Genome-wide molecular diversity analyses identify wild Cicer as reservoirs of variations for chickpea improvement

Abstract As climate change intensifies abiotic and biotic stresses, expanding the genetic base of cultivated chickpea ( Cicer arietinum ) is crucial for sustaining global pulse production. Modern chickpea cultivars have a narrow genetic base, restricting genetic gain especially for adaptation to environmental stresses, soil constraints and disease resistance. The wild Cicer species, particularly Cicer reticulatum and Cicer echinospermum , represent valuable reservoirs of genetic diversity for the improvement of existing chickpea cultivars, but their potential has not been fully exploited. Here, we evaluated genome-wide diversity and population structure in 317 Cicer accessions, comprising C. reticulatum (234), C . echinospermum (68) and C. arietinum (15), using 5792 high-confidence DArTseq SNP and 4628 SilicoDArT markers. We observed moderate polymorphic information content values, ranging from 0.25 (DArTseq SNPs) to 0.30 (SilicoDArT), indicating a medium level of informativeness and demonstrating that both marker systems are appropriate for diversity analysis for identifying useful variation for chickpea breeding. Genetic diversity indices revealed high diversity in C. reticulatum accessions. Analysis of molecular variance indicated that most molecular variation occurred within species rather than among species, indicating substantial intraspecific variation that can be exploited in chickpea breeding programs. Principal coordinates and neighbour-joining analyses resolved clear clustering at the species-level, confirming close genetic relationships between C. arietinum and C. reticulatum . The probability of identity-by-descent analysis and genome-wide linkage disequilibrium revealed extensive diversity in C. reticulatum compared to C. arietinum and C. echinospermum . Overall, this study establishes that high allelic diversity present in C. reticulatum accessions can be accessed for cultivated chickpea improvement.