Open Access Highly Accessed Research article

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

Eduard D Akhunov12, Alina R Akhunova12, Olin D Anderson3, James A Anderson4, Nancy Blake5, Michael T Clegg6, Devin Coleman-Derr3, Emily J Conley4, Curt C Crossman3, Karin R Deal1, Jorge Dubcovsky1, Bikram S Gill7, Yong Q Gu3, Jakub Hadam7, Hwayoung Heo5, Naxin Huo3, Gerard R Lazo3, Ming-Cheng Luo1, Yaqin Q Ma18, David E Matthews9, Patrick E McGuire1, Peter L Morrell4, Calvin O Qualset1, James Renfro3, Dindo Tabanao104, Luther E Talbert5, Chao Tian1, Donna M Toleno6, Marilyn L Warburton1112, Frank M You1, Wenjun Zhang1 and Jan Dvorak1*

Author Affiliations

1 Department of Plant Sciences, University of California, Davis, CA 95616, USA

2 Department of Plant Pathology, KSU, Manhattan, KS 66506, USA

3 Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA

4 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA

5 Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA

6 Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA

7 Department of Plant Pathology, Kansas State University, Manhattan KS 66506, USA

8 Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA

9 USDA-ARS, Cornell University, Ithaca, NY 14853, USA

10 Philippine Rice Research Institute, Maligaya, Nueva Ecija, Philippines

11 The International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico, D.F., Mexico

12 Corn Host Plant Research Resistance Unit, USDA/ARS MSU MS 39762, USA

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BMC Genomics 2010, 11:702  doi:10.1186/1471-2164-11-702

Published: 14 December 2010

Additional files

Additional file 1:

Table S1 summarizes estimates of nucleotide polymorphism θw and nucleotide diversity θπ at the replacement (N) and silent (S) codon positions, and noncoding portions of genes and the ratios of diversity at the replacement and silent codon positions in genes in the individual chromosomes of the A and B genomes of T. dicoccoides population from the Diyarbarkir region in Turkey. Table S2 summarizes estimates of nucleotide polymorphism θw and nucleotide diversity θπ at the replacement (N) and silent (S) codon positions and in noncoding portions of genes and the ratios of diversity at the replacement and silent codon positions in the A, B, and D genomes of T. aestivum. Figure S1 is a neighbor joining unrooted tree of 476 T. aestivum accessions constructed from Nei's genetic distances computed from RFLP at 131 loci. The tree depicts genetic relationships among 13 T. aestivum lines used for resequencing and SNP discovery. Figures S2 and S3 show the numbers of haplotypes per gene along the A-genome and B-genome chromosomes, respectively, in T. aestivum and wild emmer (T. dicoccoides) in the Diyarbakir region in Turkey. Figure S4 shows the numbers of haplotypes per gene along the D-genome chromosomes in T. aestivum. Figure S5 is a neighbor joining unrooted tree of 55 wild emmer (T. dicoccoides) accessions from the Diyarbakir region in Turkey constructed from Nei's genetic distances computed from RFLP at 153 loci. The tree depicts genetic relationships among 10 wild emmer accessions used for resequencing and SNP discovery in wild emmer.

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Additional file 2:

Table S1 is an Xcel table summarizing locus diversity measures in the A, B, and D genomes of T. aestivum, the A and B genomes of Diyarbakir population of wild emmer, and the D genome of synthetic wheats. Table S1 further shows synteny of the diversity map with the wheat deletion-bin maps and the rice 12 pseudomolecules.

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