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 * 1 International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India *Address for correspondence: [email protected] 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