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Regulation of
flower and post
embryonic
development
Jasmonic acid
biosynthesis
and metabolic
process
Cell death,
regulation of meiosis
and cell cycle
Senescence
Response to
carbohydrate
stimulus and
desiccation
Inclusive Market-Oriented Development (IMOD) –
our approach to bringing prosperity in the drylands.
ICRISAT is a member of the CGIAR Consortium.
Heat stress imposition - growth chamber
Heat stress/high temperatures during flowering and pod development is increasingly becoming a major constraint in
chickpea production. Heat tolerant varieties are needed for improving chickpea yields in warm season environments and late sown
conditions. With an objective of identifying genes and/or markers associated with heat tolerance for accelerated development of heat
tolerant chickpea varieties RNA-Seq based transcriptome analysis was performed. Vegetative (leaves and roots) and reproductive (leaves,
roots and flowers) tissues of six contrasting heat responsive (tolerant - ICCV 92944, ICC 1356, ICC 15614 and sensitive - ICC 5912, ICC 4567,
ICC 10685) genotypes were selected for the study. A total of ~514 million reads were generated and alignment of these reads against the
comprehensive chickpea transcriptome assembly (CaTA v2) resulted in covering of 44,185 out of 46,369 transcript assembly contigs. A total
of 6,799 genes including 1,172 novel genes were significantly differentially expressed with a log2 fold change of ≥2 between tolerant and
sensitive genotypes. A set of 56 differentially expressed genes belonging to abiotic stress family proteins was selected for further
validation using quantitative real time PCR. Furthermore, >22,456 single nucleotide polymorphisms (SNPs)/INDELs were identified between
lines that are the parental genotypes of two mapping populations (ICC 15614
ICC 4567 and ICC 1356
ICC 4567). Novel genes along with
the marker resources identified in this study should help breeders in developing heat tolerant chickpea lines in efficient manner.
Abstract
Stress responsive pathways
RNA-Seq and data analysis
Himabindu Kudapa, Gaurav Agarwal, Dadakhalandar Doddamani, Vinay Kumar, Aamir W Khan,
Annapurna Chitikineni, Krishnamohan Katta, Pooran M Gaur, L Krishnamurthy,
Rajeev K Varshney*
1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
*Address for correspondence: r.k.varshney@cgiar.org
Differentially expressed genes (DEGs)
Acknowledgements Financial support from Generation Challenge Programme (GCP) is
gratefully acknowledged. Tanks are due to Jaipal for technical help. This work has been
undertaken as part of the CGIAR Research Program on Grain Legumes.
Identification and validation of heat stress responsive
genes in chickpea (Cicer arietinum L.)
Vegetative stage Reproductive stage RNA
RNA-Seq
Data analysis
qRT- PCR assays
Candidate gene
identification
S. No Genotype Tolerant/
sensitive
1 ICCV 92944 T
2 ICC 1356 T
3 ICC 15614 T
4 ICC 5912 S
5 ICC 4567 S
6 ICC 10685 S
• Seven days exposure to
day/night temperature: 35/25ºC
• Tissues harvested at vegetative
and reproductive stages
Genotype Differentially expressed genes (DEGs)
up- novel
up-
down- novel
down-
ICCV 92944 vs ICC 5912
vs ICC 4567
vs ICC 10685
1,177
80
1,221
114
29
157
187
158
160
44
50
45
ICC 1356 vs ICC 5912
vs ICC 4567
vs ICC 10685
958
95
1102
93
28
143
307
309
210
53
65
48
ICC 15614 vs ICC 5912
vs ICC 4567
vs ICC 10685
1,055
149
1150
115
38
165
278
160
138
56
38
37
Total Reads generated: 514 million
Reads mapped: 505 million
Number of contigs subjected for BLASTX annotation: 5,522
Number of contigs annotated : 5,422, E-value: ≤1e-5
Functionally categorized based on Gene Ontology: 4,649
Down-regulated genes
Up-regulated genes
Identified 6,781 differentially expressed genes
including 1,172 novel genes
Pathways involved in regulation of flower and post embryonic
development, Jasmonic acid biosynthesis etc identified
20,707 SNPs and 179 Indels identified in contrasting heat
responsive genotypes
Validated 56 selected stress responsive genes and identified
candidate heat responsive genes
Summary Transport of Boron,
dipeptides, acidic amino
acids, urea, myoinosiol,
adenine nucleotide
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