Genome-wide association analysis for plant height in foxtail millet (Setaria italica L.) germplasm resources in Shanxi, China

A suitable plant height can effectively enhance the nutrient utilization efficiency and lodging resistance of millet. This study utilized 313 local millet varieties from Shanxi as an association group. Plant height was investigated in five different environments, followed by whole-genome deep resequencing. After quality control of the data, 3,160,066 SNP markers uniformly distributed across the nine chromosomes of millet were obtained for genome-wide association analysis (GWAS) of plant height. Eight QTL loci significantly associated with plant height were identified, with each locus explaining 7.13% to 12.08% of the phenotypic variation. Within the 25 kb upstream and downstream confidence intervals of these eight stable QTL loci, forty candidate genes were discovered. Integrating gene annotation information, six candidate genes were identified to be primarily involved in hormone synthesis, cell division regulation, signal transduction, and carbohydrate metabolism. Haplotype analysis revealed that the superior haplotype Hap2 of the candidate gene Millet_GLEAN_10031852 can effectively reduce plant height.