Major QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified in Chickpea (Cicer arietinum L.)

Abstract

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.

Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes

“…Functional genomics facilitates the elucidation of the important role of candidate genes for expression of tolerance against abiotic stress in crop plants [ 172 , 173 , 174 ]. Among cool season grain legumes, five HSP90 candidate genes ( Ca_25811 , Ca_23016 , Ca_09743 , Ca_17680 and Ca_25602 ) have been identified in chickpea through RNA-sequencing analysis of leaf, flower and roots at different growth stages [ 166 ].…”

“…Mining of the candidate genes for heat tolerance revealed 236 genes in 2.28 Mb (44.6–46.9 Mb) region in CaLG05 and 550 genes in 6.50 Mb (7.85–14.35 Mb) in CaLG06 in chickpea. Functional categorization showed association of many genes with biological processes (168 genes in CaLG05 and 365 genes in CaLG06) in the two genomic regions [ 172 ]. Gene ontology classification revealed that these putative candidate genes (11 in CaLG05 and 14 in CaLG06) known to function, directly or indirectly, as heat-stress response genes in several plant species.…”

Translational Chickpea Genomics Consortium to Accelerate Genetic Gains in Chickpea (Cicer arietinum L.)

“…To develop trait associated markers, available genomic information on candidate regions for drought and FW was collected from previous studies and focused on the identification of major QTL regions [12,14,15,[18][19][20]. For drought, a total of 26 genes identified in the "QTL-hotspot" region containing 24 SNPs were used to develop molecular markers for use in early generation selection.…”

“…As a result, 10 SNP panel for drought was developed and tested for early generation selection for the backcross progenies (Table 1). Similarly, for the development of FW markers, genomic information on candidate regions of QTL associated with FW resistance was assembled from the studies [18][19][20] (Table 1 and Table S1). We used these markers on the backcross progenies and validated their usefulness in chickpea breeding programs.…”

“…In recent years, the tremendous progress made in developing novel genomic tools in chickpea, such as the draft genome sequence [6], several millions of SNP markers from whole genome sequence information on germplasm lines [7][8][9] and cost-effective genotyping platforms including low-to high-density SNP arrays [10,11]. Likewise, QTLs and markers associated with abiotic stresses like drought [12][13][14][15], heat [16] and salinity [17], and biotic stresses like fusarium wilt (FW) [18,19] and Ascochyta blight (AB) [18,20] are available for chickpea improvement. These have facilitated marker-assisted selection/introgression in chickpea breeding programs.…”