Developing an Original Genetic Map and QTL Analysis for Submergence Tolerance in Nigerian Lowland Rice Germplasm

Flash flooding affects millions of hectares of lowland rice in the South South and South East zones of Nigeria annually, and developing locally adapted submergence-tolerant varieties requires understanding the genetic control of this trait in Nigerian rice germplasm, which remains uncharacterised in the scientific literature. This study developed an original genetic map and conducted QTL analysis for submergence tolerance in a Nigerian rice mapping population. A biparental cross was made between a submergence-sensitive Nigerian elite line (FARO 44) and a tolerant landrace collected from the Niger Delta floodplains. One hundred and eighty F3 lines were developed and phenotyped for submergence tolerance (percent survival after 14-day complete submergence, shoot elongation rate, and chlorophyll retention) at Bayelsa and Delta State experimental sites over two seasons. A genetic linkage map was constructed using 256 polymorphic SNP markers. Composite interval mapping identified seven QTL regions significantly associated with submergence survival, the largest on chromosome 9 (LOD 18.4) corresponding to the known Sub1 locus. Unexpectedly, a second large-effect QTL on chromosome 3 (LOD 11.2), not previously described in Sub1-containing germplasm, contributed 23 percent of phenotypic variance for survival. This novel QTL was validated in a MAGIC population using bioinformatic fine-mapping and shown to co-locate with a RING domain ubiquitin ligase gene involved in ethylene signalling. The study makes original contributions to QTL mapping methodology and identifies a novel submergence tolerance locus with significant implications for Nigerian lowland rice breeding.

Keywords: submergence tolerance, rice QTL mapping, genetic map, lowland rice, Nigeria