Genetics, Vol. 166, 1503-1516, March 2004, Copyright © 2004

Multiple Loci and Epistases Control Genetic Variation for Seed Dormancy in Weedy Rice (Oryza sativa)

Xing-You Gua, Shahryar F. Kianiana, and Michael E. Foleyb
a Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105
b Biosciences Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Fargo, North Dakota 58105

Corresponding author: Michael E. Foley, 1605 Albrecht Blvd., USDA-Agricultural Research Service, Fargo, ND 58105., foleym{at}fargo.ars.usda.gov (E-mail)

Communicating editor: R. W. DOERGE

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 rice genome was constructed on the basis of 156 BC1 [EM93-1 (nondormant 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 QTL, 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 x 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 four, six, and six QTL, respectively. The higher-order epistases strongly suggest the presence of genetically complex networks in the regulation of variation for seed dormancy in natural populations and make it critical to select for a favorable combination of alleles at multiple loci in positional cloning of a target dormancy gene.




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