Mapping epistatic QTL with one-dimensional genome searches

J.L. Jannink, R.C. Jansen

    Research output: Contribution to journalArticleAcademicpeer-review

    109 Citations (Scopus)

    Abstract

    The discovery of epistatically interacting QTL is hampered by the intractability and low power to detect QTL in multidimensional genome searches. We describe a new method that maps epistatic QTL by identifying loci of high QTL by genetic background interaction. This approach allows detection of QTL involved not only in pairwise but also higher-order interaction, and does so with one-dimensional genome searches. The approach requires large populations derived from multiple related inbred-line crosses as is more typically available for plants. Using maximum likelihood, the method contrasts models in which QTL allelic values are either nested within, or fixed over, populations. We apply the method to simulated doubled-haploid populations derived from a diallel among three inbred parents and illustrate the power of the method to detect QTL of different effect size and different levels of QTL by genetic background interaction. Further, we show how the method can be used in conjunction with standard two-locus QTL detection models that use two-dimensional genome searches and find that the method may double the power to detect first-order epistasis.
    Original languageEnglish
    Pages (from-to)445-454
    JournalGenetics
    Volume157
    Publication statusPublished - 2001

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