Integrating multilocus genome-wide association studies in chickpea landraces to discern the genetics of drought tolerance

Abstract

In chickpea breeding, drought is a major concern and a complex trait controlled by several genes. To develop drought-tolerant varieties, it is essential to use the available germplasm and genomic resources. Over the years, the landraces have proven to be a good source for the dissection of genes for different yield and yield-related traits. The present investigation for marker–trait associations (MTAs) and candidate gene identification was conducted by studying 125 chickpea landraces collected from the West Asia and North Africa (WANA) region, along with 4 varieties suitable for irrigated and rainfed environments. This study analyzed 13 physio-morphological traits in 2 consecutive years at two isolated locations (IARI, New Delhi, and Dharwad). A strong correlation coefficient was observed between the trait seed yield (SY) and biological yield (BY) under both conditions. The Drought Susceptibility Index (DSI) ranged from 0.02 to 1.84 and 0.10 to 2.04 at the IARI, New Delhi and Dharwad locations, respectively. The genotypic data of 6,367 single nucleotide polymorphisms (SNPs) distributed across the genome were used for genetic diversity study, population structure, and genome-wide association study (GWAS). The average polymorphic information content (PIC) value observed was 0.25, and the average linkage disequilibrium (LD) decay distance was 152,269 bp across the genome. A total of four subgroups were observed within the population for genotypic data. Fixed and random model Circulating Probability Unification (FarmCPU) was used for the GWAS analysis, which considered both fixed- and random-effect models. A total of 52 significant SNPs were reported in both irrigated and rainfed conditions at low locations; 7 SNPs were associated with more than one trait, which may have pleiotropic effects. Significant SNPs were annotated in the pulse database. The identified genomic region found in or near MTA under rainfed conditions encodes for guard cell hydrogen peroxide-resistant1 (GHR1), late embryogenesis-abundant, E3 ubiquitin-protein ligase, walls are thin1 (WAT1), and beta-galactosidase that are known to be associated with drought tolerance.