Research Projects

Chickpea (Cicer arietinum) is an important legume, valued for its nutritional, agronomic, and economic significance. Despite its adaptability, its susceptibility to cold stress remains a major limitation. This vulnerability stems from a narrow genetic base shaped by domestication bottlenecks, due to a shift from autumn- to spring-sowing to escape Ascochyta blight. This shift led to the loss of key adaptive traits like vernalization response and cold tolerance, making modern cultivars highly sensitive to cold stress. In contrast, wild chickpea progenitors have evolved in harsh cold environments and harbor valuable alleles for cold tolerance. However, their use in breeding has been limited by hybridization barriers and a lack of genomic resources. Fortunately, two wild species within the primary gene pool, Cicer reticulatum (Cr) and Cicer echinospermum (Ce) have shown successful hybridization with cultivated chickpea. Understanding the molecular basis of cold tolerance in these crossable wild species could help identify novel alleles for introgression breeding. Independent studies have identified a common region on chromosome 3 associated with cold tolerance, vernalization, and flowering time in wild chickpea. These interrelated traits were likely modified during domestication through a selective sweep in this region. Yet, the regulatory mechanisms and functional variants within this pleiotropic locus remain poorly understood due to reference bias, limiting their use in chickpea improvement. Traditional genomics relying on a single reference genome often misses novel alleles, genes, or isoforms that are absent in the reference. In contrast, pan-transcriptomic approaches offer a more comprehensive, reference-independent view, enabling the detection of novel genes, allele-specific expression, and alternative splice forms often underrepresented in the cultivated gene pool. To overcome these limitations, we propose constructing a high-resolution, haplotype-aware chickpea pan-transcriptome by integrating long-read (PacBio Iso-Seq) and short-read (Illumina RNA-Seq) data from cold-stressed wild (Cr, Ce) and cultivated (cold-tolerant and sensitive) accessions. This will allow us to capture genotype-, tissue-, and condition-specific expression and splicing patterns relevant to cold adaptation while avoiding reference bias. By integrating this transcriptomic data with structural variants (SVs), GWAS, and QTLs, especially from the selective sweep regions, we aim to identify key functional variants and regulatory modules associated with cold tolerance. This will support the discovery of novel natural alleles for breeding cold-resilient chickpea without compromising domestication gains. If successful, this project will enhance fundamental understanding of cold stress response in chickpea and deliver a valuable genomic resource for breeders, including candidate genes and markers for introgression breeding and functional SVs for precision genome editing.