Potato and sweetpotato genomics
Tolerance and other genes
Potato: Drought tolerance genes and traits
Sweetpotato: Gene Ind...
Genetic and genomic resources for
sweetpotato
Sweetpotato genetic and genomic resources
22.000 ESTs
1500 gene sequences
1 Bac
2 Low resolution maps
~100 SSR markers
LD ...
Access to biodiversity: Composite Genotype Set
480 accessions
•Biodiversity
•High β-carotene
•High starch
•High iron and z...
Gene sequences
Enriched for stress-related genes
2 cDNA libraries
454 sequencing
Read assembly
Annotation
vv
Gene Index Annotation
39.299 annotated sequences – 24.763 unique sequences
cell, 19341
organelle,
15130
virion, 12
symp...
Sweetpotato Gene Index
Sweetpotato Gene Index
Sweetpotato Gene Index
Sweetpotato Gene Index
Raul Cordova
Jaime Arturo Pacheco
Gene Index
Functional genomics
-Candidate gene sequences
-Microarray probes
New gene-based
SSR and SNP marker
SSR Marker
http://gcpcr.grinfo.n
et/index.php?app=da
tasets&inc=file_detail
s&file_id=900
3/4
SSR Marker
Other New Marker
Diversity Arrays DArT
Conserved Ortholog Set - COSII
Marker Application:
Genepool structure
Improved Varieties, breeding lines
Landraces:
Latin America and the Caribbean
Sub-S...
Marker application: Mapping
Population: Ipomoea trifida (2n) Marker:
~38 SSR
345 – 600 DArT
Map:
In progress
108 plants es...
Potato abiotic stress tolerance
Potato Development Targets
Abiotic stress tolerance is complex…
Environmental constraints
• Variability of natural climate
stress events
Genetic cons...
Improving potato drought tolerance
Drought-
tolerant
potato
• Yield losses <30%
at a 40 day drought
spell during bulking
•...
Testing environments
1/4
Physiological traits
CLONE: CANCHANCLONE: CANCHAN
Stricter stomatal control, increased WUE
Osmotic adjustment
Higher water...
Some, but not all key Persons
Some, but not all key Persons
Some, but not all key Persons
Some, but not all key Persons
Some, but not all key Persons
Some, but not all key Persons
Genomic Analysis
Water saver
Water spender
Dehydration tolerant
control drought
resistant
control drought
susceptible
Cand...
Metabolites
134** 20
2316* 153
14410* 5882
11297 13999
143** 16
21017** 4035
244* 34
690 224
711* 105
1478* 719
258 68
12 ...
Potato drought tolerance traitsPotato drought tolerance traits
Drought PP2C
PSI and II-related genes
Chlororespiration-rel...
Candidate gene marker
Components:
•PGSC-Gene models
•TIGR EST database
•QualitySNP (Tang et al. 2006)
•HaploSNPer (Tang et...
Association genetics study
Germplasm panel Marker Phenotyping
Population structure:
60 mapped SSR
QTL:
250 (partially) map...
Acknowledgments
Sweetpotato Genetic Resources
CIP HQ
David Tay
Rosalina Tincopa
Genoveva Rossel
Omar Palomino
Raul Cordoba...
Molecular Breeding in Vegetables
Molecular Breeding in Vegetables
Drought tolerance genes and traits/Gene Index and markers
Drought tolerance genes and traits/Gene Index and markers
Drought tolerance genes and traits/Gene Index and markers
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Drought tolerance genes and traits/Gene Index and markers

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Seminar - Roland Schafleitner - July 23, 2010

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Drought tolerance genes and traits/Gene Index and markers

  1. 1. Potato and sweetpotato genomics Tolerance and other genes Potato: Drought tolerance genes and traits Sweetpotato: Gene Index and markers
  2. 2. Genetic and genomic resources for sweetpotato
  3. 3. Sweetpotato genetic and genomic resources 22.000 ESTs 1500 gene sequences 1 Bac 2 Low resolution maps ~100 SSR markers LD cDNA microarray •Composite Genotype Set •Gene sequences •Markers •Map
  4. 4. Access to biodiversity: Composite Genotype Set 480 accessions •Biodiversity •High β-carotene •High starch •High iron and zinc contents •Nematode, virus and drought resistance -Pathogen-free in vitro plants ready for international distribution -Morphological information and molecular fingerprints (SSR genotypes) available 480 accessions •Biodiversity •High β-carotene •High starch •High iron and zinc contents •Nematode, virus and drought resistance -Pathogen-free in vitro plants ready for international distribution -Morphological information and molecular fingerprints (SSR genotypes) available http://gcpcr.grinfo.net/files/cr_files/gcpcr_file832.xls Composite Genotype SetComposite Genotype Set CIP Ipomoea batatas collection: 5,961 accessions CIP Ipomoea batatas collection: 5,961 accessions
