Identification of QTL for seed dormancy from weedy rice and its application to elite rice cultivar ‘Ninggeng 4’

Abstract

Seed dormancy is a complex agronomic trait that is not only controlled by genetics but also influenced by environmental conditions. Novel seed dormancy genes could improve rice yield and quality by preventing losses due to pre-harvest sprouting (PHS). Although there have been many reported studies related to seed dormancy in rice, little is known about seed dormancy genes derived from weedy rice. We used a weedy rice line ‘Ludao’ (with strong seed dormancy) as the donor parent and elite japonica variety ‘Ninggeng 4’ (with weak seed dormancy) as a recurrent parent for backcrossing. A BC4F2 population was developed for gene mapping, and germination percentage was used as the phenotype. Four quantitative trait loci (QTLs), qSdr7-1, qSdr7-2, qSdr7-3, and qSdr7-4, were identified on chromosome 7. Seed dormancy alleles of the QTLs were all derived from ‘Ludao.’ Located between markers RM21103 and RM5672, qSdr7-2 had the largest effect and explained 27.2% of the phenotypic variation with a LOD score of 14.5. Based on the closest linked marker for locus qSdr7-2, we developed near-isogenic lines (NILs) with the qSdr7-2 allele from ‘Ludao’ in ‘Ninggeng 4’ background. The qSdr7-2-NILs, which have strong seed dormancy and elite agronomic traits, should be useful as a parent in breeding for PHS resistance.