[Identification of drought-responsive genes of foxtail millet by genome-wide association studies and transcriptome...

Foxtail millet (Setaria italica L.) is a C₄ crop mainly cultivated in the semi-arid regions of northern China. With strong drought tolerance and rich genetic resources, this crop serves as an excellent model for the identification of drought tolerance genes in crops. Currently, the identification of drought tolerance genes in foxtail millet primarily relies on the transcriptomic analysis of individual drought-tolerant varieties. However, the research on the quantitative genetics of drought tolerance in foxtail millet is limited, which results in a scarcity of elite haplotypes available for the breeding of drought-tolerant foxtail millet varieties. This study aims to systematically identify genetic loci and key candidate genes linked to drought tolerance in foxtail millet. In this study, we used 400 core germplasm accessions of foxtail millet as research materials to observe the growth status and survival rate of foxtail millet plants under normal and drought conditions, and selected 16 extremely drought-tolerant and 45 extremely drought-intolerant varieties. The genome-wide association studies (GWAS) identified a new drought tolerance-related genetic locus on chromosome 4. Combining gene function analysis, transcriptomic analysis of materials with extreme phenotypes, and haplotype analysis of candidate genes, we found that SiCIPK24 and MYB may be involved in the regulation of drought tolerance in foxtail millet. Additionally, transcriptome data showed that the MAPK signaling pathway, phenylpropanoid metabolism, and plant hormone signaling pathways were affected by drought. The drought tolerance loci and potential drought resistance genes, as well as their elite haplotypes identified in this study, lay a foundation for the breeding of drought-tolerant foxtail millet varieties.