title: Identification of Genetic Differentiation between Waxy and Common Maize by SNP Genotyping.
abstract: 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.
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Derong
authors.initials: D
authors.lastname: Hao
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Zhenliang
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Yujing
authors.initials: Y
authors.lastname: Cheng
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Chen
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Huhua
authors.initials: H
authors.lastname: Lu
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Yuxiang
authors.initials: Y
authors.lastname: Mao
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Mingliang
authors.initials: M
authors.lastname: Shi
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Xiaolan
authors.initials: X
authors.lastname: Huang
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Guangfei
authors.initials: G
authors.lastname: Zhou
authors.affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Xue
mesh_terms: D014644:Genetic Variation; D015810:Linkage Disequilibrium; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics*