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

BMC Genomics

Research Article

James A Anderson¹  Emily J Conley¹  Peter L Morrell¹  Dindo Tabanao²  Michael T Clegg³  Donna M Toleno³  Jakub Hadam⁴  Bikram S Gill⁴  Hwayoung Heo⁵  Luther E Talbert⁵  Nancy Blake⁵  Jan Dvorak⁶  Karin R Deal⁶  Calvin O Qualset⁶  Frank M You⁶  Patrick E McGuire⁶  Chao Tian⁶  Jorge Dubcovsky⁶  Wenjun Zhang⁶  Ming-Cheng Luo⁶  Yaqin Q Ma⁷  Eduard D Akhunov⁸  Alina R Akhunova⁸  Yong Q Gu⁹  Devin Coleman-Derr⁹  Gerard R Lazo⁹  Curt C Crossman⁹  James Renfro⁹  Olin D Anderson⁹  Naxin Huo⁹  Marilyn L Warburton^1,10  David E Matthews^1,11 

[1] Department of Agronomy and Plant Genetics, University of Minnesota, 55108, St. Paul, MN, USA;Department of Agronomy and Plant Genetics, University of Minnesota, 55108, St. Paul, MN, USA;Philippine Rice Research Institute, Maligaya, Nueva Ecija, Philippines;Department of Ecology and Evolutionary Biology, University of California, 92697, Irvine, CA, USA;Department of Plant Pathology, Kansas State University, 66506, Manhattan, KS, USA;Department of Plant Sciences and Plant Pathology, Montana State University, 59717, Bozeman, MT, USA;Department of Plant Sciences, University of California, Davis, CA95616, USA;Department of Plant Sciences, University of California, Davis, CA95616, USA;Department of Botany and Plant Sciences, University of California, 92521, Riverside, CA, USA;Department of Plant Sciences, University of California, Davis, CA95616, USA;Department of Plant Pathology, KSU, 66506, Manhattan, KS, USA;Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, 94710, Albany, CA, USA;The International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico, D.F., Mexico;Corn Host Plant Research Resistance Unit, USDA/ARS MSU MS 39762, USA;USDA-ARS, Cornell University, 14853, Ithaca, NY, USA;

关键词: Single Nucleotide Polymorphism Marker;    Tetraploid Wheat;    Wild Emmer;    Homoeologous Group;    Single Nucleotide Polymorphism Discovery;   

DOI  :  10.1186/1471-2164-11-702

 received in 2010-04-27, accepted in 2010-12-14,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundA genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.ResultsNucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.ConclusionsIn a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

【 授权许可】

Unknown   
© Akhunov et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.