Developmental Mechanisms of Seed Dormancy Revealed by Map-Based Cloning of a Major Quantitative Trait Locus from Rice (Oryza sativa)

Seed dormancy is a key adaptive trait for wild species and also one of major domestication-related traits for crops. Of the 10 quantitative trait loci (QTL) identified for seed dormancy in a weedy rice system developed from our previous research, qSD12 locus displayed the largest effect on delaying germination. High-resolution mapping and progeny population analysis delimited qSD12 to a genomic region of <80 kb including 3 adjacent candidate genes (SD12a, SD12b and SD12c) interspaced by a group of 6 tandem transposon/retrotransposon (TP/RTP). SD12a and SD12c encode predicted bHLH domain-containing transcription factors while SD12b encodes a hypothetical protein. Phylogenetic analysis for the ~2Mb region flanking the QTL using 188 accessions of wild (72 rufipogon,7 nivara, 11 outgroup), weedy (12) and cultivated (86, mainly landraces) rice demonstrated that SS18-2 is exclusively clustered with 54 rufipogon accessions and the SS18-2-like haplotype is not present in the cultivated genotypes tested, suggesting that some of the seed dormancy genes may have been eliminated at the beginning of the domestication. Gene expression analyses indicated that all three genes are mainly expressed in developing embryos to regulate the seed dormancy development. RNA-sequence analysis identified a pool of candidate genes differentially expressed in developing embryos from three isogenic lines; and the downstream genes mainly consist of those with predicted functions for responses to abiotic stimuli and heat shock proteins. The findings from this research provide a unique model to explain evolutionary and developmental mechanisms of seed dormancy in grass species and candidate genes to manipulate germination capability in rice breeding programs.