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First published online October 8, 2008; 10.1104/pp.108.127902 Plant Physiology 148:1740-1759 (2008) © 2008 American Society of Plant Biologists OPEN ACCESS ARTICLE
Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean1,[W],[OA]Department of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.B.C.); Institut de Biotechnologie des Plantes, UMR CNRS 8618, INRA, Université Paris Sud, 91 405 Orsay, France (N.W.G.C., M.S., V.T., V.G.); Genoscope/Commissariat à l'Energie Atomique-Centre National de Séquençage, 91 057 Evry, France (A.C., S.S., B.S.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (S.D., H.L., M.O., I.S., J.Y., B.A.R.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (A.N.E., D.I., B.E.P., S.S.-B., J.J.D.); Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (N.G., J.M., A.N., M.B.R., D.M.T., M.A.S.M.); Department of Agronomy, Purdue University, West Lafayette, Indiana 47907 (C.S.H., S.J., J.W.); Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (B.E.P.); and Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211 (M.B.R.)
The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
1 This work was supported by the National Science Foundation Plant Genome Research Program (grant no. DBI–0321664 to R.W.I., M.A.S.M., N.D.Y., B.A.R., and J.J.D.) and by a grant from Genoscope/Commissariat à l'Energie Atomique-Centre National de Séquençage (to V.G.). A.N.E. was supported by a National Science Foundation Systematics Award (grant no. DEB–0516673). 2 Present address: Trait Genetics and Technology, Dow AgroSciences LLC, Indianapolis, IN 46268. 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: Roger W. Innes (rinnes{at}indiana.edu). [W] The online version of this article contains Web-only data. [OA] Open Access articles can be viewed online without a subscription. www.plantphysiol.org/cgi/doi/10.1104/pp.108.127902 * Corresponding author; e-mail rinnes{at}indiana.edu. Received August 10, 2008; accepted October 6, 2008; published October 8, 2008. This article has been cited by other articles:
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