Genome-wide association analysis and candidate gene identification for plant height in Shanxi local foxtail millet varieties

Plant height is pivotal for lodging resistance, harvestability, and yield potential in foxtail millet ( Setaria italica ). Here, we evaluated plant height in 209 diverse Shanxi local foxtail millet landraces across three contrasting environments and performed whole-genome resequencing of these accessions (mean depth ~38×). After standard filtering, 833,157 high-quality single nucleotide polymorphisms (SNPs) were retained. Neighbor-joining and principal component analysis consistently resolved four genetic groups with minor differences in sample assignment. A mixed linear model GWAS detected four loci significantly associated with plant height, including three loci not reported previously. Comparative genomics with rice and Arabidopsis shortlisted ten candidate genes; notably, SETIT_033071mg showed stem-specific high expression at the shooting stage in model variety Yugu1, with low expression elsewhere. Haplotype analysis of SETIT_033071mg in our GWAS panel (209 accessions evaluated across three environments) and an expanded diversity panel (313 accessions evaluated across five field environments) resolved multiple major haplotypes, among which H2 was consistently associated with reduced plant height across environments. These findings refine the genomic basis of plant height in foxtail millet and provide actionable targets for marker development for breeding lodging-resistant cultivars.