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Open Access Highly Accessed Research article

The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction

Jean-Francois Hocquette12*, Carine Bernard-Capel3, Veronique Vidal4, Beline Jesson4, Hubert Levéziel56, Gilles Renand78 and Isabelle Cassar-Malek12

Author affiliations

1 INRA, UMR1213, Unité de Recherches sur les Herbivores, Theix, Saint-Genès-Champanelle, F-63122, France

2 VetAgro Sup, UMR1213, Unité de Recherches sur les Herbivores, Saint Genès Champanelle, F-63122, France

3 Institut de l’Elevage, Service Aptitudes et Sélection des Races Allaitantes, Aubière, F-63170, France

4 IMAXIO, Biopôle Clermont-Limagne, Saint-Beauzire, F-63360, France

5 INRA, UMR1061, Unité de Génétique Moléculaire Animale, Limoges, F-87060, France

6 Université de Limoges, UMR1061, Unité de Génétique Moléculaire Animale, Limoges, F-87060, France

7 INRA, UMR1313, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, F-78352, France

8 AgroParisTech, INRA UMR1313, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, F-78352, France

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Citation and License

BMC Veterinary Research 2012, 8:135  doi:10.1186/1746-6148-8-135

Published: 15 August 2012

Abstract

Background

Previous research programmes have described muscle biochemical traits and gene expression levels associated with beef tenderness. One of our results concerning the DNAJA1 gene (an Hsp40) was patented. This study aims to confirm the relationships previously identified between two gene families (heat shock proteins and energy metabolism) and beef quality.

Results

We developed an Agilent chip with specific probes for bovine muscular genes. More than 3000 genes involved in muscle biology or meat quality were selected from genetic, proteomic or transcriptomic studies, or from scientific publications. As far as possible, several probes were used for each gene (e.g. 17 probes for DNAJA1). RNA from Longissimus thoracis muscle samples was hybridised on the chips. Muscles samples were from four groups of Charolais cattle: two groups of young bulls and two groups of steers slaughtered in two different years. Principal component analysis, simple correlation of gene expression levels with tenderness scores, and then multiple regression analysis provided the means to detect the genes within two families (heat shock proteins and energy metabolism) which were the most associated with beef tenderness. For the 25 Charolais young bulls slaughtered in year 1, expression levels of DNAJA1 and other genes of the HSP family were related to the initial or overall beef tenderness. Similarly, expression levels of genes involved in fat or energy metabolism were related with the initial or overall beef tenderness but in the year 1 and year 2 groups of young bulls only. Generally, the genes individually correlated with tenderness are not consistent across genders and years indicating the strong influence of rearing conditions on muscle characteristics related to beef quality. However, a group of HSP genes, which explained about 40% of the variability in tenderness in the group of 25 young bulls slaughtered in year 1 (considered as the reference group), was validated in the groups of 30 Charolais young bulls slaughtered in year 2, and in the 21 Charolais steers slaughtered in year 1, but not in the group of 19 steers slaughtered in year 2 which differ from the reference group by two factors (gender and year). When the first three groups of animals were analysed together, this subset of genes explained a 4-fold higher proportion of the variability in tenderness than muscle biochemical traits.

Conclusion

This study underlined the relevance of the GENOTEND chip to identify markers of beef quality, mainly by confirming previous results and by detecting other genes of the heat shock family as potential markers of beef quality. However, it was not always possible to extrapolate the relevance of these markers to all animal groups which differ by several factors (such as gender or environmental conditions of production) from the initial population of reference in which these markers were identified.

Keywords:
Predictors; Beef; Tenderness; Array; Gene expression