  5. 5. Gene sequences Enriched for stress-related genes 2 cDNA libraries 454 sequencing Read assembly Annotation
  6. 6. vv Gene Index Annotation 39.299 annotated sequences – 24.763 unique sequences cell, 19341 organelle, 15130 virion, 12 symplast, 10 macromolecul. complex, 4487 membrane- enclosed lumen, 1842 envelope, 1159 extracellular region, 592 grow th, 506 multi-organism process, 935 reproduction, 1449 multicellular organismal process, 2452 developmental process, 2767 localization, 2852 biological regulation, 4183 response to stimulus, 4832 anatomical structure formation, 496 immune system process, 314 rhythmic process, 80 viral reproduction, 30 cellular process, 12576 metabolic process, 11133 binding, 10242 catalytic activity, 9097 antioxidant activity, 155 nutrient reservoir activity, 247 molecular transducer activity, 326 electron carrier activity, 352 transporter activity, 1656 transcription regulator activity, 1157 structural molecule activity, 1020 enzyme regulator activity, 437 translation regulator activity, 386 Cellular location Biological function Molecular process
  7. 7. Sweetpotato Gene Index
  8. 8. Sweetpotato Gene Index
  9. 9. Sweetpotato Gene Index
  10. 10. Sweetpotato Gene Index Raul Cordova Jaime Arturo Pacheco
  11. 11. Gene Index Functional genomics -Candidate gene sequences -Microarray probes New gene-based SSR and SNP marker
  12. 12. SSR Marker http://gcpcr.grinfo.n et/index.php?app=da tasets&inc=file_detail s&file_id=900 3/4
  13. 13. SSR Marker
  14. 14. Other New Marker Diversity Arrays DArT Conserved Ortholog Set - COSII
  15. 15. Marker Application: Genepool structure Improved Varieties, breeding lines Landraces: Latin America and the Caribbean Sub-Saharan Africa East and South-East Asia Oceania North Africa I. trifida Jonathan Feng Shu Bai Xushu 18 Jewel Wagabolige Yanshu 1 Beauregard I. trifida parent 1 I. trifida parent 2 Jonathan Feng Shu Bai Xushu 18 Jewel Wagabolige Yanshu 1 Beauregard Jonathan Feng Shu Bai Xushu 18 Jewel Wagabolige Yanshu 1 Beauregard I. trifida I. trifida LAC
  16. 16. Marker application: Mapping Population: Ipomoea trifida (2n) Marker: ~38 SSR 345 – 600 DArT Map: In progress 108 plants established in vitro Easy to handle linkage map Comparative genomics among sweetpotato and other crops Easy to handle linkage map Comparative genomics among sweetpotato and other crops
  17. 17. Potato abiotic stress tolerance
  18. 18. Potato Development Targets
  19. 19. Abiotic stress tolerance is complex… Environmental constraints • Variability of natural climate stress events Genetic constraints • Tolerance traits might be polygenic and epistatic • Gene x environment interactions Difficult selection under natural stress conditions Interactions between genes and genetic background Not all tolerance traits work in all environments Efficient breeding requires information on theEfficient breeding requires information on the genetic and physiological basis of tolerance traitsgenetic and physiological basis of tolerance traits
  20. 20. Improving potato drought tolerance Drought- tolerant potato • Yield losses <30% at a 40 day drought spell during bulking • -minimum yield 25t/ha (~600 g/plant) • No tuber defects Drought- tolerant potato • Yield losses <30% at a 40 day drought spell during bulking • -minimum yield 25t/ha (~600 g/plant) • No tuber defects Field screening of germplasm collection (Chujoy % Cabello) Field screening of germplasm collection (Chujoy % Cabello) Identification of drought tolerance traits Identification of drought tolerance traits Trait-marker associationTrait-marker association BreedingBreeding Many susceptible and a few tolerant clones Screening tools
  21. 21. Testing environments
  22. 22. 1/4
  23. 23. Physiological traits CLONE: CANCHANCLONE: CANCHAN Stricter stomatal control, increased WUE Osmotic adjustment Higher water uptake capacity :: Stomatal resistance (s cm -1 ) 37 days after drought 0.00 2.00 4.00 6.00 8.00 10.00 12.00 14.00 16.00 Well-watered Drought Well-watered Drought 397077.16 397077.16 380389.1 380389.1 Osmotic potential (MPa) 39 days after drought 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Well-watered Drought Well-watered Drought 397077.16 397077.16 380389.1 380389.1
