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Genome-Wide Association Studies of Ear Traits in Maize
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This study was aimed at finding genetic markers or genes that are associated with ear traits important to maize by genome-wide association study (GWAS) based on the USDA maize GWAS panel consisting of diverse inbred lines that represent the genetic variation and diversity of maize present at the world-wide maize public breeding programs. This study phenotyped 263 diverse inbred lines of the GWAS panel for seven ear traits: grain weight per plant (GW), ear weight per plant (EW), ear length (EL), kernel-row length (KL), ear diameter (ED), number of kernel rows (KR), and cob diameter (CD) in College Station, Texas from 2017 to 2019, and in Lubbock, Texas in 2018. These 263 inbred lines were genotyped using the whole genome shotgun sequencing reads, having an average coverage of 7.0 x, with high performance computing clusters and the maize inbred line B73 genome as the reference genome. A total of 1,553,207 quality single nucleotide polymorphism (SNP markers were identified after filtering with a base-calling quality score of ≤ Q30, missing rate of ≥0.1, and minor allele frequency (MAF) of ≤0.1. Population structure was stratified by population structure analysis, principle component analysis, and phylogenetic tree, respectively, together indicating that the USDA GWAS panel consists of six subpopulations: stiff stalk (SS), non-stiff stalk (NSS), tropical-subtropical (TS), popcorn, sweet corn, and mixed. By constructing a general linear model (GLM) with kinship matrix as covariate, three SNP markers were identified that were associated with ear traits at a significance level of -log10(P) = 7.0. Three candidate genes and three SNPs that were previously characterized were identified near these SNPs. These results have provided the candidate genes controlling the traits and SNP markers necessary for enhanced breeding for these traits through marker-based breeding.
Bai, Gali (2020). Genome-Wide Association Studies of Ear Traits in Maize. Master's thesis, Texas A&M University. Available electronically from