Genome-wide Association Analysis and Candidate Gene Identification of Plant Height in Dabaigu (Foxtail Millet)

Abstract Plant height is pivotal for lodging resistance, harvestability, and yield potential in foxtail millet (Setaria italica). We phenotyped 209 diverse Dabaigu accessions across three contrasting environments and performed whole-genome resequencing (mean depth ~38×). After standard filtering, 833,157 high-quality 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 (EMMAX) detected four loci significantly associated with plant height. Comparative genomics with rice and Arabidopsis shortlisted ten candidates; notably, SETIT_033071mg showed stem-specific high expression at the shooting stage in Yugu1, with low expression elsewhere. Haplotype analysis of SETIT_033071mg in an expanded panel of 313 accessions across five field sites resolved six gene haplotypes (H1–H6), among which H2 was consistently associated with reduced plant height across environments. In parallel, we developed a KASP assay (kPH8552) tagging the lead SNP at qPH2.2 (distinct from the SETIT_033071mglocus). In the Dabaigu panel, the assay achieved an 80.4% call rate (G:G=74; T:T=94), and the T allele was consistently associated with reduced height by −4.48 cm (BLUE; P = 0.044). These findings refine the genomic basis of plant height in foxtail millet and provide actionable targets and a candidate marker for breeding lodging-resistant, semi-dwarf cultivars, pending validation in independent populations.