Mapping of Sihc1, which controls hull color, using a high-density genetic map based on restriction site-associated DNA sequencing in foxtail millet [Setaria italica (L.) P. Beauv.]

摘要

Hull color (HC) in foxtail millet appears to be a major indicator of nutritional quality. To attempt to identify and characterize the gene or quantitative trait locus (QTL) related to HC and to provide a basis for quality and yield breeding of foxtail millet, a restriction site-associated DNA sequencing (RAD-seq) analysis was employed to reveal genome-wide single nucleotide polymorphisms (SNPs) and to genotype the F-2 progeny from a cross between two cultivars: Heizhigu with green HC and Changnong 35 with yellow HC. A high-density linkage map spanning 1542.87 cM was constructed using 1694 bin markers, consisting of 46,256 SNP markers, and a QTL locus controlling HC was identified and temporarily named as Sihc1 (Setaria italica hull color). Results showed that Sihc1 was located in the interval between markers M33926512 and M34281352 on the end of chromosome 6, and explained 80.26% of the phenotypic variation with a logarithm of odds ratio of 93.46. The additive and dominant effects of Sihc1 were 1.0025 and -0.9991, respectively. Sihc1 was narrowed to a 354.84 kb physical region, inclusive of 30 open reading frames, and further analysis suggested that Seita. 6G226500, Seita. 6G226800, Seita. 6G228300, and Seita. 6G228600 might be the key candidates of Sihc1.