A muscle transcriptome analysis identifies positional candidate genes for a complex trait in pig

Abstract

Muscle tenderness is an important complex trait for meat quality and thus for genetic improvement through animal breeding. However, the physiological or genetic control of tenderness development in muscle is still poorly understood. In this work, using transcriptome analysis, we found a relationship between gene expression variability and tenderness. Muscle (longissimus dorsi) samples from 30 F(2) pigs were characterized by Warner-Bratzler Shear Force (WBSF) on cooked meat as a measurement of muscle tenderness. Gene expression levels were measured using microarrays for 17 muscle samples selected to represent a range of WBSF values. Using a linear regression model, we determined that samples with WBSF values above 30 N could be effectively analysed for genes exhibiting a significant association of their expression level on shear force (false discovery rate <0.05). These genes were shown to be involved in three functional networks: cell cycle, energy metabolism and muscle development. Twenty-two genes were mapped on the pig genome and 12 were found to be located in regions previously reported to contain quantitative trait loci (QTL) affecting pig meat tenderness (chromosomes 2, 6 and 13). Some genes appear therefore as positional candidate genes for QTL.

Functional analysis of muscle gene expression profiles associated with tenderness and intramuscular fat content in pork

“…The most significant molecular and cellular functions for tenderness were protein synthesis, cellular assembly, and cell cycle (Table 2), emphasising the importance of cellular growth-related pathways in defining tenderness. Lobjois et al (2008) profiled gene Fig. 3.…”

“…It is estimated that 80-90% of all cellular proteins are ultimately degraded by the proteasome pathway and many studies report enhanced proteasome expression during muscle atrophy (Goll et al, 2008). While, Lobjois et al (2008) in studies of tenderness in pork, identified differential expression of only one ubiquitination process gene (CDC34) in relation to shear force, their studies focused on ultimate tenderness, whereas our samples differed in early post mortem and not ultimate tenderness, suggesting that the proteasome may be important for rate of tenderisation. Bovine proteomic studies have shown that 27s proteasome subunit abundance is correlated with shear force in bovine Musculus rectus abdominus (Oury, Picard, Briand, Blanquet, & Dumont, 2009), that muscle concentrations of the proteasome complex are stable over the post mortem period (Dutaud et al, 2006), and that laboratory inhibition of the bovine proteasome impaired the degradation of structural and sarcoplasmic proteins (Houbak, Ertbjerg, & Therkildsen, 2008).…”

Additive effects of 19 porcine SNPs on growth rate, meat content and selection index

“…Several SNPs (TNNT3, CYP2E, CAST A499C), which showed additive effects on analysed traits in our study, were shown (by other authors) to be also associated with meat quality traits, e.g. tenderness, pH, intramuscular fat content, muscle colour, scatole content (Lobjois et al 2008;Amills et al 2005;Lin et al 2006;Arnyasi et al 2006;Krzecio et al 2005). They are promising candidates for simultaneous improvement of both types of traits (quantity and quality of meat), which is one of the most challenging tasks of marker assisted selection applied to pig breeding.…”

Recent advances in omic technologies for meat quality management

“…The causal polymorphism has not yet been identified. Among the 272 genes with a regulated expression by at least one eQTL, five genes (ACOX1, FKBP8, LDHA, NEB, and SEPW1) have their expression level correlated with the Warner-Bratzler SF (Lobjois et al, 2008); no cis-eQTL was identified for these genes.…”

“…Among these genes, 12 were localized on four chromosome regions of interest (QTL) on chromosomes 2, 6 and 13. This enabled us to propose positional and functional candidate genes to explain the effects observed by these QTL (Lobjois et al, 2008). About half of these genes are unknown or involved in unexpected functions related to MQ traits.…”