In the context of climate change, heat stress during the reproductive stages of chickpea (Cicer arietinum L.) leads to significant yield losses. In order to identify the genomic regions responsible for heat stress tolerance, a recombinant inbred line population derived from DCP 92-3 (heat sensitive) and ICCV 92944 (heat tolerant) was genotyped using the genotyping-by-sequencing approach and evaluated for two consecutive years (2017 and 2018) under normal and late sown or heat stress environments. A high-density genetic map comprising 788 single-nucleotide polymorphism markers spanning 1,125 cM was constructed. Using composite interval mapping, a total of 77 QTLs (37 major and 40 minor) were identified for 12 of 13 traits. A genomic region on CaLG07 harbors quantitative trait loci (QTLs) explaining >30% phenotypic variation for days to pod initiation, 100 seed weight, and for nitrogen balance index explaining >10% PVE. In addition, we also reported for the first time major QTLs for proxy traits (physiological traits such as chlorophyll content, nitrogen balance index, normalized difference vegetative index, and cell membrane stability). Furthermore, 32 candidate genes in the QTL regions that encode the heat shock protein genes, heat shock transcription factors, are involved in flowering time regulation as well as pollen-specific genes. The major QTLs reported in this study, after validation, may be useful in molecular breeding for developing heat-tolerant superior lines or varieties.

Background: Chickpea (Cicer arietinum L.) contributes 75% of total pulse production. Being cheaper than animal protein, makes it important in dietary requirement of developing countries. Weed not only competes with chickpea resulting into drastic yield reduction but also creates problem of harboring fungi, bacterial diseases and insect pests. Chemical approach having new herbicide discovery has constraint of limited lead molecule options, statutory regulations and environmental clearance. Through genetic approach, transgenic herbicide tolerant crop has given successful result but led to serious concern over ecological safety thus non-transgenic approach like marker assisted selection is desirable. Since large variability in tolerance limit of herbicide already exists in chickpea varieties, thus the genes offering herbicide tolerance can be introgressed in variety improvement programme. Transcriptome studies can discover such associated key genes with herbicide tolerance in chickpea. Results: This is first transcriptomic studies of chickpea or even any legume crop using two herbicide susceptible and tolerant genotypes exposed to imidazoline (Imazethapyr). Approximately 90 million paired-end reads generated from four samples were processed and assembled into 30,803 contigs using reference based assembly. We report 6,310 differentially expressed genes (DEGs), of which 3,037 were regulated by 980 miRNAs, 1,528 transcription factors associated with 897 DEGs, 47 Hub proteins, 3,540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM), 13,778 genic Single Nucleotide Polymorphism (SNP) putative markers and 1,174 Indels. Randomly selected 20 DEGs were validated using qPCR. Pathway analysis suggested that xenobiotic degradation related gene, glutathione S-transferase (GST) were only up-regulated in presence of herbicide. Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed. Study further reveals the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and of thaumatin-like genes in herbicide resistance. Conclusion: Reported DEGs can be used as genomic resource for future discovery of candidate genes associated with herbicide tolerance. Reported markers can be used for future association studies in order to develop marker assisted selection (MAS) for refinement. In endeavor of chickpea variety development programme, these findings can be of immense use in improving productivity of chickpea germplasm.