Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in Rice

Alkaline soil is characterized by high soluble salt content, elevated pH levels, and ionic imbalance, all of which collectively intensify the harmful effects of alkaline stress on plants. To gain molecular insights into alkaline tolerance (AT), we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage. A total of 2 929 764, 2 059 114, and 1 365 868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies (GWAS) in the entire population as well as in the xian and geng subpopulations, respectively. Candidate genes and their superior haplotypes were further identified through gene-based association, haplotype analysis, and gene function annotation. In total, 99 QTLs were…