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GRM 2013: Asian Maize Drought Tolerance (AMDROUT) Project -- BS Vivek


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GRM 2013: Asian Maize Drought Tolerance (AMDROUT) Project -- BS Vivek

  1. 1. Asian Maize Drought Tolerance (AMDROUT) Project SP3 PROJECT G4008.56 Principal Investigator: B. S. Vivek
  2. 2. Project Details Grant Period:  (Start: Nov 08) (End: Oct 2013)  No cost extension to July 2014
  3. 3. What? Drought tolerant lines  using Marker Assisted Recurrent Selection (MARS) based on genome-wide selection (GWS) Yellow drought tolerant inbred lines Proof of concept for MARS-GWS Scientists trained in molecular breeding Principle Outputs
  4. 4. Why? 80% of maize in Asia is grown under rain-fed conditions and prone to drought stress
  5. 5. Drought in Asia  …wheat and maize harvests will be strongly affected by droughts …unless states ..can quickly adapt their agricultural practices  China, Indonesia and Pakistan were relatively well-placed to adapt to climate change. India was found to have one of the lowest capacities to adapt ….its maize production (in C and N India)
  6. 6. 2012: The worst drought US witnessed in recent decades Source: Bob Nielsen (Purdue University) • Sixth worst departure from yield trend since 1866! • Yield estimate would be 23% lower than predicted in 2012… • Drought coupled with heat stress • Possible global implications in terms of maize prices Wherever you are, …you need stress resilience to ensure stable performance
  7. 7. Collaboration  Dr. B. S. Vivek, CIMMYT-India  Girish Kumar Krishna, CIMMYT-India  V. Vengadessan , CIMMYT-India  P. H. Zaidi, CIMMYT-India  Le Quy Kha, NMRI, Vietnam  Pichet Grudloyma, NSFCRC, Tak Fa, Thailand  I.S. Singh, Krishidhan Seeds, India  R. Babu, CIMMYT-India  Eureka Ocampo, Institute of Plant Breeding, UPLB, Philippines  Fan Xingming, YAAS, Kunming, China  M. Azrai, ICERI, Maros, Indonesia  R.P. Singh, Syngenta, India  J. Burgeño, CIMMYT-Mexico  J. Crossa, CIMMYT-Mexico
  8. 8. Final irrigation before imposing drought Drought Phenotyping Optimal Management Managed Drought Drought expression at flowering Typical genotypic variability under drought
  9. 9. Form S2 x tester (CML474) Evaluate test crosses (At least 3 drought + 3 optimal sites) Calculate marker effects (MARS-GWS) Form C1 with best S2 lines based on phenotype data Genotype S2 families: 350 polymorphic whole genome SNPs: Kbioscience KASPar assay Form c1F2 (recombine best looking c1 plants) C2 S6 Genotype-only selection (24 plants with highest GEBVs recombined) •CML470 •VL1012767 •VL1012764 •CML472 S2 F2 (S1) F1 P1 P2x4 elite yellow Asian lines (lack drought tolerance) 2 African white drought tolerant donors •CML444 •CML440 Populations •AMDROUT1: CML470/CML444 •AMDROUT2: VL1012767/CML444 •AMDROUT5/6: VL1012764/CML444//CML472xCML440 Genotype C1 plants Calculate Genomic Estimated Breeding Values (GEBVs) using marker effects How? Genome Wide Selection (GWS)
  10. 10. Mean Lines developed by pedigree selection Lines selected for recombination from C0 phenotyping Cycle 3 MARS lines Population of random lines extracted from a cross MARS increases the frequency of favorable alleles Moves the mean of the selected population beyond the original distribution MARS / GWS
  11. 11. Sl. No. AMDROUT Population Number Population Type Data from K BioScience Marker effects available GEBVs available No. of individuals in the population No. of SNPs assayed 1 AMDROUT1 F2:F3 294 340 Yes No 2 AMDROUT1 Cycle-1 242 318 Yes 3 AMDROUT1 Cycle-2 347 278 Yes 4 AMDROUT2 F2:F3 188 376 Yes No 5 AMDROUT2 Cycle-1 258 351 Yes 6 AMDROUT2 Cycle-2 346 271 Yes 7 AMDROUT5 F2:F3 197 421 Yes 8 AMDROUT6 F2:F3 183 340 Yes 9 AMDROUT5/6 Cycle-1 352 425 Yes 10 AMDROUT5/6 Cycle-2 252 399 Yes
  12. 12. @60% gain @40% gain @80% gain 0.0 1.0 2.0 3.0 4.0 5.0 6.0 0.00 0.50 1.00 1.50 2.00 2.50 3.00 3.50 days t/ha Cycles of selection GY ASI Genetic Gains for Grain Yield under Drought: AMDROUT1 1 location 3 reps 2 row plots H 0.74 c1 c2: Marker-only selection @ per cent gain over F2
  13. 13. @50% @40% @60% 0.00 0.50 1.00 1.50 2.00 2.50 3.00 t/ha Cycles of selection GY GY Genetic Gains for Grain Yield under Drought: AMDROUT2 1 location 3 reps 2 row plots H 0.74 @ per cent gain over F2 c1 c2: Marker-only selection
