Unraveling genetic diversity and loci conferring leaf blast resistance in East and Southern African rice germplasm

Abstract Rice blast remains a major disease, causing severe yield losses in rice‐producing regions and posing a threat to global food security. Understanding genetic variation within germplasms is crucial for identifying locally adapted genotypes with beneficial alleles for improving resistance to this disease. This study aimed to characterize the genetic diversity of 261 East and Southern African (ESA) rice accessions and their relationships with the global 3K rice panel, and to identify genetic loci associated with leaf blast resistance. We analyzed genetic diversity using population structure and diversity metrics, and conducted genome‐wide association studies (GWASs) with SUPER (settlement of mixed linear model under progressively exclusive relationship) and BLINK (Bayesian information and linkage‐disequilibrium iteratively nested keyway) models to detect marker‐trait associations (MTAs) for blast resistance. The ESA panel revealed five genetically diverse subpopulations, which, while distinct from most 3K accessions, clustered with indica and aus types, and showed moderate to high nucleotide diversity ( π = 0.10–0.45) with major diversity hotspots identified. GWAS detected several significant MTAs for blast resistance, including a major quantitative trait loci, qBL4 , on chromosome 4, which accounted for 20.6% of variance and contained candidate resistance genes such as LOC_Os04g51030, a wall‐associated kinase. Favorable haplotypes at this locus led to a significant reduction in disease severity, suggesting these genetic variants are valuable resources for breeding durable, broad‐spectrum blast‐resistant rice varieties.