Open Access Research article

Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs

Pierre Cherel1, José Pires1, Jérôme Glénisson1, Denis Milan2, Nathalie Iannuccelli2, Frédéric Hérault34, Marie Damon56 and Pascale Le Roy34*

Author Affiliations

1 Hendrix-Genetics RTC, 100 avenue Denis-Papin, St-Jean-de-Braye, France

2 INRA, UR444 Laboratoire de Génétique Cellulaire, 31320 Castanet-Tolosan, France

3 INRA, UMR0598, Génétique Animale, 35042 Rennes cedex, France

4 Agrocampus Ouest, UMR0598, Génétique Animale, 35042 Rennes cedex, France

5 INRA, UMR1079 SENAH, 35590 Saint-Gilles, France

6 Agrocampus Ouest, UMR1079 SENAH, 35590 Saint-Gilles, France

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BMC Genetics 2011, 12:76  doi:10.1186/1471-2156-12-76

Published: 29 August 2011

Additional files

Additional file 1:

Suggestive QTLs detected for meat quality, carcass composition and growth traits. Suggestive QTLs detected in the F2 population excluding carriers of either RYR1 or PRKAG3 mutations, at 5% and 1% chromosome-wise significance levels.

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Additional file 2:

QTL detection LRT profiles for carcass composition traits on chromosomes SSC5, SSC11 and SSC13. LRT profiles for groups of carcass composition traits where significant and suggestive QTL were detected at neighbouring locations.

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Additional file 3:

Detection of RYR1 and PRKAG3 mutations in the control population. The numbers of records for each genotype are tabulated with corresponding mutation frequency for a selection of traits. QTL detection results including or excluding mutation carriers are summarized for the RYR1 mutation on SSC6 and the PRKAG3 mutation on SSC15.

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Additional file 4:

Sex-averaged genetic maps. Genetic map of 18 pig autosomes used for QTL detection including the list of marker names and positions for all genetic markers used. Individual marker positions are expressed in Haldane mapping distance function from the first marker in each linkage group. Primer sequence information for complementary genetic markers not available in reference genetic maps is included.

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Additional file 5:

Estimated variance components in analyses fitted at all significant and suggestive QTL positions. All variance components are reported in trait units; genetic components (additive and QTL effects) are reported as percentage of total variance.

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Additional file 6:

Chromosome-wise significance thresholds. Chromosome-wise thresholds as quantiles of the distribution of QTL detection statistical test used when applied to phenotypes simulated under the null hypothesis (polygenic additive model, H0: h2 = 30%).

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