Drought tolerance genes and traits/Gene Index and markers

Potato and sweetpotato genomics Tolerance and other genes Potato: Drought tolerance genes and traits Sweetpotato: Gene Index and markers

Genetic and genomic resources for sweetpotato

Sweetpotato genetic and genomic resources •Composite Genotype Set •Gene sequences •Markers •Map 22.000 ESTs 1500 gene sequences 1 Bac 2 Low resolution maps ~100 SSR markers LD cDNA microarray

Access to biodiversity: Composite Genotype Set Composite Genotype Set CIP Ipomoea batatas collection: CIP Ipomoea batatas collection: 480 accessions 480 accessions 5,961 accessions 5,961 accessions •Biodiversity •Biodiversity •High β-carotene •High β-carotene •High starch •High starch •High iron and zinc contents •High iron and zinc contents •Nematode, virus and drought resistance •Nematode, virus and drought resistance -Pathogen-free in vitro plants ready for international -Pathogen-free in vitro plants ready for international distribution distribution -Morphological information and molecular -Morphological information and molecular fingerprints (SSR genotypes) available fingerprints (SSR genotypes) available http://gcpcr.grinfo.net/files/cr_files/gcpcr_file832.xls

Gene sequences Enriched for stress-related genes Annotation Read assembly 454 sequencing 2 cDNA libraries

Gene Index Annotation 39.299 annotated sequencesv– 24.763 unique sequences v extracellular anatomical immune viral translation electron envelope, molecular region, 592 structure system reproduction, regulator carrier activity, 1159 transducer nutrient grow th, 506 formation, 496 process, 314 30 activity, 386 352 activity, 326 reservoir membrane- virion, 12 enzyme activity, 247 enclosed multi-organism symplast, 10 rhythmic regulator lumen, 1842 process, 935 activity, 437 antioxidant process, 80 reproduction, activity, 155 macromolecul. 1449 structural complex, 4487 molecule cellular multicellular process, activity, 1020 organismal 12576 cell, 19341 transcription process, 2452 binding, 10242 regulator developmental activity, 1157 process, 2767 localization, transporter 2852 activity, 1656 biological organelle, metabolic regulation, catalytic 15130 process, 4183 response to activity, 9097 stimulus, 4832 11133 Cellular location Biological function Molecular process

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: I. trifida parent 2 I. trifida parent 1 I. trifida Genepool structure I. trifida Improved Varieties, breeding lines Landraces: LAC Latin America and the Caribbean Sub-Saharan Africa East and South-East Asia Oceania North Africa Jonathan Yanshu 1 Feng Shu Bai Xushu 18 I. trifida Jewel Wagabolige Beauregard

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 Easy to handle linkage map Comparative genomics among sweetpotato and other crops Comparative genomics among sweetpotato and other crops

Potato abiotic stress tolerance

Potato Development Targets

Abiotic stress tolerance is complex… Environmental constraints Difficult selection under natural • Variability of natural climate stress conditions stress events Genetic constraints • Tolerance traits might be Interactions between genes and polygenic and epistatic genetic background Not all tolerance traits work in all • Gene x environment interactions environments Efficient breeding requires information on the genetic and physiological basis of tolerance traits

Improving potato drought tolerance Field screening of Field screening of germplasm collection germplasm collection (Chujoy % Cabello) (Chujoy % Cabello) Drought- Drought- Many susceptible and a few tolerant clones tolerant tolerant potato potato Identification of drought Identification of drought • Yield losses <30% • Yield losses <30% tolerance traits at a 40 day drought at a 40 day drought tolerance traits spell during bulking spell during bulking • -minimum yield • -minimum yield 25t/ha (~600 g/plant) 25t/ha (~600 g/plant) Trait-marker association Trait-marker association Screening tools • No tuber defects • No tuber defects Breeding Breeding

Testing environments

Physiological traits CLONE: CANCHAN CLONE: CANCHAN : -1 Stomatal resistance (s cm ) 37 days after drought 16.00 14.00 12.00 10.00 8.00 6.00 4.00 2.00 0.00 Well-watered Drought Well-watered Drought 397077.16 397077.16 380389.1 380389.1 Osmotic potential (MPa) 39 days after drought 3.0 2.5 2.0 Stricter stomatal control, increased WUE 1.5 1.0 Osmotic adjustment 0.5 0.0 Well-watered Drought Well-watered Drought Higher water uptake capacity 397077.16 397077.16 380389.1 380389.1

Some, but not all key Persons

Genomic Analysis resistant susceptible control drought control drought Water saver Water spender Dehydration tolerant Candidate Tolerance Gene List

