Genome‐wide discovery ofDNApolymorphisms via resequencing of chickpea cultivars with contrasting response to drought stress

Abstract

Drought stress limits plant growth, resulting in a significant yield loss in chickpea. The diversification in genome sequence and selective sweep of allele(s) in different genotypes of a crop plant may play an important role in the determination of agronomic traits, including drought stress response. We investigated, via whole genome res-

An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea

“…We identified all the transcripts located within the drought tolerance associated known QTL regions 49 – 52 and analyzed their expression profiles using RNA-seq data of a drought-tolerant (Dtol; ICC 4958) and a drought-sensitive (Dsen; ICC 1882) chickpea genotype under control (CT) and drought stress (DS) conditions at early reproductive (ER) and late reproductive (LR) stages from our previous study 53 . Further, the differentially expressed transcripts were examined for the presence of DNA polymorphisms that differentiate drought-sensitive and drought-tolerant chickpea genotypes 54 . The analysis revealed a total of 65 differentially expressed transcripts that harbored the DNA polymorphisms within the transcripts and/or their promoter regions (Supplementary Data 10 ).…”

“…8b and Supplementary Table 6 ). Several TFs cognate to these cis -regulatory motifs have been implicated in drought stress responses/tolerance 54 – 57 . These transcripts and/or alleles represent important candidates for prioritization to validate their role in drought tolerance.…”

“…Next, we demonstrated the application of reference transcriptome assembly to identify the candidate transcripts that may govern drought and salinity stress responses. Via the integration of the known QTLs associated with drought 49 – 52 and salinity 58 – 60 tolerance, differential gene expression in/between the sensitive and tolerant genotypes under stress conditions, and DNA polymorphisms that differentiate sensitive and tolerant genotypes 54 , 61 , at least 10 drought-responsive and four salinity-responsive transcripts were identified that harbored DNA polymorphisms within the cis- regulatory motifs representing the binding sites of important TFs. Many of these TFs and the target genes have been implicated in the regulation of the biological processes associated with drought and/or salinity stress responses/tolerance 54 – 57 , 62 , 63 .…”

“…Via the integration of the known QTLs associated with drought 49 – 52 and salinity 58 – 60 tolerance, differential gene expression in/between the sensitive and tolerant genotypes under stress conditions, and DNA polymorphisms that differentiate sensitive and tolerant genotypes 54 , 61 , at least 10 drought-responsive and four salinity-responsive transcripts were identified that harbored DNA polymorphisms within the cis- regulatory motifs representing the binding sites of important TFs. Many of these TFs and the target genes have been implicated in the regulation of the biological processes associated with drought and/or salinity stress responses/tolerance 54 – 57 , 62 , 63 . In addition, 12 drought and/or salinity stress-responsive transcripts located on the refined QTL-hotspot _a and b regions on chromosome 4 associated with drought tolerance were identified.…”

Raising crops for dry and saline lands: Challenges and the way forward

“…Of these, 2488 SNPs had a high impact due to the gain of stop codons, variations in splice acceptors and splice donors, and the loss of start codons. Similarly, analysis of WGRS data obtained from nine chickpea genotypes (3 of which were drought‐sensitive and 6 were drought‐tolerant) led to the identification of 36,406 SNPs and 3407 insertions or deletions that distinguish the drought‐sensitive and drought‐tolerant genotypes (Rajkumar et al, 2022). Moreover, Tang et al (2022) identified 66 U‐box genes encoding ubiquitin ligases in the potato genome.…”