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Title: Recent demography drives changes in linked selection across the maize genome

Author
item Beissinger, Timothy
item WANG, LI - Iowa State University
item CROSBY, KATE - University Of California
item DURVASULA, ARUN - University Of California
item HUFFORD, MATTHEW - Iowa State University
item ROSS-IBARRA, JEFFREY - University Of California

Submitted to: Nature Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/5/2016
Publication Date: 6/13/2016
Publication URL: http://handle.nal.usda.gov/10113/62707
Citation: Beissinger, T.M., Wang, L., Crosby, K., Durvasula, A., Hufford, M.B., Ross-Ibarra, J. 2016. Recent demography drives changes in linked selection across the maize genome. Nature Plants. doi:10.1038/nplants.2016.84.

Interpretive Summary: Maize, which is among the world's most important crops for food, feed, and fuel, was not always the high-yielding crop we are familiar with today. Instead, maize resulted from human imposed selection operating on a leafy grass called teosinte. ARS researchers studied the types of selection that transformed teosinte into maize, as well as the population size expansion and contraction that occurred during this process. We observe that approximately 5% of the teosinte contributed genetically to modern maize, and that after going through this so-called "bottleneck", maize population size ballooned to be orders of magnitude larger than that of teosinte. Selection favoring new beneficial mutations within genes has contributed little to maize evolution, while selection against harmful mutations appears to have contributed substantially. Our most important finding is that the recent ballooning of maize population size allows selection in maize to operate much more effectively than it did in the past. Maize breeders and geneticists can use this knowledge to predict which genetic variations may prove harmful and/or beneficial to further improve the crop.

Technical Abstract: The interaction between genetic drift and selection in shaping genetic diversity is not fully understood. In particular, a population's propensity to drift is typically summarized by its long-term e_ective population size (Ne), but rapidly changing population demographics may complicate this relationship. To better understand how changing demography impacts selection, we investigated linked selection in the genomes of 23 domesticated maize and 13 wild maize (teosinte) individuals. We show that maize went through a domestication bottleneck with a population size of approximately 5% that of teosinte before it experienced rapid expansion post-domestication. We observe that hard sweeps on genic mutations are not the primary force driving maize evolution. As expected, a reduced population size during domestication decreased the e_ciency of purifying selection to purge deleterious alleles from maize, but rapid expansion after domestication has since increased the e_ciency of purifying selection to levels exceeding those seen in teosinte. This _nal observation demonstrates that rapid demographic change can have wide-ranging impacts on diversity that conict with would-be expectations based on long-term Ne.