Multi-locus genome-wide association studies reveal genomic regions associated with sodicity tolerance in rice

Rice is a major food crop and serves as the primary food source for over half of the world's population, particularly in Asia. However, its cultivation is constrained by several abiotic stresses, notably sodicity, which significantly reduces productivity and is expected to worsen in the near future. In this study, a genome-wide association study (GWAS) was conducted to identify genomic regions and candidate genes associated with sodicity tolerance in rice. A rice association mapping panel consisting of 150 genotypes was evaluated for sodicity tolerance traits across four environments and genome-wide single nucleotide polymorphisms (SNPs) obtained using genotyping-by-sequencing (GBS) approach. The results revealed high phenotypic variation and heritability for six sodicity tolerance traits across the evaluated environments. The high-quality SNPs obtained were subjected to linkage disequilibrium (LD) block construction, resulting in 5,459 tag-SNPs, which were used for population structure and GWAS analyses. Population structure analysis revealed nine distinct sub-populations (k = 9) within the panel. GWAS, using three multi-locus models, identified 27 consistent and stable marker-trait associations (MTAs) for six sodicity tolerance traits across 10 chromosomes. A candidate gene search within the corresponding LD block regions identified 57 putative candidate genes associated with sodicity tolerance. Furthermore, gene-based haplotype analysis was conducted for these candidates and revealed that four genes-encoding ADP-glucose pyrophosphorylase, phenolics efflux transporter, DUF1296 family proteins, and F-box domain-containing proteins-exhibited significant differences among their haplotype groups. These candidate genes may serve as valuable resources for rice genetic improvement programs aimed at developing sodicity-tolerant rice cultivars.