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Applying QTL analysis to conservation genetics

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Abstract

Both analytical and molecular tools currently exist that can be used to prolifically apply quantitative trait loci (QTL) analysis to the study of natural populations. In this communication, we review and exemplify the use of QTL mapping tools and genetic modeling for conservation geneticists. We simulate populations inspired by relevant cases that can be encountered in the field and analyze them using the recently developed flexible intercross analysis (FIA) method. We then reanalyze these results with the also recently developed natural and orthogonal interactions (NOIA) model of genetic effects. Next, we further exemplify the potential of genetic modeling for the interpretation of the output of QTL analyses by reviewing studies on hybrids between wild individuals and their domesticated relatives. Based on the results here presented we emphasize several points that are pertinent in conservation genetics including (i) the advantages of FIA as a powerful tool to be applied to line crosses in which the parental lines are not inbred, (ii) the importance of obtaining estimates of genetic effects that are adequate to address the research issue under consideration, (iii) the versatility of genetic modeling, particularly NOIA, to dissect complex genetic architectures and (iv) the possibility of using currently available methods to address non-equilibrium multiallelic systems.

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Abbreviations

ESU:

Evolutionary significant unit

FIA:

Flexible intercross analysis

IBD:

Identity by descent

NOIA:

Natural and orthogonal interactions

QTL:

Quantitative trait loci

TS:

Transgressive segregation

VC:

Variance components

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Acknowledgments

Örjan Carlborg, Ania Pino-Querido and Lars Rönnegård and two reviewers have provided valuable comments on the manuscript. JAC acknowledges funding by an “Isidro Parga Pondal” contract from the Xunta de Galicia. ALR was funded by the Marie Curie Fellowship EIF-220558.

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Author notes

  1. Arnaud Le Rouzic

    Present address: Laboratoire Évolution, Génome, Spéciation, CNRS UPR9034, 91198, Gif-sur-Yvette, France

Authors and Affiliations

  1. Department of Animal Breeding and Genetics, Swedish University of Agriculture, Uppsala, Sweden

    François Besnier

  2. Center for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway

    Arnaud Le Rouzic

  3. Department of Genetics, University of Santiago de Compostela, Lugo, Spain

    José M. Álvarez-Castro

Authors
  1. François Besnier
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  2. Arnaud Le Rouzic
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  3. José M. Álvarez-Castro
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Corresponding author

Correspondence to José M. Álvarez-Castro.

Additional information

François Besnier and Arnaud Le Rouzic have contributed equally to this work.

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Besnier, F., Le Rouzic, A. & Álvarez-Castro, J.M. Applying QTL analysis to conservation genetics. Conserv Genet 11, 399–408 (2010). https://doi.org/10.1007/s10592-009-0036-5

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