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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #271352

Title: Comparative population genomics of maize domestication and improvement

item HUFFORD, MATTHEW - University Of California
item XU, XUN - Beijing Genome Institute
item VAN HEERWAARDEN, JOOST - University Of California
item PYHAJARVI, TANJA - University Of California
item CHIA, JER-MING - Cold Spring Harbor Laboratory
item CARTWRIGHT, REED - Rice University
item ELSHIRE, ROBERT - Cornell University
item GLAUBITZ, JEFFREY - Cornell University
item Guill, Katherine
item KAEPPLER, SHAWN - University Of Wisconsin
item LAI, JINSHENG - China Agricultural University
item MORRELL, PETER - University Of Minnesota
item SHANNON, LAURA - University Of Wisconsin
item SONG, CHI - Beijing Genome Institute
item SPRINGER, NATHAN - University Of Minnesota
item SWANSON-WAGNER, RUTH - University Of Minnesota
item TIFFIN, PETER - University Of Minnesota
item WANG, JUN - Beijing Genome Institute
item ZHANG, GENGYUN - Beijing Genome Institute
item DOEBLEY, JOHN - University Of Wisconsin
item McMullen, Michael
item Ware, Doreen
item Buckler, Edward - Ed
item YANG, SHUANG - Beijing Genome Institute
item ROSS-IBARRA, JEFFREY - University Of California

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.