Kernel moisture content at harvest stage (KMC) is an important factor affecting maize production, especially for mechanical harvesting. We investigated the genetic basis of KMC using an association panel comprising of 144 maize inbred lines that were phenotypically evaluated at two field trial locations. Significant positive or negative correlations were identified between KMC and a series of other agronomic traits, indicating that KMC is associated with other such traits. Combining phenotypic values and the Maize SNP3K Beadchip to perform a genome-wide association study revealed eight single nucleotide polymorphisms (SNPs) associated with KMC at P ≤ 0.001 using a mixed linear model (PCA+K). These significant SNPs could be converted into five quantitative trait loci (QTLs) distributed on chromosomes 1, 5, 8, and 9. Of these QTLs, three were colocalized with genomic regions previously reported. Based on the phenotypic values of the alleles corresponding to significant SNPs, the favorable alleles were mined. Eight maize inbred lines with low KMC and harboring favorable alleles were identified. These QTLs and elite maize inbred lines with low KMC will be useful in maize breeding.
Waxy maize (Zea mays L. var. ceratina) is an important vegetable and economic crop that is thought to have originated from cultivated flint maize and most recently underwent divergence from common maize. In this study, a total of 110 waxy and 110 common maize inbred lines were genotyped with 3072 SNPs to evaluate the genetic diversity, population structure, and linkage disequilibrium decay as well as identify putative loci that are under positive selection. The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms. Principal coordinate analysis and neighbor-joining cluster analysis consistently classified the 220 accessions into two major groups and a mixed group with mixed ancestry. Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups. The LD decay distance (1500–2000 kb) in waxy maize was lower than that in common maize. Fourteen candidate loci were identified as under positive selection between waxy and common maize at the 99% confidence level. The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.
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