RosBREED: Testing Genotyping By Sequencing in Strawberry
RosBREED: Testing Genotyping By Sequencing in Strawberry RosBREED: Testing Genotyping By Sequencing in Strawberry
RosBREED: Testing Genotyping By Sequencing in Strawberry Natalia Salinas, Jill Bushakra, Chad Finn, Eric van de Weg, Dan Sargent, Ksenija Gasic, Bradley Rauh and Nahla Bassil
- Page 2 and 3: Outline of Presentation What is GB
- Page 4 and 5: Genotyping by Sequencing (GBS) (Els
- Page 6 and 7: Genotyping by Sequencing (GBS) •
- Page 8 and 9: GBS in Strawberry
- Page 10 and 11: Strawberry Germplasm Jucunda R_Sove
- Page 12 and 13: Strawberry Progress Report
- Page 14 and 15: Strawberry Progress Report • Sequ
- Page 16: Questions www.rosbreed.org
<strong>RosBREED</strong>: <strong>Test<strong>in</strong>g</strong><br />
<strong>Genotyp<strong>in</strong>g</strong> <strong>By</strong> <strong>Sequenc<strong>in</strong>g</strong><br />
<strong>in</strong> <strong>Strawberry</strong><br />
Natalia Sal<strong>in</strong>as, Jill Bushakra, Chad F<strong>in</strong>n, Eric van de Weg,<br />
Dan Sargent, Ksenija Gasic, Bradley Rauh and Nahla Bassil
Outl<strong>in</strong>e of Presentation<br />
What is GBS<br />
GBS <strong>in</strong> <strong>Strawberry</strong><br />
Progress Report
<strong>Genotyp<strong>in</strong>g</strong> by <strong>Sequenc<strong>in</strong>g</strong>
<strong>Genotyp<strong>in</strong>g</strong> by <strong>Sequenc<strong>in</strong>g</strong> (GBS)<br />
(Elshire et al. 2011)<br />
• Reduced representation sequenc<strong>in</strong>g
<strong>Genotyp<strong>in</strong>g</strong> by <strong>Sequenc<strong>in</strong>g</strong> (GBS)<br />
• Advantages<br />
(Elshire et al. 2011, Poland & Rife 2012)<br />
- Relatively simple and fast protocol<br />
- Relatively low cost ($~30/sample)<br />
- High-throughput<br />
- High-density SNP discovery<br />
- <strong>Sequenc<strong>in</strong>g</strong> of potentially un-accessed regions of<br />
the genome<br />
- Requires no reference genome<br />
- Can be tailored for each species
<strong>Genotyp<strong>in</strong>g</strong> by <strong>Sequenc<strong>in</strong>g</strong> (GBS)<br />
• Disadvantages<br />
(Elshire et al. 2011, Poland & Rife 2012)<br />
- Miss<strong>in</strong>g data from technical issues<br />
- Library complexity, under-represented or overrepresented<br />
sequences<br />
- Miss<strong>in</strong>g data from biological issues<br />
- Presence/absence variation, polymorphic RE<br />
sites, differential methylation
<strong>Genotyp<strong>in</strong>g</strong> by <strong>Sequenc<strong>in</strong>g</strong> Uses
GBS <strong>in</strong> <strong>Strawberry</strong>
GBS <strong>in</strong> <strong>Strawberry</strong><br />
Goal: Compare GBS and Axiom ® for<br />
generation and utility of markers for<br />
Pedigree-Based Analysis and Genome-Wide<br />
Selection<br />
- ‘Redgauntlet’ x ‘Hapil’ (51 progeny)<br />
- ‘Holiday’ x ‘Korona’ (17 progeny)<br />
- ‘Honeoye’ x ‘Tribute’ (4 progeny)<br />
- ‘Tribute’ x MSU_56 (3 progeny)<br />
- Sequenced SNP panel <strong>in</strong>dividuals (4)<br />
- Founders, diverse <strong>in</strong>dividuals
<strong>Strawberry</strong> Germplasm<br />
Jucunda<br />
R_Sovereign<br />
Howard_17<br />
Aberdeen<br />
US_3763<br />
Climax<br />
Fairfax<br />
NJ_1051<br />
Sparkle<br />
Talisman<br />
Juspa<br />
P_Beauty<br />
Gorella<br />
Induka<br />
Tamella<br />
Korona<br />
OSC_1765<br />
S_Sengana
<strong>Strawberry</strong> Germplasm<br />
F.chiloensis<br />
UNK17<br />
FRA_1702<br />
FRA_1697<br />
JH_101-1<br />
RH30xLH50-4<br />
FVC_8-1<br />
FVC_8-2<br />
FVC_8-3<br />
FVC_8-4<br />
FVC_8-5
<strong>Strawberry</strong> Progress Report
<strong>Strawberry</strong> Progress Report<br />
• GBS library<br />
Bioanalyzer<br />
results<br />
-Fragment sizes<br />
ma<strong>in</strong>ly ~200bp<br />
-No significant<br />
adapter dimer
<strong>Strawberry</strong> Progress Report<br />
• <strong>Sequenc<strong>in</strong>g</strong> results<br />
- 100bp s<strong>in</strong>gle-end reads<br />
- Total sequences 188 million raw reads<br />
- 49% GC content<br />
• Next step: Data analysis
Acknowledgements<br />
This project is supported by the Specialty<br />
Crop Research Initiative of USDA’s<br />
National Institute of Food and Agriculture
Questions<br />
www.rosbreed.org
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