Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants

DOI PDF 被引用文献2件
  • Linda Cardle
    Scottish Crop Research Institute, Dundee DD2 5DA, Scotland, United Kingdom
  • Luke Ramsay
    Scottish Crop Research Institute, Dundee DD2 5DA, Scotland, United Kingdom
  • Dan Milbourne
    Scottish Crop Research Institute, Dundee DD2 5DA, Scotland, United Kingdom
  • Malcolm Macaulay
    Scottish Crop Research Institute, Dundee DD2 5DA, Scotland, United Kingdom
  • David Marshall
    Scottish Crop Research Institute, Dundee DD2 5DA, Scotland, United Kingdom
  • Robbie Waugh
    Scottish Crop Research Institute, Dundee DD2 5DA, Scotland, United Kingdom

書誌事項

公開日
2000-10-01
権利情報
  • https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model
DOI
  • 10.1093/genetics/156.2.847
公開者
Oxford University Press (OUP)

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説明

<jats:title>Abstract</jats:title> <jats:p>The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSRs was one every 6.04 kb in genomic DNA, decreasing to one every 14 kb in ESTs. SSR frequency and type differed between coding, intronic, and intergenic DNA. Similar frequencies were found in other plant species. On the basis of these findings, an approach is proposed and demonstrated for the targeted isolation of single or multiple, physically clustered SSRs linked to any gene that has been mapped using low-copy DNA-based markers. The approach involves sample sequencing a small number of subclones of selected randomly sheared large insert DNA clones (e.g., BACs). It is shown to be both feasible and practicable, given the probability of fortuitously sequencing through an SSR. The approach is demonstrated in barley where sample sequencing 34 subclones of a single BAC selected by hybridization to the Big1 gene revealed three SSRs. These allowed Big1 to be located at the top of barley linkage group 6HS.</jats:p>

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  • Genetics

    Genetics 156 (2), 847-854, 2000-10-01

    Oxford University Press (OUP)

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