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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION OF FUNCTIONAL SEQUENCE IN PLANT GENOMES THROUGH BIOINFORMATIC, GENOMIC, AND GENETIC APPROACHES

Location: Plant, Soil and Nutrition Research

Title: Comparative population genomics of maize domestication and improvement

Authors
item Hufford, Matthew -
item Xu, Xun -
item Van Heerwaarden, Joost -
item Pyhajarvi, Tanja -
item Chia, Jer-Ming -
item Cartwright, Reed -
item Elshire, Robert -
item Glaubitz, Jeffrey -
item Guill, Katherine
item Kaeppler, Shawn -
item Lai, Jinsheng -
item Morrell, Peter -
item Shannon, Laura -
item Song, Chi -
item Springer, Nathan -
item Swanson-Wagner, Ruth -
item Tiffin, Peter -
item Wang, Jun -
item Zhang, Gengyun -
item Doebley, John -
item McMullen, Michael
item Ware, Doreen
item Buckler, Edward
item Yang, Shuang -
item Ross-Ibarra, Jeffrey -

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 19, 2012
Publication Date: June 3, 2012
Citation: Hufford, M., Xu, X., Van Heerwaarden, J., Pyhajarvi, T., Chia, J., Cartwright, R., Elshire, R., Glaubitz, J., Guill, K.E., Kaeppler, S., Lai, J., Morrell, P., Shannon, L., Song, C., Springer, N., Swanson-Wagner, R., Tiffin, P., Wang, J., Zhang, G., Doebley, J., McMullen, M.D., Ware, D., Buckler IV, E.S., Yang, S., Ross-Ibarra, J. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics. 44:808-811. DOI: 10.1038/ng.2309.

Interpretive Summary: Domesticates are striking examples of rapid evolution and formed the basis of Darwin’s ideas of natural selection. Our assessment of maize domestication and breeding delves into this 10,000-year evolutionary experiment through a novel combination of genomic and transcriptomic analyses. We find a wide array of selected genes and discover that selection has been stronger during initial domestication than subsequent breeding. We find that modern breeding has selected for complementation in gene expression between heterotic groups and has sampled a mere fraction of the diversity available in wild relatives, stressing the importance of incorporating exotic germplasm in breeding and transgenic efforts.

Technical Abstract: Domestication and modern breeding represent exemplary case studies of evolution in action. Maize is an outcrossing species with a complex genome, and an understanding of maize evolution is thus relevant for both plant and animal systems. This study is the largest plant resequencing effort to date, and our targeted sampling allows characterization of selection during two distinct bouts of selection. Our comprehensive comparative analysis of expression and population genomic data will serve as a model for studying the genetic basis of evolutionary change, and our results provide a number of testable hypotheses about crop evolution and propose methods for improvement.

Last Modified: 8/22/2014
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