Conuping BSA-Seq and RNA-Seq Reveal the Molecular Pathway and Genes Associated with the Plant Height of Foxtail Millet (Setaria italica)

Foxtail millet (Setaria italica) plays an important role in C4 crop research and agricultural development in arid areas due to its short growth period, drought tolerance, and barren tolerance. Exploration of the dwarfing mechanism and the dwarf genes of foxtail millet can provide a reference for dwarf breeding and dwarf research of other C4 crops. In this study, genetic analysis was performed using phenotypic data, candidate genes were screened by bulk segregant analysis sequencing (BSA-Seq); differentially expressed genes and metabolic pathways in different strains of high samples were analyzed by RNA sequencing (RNA-Seq). The association analysis of BSA-Seq and RNA-Seq further narrowed the candidate range. As a result, a total of three quantitative trait loci (QTLs) and nine candidate genes related to plant height were obtained on chromosomes I and IX. Based on the functional prediction of the candidate genes, we propose a hypothetical mechanism for the formation of millet dwarfing, in which, metabolism and MAPK signaling play important roles in the formation of foxtail millet plant height.