AUTHOR=Harish D. , Pappula Reddy Sneha Priya , Kumar Neeraj , Bharadwaj Chellapilla , Kumar Tapan , Parida Swaroop , Patil Basavanagowda S. , Kumar Sudhir , Jain Pradeep K. , Kumar Yogesh , Varshney Rajeev K. 

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

JOURNAL=Frontiers in Sustainable Food Systems

VOLUME=Volume 8 - 2024

YEAR=2024

URL=https://www.frontiersin.org/journals/sustainable-food-systems/articles/10.3389/fsufs.2024.1389970

DOI=10.3389/fsufs.2024.1389970

ISSN=2571-581X

ABSTRACT=In chickpea breeding, drought is of major concern and it is a complex trait controlled by numerous genes. To develop drought-tolerant varieties, it is essential to use the available germplasm and genomic resources. Over 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 Association's (MTA's) and candidate gene identification was carried out by studying 125 chickpea landraces collected from WANA (West Asia and North Africa) region and 4 varieties suitable under irrigated and rain-fed environment for 13 physio-morphological traits in two 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. Drought Susceptibility Index (DSI) ranged from 0.02 to 1.84 and 0.10 to 2.04 at IARI, New Delhi and Dharwad locations, respectively. The genotypic data of 6367 SNPs (single nucleotide polymorphisms) distributed across the genome were used for genetic diversity study, population structure, and GWAS (genome-wide association study). The average PIC (polymorphic information content) value observed was 0.25 and the average LD (linkage disequilibrium) decay distance was 152269 bp across the genome. Total 4 subgroups were observed within the population for genotypic data. Fixed and random model Circulating Probability Unification (FarmCPU) was used for 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 GHR1 (Guard Cell Hydrogen Peroxide-Resistant1), Late embryogenesis abundant, E3 Ubiquitin-protein ligase, WAT1 (Walls are thin1), beta-galactosidase, that are known to be associated with drought tolerance.