Genome-wide association analysis for drought tolerance and component traits in groundnut gene pool

Abstract

The potential production and productivity of groundnuts are limited due to severe drought stress associated with climate change. The current study aimed to identify genomic regions and candidate genes associated with drought tolerance and component traits for gene introgression and to guide marker-assisted breeding of groundnut varieties. Ninety-nine genetically diverse groundnut genotypes were phenotyped under drought-stressed and non-stressed field conditions in 2018/19 and 2019/20, and using the LeasyScan platform under non-stressed conditions in 2019/20 at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)/India. The samples were genotyped using 48 K single nucleotide polymorphisms (SNPs) markers at the University of Georgia/USA. Phenotypic data was collected on 17 agronomic traits and subjected to statistical analyses. The SNP data were computed, and population structure was inferred using a Bayesian clustering method in Structure version 2.3.4, while linkage disequilibrium was calculated using the GAPIT program in R software. Marker-trait associations were deduced using Tassel 5.2.86. Significant phenotypic variations were recorded for drought tolerance and the assessed agronomic traits. GWAS analysis using PCA + K and Q + K models identified significant SNPs associated with leaf area (1 SNP), leaf area Index (1 SNP), specific leaf area (1 SNP), leaf relative water content (43 SNPs), number of primary branches (1 SNP) and hundred seed weight (1 SNP). Forty-seven and one marker-trait associations were detected under drought-stressed and non-stressed conditions, respectively. The candidate genes and markers identified in the current study are useful for accelerated groundnut breeding targeting drought tolerance and market-preferred traits.