University Library
  • Login
A gateway to Melbourne's research publications
Minerva Access is the University's Institutional Repository. It aims to collect, preserve, and showcase the intellectual output of staff and students of the University of Melbourne for a global audience.
View Item 
  • Minerva Access
  • Veterinary and Agricultural Sciences
  • Agriculture and Food Systems
  • Agriculture and Food Systems - Research Publications
  • View Item
  • Minerva Access
  • Veterinary and Agricultural Sciences
  • Agriculture and Food Systems
  • Agriculture and Food Systems - Research Publications
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

    A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors

    Thumbnail
    Download
    A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors (222.3Kb)

    Citations
    Scopus
    Web of Science
    Altmetric
    24
    22
    Author
    MacLeod, I. M.; Meuwissen, T. H. E.; Hayes, B. J.; Goddard, M. E.
    Date
    2009
    Source Title
    Genetics Research
    Publisher
    Cambridge University Press
    University of Melbourne Author/s
    MacLeod, Iona; Goddard, Michael
    Affiliation
    Melbourne School of Land and Environment
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    MacLeod, I. M., Meuwissen, T. H. E., Hayes, B. J. & Goddard, M. E. (2009). A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors. Genetics Research, 91(6), 413-426.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/33006
    DOI
    10.1017/S0016672309990358
    Description

    © 2010 Cambridge University Press. Online edition of the journal is available at http://journals.cambridge.org/action/displayJournal?jid=grh

    Abstract
    The patterns of linkage disequilibrium (LD) between dense polymorphic markers are shaped by the ancestral population history. It is therefore possible to use multilocus predictors of LD to infer past population history and to infer sharing of identical alleles in quantitative trait locus (QTL) studies. We develop a multilocus predictor of LD for pairs of haplotypes, which we term haplotype homozygosity (HHn) : the probability that any two haplotypes share a given number of n adjacent identical markers or ‘runs of homozygosity’. Our method, based on simplified coalescence theory, accounts for recombination and mutation. We compare our HHn predictions, with HHn in simulated populations and with two published predictors of HHn. Our method performs consistently better across a range of population parameters, including populations with a severe bottleneck followed by expansion, compared to two published methods. We demonstrate that we can predict the pattern of HHn observed in dense single nucleotide polymorphisms (SNPs) genotyped in a cattle population, given appropriate historical changes in population size. Our method is practical for use with very large numbers of individuals and dense genome wide polymorphic DNA data. It has potential applications in inferring ancestral population history and QTL mapping studies.
    Keywords
    genetics research; linkage disequilibrium; multilocus predictors; identical alleles; quantitative trait locus; haplotypes; ancestral population history

    Export Reference in RIS Format     

    Endnote

    • Click on "Export Reference in RIS Format" and choose "open with... Endnote".

    Refworks

    • Click on "Export Reference in RIS Format". Login to Refworks, go to References => Import References


    Collections
    • Agriculture and Food Systems - Research Publications [542]
    Minerva AccessDepositing Your Work (for University of Melbourne Staff and Students)NewsFAQs

    BrowseCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects
    My AccountLoginRegister
    StatisticsMost Popular ItemsStatistics by CountryMost Popular Authors