI:
September 1, 1989-August 31, 1990.
3. Tamalynn Stockton, Postdoctoral fellow from December 1, 1989 to June 15, 1992. Current
occupation: postdoctoral fellow, USDA Plant Gene Expression Center, Albany, CA
4. Siu-Mui Tsai, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo,
Piracicaba, Brazil: September 1, 1990- February 28, 1992
5. Gabriella Sonnante, Istituto di Germoplasma, Bari, Italy: January 1, 1991- December 31, 1991.
Currrent position: researcher, Istituto di Germoplasma, Bari
6. Maria Cigales, Universidad de Colima, Mexico: January 1, 1992 - December 31, 1992.
Current postion: Faculty, Universidad de Colima
7. Rosanna Freyre, postdoctoral geneticist, September 1, 1993 - July 31, 1996. Current position:
Adjunct professor, Univ. of New Hampshire
8. Cristina Menéndez, postdoctoral geneticist, 1994-1995. Current position: University of
Pamplona, Spain
9. Roberto Papa, visiting scientist, University of Ancona, Italy, January 1996-August 1997.
Current position: Faculty, University of Ancona
10. Rémy Pasquet, IRD (previously ORSTOM), France: April 1996-April 1997. Current
location: ICIPE, Nairobi, Kenya.
11. Alonso Gonzalez, postdoc, January 1997- December 1998. Current position: CSIRO,
Darwin, Australia
12. Patricia Colunga GarciaMarin, visiting scientist, CICY, Mérida, Yucatan, Mexico, December
1998 -February 2000
13. Daniel Zizumbo, visiting scientist, CICY, Mérida, Yucatan, Mexico, December 1998 -
February 2000
14. Juan José Ferreira, Dpto. Hortofruticultura- CIATA, Villaviciosa, Asturias, Spain; October -
December 1999
15. Valérie Geffroy, visiting postdoctoral geneticist: April 2000 - July 2001. Current position:
researcher, Institut National de la Recherche Agronomique, Orsay, France
16. Valérie Poncet, visiting postdoctoral geneticist: September 2000 - August 2001. Current
position: Institut de Recherches pour le Développement, France
17. Ana María Torres, visiting scientist, December 2000 - February 2001. Permanent position:
Centro de Investigacion y Formacion Agraria (CIFA Alameda del Obispo), Dpto. Mejora y
Agronomia (Leguminosas), University of Córdoba, Spain
18. Cristina Mapes, visiting scientist, Jardín Botánico, Universidad Nacional Autónoma de
México: January 2001 - January 2002.

19. Diaga Diouf, visiting scientist, Faculty at Université Cheikh AntDeara Diop, Dakar, Senegal:
March-June 2003
20. Yonas Feleke (Ethiopia; until December 2003) – Visiting student of the University of Nairobi
(sandwich program) - Thesis: Genetic diversity and phylogeny of Vigna unguiculata and related
species (in collaboration with R. Pasquet, IRD, France)
21. Luca Pallottini (Italy; March to August 2003) - Visiting student of the University of Padova:
Genetic diversity of beans and bean genomics. Plant breeder, Italy.
22. Hani Antoun, visiting scientist, Faculty at the Université Laval, Québec: August 2003 -
August 2004
23. Margaret Gutiérrez, visiting scientist, INIA, Venezuela: August - November 2004
24. María de la Fuente, visiting scientist, Missión Biológica, Galicia, Spain: November -
December 2004
25. Rajendra Malhotra, visiting scientist, ICARDA, Aleppo, Syria: August - November 2005
26. José de Jesús Luna Ruíz, visiting scientist, Faculty at Universidad Autónoma de
Aguascalientes: September 2005 - May 2006
27. Pilar Ramírez Fonseca, visiting scientist, Faculty at Universidad de Costa Rica: November-
December 2006
28. Juliano Lino Ferreira (Brazil: January 2006-2007); Visiting student of the Universidade
Federal de Viçosa, MG, Brazil (in collaboration with A. Borem)
29. Daniel Zizumbo, visiting scientist, Centro de Investigaciones Científicas del Yucatán,
Mérida, Mexico: August 2007-August 2008
30. Patricia Colunga, visiting scientist, Centro de Investigaciones Científicas del Yucatán,
Mérida, Mexico: August 2007-August 2008
31. J. Vicente Gomes dos Santos, visiting student, ESALQ, Universidade de Sao Paulo: August
2008-March 2009
32. Pedro Soares Vidigal Filho, visiting scientist, Universidade Estadual de Maringá, PR, Brasil,
December 2008-December 2009.
33. Maria Celeste Gonçalves Vidigal, visiting scientist, Universidade Estadual de Maringá, PR,
Brasil, December 2008-December 2009.
34. Marta Galván, visiting scientist, INTA, Salta, Argentina: August - December 2009.
35. Tania Gioia, visiting student, Università degli Studi della Basilicata: March 2009 -
36. Augusto Gomez Guimaraes, visiting student, ESALQ, Universidade de Sao Paulo: April-
September 2010
37. Sun Lei, visiting student, Jilin Academy of Agricultural Sciences, Chanchun, China: October
2010-
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