Genetic improvement of resistance to preharvest sprouting using a major QTL allele for embryo dormancy in rice.

Lack of seed dormancy (SD) often causes pre-harvest sprouting (PHS) or inadequate germination in cereal crops and seed production. This research aimed to integrate a dormancy (D) allele isolated from weedy rice at qSD12 into the genetic background of a restoration-of-fertility line (RFL) to mitigate the PHS and germination problems. A hybrid F2 population was developed to map quantitative trait loci (QTLs) and model their epistatic and genotype-by-environment interactions. Twelve QTLs for flowering time (FT, 3), plant height (5) or SD (4) were identified. Of the 4 SD loci, qSD12 explained most of the phenotypic variance (R2 = 0.34), and 2 (qSD3 & qSD6) have the D alleles from the RFL. qSD12 interacted with qSD3 or qSD7-2, with the presence of the D allele at qSD12 increasing the effects of the others, as well as the duration of seed storage at 24 or 40 ˚C for dormancy release. The F2 plant-derived F4 to F6 lines were marker-assisted selected. The major effect of qSD12 on seed germination and on-panicle sprouting was confirmed with the F4 and F5 lines, respectively. A sample of F2 plant-derived backcross (BC1F1) plants, which are heterozygous for 2-4 of the SD QTLs, was evaluated for agronomic traits and genotyped with an array of SNP markers. Recurrent backcrossing with the RFL and genomic selection are used to pyramid the D alleles from qSD12 and other locus/loci to develop new varieties and RF lines with improved resistance to PHS. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-025-01623-8.