J. Anim Sci.
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J. Anim. Sci. 2005. 83:2289-2296
© 2005 American Society of Animal Science

ANIMAL GENETICS

Large-scale, multibreed, multitrait analyses of quantitative trait loci experiments: The case of porcine X chromosome1

M. Pérez-Enciso*,{dagger},2, A. Mercadé{dagger}, J. P. Bidanel{ddagger}, H. Geldermann§, S. Cepica#, H. Bartenschlager§, L. Varona, D. Milan|| and J. M. Folch{dagger}

* Institut Català de Recerca i Estudis Avançats, Lluis Companys 23, Barcelona 08010, Spain; and {dagger} Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain; and {ddagger} Station de Génétique Quantitative et Appliquée, INRA, 78352 Jouy-en-Josas, France; and § Department of Animal Breeding and Biotechnology, University of Hohenheim, D-70593 Stuttgart, Germany; and # Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Libechov, Czech Republic; and Àrea de Producció Animal, Centre UdL-IRTA, Alcalde Rovira Roure 177, Lleida, 25198, Spain; and and || Laboratoire de Génétique Cellulaire, INRA, 31326 Castanet-Tolosan, France

2 Correspondence: Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (phone: 34 93 581 4225; fax: 34 93 5812106; e-mail: miguel.perez{at}uab.es)

A QTL analysis of multibreed experiments (i.e., crossed populations involving more than two founder breeds) offers clear advantages over classical two-breed crosses, among them increased power and a more comprehensive coverage of the total genetic variability in the species. An alternative to designed multibreed crosses is to reanalyze jointly several experiments involving different breeds. We report a multibreed, multitrait QTL analysis of SSCX that involves five different crosses, six breeds, and almost 3,000 genotyped individuals using a truly multibreed strategy to allow for any number of founder breed origins. Traits analyzed were growth, fat thickness, carcass length, and shoulder and ham weights. Generally, the joint analysis resulted in more significant QTL than the single-experiment analyses. We show that the QTL for fatness, which is highly significant (nominal P < 10–43), is of Asiatic origin (Meishan). The next most significant QTL (nominal P < 10–15) affected ham weight and seems to be segregating only between Large White and the rest of the breeds. A multitrait, multi-QTL analysis suggests that these are two distinct loci. Additionally, a locus segregating only between Iberian and Landrace affects live weight. The advantages of joint, multibreed analyses clearly outweigh their potential risks.

Key Words: Fatness • Growth • Pig • Quantitative Trait Locus • Sex Chromosome






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