Identities and Regulatory Mechanisms of Seed Dormancy Genes Map-Based Cloned from Rice

Seed dormancy is divergent between cereal crops and wild relatives. This divergence in rice is accounted for by >10 quantitative trait loci (QTL), with ~80% of them having the dormancy-enhancing alleles derived from weedy rice. Loci SD7-1, SD1-2, SD7-2 and SD12 have been map-based cloned and characterized for molecular identities and regulatory mechanisms. SD7-1 encodes a bHLH family transcription factor (bHLH-TF) expressed in early developing seeds to control coat-imposed dormancy by promoting abscisic acid (ABA) synthesis and to produce red pigments in the lower epidermal cells of the pericarp tissue by activating the flavonoid biosynthesis pathway. SD1-2 encodes a gibberellin (GA) biosynthesis enzyme and its loss-of-functional mutations delayed endosperm development, desiccation acquisition and germination. SD7-2 encodes a protein kinase phosphorylating the DELLA protein SLR1, a core negative regulator of GA signaling, to delay seed after-ripening and germination. SD12 contributed most to the phenotypic variation and its effect on seed dormancy is enhanced by high seed developing temperatures. Underlying SD12 are three tightly linked genes encoding two bHLH-TFs and one hypothetic protein; the linked genes control embryo dormancy by promoting the expression of genes encoding heat-shock and late embryogenesis abundant proteins to enhance desiccation tolerance. Identities of the cloned genes demonstrated that natural variation in seed dormancy is largely regulated at a transcriptional level or by modifying GA or ABA signaling pathways in component tissues of developing or after-ripening seeds. These genes are being used to develop a new technique to mitigate transgene flow into weedy rice.