Genome-wide association analysis of drought resistance and yield-related traits in maize inbred lines in Northwest China

Abstract Background Drought stress is a primary constraint on global maize production, significantly impairing plant growth, reproductive synchrony, and grain yield. To address this challenge, we aimed to identify SNPs and candidate genes associated with maize drought tolerance, with emphasis on grain yield (GY) and its drought resistance index (DRI). Results A panel of 202 maize inbred lines was evaluated for plant height (PH), anthesis–silking interval (ASI), and GY under well-watered (WW) and drought stress (DS) conditions over two years. Genome-wide association analyses (GWAS) were performed using 42,410 single-nucleotide polymorphisms and a mixed linear model (MLM) accounting for population structure and kinship. Drought stress reduced PH and GY and prolonged the ASI. A total of 158 nonredundant significant SNPs were identified, including 12 loci that were repeatedly detected across datasets. Thirty-six SNPs were associated with the DRI_GY, six of which were also significantly associated with GY under DS in 2023. Integration of favorable-allele profiles with the DRI showed that maize lines with higher DRI values generally carried more favorable alleles. A total of 142 candidate genes were identified within the associated intervals of SNPs carrying favorable alleles for DRI_GY, including Zm00001d026018 , which encodes ZmCPK4 . Heterologous overexpression of ZmCPK4 in Arabidopsis enhanced drought tolerance. Conclusions This study identified SNPs and candidate genes provide genomic resources for functional validation, marker-assisted selection, and the development of drought-tolerant, high-yielding maize cultivars.