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

Abstract

BackgroundPrevious 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.ResultsWe 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.ConclusionThis 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.

Adaptive traits of indigenous cattle breeds: The Mediterranean Baladi as a case study

“…It turned out, however, that the genes related to energy and lipid metabolism may be specific to animal type and thus, are limited in their ability to predict beef tenderness across environmental conditions and genders, presumably due to the plasticity of the metabolic status (Hocquette et al, 2012). This goes in line with previous notion supplied by Hocquette et al (2007) that "the major genes causing variability for similar traits in different species or breeds are rarely the same".…”

“…Indeed, the chaperone activity of sHSP and their role in maintaining protein integrity interfere with proteolytic degradation of actin and myosin (Bernard et al, 2007;Kim et al, 2008). Meat tenderness was negatively correlated also with other HSP members, DNAJA1 (HSP40), HSP70 and some sHSP including HSP27 (Hocquette et al, 2012). HSP40 is a co-chaperone of HSP70 and the HSP40/HSP70 complex is known to directly inhibit apoptosis, supportive of the hypothesis that programmed cell death is significant for tenderization of meat during ageing .…”

“…For example, a series of genes belonging to the energy and lipid metabolism family were associated with beef tenderness in Charolais cattle, suggesting a positive contribution of intramuscular fat. These included the adipocyte fatty acid binding protein (FABP4), fatty acid synthase (FASN), diacylglycerol O-acyltransferase2 (DGAT2), peroxisome proliferator-activated receptor (PPAR-γ) and hydroxyacyl-Coenzyme A dehydrogenize beta subunit (HADH-B), the positive association of which explained approximately 70% of the total variability in tenderness in a reference group of bull calves (Hocquette et al, 2012). As a whole, these gene products "cover" attributes of muscle characteristics of live animals and proteolytic activity during post mortem ageing, both determinants of beef quality.…”

Muscle metabolism in sheep and cattle in relation to high rigor temperature – overview and perspective

“…In addition, Bernard et al (2007) indicated that sHSP27 was positively related to improved tenderness, flavour and juiciness of meat, which may or may not relate to heat tolerance or other stressors involved in meat quality expression. This study is supported by findings confirming the relationship between two gene families (heatshock proteins and energy metabolism) and beef quality, although the markers found for beef quality could not be universally extrapolated (Hocquette et al 2012). The interested reader is directed to a recent review on the role of sHSP in meat tenderness (Lomiwes et al 2014), which gives an overview of the basic structure and function of sHSP and their possible role in post-mortem muscle and hence effects on meat quality.…”

Relationships between DNAJA1 Expression and Beef Tenderness: Effects of Electrical Stimulation and Post-mortem Aging in two Muscles

“…However, further work showed that DNAJA1 was not the only gene belonging to the heat shock protein family related to tenderness and that the genes individually correlated with tenderness are not consistent across genders and slaughtering years in Longissimus thoracis muscle from the Charolais breed indicating the strong influence of rearing conditions on the relationships between DNAJA1 expression and beef palatability (Hocquette et al, 2012). This may be explained by the fact that developmental age and management factors influence DNAJA1 expression at the mRNA or protein levels .…”