Submitted to: Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/16/2003
Publication Date: 3/20/2004
Citation: Gu, X.-Y., Kianian, S., Foley, M.E. 2004. Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa). Genetics. 166:1503-1516. Interpretive Summary: Although seed dormancy is a key characteristic of weedy plants, mechanism governing seed dormancy are unknown. We seek to map and clone dormancy genes from rice to elucidate mechanism governing seed dormancy in weedy grasses. To this end, we developed a backcross population using the weedy strain of rice called SS18-2 and constructed a genetic linkage map. Using seed germination data, the linkage map, and genetic software, we identified several genes that regulate dormancy in this population over a 21 day period of afterripening. Finally, we discovered that most of these gene interact with one another and with other genes in the population to control the expression of seed dormancy.
Technical Abstract: Weedy rice has much stronger seed dormancy than cultivated rice. A wild-like weedy strain SS18-2 was selected to investigate the genetic architecture underlying seed dormancy, a critical adaptive trait in plants. A framework genetic map covering the whole rice genome was constructed based on 156 BC1 [EM93-1(non-dormant breeding line)//EM93-1/SS18-2] individuals. The mapping population was replicated using a split-tiller technique to control and better estimate the environmental variation. Dormancy was determined by germination of seeds after 1, 11, and 21 days of after-ripening (DAR). Six dormancy QTLs, designated as qSDS-4, -6, -7-1, -7-2, -8, and -12, were identified. The locus qSDS-7-1 was tightly linked to the red pericarp color gene Rc. A QTL×DAR interaction was detected for qSDS-12, the locus with the largest main effect at 1, 11, and 21 DAR (R2 = 0.14, 0.24, and 0.20, respectively). Two, three, and four orders of epistases were detected with 4, 6, and 6 QTL, respectively. The higher-order epistases strongly suggests the presence of genetically complex networks in the regulation of variation for seed dormancy in natural populations, and makes it critical to select for a favorable combination of alleles at multiple loci in positional cloning of a target dormancy gene.