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Research Program- Genetic Gains
Presentation at the 98th
Governing Board meeting
Program Committee
20 April 2021
Upstream ...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
Trends Plant Sci 2020
 Illumina ...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
 1.8 Tb sequence data generated ...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
Global chickpea genetic variation...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
 50K SNP panel
 $ 55 per sample...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
Pusa Chickpea Manav in India
Fusa...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
Genomics foundation for future br...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021 8
 The functional flours market ...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
Fresh high moisture flours prepa...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
What: Mutations in target fad and...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
Sequence confirmation of key lipa...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
Summary
 Genome sequencing work ...
Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
Thank You
Questions?
13
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Genetic Gains Governing Board April 2021

ICRISAT Governing Board concludes its third virtual board meeting

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Genetic Gains Governing Board April 2021

  1. 1. Research Program- Genetic Gains Presentation at the 98th Governing Board meeting Program Committee 20 April 2021 Upstream research for crop improvement: Genome sequencing in chickpea & Gene editing in pearl millet
  2. 2. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 Trends Plant Sci 2020  Illumina sequencing used to generate 153.01 Gb  73.8% of the genome is captured in scaffolds  Genome analysis predicted 28,269 genes Genome, pangenome/super pangenome Super pan genome Sequencing single genome not enough…
  3. 3. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021  1.8 Tb sequence data generated (5 X to 14 X)  4.9M SNPs, 596K Indels, 4.9K CNVs, 60.7K PAVs & 70K SVs  Domestication analysis reported 122 candidate genomic regions that underwent selection  Selection sweep analysis reported a significant reduction in diversity from wild to landraces to breeding lines  Center of origin determined  Genes associated with drought- and heat- tolerance identified
  4. 4. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 Global chickpea genetic variations by sequencing 3,366 accessions  Total data: 3.7 – 25 Gbp per line, ~12X (5X – 33X)  Species differentiation, genetic bottlenecks  Migration route of chickpea  Genomic breeding foundation A chickpea pan-genome identified 1,216 new gene models for chickpea. Genetic distance based on geographic regions provides insights on chickpea migration Nature, under revision
  5. 5. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021  50K SNP panel  $ 55 per sample  Genetic mapping  5K SNP panel  $ 6 per sample  Genomic selection Cost-effective genotyping platforms  48 SNP panel  hybridity testing & seed quality control  $2 per sample  Molecular breeding for drought, fusarium wilt & Aschochyta blight resistance Resistance allele Heterozygous allele Susceptible allele 1. Axiom®CicerSNP array 3. CaQC SNP panel 2.Targeted GBS AgriSeqTM NGS Platform 4. 10 SNP Panel
  6. 6. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 Pusa Chickpea Manav in India Fusarium wilt (FW) resistance with 28% yield advantage released in India Plant Genome 2021 Pusa 372 Pusa 362 DCP 92-3 Products from genomics-assisted breeding AVT 2: 3 drought tolerance & 1 FW resistance AVT 1: 5 drought tolerance & 2 FW resistance Pusa 391
  7. 7. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 Genomics foundation for future breeding a. Optimal contributions selection b. Bayesian Generalized Linear Regression c. WhoGEM prediction machine d. Haplotype-based local GEBVs  19.10 million haplo-pheno combinations were analysed  24 consistent and stable superior haplotypes for 100 seed weight, days to maturity, pods per plant, plot yield, and plant height Haplotype-based breeding Genomic Prediction a. b. c. d.
  8. 8. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 8  The functional flours market is growing to be USD 78.00 billion by 2022 at a CAGR of 7.82%.  The global Millets market was valued at USD 9 Billion in 2018 and is projected to touch USD 12 Billion by 2025, developing at a CAGR of 4.5 % from 2019 to 2025. Rancidity in milled pearl millet is a major issue  Unpleasant odour and taste within 5-10 days making its storage challenging posing major hindrance for wider consumer acceptability  Lack of demand from industry result in low economic incentives to farmers Knowledge gap:  Post-harvesting and/or pre-milling techniques some extent can reduce the rancidity  Less information in permanent solution to overcome the rancidity in pearl millet Issues to be addressed: • Finding the key genetic factors to be targeted to improve the shelf life of pearl millet flour Gene editing for rancidity in pearl millet
  9. 9. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 Fresh high moisture flours prepared and aged for 21 days at room temperature; Dry flour stored at accelerated conditions (35 °C & 70% RH) Descriptive sensory analysis for odour nuisance carried out Biochemical profiling of surrogates for enzymatic and oxidative rancidity done Total Lipids extracted and analyzed by GC – quantitatively Profiling pearl millet inbreds
  10. 10. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 What: Mutations in target fad and lipase genes to prevent oxidative and enzymatic rancidity How: CRISPR for single and double cuts with no repair template ( SDN1) A to G substitutions created frame shift mutations in Fad2a gene Strong pleotropic effect, small panicle and reduced seed set observed in these edits; additional gRNAs designed for other Fad2a, 2b alleles Rancidity trait pipeline- CRISPR
  11. 11. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 Sequence confirmation of key lipases show higher affinity to TAG components  Elucidated the molecular mechanisms and candidate gene(s) for a possible genetic solution to increase shelf-life of milled pearl millet.  Structural variation in contrasting pearl millet lines identified  Dysfunctional pearl millet lipase gene is responsible for reduced rancidity in milled flour. Underlying molecular mechanisms * Intact lipase (WT) Mutant LR2 Mutant LR 1 Functional validation in yeast expression system reveal significantly lower lipid degradation activity in mutant alleles (from low rancid lines) compared to intact WT lipase (isolated from high-rancid line)  m o l/g D W 0 h 6 h 1 D 2 D 4 D 5 D 7 D 0 5 0 1 0 0 1 5 0 I3 I7 Total TAG (µmoles/g DW) Mobilization of storage lipid reserve in contrasting pearl millet lines during germination
  12. 12. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 Summary  Genome sequencing work has established ICRISAT as centre of excellence in dryland by contributed to basic and strategic science and capacity building in developing countries  NARS partners with ICRISAT developed and released high-yielding chickpea varieties through genomics-assisted breeding in Ethiopia and India  ICRISAT together with Corteva Agriscience has embarked on gene editing technology to address the rancidity issue in pearl millet.  A dysfunctional pearl millet lipase gene responsible for reduced rancidity has been identified for gene editing  Integration of upstream science in crop improvement for addressing complex issues in international agriculture 12
  13. 13. Presentation at the 98th ICRISAT Governing Board Meeting Program Committee 20 April 2021 Thank You Questions? 13

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