New seed dormancy loci detected from weedy rice-derived advanced populations with major QTL alleles removed from the background

Domestication of cereal crops from wild relatives tended to eliminate seed dormancy. Our objective was to identify all the detectable seed dormancy loci that differentiated between a weedy and a cultivated line of rice to understand the impact of domestication on distribution of dormancy genes. Three additional dormancy quantitative trait loci (QTLs) were identified from two BC1F1 plant-derived F2 populations, in which the five previously known QTL-containing segments from the weedy rice donor were substituted by the genome of the recurrent parent. The three new QTLs that accounted for 8–11% phenotypic variance in the F2s were confirmed with three BC1F2 plant-derived F3 populations. Counting the seven previously identified QTLs, the parental lines differentiate at a total of ten dormancy loci that vary in dominance from dominant, partially dominant, co-dominant, to recessive types. The weedy and cultivated parents contribute dormancy alleles to eight and two of the ten loci, respectively. The two loci were newly detected. We concluded that a large proportion (8/10) of seed dormancy genes have been eliminated during domestication. The minor proportion (2/10) of dormancy genes retained in cultivars could be masked by those with a relatively large effect in a primary segregating population.