A genome-wide association study identifies genes associated with cuticular wax metabolism in maize.

The plant cuticle is essential in plant defense against biotic and abiotic stresses. To systematically elucidate the genetic architecture of maize (Zea mays L.) cuticular wax metabolism, two cuticular wax-related traits, the chlorophyll extraction rate (CER) and water loss rate (WLR) of 389 maize inbred lines, were investigated and a genome-wide association study (GWAS) was performed using 1.25 million single nucleotide polymorphisms (SNPs). In total, 57 non-redundant quantitative trait loci (QTL) explaining 5.57%-15.07% of the phenotypic variation for each QTL were identified. These QTLs contained 183 genes, among which, 21 strong candidates were identified based on functional annotations and previous publications. Remarkably, 3 candidate genes that express differentially during cuticle development encode β-ketoacyl-CoA synthase (KCS). While KCS19was known to be involved in cuticle wax metabolism, KCS12 and KCS3 functions were not reported. The association between KCS12 and WLR was confirmed by re-sequencing 106 inbred lines, and the variation of WLR was significant between different haplotypes of ZmKCS12. In this study, the loss-of-function mutant of ZmKCS12 exhibited wrinkled leaf morphology, altered wax crystal morphology, and decreased C32 wax monomer levels, causing an increased water loss rate and sensitivity to drought. These results confirm that ZmKCS12 plays a vital role in maize C32 wax monomers synthesis and is critical for drought tolerance. In sum, through GWAS of two cuticular wax-associated traits, this study reveals comprehensively the genetic architecture in maize cuticular wax metabolism and provides a valuable reference for the genetic improvement of stress tolerance in maize.