Multi-environment dissection of the genetic architecture of grain color and milling-related recovery traits in foxtail millet.

Multi-environment QTL analysis uncovered reproducible and novel loci underlying grain color and milling-related recovery traits in foxtail millet, and Seita.5G392600 was prioritized as a putative candidate gene for kernel yellowness and a potential breeding target. Grain appearance and processing quality are major determinants of the market value and end-use performance of foxtail millet, yet the genetic basis of these traits remains incompletely understood, particularly for kernel color and milling-related recovery traits. Here, we used 256 recombinant inbred lines derived from Jingu 21 × Chuang 29 and an ultra-high-density bin map generated by whole-genome resequencing to dissect the genetic architecture of grain color and milling-related recovery traits across eight environments. Three hull color traits (L, a, b), three kernel color traits (L, a, b), and two milling-related recovery traits, percentage of grain weight per panicle (PGWP) and percentage of kernel weight (PKW), were evaluated. In total, 74 QTL occurrences were identified and integrated into 45 distinct QTLs, including 11 reproducible loci detected in at least two environments and 34 environment-specific loci. Based on physical overlap with previously reported regions, 39 QTLs were considered putatively novel, whereas six co-localized with previously reported loci. We also identified seven multi-trait QTL clusters on chromosomes 1, 2, 3, 5, and 9. Candidate gene prioritization identified 11 genes within major QTL intervals. Among them, Seita.5G392600, encoding a putative glycosyltransferase, was prioritized as a putative candidate gene for kernel yellowness based on QTL co-localization, haplotype association, and detectable expression during grain development. The rare haplotype of Seita.5G392600 associated with higher kernel yellowness may provide useful variation for kernel color improvement, although further validation is required. These findings advance our understanding of the genetic architecture of grain appearance and milling-related recovery traits in foxtail millet and provide targets for fine mapping, functional validation, and marker-assisted improvement.