High yielding rain-fed lowland rice cultivars are sensitive to complete submergence stress of more than four days. In Nigeria, rice farms on about 3.6 million ha of rain-fed lowland areas are adversely affected by submergence stress. Consequently, farmers in the major rice producing states of the country lose their entire crop to flooding each year. The identification of a major quantitative traits locus (QTL) on chromosome 9, designated as sub1, has provided the opportunity to apply marker

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... sted selection to develop submergence tolerant varieties. This study was undertaken to introgress sub 1 into the genetic background of Nigerian lowland rice mega variety (WITA 4) and assess the ability of WITA 4 with sub 1 to withstand submergence stress. Swarna Sub1, one of the FR13A-derived submergence tolerant varieties developed by IRRI, was crossed to WITA 4, a submergence intolerant Nigerian mega variety to produce F1 hybrid. The derived BC1F2 progenies were genotyped and BC1F3 phenotyped. The results of genotyping, using two markers, namely ART5 and SC3, revealed that 18 BC1F3 plants were found carrying Swarna Sub 1 allele of ART5 while 41 BC1F3 carried WITA 4 allele of ART5. Twenty progenies were found carrying Swarna Sub 1 allele of SC3 while 37 plants carried WITA 4 allele. Two plants carried both alleles (H). Seventeen plants were observed to carry Swarna Sub 1 alleles at both markers loci while a total of 36 progenies were observed to carry WITA 4 alleles at both markers loci. The results of the phenotypic screening showed that 12 plants recorded percentage survival above 60%. The two markers showed high selection accuracies, and selection based on the markers could satisfactorily meet the needs of breeding for submergence.