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The Role of Epistasis in the Control of Complex Traits

The Role of Epistasis in the Control of Complex Traits. Ö rjan Carlborg and Chris Haley Roslin Institute. Epistasis. Epistasis = interactions between alleles at different loci Relatively neglected in quantitative genetics

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The Role of Epistasis in the Control of Complex Traits

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  1. The Role of Epistasis in the Control of Complex Traits Örjan Carlborg and Chris Haley Roslin Institute

  2. Epistasis • Epistasis = interactions between alleles at different loci • Relatively neglected in quantitative genetics • More attention in qualitative genetics where several types of epistasis has been found for e.g. coat colour phenotypes

  3. Examples of classic epistasis Hybrid dysgenesis

  4. Epistasis and QTL • Most QTL mapping studies focus on detection of marginal effects assuming absence of epistasis • Assumption of no epistasis based on low estimates of epistatic variances from quantitative genetic studies • Some studies have searched for epistasis between QTL with significant marginal effects

  5. Why consider epistasis? • Similar cellular mechanisms affect quantitative and qualitative traits • Increased power to detect QTL which mediate their effects through interactions • Epistasis could bias estimates of additive and dominance effects • Epistasis could help in the interpretations of QTL mapping results

  6. Methodology to detect epistasis • Need procedure to detect QTL with marginal effects as well as entirely epistatic QTL • One option (Carlborg and Andersson, 2002):

  7. Increased power to detect QTL • Possible to detect novel QTL pairs with very small or no marginal effects at all possible for the individual QTL • Increased support for QTL with close to significant marginal effects

  8. New epistatic QTL detected • Some QTL can not be detected by their marginal effects • E.g. QTL pair affecting hatch weight in chicken

  9. New epistatic QTL detected • Simultaneous mapping of epistatic QTL increases significance for some QTL with minor marginal effects

  10. Bias in estimation of QTL effects • Estimates of marginal genetic effects are the average effect of the alleles at a locus across all alleles at all other genomic loci • By identifying interactions between loci one can obtain additional information about e.g. • In which genetic background a QTL has its most influential effects • How further studies should be designed to maximise the chance to replicate a QTL

  11. Bias in estimation of QTL effects

  12. Additional variance explained • The estimates of the relative amount of variance attributable to epistasis depend on the genetic model used in the study • The simplest and most commonly used model is that of Mather and Jinks • Alternatives include the Cockerham model

  13. Additional variance explained • Epistasis explains a considerable portion of the genetic variance (Mather-Jinks model)

  14. Genetic mechanisms of epistasis • By understanding more about the nature of QTL interactions, one can: • Be more precise when selecting candidate genes • Better select the strategy for replicating a QTL • Get higher efficiency in marker assisted selection (MAS) • Need to explore Genotype-Phenotype patterns for epistatic QTL

  15. Genetic mechanisms of epistasis • Chicken F2 intercross between growth and layer selection lines: • 21 epistatic QTL pairs detected • 17 pairs could be associated with one of 4 types of epistasis

  16. Genetic mechanisms of epistasis • Chicken F2 intercross – 4 common types of epistasis:

  17. Conclusions • Epistasis is abundant • Epistasis increases power in QTL mapping • Novel QTL detected and more variance explained • Epistasis might be needed to replicate QTL findings and clone QTL • Can not understand control of complex traits without considering epistasis

  18. Acknowledgements • Roslin Institute • Dave Burt, Paul Hocking, DJ deKoning • Swedish University of Agricultural Sciences • Leif Andersson, Per Jensen, Susanne Kerje, Karin Schutz • The Knut and Alice Wallenberg foundation • NGSSC • BBSRC

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