Conservation Genetics

, Volume 11, Issue 2, pp 399–408 | Cite as

Applying QTL analysis to conservation genetics

  • François Besnier
  • Arnaud Le Rouzic
  • José M. Álvarez-Castro
Research Article


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.


QTL analysis Genetic modeling Wild-domestic hybrids Segregation of alleles Chicken 



Evolutionary significant unit


Flexible intercross analysis


Identity by descent


Natural and orthogonal interactions


Quantitative trait loci


Transgressive segregation


Variance components



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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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • François Besnier
    • 1
  • Arnaud Le Rouzic
    • 2
    • 3
  • José M. Álvarez-Castro
    • 4
  1. 1.Department of Animal Breeding and GeneticsSwedish University of AgricultureUppsalaSweden
  2. 2.Center for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
  3. 3.Laboratoire Évolution, Génome, SpéciationGif-sur-YvetteFrance
  4. 4.Department of GeneticsUniversity of Santiago de CompostelaLugoSpain

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