Longissimus muscle transcriptome profiles related to carcass and meat quality traits in fresh meat Pietrain carcasses

High quality pork is consumed as fresh meat, whereas other carcasses are used in the processing industry. Meat quality is determined measuring technical muscle variables. The objective of this research was to investigate the molecular regulatory mechanisms underlying meat quality differences of pork originating from genetically different Pietrain boars. Pietrain boars were approved for high meat quality using a DNA marker panel. Other Pietrain boars were indicated as average. Both groups produced litters in similar Pietrain sows. The LM were sampled from 9 carcasses produced by approved boars and 8 carcasses of average boars. Total RNA was isolated, and an equal portion of each sample was pooled to make a reference sample representing the mean of all samples. Each sample was hybridized on microarrays against the reference in duplicate using a dye swaps design. After normalization and subtraction of 2 times the background, only genes expressed in at least 5 carcasses were analyzed. For all analyses the mean of the M-values relative to the reference (i.e., fold change), were used. Sixteen genes showed significant linear or quadratic associations between gene expression and meat color (Minolta a* value, Minolta L* value, reflection, pH 24 h) after Bonferroni correction. All these genes had expression levels similar to the reference in all carcasses. Studying association between gene expression levels and meat quality using only genes with expression statistically differing from the reference in at least 5 carcasses revealed 29 more genes associating with the technological meat quality variables, again with meat color as a main trait. These associations were not significant after Bonferroni correction and explained less of the phenotypic variation in the traits. Bioinformatics analyses with The Database for Annotation, Visualization and Integrated Discovery (DAVID) using the list of genes with more than 2-fold changed expression level revealed that these genes were mainly found in muscle-specific processes, protein complexes, and oxygen transport, and located to muscle-specific cellular localizations. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed pathways related to protein metabolism, cellular proliferation, signaling, and adipose development differing between the 2 groups of carcasses. Approved meat carcasses showed less variation in gene expression. The results highlight biological molecular mechanisms underlying the differences between the high meat quality approved and average boars.