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