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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Patterns of Selection and Tissue-Specific Expression among Maize Domestication and Crop Improvement Loci^1,[W],[OA]

Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 (K.M.H., B.S.G.); Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (P.C., D.H.W.); Plant, Soil, and Nutrition Research Unit, United States Department of Agriculture-Agricultural Research Service, Cold Spring Harbor, New York 11724 (D.H.W.); and Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, and the Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211 (M.D.M.)

The domestication of maize (Zea mays sp. mays) from its wild progenitors represents an opportunity to investigate the timing and genetic basis of morphological divergence resulting from artificial selection on target genes. We compared sequence diversity of 30 candidate selected and 15 reference loci between the three populations of wild teosintes, maize landraces, and maize inbred lines. We inferred an approximately equal ratio of genes selected during early domestication and genes selected during modern crop breeding. Using an expanded dataset of 48 candidate selected and 658 neutral reference loci, we tested the hypothesis that candidate selected genes in maize are more likely to have transcriptional functions than neutral reference genes, but there was no overrepresentation of regulatory genes in the selected gene dataset. Electronic northern analysis revealed that candidate genes are significantly overexpressed in the maize ear relative to vegetative tissues such as maize shoot, leaf, and root tissue. The maize ear underwent dramatic morphological alteration upon domestication and has been a continuing target of selection for maize yield. Therefore, we hypothesize that genes targeted by selection are more likely to be expressed in tissues that experienced high levels of morphological divergence during domestication and crop improvement.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Brandon S. Gaut (bgaut{at}uci.edu).

^[W] The online version of this article contains Web-only data.

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www.plantphysiol.org/cgi/doi/10.1104/pp.107.098988

^* Corresponding author; e-mail bgaut{at}uci.edu; fax 949–824–2181.

Received March 6, 2007; accepted May 9, 2007; published May 11, 2007.

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