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The analysis of QTL by simultaneous use of the full linkage map

Journal Article


Abstract


  • An extension of interval mapping is presented

    that incorporates all intervals on the linkage map simultaneously.

    The approach uses a working model in which

    the sizes of putative QTL for all intervals across the

    genome are random effects. An outlier detection method

    is used to screen for possible QTL. Selected QTL are

    subsequently fitted as fixed effects. This screening and

    selection approach is repeated until the variance component

    for QTL sizes is not statistically significant.

    A comprehensive simulation study is conducted in which

    map uncertainty is included. The proposed method is

    shown to be superior to composite interval mapping in

    terms of power of detection of QTL. There is an increase

    in the rate of false positive QTL detected when using the

    new approach, but this rate decreases as the population

    size increases. The new approach is much simpler computationally.

    The analysis of flour milling yield in a

    doubled haploid population illustrates the improved power

    of detection of QTL using the approach, and also shows

    how vital it is to allow for sources of non-genetic variation

    in the analysis.

Authors


  •   Verbyla, Ari P. (external author)
  •   Cullis, Brian R.
  •   Thompson, Robin (external author)

Publication Date


  • 2007

Citation


  • Verbyla, A. P.., Cullis, B. R. & Thompson, R. (2007). The analysis of QTL by simultaneous use of the full linkage map. Theoretical and Applied Genetics, 116 (1), 95-111.

Scopus Eid


  • 2-s2.0-36349032332

Ro Metadata Url


  • http://ro.uow.edu.au/infopapers/2096

Has Global Citation Frequency


Number Of Pages


  • 16

Start Page


  • 95

End Page


  • 111

Volume


  • 116

Issue


  • 1

Place Of Publication


  • Germany

Abstract


  • An extension of interval mapping is presented

    that incorporates all intervals on the linkage map simultaneously.

    The approach uses a working model in which

    the sizes of putative QTL for all intervals across the

    genome are random effects. An outlier detection method

    is used to screen for possible QTL. Selected QTL are

    subsequently fitted as fixed effects. This screening and

    selection approach is repeated until the variance component

    for QTL sizes is not statistically significant.

    A comprehensive simulation study is conducted in which

    map uncertainty is included. The proposed method is

    shown to be superior to composite interval mapping in

    terms of power of detection of QTL. There is an increase

    in the rate of false positive QTL detected when using the

    new approach, but this rate decreases as the population

    size increases. The new approach is much simpler computationally.

    The analysis of flour milling yield in a

    doubled haploid population illustrates the improved power

    of detection of QTL using the approach, and also shows

    how vital it is to allow for sources of non-genetic variation

    in the analysis.

Authors


  •   Verbyla, Ari P. (external author)
  •   Cullis, Brian R.
  •   Thompson, Robin (external author)

Publication Date


  • 2007

Citation


  • Verbyla, A. P.., Cullis, B. R. & Thompson, R. (2007). The analysis of QTL by simultaneous use of the full linkage map. Theoretical and Applied Genetics, 116 (1), 95-111.

Scopus Eid


  • 2-s2.0-36349032332

Ro Metadata Url


  • http://ro.uow.edu.au/infopapers/2096

Has Global Citation Frequency


Number Of Pages


  • 16

Start Page


  • 95

End Page


  • 111

Volume


  • 116

Issue


  • 1

Place Of Publication


  • Germany