GWAS and gene co-expression network analysis reveal the genetic control of seed germination under salt stress in...

GWAS and WGCNA uncovered ZmKCH5 involved in seed germination under salt stress. Role of ZmKCH5 in modulating salt-germination ability was validated via overexpression in Arabidopsis and knockout in maize. Seed germination ability in salinized soil is a crucial factor affecting maize productivity. Herein, genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) were combined to elucidate the genetic control of seed germination ability under salt stress in maize. A total of 50 single nucleotide polymorphisms (SNPs) and 537 candidate genes were associated with seed germination traits under salt stress using GWAS. Meanwhile, transcriptome libraries at five salt-germination stages were constructed using two inbred lines with contrasting salt tolerances. We uncovered 19,929 differentially expressed genes (DEG) that were differentially responsive to salt stress during seed germination. The 221 overlaps between the 537 candidate genes and 19,929 DEGs were subjected to WGCNA based the gene expression values, detecting a salt stress-related module and four hub genes. Zm00001d011473, one of the hub genes, encodes the potassium channel protein 5 (ZmKCH5). Gene-based association analysis indicated that the variants in ZmKCH5 affected post-germinated root growth and salt tolerance, with "GA" being the favorable haplotype. Overexpression in Arabidopsis and knockout in maize indicated that ZmKCH5 positively mediated seed germination rate and primary root growth under salt stress. These findings will contribute to understanding the genetic and molecular mechanisms underlying maize seed germination under salt stress.