Genetic linkage map construction and QTL mapping for panicle-related traits in foxtail millet (Setaria italica (L.) P. Beauv.)

Panicle-related traits are important factors affecting foxtail millet yield and detecting the underlying genetic basis is imperative. In this study, we constructed a genetic linkage map using the F ₂ population crossed by Changsheng07 and Donggu218, two foxtail millet materials with significant differences in panicle-related traits. The genetic linkage map included 159 SSR markers and 37 Indel markers, covering 1545.5 cM, with average distance of 7.89 cM between adjacent markers. According to the phenotypes of nine panicle-related traits in F _2:3 families, a total of 22 quantitative trait loci (QTL) were identified, which could explain the phenotypic variation of 0.06–50.14%. Among them, the increased effect allele of 16 QTL were derived from the parent Changsheng07, and seven QTL ( qMPL3.1 , qMPL5 , qMPW2 , qSD5 , qTGW5.1 , qTGW5.2 and qGL5 ) were major QTL, which explained the phenotypic variation of 11.41, 12.78, 13.75, 34.81, 50.14, 40.28 and 11.32, respectively. Moreover, we found that a class II formin Seita.5G078800 may be the candidate gene in the mapping intervals of qMPL5 , qSD5 , qTGW5.2 and qGL5 . These results will lay a foundation for cloning and molecular mechanism analysis of candidate genes, and provide a theoretical basis for molecular marker-assisted selection breeding for high yield in foxtail millet.