Dominique Rocha

Pig Longissimus lumborum proteome: Part II: Relationships between protein content and meat quality

Gender, rearing environment and breed of sire influenced 50.5% of the matched protein spots of the soluble fraction and some meat quality traits [Kwasiborski, A., Sayd, T., Chambon, C., Santé-Lhoutellier, V., Rocha, D., & Terlouw, C. (2008). Muscle proteome in pigs: Part I: Effects of genetic background, rearing environment and gender. Meat Science]. Multiple regression analyses determined that 1 or 2 proteins explained between 24% and 85% of variability in Longissimus meat quality. Regression models differed between treatment groups, but relationships between proteins and meat quality traits seemed to be related to common underlying mechanisms. Thus, proteins retained in models for ultimate pH, lightness, drip, thawing and cooking loss were related to the glycolytic pathway, phosphate transfer, or fibre type composition. Another model for thawing loss retained proteins related to denaturation of myofibrils or lipid content. The models for redness involved proteins related to post-mortem oxidative activity. Thus, proteins correlated with meat quality traits were related to biochemical mechanisms known to be involved in meat quality. Relative contributions of these mechanisms may vary according to gender, sire breed or rearing environment.

Pig Longissimus lumborum proteome: Part I. Effects of genetic background, rearing environment and gender

A 2×2×2 factorial experiment on Longissimus lumborum of 24 pigs found that rearing environment (indoors or outdoors), breed of sire (Duroc or Large White), and gender (female or castrated male) influenced 22, 10, and 88 proteins of the soluble fraction, respectively, containing 220 matched spots in total. Some proteins were influenced by more than one main effect. Outdoor rearing resulted in lower levels of enzymes of the glycolytic pathway suggesting a more oxidative metabolism. Breed of sire slightly altered the balance of enzymes of the glycolytic pathway. Gender had profound effects. In particular, different enzyme levels suggest a more lipid oriented energy metabolism, and a higher extractability of myofibrillar proteins suggest altered control of the contractile apparatus, in castrated males. Differences in extractability did not explain the profound gender effects. Glycogen content, ultimate pH, drip and thawing losses showed main or interactive effects of the three treatment factors.

Gene expression in Large White or Duroc-sired female and castrated male pigs and relationships with pork quality.

This study assessed expression of 12 genes in 24 pig longissimus samples earlier subjected to a proteomic study by our group. Genes were selected on the basis of the earlier proteomic results. Pigs differed in rearing environment (indoors or outdoors), sire breed (Duroc or Large White) and gender (female or castrated male). At slaughter they experienced different stress conditions. The proportion of gene expression changes influenced by treatment factors was consistent with the proportion of protein changes in an earlier proteomic analysis of the same pigs. Expression levels of genes were often correlated. Gene expression was generally not correlated with the levels of the corresponding protein. Finally, most meat quality traits were correlated with the expression of at least one of the studied genes. The most meaningful of these was the association of a slower pH decline with lower levels of HSP72 expression and higher levels of HSP72 protein. ANXA2 and cMDH expression were also associated with various meat quality traits. These relationships may be related to pre-slaughter stress levels and fibre type composition.

Usp9y (ubiquitin-specific protease 9 gene on the Y) is associated with a functional promoter and encodes an intact open reading frame homologous to Usp9x that is under selective constraint.

Sequences complementary to the X-linked ubiquitin-specific protease gene Usp9x (Dffrx) have been shown to map to the Sxrb interval of the mouse Y Chromosome (chr) and to be expressed in a testis-specific manner. In humans, ubiquitously expressed functional homologues (USP9Y and USP9X DFFRY/DFFRX) are present on both sex chromosomes, whereas in mouse it remains to be demonstrated that the Y-linked sequences encode a functional protein. In this paper, it is shown that the Usp9y gene encodes a potentially functional ubiquitin-specific protease possessing a core promoter region that shares several features characteristic of other testis-specific genes. Analysis of synonymous and nonsynonymous nucleotide changes suggests that there is constraint on the amino acid sequence of both the mouse Usp9x and Usp9y genes, a finding that mirrors similar analysis of the human orthologs. Thus, in both mouse and human, selection is acting to maintain the amino acid sequence of the X and Y-linked genes. This indicates that in both species the genes on each sex chromosome continue to encode an important function.

Chromosomal assignment of the porcine NALP5 gene, a candidate gene for female reproductive traits

NALP5, also known as MATER (maternal antigen that embryos require), is an oocyte-specific maternal effect gene required for early embryonic development. Because of the specificity of NALP5 expression, and its role in female fertility, NALP5 is an interesting candidate gene for economically important female reproductive traits. Here we describe the chromosomal assignment of the porcine NALP5 gene to the long arm of pig chromosome 6 (SSC6q21-22), a region known to harbour several reproduction quantitative trait loci.

Characterization of the porcine FSCN3 gene: cDNA cloning, genomic structure, mapping and polymorphisms.

Fascin 3 (FSCN3)is a testis-specific actin-bundling protein involved in spermatid development. Here we describe the molecular characterisation of the porcine FSCN3 gene. The 1,800-bp cDNA sequence contains a 1,497-bp open reading frame encoding a protein of 498 amino acids with a calculated molecular mass of 56.2 kDa and an isoelectric point of 6.82. The porcine FSCN3 protein shares high identity with other mammalian FSCN3. The FSCN3 gene contains seven exons, spans approximately 9 kb, and maps to pig chromosome 18. We also identified 24 DNA polymorphisms.

Allelic variation of the porcine α-1,3-galactosyltransferase 1 (GGTA1) gene

The alpha-1,3-galactosyltransferase 1 enzyme (GGTA1) produces the α-Gal epitopes, responsible for pig-to-human hyperacute xenograft rejection. Recently, efforts have been directed at inactivating the porcineGGTA1 gene in order to reduce hyperacute rejection. As very little is known about the genetic variability of this key gene among pig breeds, we investigated the variation in its nucleotide sequence, by amplification of the entire coding region with the use of polymerase chain reaction followed by DNA sequencing. Eight commercial pig populations were analysed and 17 single nucleotide polymorphisms (SNPs) were detected: 11 in intronic regions and 6 in the 3′ untranslated region (UTR). No SNPs change the encoded protein; however, 8 of these SNPs may alter the transcriptional regulation and pre-mRNA splicing ofGGTA1.