Fine mapping of qSdr9 , a novel locus for seed dormancy (SD) in weedy rice, and development of NILs with a strong SD allele

Lack of seed dormancy, a major cause of pre-harvest sprouting in rice and other cereal crops, causes significant reductions in grain yield and quality. Weedy rice is often strongly dormant; therefore, quantitative trait loci (QTLs) related to seed dormancy in weedy rice “Ludao” could be useful for improving pre-harvest sprouting resistance in the important japonica variety “Ninggeng 4.” To identify SD QTLs in variety Ludao, we constructed an advanced backcross population (BC6F2) of Ninggeng 4 with Ludao as the donor parent by marker-assisted backcrossing followed by SD phenotyping. The consistently detected QTL qSdr9 on chromosome 9L explained 18.09% of the phenotypic variance, and the Ludao allele decreased germination percentage by 10.78%. qSdr9 was fine-mapped to a 586.60 kb region between markers QNU9–10 and RM5777. Based on the closest linked marker for locus qSdr9, we developed near-isogenic lines with the qSdr9 allele from Ludao in Ninggeng 4 background. The qSdr9 near-isogenic lines with strong SD will be useful as parents in breeding for pre-harvest sprouting resistance.