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

Panicle-related traits are important factors affecting the final yield of foxtail millet, and it is imperative to detect their underlying genetic basis. In this study, we constructed a genetic linkage map using the F₂ population crossed by Changsheng07 and Donggu218, two foxtail millet lines 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. Quantitative trait loci (QTL) mapping was conducted by combining the genetic linkage map and the phenotypic data of nine panicle-related traits in F_2:3 families, and a total of 22 QTL were identified, with phenotypic variation explained (PVE) of 0.06-50.14%. Among them, the increased effect alleles 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, 13 of 22 QTL formed four QTL clusters. These results will lay a foundation for the cloning and functional analysis of candidate genes involved in panicle development, and provide a theoretical basis for breeding high yield varieties through molecular marker-assisted selection in foxtail millet.

The online version contains supplementary material available at 10.1007/s11032-025-01594-w.