ICRISAT Governing Board concludes its third virtual board meeting

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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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
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13. Presentation at the 98th ICRISAT Governing Board Meeting
Program Committee 20 April 2021
Thank You
Questions?
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