  24. 24. Some, but not all key Persons
  25. 25. Some, but not all key Persons
  26. 26. Some, but not all key Persons
  27. 27. Some, but not all key Persons
  28. 28. Some, but not all key Persons
  29. 29. Some, but not all key Persons
  30. 30. Genomic Analysis Water saver Water spender Dehydration tolerant control drought resistant control drought susceptible Candidate Tolerance Gene List
  31. 31. Metabolites 134** 20 2316* 153 14410* 5882 11297 13999 143** 16 21017** 4035 244* 34 690 224 711* 105 1478* 719 258 68 12 12 2083** 558 Arabinose Galactose Glucose Sucrose Xylose Fructose Melibiose Raffinose Pinitol Inositol Trehalose Mannitol Proline 36 54 505 399 14853 11606 11532 15291 128 68 15717 14789 104** 12 260 400 604* 91 1723 4333 84 80 16 27 804* 300 Drought Control Drought Control 30 Tolerant Susceptible
  32. 32. Potato drought tolerance traitsPotato drought tolerance traits Drought PP2C PSI and II-related genes Chlororespiration-related gene ASR TFs Redox regulation Lipid transferLEA, chaperonesRFO, AS-Metabolism ABA sensitivity AOS detoxification AOS ABAPhospholipase C and D 40 GA levels Stomatal closureGrowth inhibition Leaf area reduction yield Root size C-partition Osmotic adjustment Protein protection Membrane modification PS I and II stress tolerance Photosynthesis yieldyield
  33. 33. Candidate gene marker Components: •PGSC-Gene models •TIGR EST database •QualitySNP (Tang et al. 2006) •HaploSNPer (Tang et al. 2008) •PolyHap (HMM)
  34. 34. Association genetics study Germplasm panel Marker Phenotyping Population structure: 60 mapped SSR QTL: 250 (partially) mapped SNPs (HRM genotyping) 160 clones from 3 CIP breeding populations and pre-breeding clones Water use efficiency Water uptake capacity Yield under drought Harvest index Water relations ABA Analysis: STRUCTURE, GeneStat Discovery
  35. 35. Acknowledgments Sweetpotato Genetic Resources CIP HQ David Tay Rosalina Tincopa Genoveva Rossel Omar Palomino Raul Cordoba Ji Young Kim Carlos Rivera Cynthia Quispe Reinhard Simon Rolando Carbonet Rocio Alagon Angie DArT Andrezej Kilian and staff E. Mondlane University Mozambique Yvone Martins Muchoa NAARI Uganda Robert Mwanga Gorettie Ssamakula Evrogen Russia Sweetpotato Genetic Resources CIP HQ David Tay Rosalina Tincopa Genoveva Rossel Omar Palomino Raul Cordoba Ji Young Kim Carlos Rivera Cynthia Quispe Reinhard Simon Rolando Carbonet Rocio Alagon Angie DArT Andrezej Kilian and staff E. Mondlane University Mozambique Yvone Martins Muchoa NAARI Uganda Robert Mwanga Gorettie Ssamakula Evrogen Russia Funding Government of Austria Government of Luxembourg GTZ Germany Funding Government of Austria Government of Luxembourg GTZ Germany Potato Stress Tolerance CIP HQ Merideth Bonierbale Raymundo Gutierrez David Tay Walter Amoros Rolando Cabello Enrique Chujoi Roberto Quiroz Carolina Barreda Diogenes Cerna Macarena Barra Amelie Gaudin Percy Rojas Carlos Alvarado CIP CAC Carlo Carli CIP ESA Fernando Ezeta Dao Huy Chien Potato Stress Tolerance CIP HQ Merideth Bonierbale Raymundo Gutierrez David Tay Walter Amoros Rolando Cabello Enrique Chujoi Roberto Quiroz Carolina Barreda Diogenes Cerna Macarena Barra Amelie Gaudin Percy Rojas Carlos Alvarado CIP CAC Carlo Carli CIP ESA Fernando Ezeta Dao Huy Chien CPRI India S.K. Pandey and his team CRP Gabriel Lippmann Daniel Evers Sylvain Legay Isabelle Levevre Virginia Tech Ruth Grene Cecilia Vasquez-Robinet Shrinivasrao Mane AAFC Canada David DeKoyer Helene Tai University of Illinois Hans Bohnert Julius Kuehn Institut Silvia Seddig Anne Pechstein Anne Badani-Dehmer CPRI India S.K. Pandey and his team CRP Gabriel Lippmann Daniel Evers Sylvain Legay Isabelle Levevre Virginia Tech Ruth Grene Cecilia Vasquez-Robinet Shrinivasrao Mane AAFC Canada David DeKoyer Helene Tai University of Illinois Hans Bohnert Julius Kuehn Institut Silvia Seddig Anne Pechstein Anne Badani-Dehmer Government of Austria Government of Luxembourg GTZ Germany Government of Austria Government of Luxembourg GTZ Germany
  36. 36. Molecular Breeding in Vegetables
  37. 37. Molecular Breeding in Vegetables

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