Identifying genetic loci associated with drought tolerance in foxtail millet (Setaria italica)

Drought is the primary factor contributing to crop yield loss. Therefore, enhancing the drought tolerance of foxtail millet, a globally significant food crop, is essential for ensuring global food security. We analyzed 425 foxtail millet samples from the Xinjiang Academy of Agricultural Sciences using 1,304,248 highly polymorphic SNPs for a genome-wide association study, and a total of 77 QTL regions were detected across three environments. Linkage disequilibrium (LD) analysis, population genetic structure analysis, K-means clustering, and phylogenetic tree construction revealed that foxtail millet in different subgroups exhibited certain regional differences. The secondary screening of QTL region genes combined with transcriptome analysis identified six genes with significant expression differences. These drought-responsive genes in foxtail millet function as protein kinases, glycosyltransferases, CTP synthetases, and transcription factors. Haplotype analysis identified 8 phenotypically distinct haplotypes in candidate genes associated with drought stress. Expression levels of genes associated with drought tolerance and yield, validated by RT-qPCR, were largely consistent with transcriptome analysis results. This study's results offer a scientifically significant reference for genetic research and improvement in foxtail millet yield under drought stress.