Isolation and mapping of two porcine skeletal muscle myosin heavy chain isoforms

Association of a single nucleotide polymorphism in the 5' upstream region of the porcine myosin heavy chain 4 gene with meat quality traits in pigs

We identified a potential molecular marker associated with meat quality traits in the myosin heavy chain 4, MYH4 gene of Landrace pigs. Sequencing revealed a single nucleotide polymorphism (SNP; g.‐1398G>T) in the 5' upstream region of MYH4. It was significantly associated with the number of type IIa muscle fibers and water‐holding capacity based on filter‐paper fluid uptake. The GG genotype groups had a greater number of type IIa fibers and a larger area composed of type IIa fibers than the other genotype group (P = 0.004 and P = 0.061, respectively). Expression level of MYH4 gene in the genotype TT or GT was higher than in genotype of GG (P < 0.0001). The T allele may enhance expression level of MYH4 gene and then the portion of IIb type fiber in the muscle be increased by the T allelle. Therefore, we suggest that the g.‐1398G>T in the 5' upstream region of the porcine MYH4 may be used as a molecular marker for meat quality traits, although its functional effect is not defined yet.

A polymorphism in the porcine miR-208b is associated with microRNA biogenesis and expressions of SOX-6 and MYH7 with effects on muscle fibre characteristics and meat quality

MicroRNAs (miRNAs) encoded by the myosin heavy chain (MHC) genes are muscle-specific miRNAs (myomiRs) and regulate the expression of MHC isoforms in skeletal muscle. These miRNAs have been implicated in muscle fibre types and their characteristics by affecting the heterogeneity of myosin. In pigs, miR-208b and miR-499 are embedded in introns of MYH7 and MYH7b respectively. Here, we identified a novel single nucleotide polymorphism (SNP) in intron 30 of MYH7 by which porcine miR-208b is encoded. Based on the association study using a total of 487 pigs including Berkshire (n = 164), Landrace (n = 121) and Yorkshire (n = 202), the miR-208b SNP (g.17104G>A) had significant effects on the proportions of types I and IIb fibre numbers (P < 0.010) among muscle fibre characteristics and on drip loss (P = 0.012) in meat quality traits. Moreover, the SNP affected the processing of primary miR-208b into precursor miR-208b with a marginal trend towards significance (P = 0.053), thereby leading to significant changes in the levels of mature miR-208b (P = 0.009). These SNP-dependent changes in mature miR-208b levels were negatively correlated with the expression levels of its target gene, SOX-6 (P = 0.038), and positively associated with the expression levels of its host gene, MYH7 (P = 0.046). Taken together, our data suggest that the porcine miR-208b SNP differentially represses the expression of SOX-6 by regulating miRNA biogenesis, thereby affecting the expression of MYH7 and the traits of muscle fibre characteristics and meat quality.

A quantitative trait locus genome scan for porcine muscle fiber traits reveals overdominance and epistasis

Muscle histochemical characteristics are decisive determinants of meat quality. The relative percentage and diameters of the different muscular fiber types influence crucial aspects of meat such as color, tenderness, and ultimate pH. Despite its relevance, however, the information on muscle fiber genetic architecture is scant, because histochemical muscle characterization is a laborious task. Here we report a complete QTL scan of muscle fiber traits in 160 animals from a F(2) cross between Iberian and Landrace pigs using 139 markers. We identified 20 genome regions distributed along 15 porcine chromosomes (SSC1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, and X) with direct and(or) epistatic effects. Epistasis was frequent and some interactions were highly significant. Chromosomes 10 and 11 seemed to behave as hubs; they harbored 2 individual QTL, but also 6 epistatic regions. Numerous individual QTL effects had cryptic alleles, with opposite effects to phenotypic pure breed differences. Many of the QTL identified here coincided with previous reports for these traits in the literature, and there was overlapping with potential candidate genes and previously reported meat quality QTL.

Cluster characterisation and temporal expression of porcine sarcomeric myosin heavy chain genes

Members of the myosin heavy chain (MyHC) gene family are subjected to temporal regulation of gene switching during development. One strategy to the identification of cis-acting regulatory elements that are involved in temporal or fibre-type specific regulation is to undertake a comparative analysis of the MyHC gene family between the pig, an important target species, and other mammals, like human whose entire genome has been recently sequenced. Towards this end, we report here on the isolation, and characterisation of the porcine cardiac (MyHC slow/beta and alpha) and skeletal MyHC (embryonic, 2a, 2x, 2b and perinatal) gene clusters, and their structural comparisons with mouse and human clusters. The genome organisation of both clusters in the pig, human and mouse is conserved as having the same gene order, similar intergenic distances, and in the same head-to-tail orientation. For a period of pre-natal muscle growth, relative expression of MyHC isoforms, as determined by TaqMan real-time RT-PCR, correlated with the gene order in the skeletal MyHC cluster (embryonic > 2a > 2x > 2b) suggesting the possible presence of DNA elements on the same side as the MyHC embryonic gene that direct temporal regulation.

