Plant Physiology Preview
Published on October 8, 2008; 10.1104/pp.108.127902
OPEN ACCESS ARTICLE
Received August 10, 2008
Accepted October 6, 2008
Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions Following Polyploidy in the Ancestor of Soybean
Roger W. Innes *, Carine Ameline-Torregrosa , Tom Ashfield , Ethalinda Cannon , Steven B. Cannon , Ben Chacko , Nicolas W. G. Chen , Arnaud Couloux , Anita Dalwani , Roxanne Denny , Shweta Deshpande , Ashley N. Egan , Natasha Glover , Christian S. Hans , Stacy Howell , Dan Ilut , Scott Jackson , Hongshing Lai , Jafar Mammadov , Sara Martin del Campo , Michelle Metcalf , Ashley Nguyen , Majesta O'Bleness , Bernard E. Pfeil , Ram Podicheti , Milind B. Ratnaparkhe , Sylvie Samain , Iryna Sanders , Beatrice Segurens , Mireille Sevignac , Sue Sherman-Broyles , Vincent Thareau , Dominic M. Tucker , Jason Walling , Adam Wawrzynski , Jing Yi , Jeff J. Doyle , Valerie Geffroy , Bruce A. Roe , M.A. Saghai Maroof , and Nevin D. Young
Department of Biology, Indiana University, Bloomington, Indiana 47405; Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108; Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011; USDA-ARS and Department of Agronomy, Iowa State University, Ames, Iowa 50011; Institut de Biotechnologie des Plantes, UMR CNRS 8618, INRA, Universite Paris Sud, 91 405 Orsay, France; Genoscope/CEA-Centre National de Sequencage, 91 057 Evry, France; Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019; L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853; Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061; Department of Agronomy, Purdue University, West Lafayette, Indiana 47907; CSIRO Plant Industry, Canberra, ACT 2601 Australia; Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
* Corresponding author; email: rinnes{at}indiana.edu.
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 base-pair region in Glycine max (soybean) centered on the Rpg1-b disease resistance gene and compared this region to a region duplicated 10-14 million years ago. These two regions were also compared to homologous regions in several related legume species (a second G. max genotype, G. 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 threefold 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 genome, in which only about a 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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