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Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean

Roger W. InnesIowa State UniversityCarine Ameline-TorregrosaIndiana University BloomingtonTom AshfieldUnited States Department of AgricultureEthalinda K. S. CannonUniversity of Minnesota Twin CitiesSteven B. CannonUniversity of Minnesota Twin CitiesBen ChackoIowa State UniversityNicolas W. G. ChenIowa State UniversityArnaud CoulouxUnited States Department of AgricultureAnita DalwaniIndiana University BloomingtonRoxanne DennyDepartment 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 ResearchShweta DeshpandeUnited States Department of AgricultureAshley N. EganDepartment 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 ResearchNatasha GloverIndiana University BloomingtonC.S. HansUnited States Department of AgricultureStacy HowellDepartment 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 ResearchDaniel C. IlutUnited States Department of AgricultureScott A. JacksonIndiana University BloomingtonHongshing LaiIndiana University BloomingtonJafar MammadovDepartment 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 ResearchSara E. Martin del CampoIowa State UniversityMichelle MetcalfUnited States Department of AgricultureAshley NguyenUnited States Department of AgricultureMajesta O’BlenessUniversity of OklahomaBernard E. PfeilUnited States Department of AgricultureRam PodichetiIndiana University BloomingtonMilind B. RatnaparkheUniversity of MissouriSylvie SamainIndiana University BloomingtonIryna SandersDepartment 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 ResearchBéatrice SegurensIowa State UniversityMireille SévignacIowa State UniversityS. Sherman-BroylesUnited States Department of AgricultureVincent ThareauDepartment 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 ResearchDominic M. TuckerIowa State UniversityJason G. WallingUnited States Department of AgricultureAdam WawrzyńskiUnited States Department of AgricultureYi JingDepartment 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 ResearchJeff J. DoyleIowa State UniversityValérie GeffroyUnited States Department of AgricultureBruce A. RoeIndiana University BloomingtonM. A. Saghai MaroofDepartment 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 ResearchNevin D. YoungIowa State University

2008en

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ABI

Annotatsiya

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.

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DOI: 10.1104/pp.108.127902

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