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

key messageMulti-environment genome-wide association study (GWAS) and haplotype analysis identified a height-reducing WAK4 (SETIT_033071mg) haplotype as a promising target for plant height improvement in foxtail millet. Plant height is pivotal for plant architecture, harvestability, and yield potential in foxtail millet (Setaria italica). Here, we evaluated plant height in 209 diverse Shanxi local foxtail millet landraces in three field environments in Jinzhong, Shanxi, during 2020-2022, and performed whole-genome resequencing of these accessions at a mean depth of approximately 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. GWAS using EMMAX, complemented by MLMM, identified four loci associated with plant height, including two loci not previously reported. Comparative genomics with rice and Arabidopsis shortlisted ten candidate genes, among which SETIT_033071mg was prioritized for further haplotype analysis based on its genomic location and functional annotation. 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 useful targets for marker development in plant height-related breeding.