Population Structure, Genetic Diversity, and Genome-Wide Association Analysis of Eastern African Rice Landraces for Climate Resilience Breeding: The Case of Complete Submergence Tolerance

Rice landraces remain a crucial reservoir of novel alleles for stress-tolerance and climate-resilience breeding in Africa. East Africa harbors a rich diversity of Oryza sativa germplasm that is under investigated for their potential to improve stress tolerance. This study characterized a panel of 259 Oryza sativa landraces collected from East Africa using a genotype-by-sequencing approach and phenotypic evaluation under complete submergence stress. The study identified 168,091 high-quality SNP markers, revealing a panel with high genetic diversity, moderate heterozygosity of 0.062, and complex population structure. Population structure analysis of the panel displayed three major subpopulations with extensive admixture, indicating long-term gene flow and local adaptation of the landraces. Genome-wide linkage disequilibrium (LD) decay at r 2 = 0.2 is approximately 57.5 kb, revealing moderate mapping resolution. To explore the breeding relevance of the panel, the study carried out a genome-wide association analysis (GWAS) for complete submergence tolerance following a linear mixed model (LMM). GWAS revealed 20 putative loci associated with submergence tolerance across chromosomes 1, 2, 4, 5, 6, 8, 9, 10, 11, and 12 based on the nominal P-value. The identified SNPs did not surpass the Bonferroni correction threshold; hence, the associations are suggestive rather than genome-wide significant. Candidate gene mining within a 115 kb linkage disequilibrium (LD) window discovered putative genes involved in cytokinin and auxin signaling, transcription regulation under an oxygen-deprived environment, stress signal transduction, and cellular maintenance activities. While the study findings are exploratory, they present the panel as a potentially valuable genetic resource for breeding strategies in the region and as a novel resource for improving abiotic stress tolerance, including submergence tolerance. The findings provide a preliminary foundation for functional validation and realistic targets for marker-assisted introgression to improve productivity in rice-producing regions of Africa.