Abstract
<jats:p>Flash flooding is a major constraint for rice production in the rainfed lowland areas in Sub-Saharan Africa. Breeding for complete submergence tolerance has progressed slowly in Africa, with tolerant varieties released in only a few countries. A breakthrough in complete submergence tolerance breeding has been the discovery and introgression of the SUB1 gene in Oryza sativa, conferring tolerance for over 14 days of complete submergence. The African rice, Oryza glaberrima, represents an underexploited reservoir of novel alleles for abiotic stress tolerance. This study evaluated 237 O. glaberrima accessions phenotyped for two seasons under 14 days of complete submergence at 1.5 m water depth, with survival recorded from 7 to 56 days after desubmergence. The panel was genotyped using a 9065 DArTseq-based SNP array, yielding 8,760 high-quality polymorphic markers distributed across all 12 chromosomes. Population structure revealed two subpopulations, and the rapid decay of linkage disequilibrium at 30 kb provided sufficient marker resolution for association mapping. Genome-wide association mapping using a linear mixed model identified 12 Bonferroni-significant SNPs on chromosomes 1, 2, 3, 4, 6, and 7. No significant SNPs were mapped to the SUB1 region on chromosome 9, suggesting an independent tolerance mechanism. Candidate genes identified include the Cytochrome P450 subfamily 72 (CYP72) gene, a lectin signaling protein, and a major QTL cluster. Collectively, these genes mediate submergence tolerance through oxidative stress detoxification, hypoxia signaling, and hormonal regulation under the quiescence strategy. The findings provide novel tolerance alleles to broaden the genetic base beyond SUB1 in Sub-Saharan Africa.</jats:p>