Mapping QTLs for submergence tolerance during germination in rice

Abstract

To understand the genetic bases of tolerance and to identify relevant quantitative trait loci (QTLs), KHAIYAN (Aus type) was crossed with IR64, a semi-dwarf, modern variety moderately sensitive to anaerobic conditions during germination. Results of screening of BC2F2 lines showed that survival percentage in IR64/KHAIYAN//IR64 population ranges from 0 to 68% with an average of 30%. A linkage map was constructed with 155 polymorphic SSR markers, resulting in a map of 1483.5 cM with a mean inter-marker distance of 9.6. Four putative QTLs were detected in this population, one each on chromosomes 1 (qAG-1), 2 (qAG-2-1), 11 (qAG-11), and 12 (qAG-12). The LOD value of these QTLs ranged from 3.66 to 5.71 with phenotypic variance in the range of 12 to 29.24%. Total phenotypic variation explained by the four QTLs was about 51.4%. The additive value of the QTL on chromosome 1 was negative, indicating that the allele from KHAIYAN increased tolerance to anaerobic conditions during germination. However, the QTLs on chromosome 2, 11, and 12 were positive indicating contribution of the alleles from IR64.