Identification of SNPs, mapping and analysis of allele frequencies in two candidate genes for meat production traits: the porcine myosin heavy chain 2B (MYH4) and the skeletal muscle myosin regulatory light chain 2 (HUMMLC2B)

Myosin is one of the most important skeletal muscle proteins. It is composed of myosin heavy chains and myosin light chains that exist with different isoforms coded by different genes. We studied the porcine myosin heavy chain 2B (MYH4) and the porcine skeletal muscle myosin regulatory light chain 2 (HUMMLC2B) genes. A single nucleotide polymorphism (SNP), identified for each gene, was used for linkage mapping of MYH4 and HUMMLC2B to porcine chromosome (Sscr) 12 and Sscr 3, respectively. The mapping of these two genes was confirmed by using a porcine-rodent radiation hybrid panel, even if for MYH4 the LOD score and the retention fraction were low. Allele frequencies at the two loci were studied in a sample of 307 unrelated pigs belonging to seven different pig breeds. Moreover the distribution of the alleles at these two loci was analysed in groups of pigs with extreme divergent (positive and negative) estimated breeding values (EBV) for four meat production traits that have undergone selection in Italian heavy pigs.

Isolation of porcine expressed sequence tags for the construction of a first genomic transcript map of the skeletal muscle in pig

To identify genes with effects on meat quality and production traits we developed an adult porcine skeletal muscle cDNA library. After pre-screening this library with seven genes highly expressed in skeletal muscle, 385 non-hybridizing clones were sequenced from both ends to yield 510 expressed sequence tags (ESTs). Together with those ESTs previously generated from this library, we have produced 701 porcine skeletal muscle ESTs. These ESTs were grouped into 306 different cDNA species and compared with the human skeletal muscle transcriptional profiles obtained from different databases. Furthermore we mapped 107 of these cDNAs using a somatic cell hybrid panel with genes mapping over all the autosomes (except on chromosome 11) and on chromosome X. The mapping of these cDNAs contributed to the construction of a first genomic transcript map of the skeletal muscle tissue in pig.

Mapping of 14 expressed sequence tags (ESTs) from porcine skeletal muscle by somatic cell hybrid analysis

Chromosomal assignments are reported for fourteen porcine expressed sequence tags (ESTs)--CALM1, CRYAB, MYH7, MYL1, PDK4, PGAM2, PYGM, REV3L, RFC1, SLN, SPTBN1, SRM160, TPM1 and YWHAG. The ESTs were derived from our porcine skeletal muscle cDNA library. The ESTs sequences selected for mapping included the presence of the 3'-untranslated region. The assignments were performed using two independent somatic cell hybrid panels providing the possibility of confirmation of the results obtained. The observed localizations are compared with the locations predicted from heterologous (human-pig, pig-human) chromosome painting data and knowledge of the map locations of the human homologues. These results add new information to the porcine genome transcript map.

Analysis of expressed sequence tags of porcine skeletal muscle

Porcine skeletal muscle genes play a major role in determining muscle growth and meat quality. Therefore, to progress towards a better understanding of the genetic factors influencing these traits, the first step is to characterize the genes expressed in skeletal muscle tissue in pig. To this aim, we constructed a porcine biceps femoris muscle cDNA library and sequenced 111 randomly isolated clones. By FASTA analysis, we identified 72 unique clones: 47 showed homology to previously identified genes in human or other mammals, 20 matched uncharacterized expressed sequence tags (ESTs), two showed no significant matches to sequences already present in DNA databases, and three other clones containing only repetitive elements were excluded from further analysis. Mitochondrial genes (16.2%), myosin heavy chain genes (9%) and the actin alpha skeletal muscle gene (9%) were the most abundant transcripts. Among the 47 identified genes several muscle-specific or predominant sequences expressed in skeletal muscle were found. The sequences of the clones matching uncharacterized human, mouse or porcine ESTs were tested by GRAIL in order to identify putative coding regions. The results of our analysis allowed the establishment of a first list of genes expressed in porcine skeletal muscle.