Genome-wide Association Study of Carotenoids in Maize Kernel.

Maize (Zea mays L.) kernel pigments mainly consist of natural pigments, such as carotenoids, which are the second largest class of natural pigments and have some functions that are healthful to humans. It is essential to analyze the genetic mechanism of carotenoid biosynthesis and establish the molecular marker technology system for the breeding of maize germplasm. In this study, we utilized an association panel comprising 244 maize inbred lines and about three million single nucleotide polymorphism (SNP) markers for the genome-wide association study (GWAS) and to preliminarily analyze the genetic bases of maize kernel carotenoids. The main carotenoids in maize kernels were found to be lutein, zeaxanthin, beta-cryptoxanthin, and beta-carotene, as determined by high-performance liquid chromatography. The GWAS revealed that a total of 826 quantitative trait loci (QTLs) were significantly associated with carotenoids contents, 35 QTLs were simultaneously mapped by at least two traits, and 87 candidate genes were located in the meta-QTL regions. Eight stable QTLs that were identified by more traits in the two environments were selected for the superior allelic variation analysis for germplasem selection. The results of this study can provide a theoretical basis for screening genes that guide kernel carotenoids selection breeding. The association panel comprised 244 excellent maize inbred lines for genome-wide association studies (GWAS). We identified 826 quantitative trait loci (QTLs) were significantly associated with carotenoids contents, and two key candidate genes. We found a germplasm IL78 with higher carotenoids and carried the superior allelic variations. In this study, the contents of four carotenoids in 244 maize inbred lines were detected and about three million single nucleotide polymorphisms (SNPs) for genome-wide association study to preliminarily analyze the genetic mechanism of maize kernel carotenoids. We identified 826 quantitative trait loci (QTLs) were significantly associated with carotenoids contents, and two key candidate genes Zm00001d029526 (CYP18) and Zm00001d023336 (wrky91) were obtained. In addition, we found a germplasm IL78 with higher carotenoids. The results of this study can provide a theoretical basis for screening genes that guide kernel carotenoids selection breeding.