  14. 14. AMDROUT1 cycles AMDROUT1c2 (Phenotypic selection followed by genotype- only selection) AMDROUT1c1F2 (Two cycles of phenotype-only selection)
  15. 15. Therefore: For grain yield under drought: one cycle of phenotypic selection followed by one cycle of genotype-only selection gives 50-100% higher genetic gain compared to two cycles of phenotype- only selection GWS is a useful methodology to improve source (breeding) populations
  16. 16. Moving on….. Nov 2013: Test crosses with cycles of selection May 2014: Drought and well watered trial information on per se and test cross performance of cycles of selection August 2014: Draft publication Meanwhile: Wet season data is being collected Second season of drought screening will be completed by May 2014
  17. 17. Germplasm Outputs Cycles of selection from bi-parental crosses between CIMMYT-Asia lines and African DT donors  AMDROUT1c3, AMDROUT2c3, AMDROUT(5x6)c3  AMDROUT1c2, AMDROUT2c2, AMDROUT(5x6)c2  AMDROUT1c1F2, AMDROUT1c2F2, AMDROUT2c2F2, AMDROUT(5x6)c1F2, AMDROUT(5x6)c2F2 Early generation lines from above cycles of selection DH lines from the above cycles?
  18. 18. Genotyping Outputs 1215 SNP data of 175 advanced lines Genetic linkage maps of two populations viz. AMDROUT1 and 2 Marker effects of SNPs for 4 bi-parental populations
  19. 19. Other Outputs Proof of Concept publication on MARS-GWS method Trained scientists  Cambridge Molecular Breeding  Maize breeding  Drought phenotyping  Data management  Visiting scientists  On site visits  Statistics, molecular breeding course planned
  20. 20. Looking further ahead: Movement of AMDROUT germplasm to farmers’ field
  21. 21. SWOT: What worked?  An opportunity to learn and implement new technology which promises to give higher genetic gain, especially under drought.  Main outputs from this project: yellow drought tolerant selection cycles starting from white African germplasm as donor. Yellow maize covers most of the Asian region, hence having such breeding material on hand again will ensure faster genetic gain. This output will be used in future breeding either as drought tolerant donor or for deriving inbred lines.  Excellent training opportunity (for field evaluation and data analysis) for collaborators.  CIMMYT locations continue to give excellent data, along with couple of other partner sites.
  22. 22. SWOT: What was difficult? There were issues with timely delivery of genotypic data from KBioscience, UK; but this issue has been taken up and resolved. Germplasm export to collaborators was slow and timely evaluation of trials was difficult. Getting good heritability of grain yield was difficult in a lot of partner locations.
  23. 23. SWOT: What was difficult?  An unforeseen insect attack by pollen eating blister beetles (Cylidrothorax tenuicollis), hitherto unseen, almost derailed the recombination of AMDROUT1 and 2  Similar to a locust swarm
  24. 24. SWOT: What was difficult? Cross selection was a challenge because tropical maize (unlike temperate maize) is very diverse (while temperate maize has a narrower based and a better defined heterotic behavior) has a shorter history of genetic improvement has inconsistent pedigree information has poorly maintained historical data
  25. 25. SWOT: What I would do different in the future? Selection of breeding populations on observed heterosis (evaluation of 3-ways between the target populations and a tester panel) rather than extrapolated heterosis (which was done here through a Design II study);  Heterotic partner known before inbreds are developed  Direct use of observed heterosis  Less reliance on extrapolation and historic information which is often poorly managed
  26. 26. SWOT: What else could have been different? Perhaps …….. Using multi-parent synthetics as the breeding material (as opposed to the bi-parental populations used here). For tropical maize, the onus on selection of the best bi-parental crosses and the right testers is too huge a risk. This risk is magnified by working with few populations (4 in this case). Using multi-parent synthetics would have potentially reduced this risk.