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

Creator: Akhunov, E.
Creator: Akhunova, A.
Creator: Anderson, O.
Creator: Anderson, J.A.
Creator: Blake, N.K.
Creator: Clegg, M.T.
Creator: Coleman-Derr, D.
Creator: Conley, E.J.
Creator: Crossman, C.C.
Creator: Deal, K.R.
Creator: Dubcovsky, J.
Creator: Gill, B.S.
Creator: Yong Qiang Gu
Creator: Hadam, J.
Creator: Hwayoung Heo
Creator: Naxin Huo
Creator: Lazo, G.R.
Creator: Ming-Cheng Luo
Creator: Yaqin Q Ma
Creator: Matthews, D.
Creator: McGuire, P.E.
Creator: Morrell, P.L.
Creator: Qualset, C.O.
Creator: Renfro, J.
Creator: Tabanao, D.
Creator: Talbert, L.E.
Creator: Chao Tian
Creator: Toleno, D.M.
Creator: Warburton, M.L.
Creator: You, F.M.
Creator: Wenjun Zhang
Creator: Dvorak, J.
Year: 2010
URI: https://hdl.handle.net/10883/21679
Language: English
Publisher: BioMed Central
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
Type: Article
Place of Publication: London
Issue: 1
Volume: 11
DOI: 10.1186/1471-2164-11-702
Description: Background: A 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.Results: Nucleotide 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.Conclusions: In 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.
Agrovoc: SINGLE NUCLEOTIDE POLYMORPHISM
Agrovoc: TETRAPLOIDY
Agrovoc: WHEAT
Agrovoc: TRITICUM DICOCCOIDES
ISSN: 1471-2164
Journal: BMC Genomics
Article number: 702


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  • Genetic Resources
    Genetic Resources including germplasm collections, wild relatives, genotyping, genomics, and IP

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