Comparative population genomics of maize domestication and improvement

• Published in: Nature genetics Vol. 44; no. 7; pp. 808 - 811
• Main Authors: HUFFORD, Matthew B, XUN XU, JINSHENG LAI, MORRELL, Peter L, SHANNON, Laura M, CHI SONG, SPRINGER, Nathan M, SWANSON-WAGNER, Ruth A, TIFFIN, Peter, JUN WANG, GENGYUN ZHANG, DOEBLEY, John, VAN HEERWAARDEN, Joost, MCMULLEN, Michael D, WARE, Doreen, BUCKLER, Edward S, SHUANG YANG, ROSS-IBARRA, Jeffrey, PYHÄJÄRVI, Tanja, CHIA, Jer-Ming, CARTWRIGHT, Reed A, ELSHIRE, Robert J, GLAUBITZ, Jeffrey C, GUILL, Kate E, KAEPPLER, Shawn M
• Format: Journal Article
• Language: English
• Published: New York, NY Nature Publishing Group 01.07.2012
• Subjects: Biological and medical sciences; Breeding - methods; Corn; Crops, Agricultural - genetics; Estimates; Evolution; Evolution, Molecular; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation, Plant; Genes; Genetic aspects; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Genome, Plant; Genomes; Genomics; Haplotypes; Metagenomics - methods; Physiological aspects; Plants; Polymorphism, Single Nucleotide; Selection, Genetic; Transcriptome - genetics; Zea mays; Zea mays - genetics; United States; Domestication; Comparative genomics
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/ng.2309

Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines. We find evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.