Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome
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  • 作者:Tatiana Belova ; Lars Gr?nvold ; Ajay Kumar…
  • 刊名:Theoretical and Applied Genetics
  • 出版年:2014
  • 出版时间:September 2014
  • 年:2014
  • 卷:127
  • 期:9
  • 页码:2029-2040
  • 全文大小:634 KB
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  • 作者单位:Tatiana Belova (1)
    Lars Gr?nvold (1)
    Ajay Kumar (2)
    Shahryar Kianian (2)
    Xinyao He (3)
    Morten Lillemo (1)
    Nathan M. Springer (4)
    Sigbj?rn Lien (5)
    Odd-Arne Olsen (1)
    Simen R. Sandve (1)

    1. Department of Plant Sciences, Norwegian University of Life Sciences, ?s, Norway
    2. Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
    3. International Maize and Wheat Improvement Center (CIMMYT), Apdo.Postal 6-641, 06600, Mexico, DF, Mexico
    4. Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
    5. Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, ?s, Norway
  • ISSN:1432-2242
文摘
Key message A total of 3,671 sequence contigs and scaffolds were mapped to deletion bins on wheat chromosome 7B providing a foundation for developing high-resolution integrated physical map for this chromosome. Abstract Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC) we are focused on assembling a reference sequence for chromosome 7B. The successful completion of the reference chromosome sequence is highly dependent on the integration of genetic and physical maps. To aid the integration of these two types of maps, we have constructed a high-density deletion bin map of chromosome 7B. Using the 270?K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. Chinese spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8?% of chromosome 7B physical length) were mapped into nine deletion bins. Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. The bin mapping results were validated using three different approaches, viz. (a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. Validation of the bin mapping results suggested a high accuracy of the assignment of 7B sequence contigs and scaffolds to the 7B deletion bins.

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