Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates

doi:10.1073/pnas.1934431100

Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates

^aDepartment of Agronomy and Range Science and ^cGenetic Resources Conservation Program, University of California, Davis, CA 95616; ^bU.S. Department of Agriculture/Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710; ^dUnité Mixte de Recherche Diversity and Genome of Crop Plants, Institut National de la Recherche Agronomique, Montpellier, 34130 France; ^eDepartment of Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506; ^fDepartment of Agronomy, University of Missouri, Columbia, MO 65211;^gU.S. Department of Agriculture/Agricultural Research Service, University of Missouri, Columbia, MO 65211; ^hDepartment of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853; ⁱDepartment of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409; ^jDepartment of Plant Sciences, Loftsgard Hall, North Dakota State University, Fargo, ND 58105-5051; ^kDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523; ^lDepartment of Agronomy and Plant Genetics, University of Minnesota, 422 Borlaug Hall, St. Paul, MN 55108-6026; and ^mDepartment of Crop and Soil Sciences, P.O. Box 646420, Washington State University, Pullman, WA 99164-6420

Communicated by M. T. Clegg, University of California, Riverside, CA, July 15, 2003 (received for review March 25, 2003)

Abstract

Loci detected by Southern blot hybridization of 3,977 expressed sequence tag unigenes were mapped into 159 chromosome bins delineated by breakpoints of a series of overlapping deletions. These data were used to assess synteny levels along homoeologous chromosomes of the wheat A, B, and D genomes, in relation to both bin position on the centromere-telomere axis and the gradient of recombination rates along chromosome arms. Synteny level decreased with the distance of a chromosome region from the centromere. It also decreased with an increase in recombination rates along the average chromosome arm. There were twice as many unique loci in the B genome than in the A and D genomes, and synteny levels between the B genome chromosomes and the A and D genome homoeologues were lower than those between the A and D genome homoeologues. These differences among the wheat genomes were attributed to differences in the mating systems of wheat diploid ancestors. Synteny perturbations were characterized in 31 paralogous sets of loci with perturbed synteny. Both insertions and deletions of loci were detected and both preferentially occurred in high recombination regions of chromosomes.