Unveiling Stagnant Flooding Tolerance in Lowland NERICAs: Genomic Insights and Breeding Prospects

Rice cultivation in the rainfed lowland ecosystem is prone to encounter substantial flooding challenges in the form of complete submergence or prolonged stagnant flooding. While the Sub1 gene enables rice plants to survive the momentary complete submergence, stagnant flooding, defined by incomplete submergence for extended periods, necessitates moderate stem elongation for survival. In this study, we characterized 60 lowland NERICA varieties under stagnant flooding (SF) conditions, identify tolerant germplasm, and detect genomic regions associated with key traits to aid breeding efforts. Phenotypic evaluations revealed significant genetic variability among the NERICA varieties, with some accessions showing 20–60% yield reduction under SF stress. The derived NERICA-L19/IR64 Sub1 RIL population showed improved grain yield under SF compared to both parents and submergence tolerant checks. A total 27 QTLs were identified associated with plant height, tiller number, panicle number, days to flowering, and grain yield. Stable and major-effect QTLs, such as qPH1.1 , qPH3.1 , and qDTF3.1 , were consistent across environments, explaining up to 48% of the phenotypic variation. Several QTLs co-localized, indicating potential pleiotropy or tight linkage. Candidate genes associated with these regions include regulators of gibberellin signaling, flowering time and other developmental processes. This study highlights the potential of lowland NERICAs as a genetic resource as well as provides molecular resources for improving stagnant flooding tolerance in rice. The integration of phenotypic data, stable QTLs, and functionally relevant candidate genes lays a foundation for marker-assisted breeding of dual-tolerant rice cultivars adapted to climate-induced flooding scenarios in sub-Saharan Africa.