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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)

Author
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 - Kate
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 - Ed
item Yang, Shuang
item Ross-ibarra, Jeffrey

Submitted to: Nature Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 3/19/2012
Publication Date: 6/3/2012
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: 8/24/2016
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