Genome-Wide Association Studies and Genomic Selection Analysis for Flowering-Related Traits in Maize Under Salt Stress

Salt stress is a major abiotic stress that restricts the growth and development of maize, often leading to irreversible yield losses when it occurs at flowering. To dissect the genetic basis of flowering-related traits under salt stress, a natural panel of 395 maize inbred lines was phenotyped for days to tasseling (DTT), days to pollen shedding (DTP), days to silking (DTS), and anthesis–silking interval (ASI) under salt-stressed field conditions. All four traits exhibited moderate-to-high heritabilities, ranging from 76.55% to 93.13%, suggesting a substantial genetic basis. GWAS using MLM, FarmCPU, and BLINK detected 42, 41, 47, and 8 unique SNPs for DTT, DTP, DTS, and ASI under salt stress, respectively, including 29 stable SNPs. A total of 292 candidate genes were identified, of which 230 had known functional annotations. KEGG pathway and GO enrichment analyses revealed two enriched pathways and five enriched GO terms, indicating that flowering time under salt stress is controlled by complex networks rather than by a few major genes or a single pathway. Among the candidate genes, Zm00001eb138380 was identified as a key candidate gene for flowering-related traits, whereas Zm00001eb335420, Zm00001eb311870, Zm00001eb091230, Zm00001eb139350, and Zm00001eb014590 were considered important candidates regulating flowering performance under saline conditions. Genomic selection (GS) prediction accuracy was 0.66 for DTT, 0.68 for DTP, 0.69 for DTS, and 0.32 for ASI using a five-fold cross-validation method. The optimal training population size and marker density were 70% and 20,000 SNPs, respectively. This study provides novel insights into the genetic basis of maize flowering-related traits under salt stress and demonstrates the potential of GS for improving flowering performance under saline conditions.