title: A Gene-Oriented Haplotype Comparison Reveals Recently Selected Genomic Regions in Temperate and Tropical Maize Germplasm.
abstract: The extensive genetic variation present in maize (Zea mays) germplasm makes it possible to detect signatures of positive artificial selection that occurred during temperate and tropical maize improvement. Here we report an analysis of 532,815 polymorphisms from a maize association panel consisting of 368 diverse temperate and tropical inbred lines. We developed a gene-oriented approach adapting exonic polymorphisms to identify recently selected alleles by comparing haplotypes across the maize genome. This analysis revealed evidence of selection for more than 1100 genomic regions during recent improvement, and included regulatory genes and key genes with visible mutant phenotypes. We find that selected candidate target genes in temperate maize are enriched in biosynthetic processes, and further examination of these candidates highlights two cases, sucrose flux and oil storage, in which multiple genes in a common pathway can be cooperatively selected. Finally, based on available parallel gene expression data, we hypothesize that some genes were selected for regulatory variations, resulting in altered gene expression.
authors.affiliation: College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.|Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: He
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Junjie
authors.identifier: http://orcid.org/0000-0002-4702-2392
authors.initials: J
authors.lastname: Fu
authors.affiliation: College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yongxiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zheng
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Zhang
authors.affiliation: College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Yang
authors.affiliation: College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Guoying
authors.initials: G
authors.lastname: Wang
mesh_terms: D002980:Climate; D018506:Gene Expression Regulation, Plant; D005809:Genes, Regulator; D005828:Genetics, Population; D018745:Genome, Plant; D006239:Haplotypes; D015810:Linkage Disequilibrium; D012641:Selection, Genetic; D013395:Sucrose / Q000378:metabolism; D014329:Tropical Climate; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism
chemical_list: D013395:Sucrose