Metabolites Tolerant Susceptible Drought Control Drought Control 134** 20 Arabinose 36 54 2316* 153 Galactose 505 399 14410* 5882 Glucose 14853 11606 11297 13999 Sucrose 11532 15291 143** 16 Xylose 128 68 21017** 4035 Fructose 15717 14789 244* 34 Melibiose 104** 12 690 224 Raffinose 260 400 711* 105 Pinitol 604* 91 1478* 719 Inositol 1723 4333 258 68 Trehalose 84 80 12 12 Mannitol 16 27 2083** 558 Proline 804* 300 30

Potato drought tolerance traits Drought Phospholipase C and D ABA PP2C ASR ABA sensitivity Root size Growth inhibition Stomatal closure GA levels Leaf area reduction AOS Photosynthesis TFs C-partition PS I and II stress tolerance Redox regulation yield yield PSI and II-related genes AOS detoxification Chlororespiration-related gene Osmotic adjustment Protein protection Membrane modification RFO, AS-Metabolism LEA, chaperones Lipid transfer 40

Candidate gene marker Components: •PGSC-Gene models •TIGR EST database •QualitySNP (Tang et al. 2006) •HaploSNPer (Tang et al. 2008) •PolyHap (HMM)

Association genetics study Germplasm panel Marker Phenotyping 160 clones from Population structure: Water use efficiency 3 CIP breeding populations 60 mapped SSR Water uptake capacity and pre-breeding clones Yield under drought QTL: Harvest index 250 (partially) mapped Water relations SNPs (HRM genotyping) ABA Analysis: STRUCTURE, GeneStat Discovery

Acknowledgments Potato Stress Tolerance Potato Stress Tolerance Sweetpotato Genetic Resources Sweetpotato Genetic Resources CIP HQ CIP HQ CPRI India CPRI India CIP HQ CIP HQ Merideth Bonierbale Merideth Bonierbale S.K. Pandey and his team S.K. Pandey and his team David Tay David Tay Raymundo Gutierrez Raymundo Gutierrez CRP Gabriel Lippmann CRP Gabriel Lippmann Rosalina Tincopa Rosalina Tincopa David Tay David Tay Daniel Evers Daniel Evers Genoveva Rossel Genoveva Rossel Walter Amoros Walter Amoros Sylvain Legay Sylvain Legay Omar Palomino Omar Palomino Rolando Cabello Rolando Cabello Isabelle Levevre Isabelle Levevre Raul Cordoba Raul Cordoba Enrique Chujoi Enrique Chujoi Virginia Tech Virginia Tech Ji Young Kim Ji Young Kim Roberto Quiroz Roberto Quiroz Ruth Grene Ruth Grene Carlos Rivera Carlos Rivera Carolina Barreda Carolina Barreda Cecilia Vasquez-Robinet Cecilia Vasquez-Robinet Cynthia Quispe Cynthia Quispe Diogenes Cerna Diogenes Cerna Shrinivasrao Mane Shrinivasrao Mane Reinhard Simon Reinhard Simon Macarena Barra Macarena Barra AAFC Canada AAFC Canada Rolando Carbonet Rolando Carbonet Amelie Gaudin Amelie Gaudin David DeKoyer David DeKoyer Rocio Alagon Rocio Alagon Percy Rojas Percy Rojas Helene Tai Helene Tai Angie Angie Carlos Alvarado Carlos Alvarado University of Illinois University of Illinois DArT DArT CIP CAC CIP CAC Hans Bohnert Hans Bohnert Andrezej Kilian and staff Andrezej Kilian and staff Carlo Carli Carlo Carli Julius Kuehn Institut Julius Kuehn Institut E. Mondlane University Mozambique E. Mondlane University Mozambique CIP ESA CIP ESA Silvia Seddig Silvia Seddig Yvone Martins Muchoa Yvone Martins Muchoa Fernando Ezeta Fernando Ezeta Anne Pechstein Anne Pechstein NAARI Uganda NAARI Uganda Dao Huy Chien Dao Huy Chien Anne Badani-Dehmer Anne Badani-Dehmer Robert Mwanga Robert Mwanga Gorettie Ssamakula Gorettie Ssamakula Funding Funding Evrogen Russia Evrogen Russia Government of Austria Government of Austria Government of Austria Government of Austria Government of Luxembourg Government of Luxembourg Government of Luxembourg Government of Luxembourg GTZ Germany GTZ Germany GTZ Germany GTZ Germany

Molecular Breeding in Vegetables

Drought tolerance genes and traits/Gene Index and markers

by International Potato Center

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