Comparative population genomics of maize domestication and improvement

Matthew B. Hufford, Xun Xu, Joost Van Heerwaarden, Tanja Pyhäjärvi, Jer Ming Chia, Reed A. Cartwright, Robert J. Elshire, Jeffrey C. Glaubitz, Kate E. Guill, Shawn M. Kaeppler, Jinsheng Lai, Peter L. Morrell, Laura M. Shannon, Chi Song, Nathan M. Springer, Ruth A. Swanson-Wagner, Peter Tiffin, Jun Wang, Gengyun Zhang, John DoebleyMichael D. McMullen, Doreen Ware, Edward S. Buckler, Shuang Yang, Jeffrey Ross-Ibarra

Research output: Contribution to journalArticle

407 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)808-811
Number of pages4
JournalNature Genetics
Volume44
Issue number7
DOIs
StatePublished - Jul 1 2012

    Fingerprint

ASJC Scopus subject areas

  • Genetics

Cite this

Hufford, M. B., Xu, X., Van Heerwaarden, J., Pyhäjärvi, T., Chia, J. M., Cartwright, R. A., Elshire, R. J., Glaubitz, J. C., Guill, K. E., Kaeppler, S. M., Lai, J., Morrell, P. L., Shannon, L. M., Song, C., Springer, N. M., Swanson-Wagner, R. A., Tiffin, P., Wang, J., Zhang, G., ... Ross-Ibarra, J. (2012). Comparative population genomics of maize domestication and improvement. Nature Genetics, 44(7), 808-811. https://doi.org/10.1038/ng.2309