Comparative transcriptome analysis and genetic dissection of vegetative branching traits in foxtail millet (Setaria italic)

Abstract

Abstract Vegetative branching including tiller and axillary branch are vital traits affecting both the plant architecture and the biomass in cereal crops. However, the mechanism underlying the formation of vegetative branching in foxtail millet is largely unknown. Here, a foxtail millet cultivar and its bushy wild relative Setaria viridis accession were used to construct segregating population to identify candidate genes regulating tiller number and axillary branch number. Transcriptome analysis using vegetative branching bud samples of parental accessions were performed, and key differentially expressed genes and pathways regulating vegetative branching were pointed out. Bulk segregant analysis on their F2:3 segregating population was carried out, and a major QTL for tiller number (qTN5.1) and two major QTLs for axillary branch number (qAB2.1 and qAB9.1) were detected. Fine-mapping strategy was further performed on F2:4 segregate population, and Seita.5G356600 encoding β- glucosidase 11 were identified as the promising candidate genes for qTN5.1, and eight genes with non-synonymous variation and expression differences in the qAB9.1 interval were finally identified as candidate genes for regulating axillary branching. Findings in this study will help to elucidate the genetic basis of vegetative branching formation of foxtail millet, and lay a foundation for breeding foxtail millet varieties with ideal vegetative branching number.