Indications of associations of the porcine FOS proto-oncogene with skeletal muscle fibre traits

Transcriptome analysis of divergent residual feed intake phenotypes in the M. longissimus thoracis et lumborum of Wannan Yellow rabbits

Introduction: Feed efficiency is an important economic trait in rabbit meat production. The identification of molecular mechanisms and candidate genes for feed efficiency may improve the economic and environmental benefits of the rabbit meat industry. As an alternative to the conventional feed conversion ratio, residual feed intake (RFI) can be used as an accurate indicator of feed efficiency. Methods: RNA sequencing was used to identify the differentially expressed genes (DEGs) in the M. longissimus thoracis et lumborum of eight Wannan Yellow rabbits with excessively high or low RFIs (HRFI or LRFI, respectively). Thereafter, Gene Ontology (GO) analysis, enrichment using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, gene set enrichment analysis (GSEA), and protein-protein interaction (PPI) network analysis was conducted. Results: In total, 445 DEGs were identified in the M. longissimus thoracis et lumborum of rabbits with high and low RFIs. The significantly enriched GO terms identified in these two groups were primarily involved in energy and mitochondrial metabolism and oxidation-reduction processes. KEGG analysis identified 11 significantly enriched pathways, including oxidative phosphorylation, PI3K-Akt signaling, and extracellular matrix-receptor interaction pathways. According to GSEA, the expressions of genes and pathways related to mitochondrial function were upregulated in HRFI rabbits, whereas genes with upregulated expressions in LRFI rabbits were related to immune response and energy metabolism. Additionally, PPI network analysis revealed five potential candidate genetic markers. Conclusion: Comparative analysis of the M. longissimus thoracis et lumborum transcriptomes in HRFI and LRFI rabbits revealed FOS, MYC, PRKACB, ITGA2, and FN1 as potential candidate genes that affect feed efficiency in rabbits. In addition, key signaling pathways involved in oxidative phosphorylation and PI3K-Akt and ECM-receptor interaction signaling impact rabbit feed efficiency. These findings will aid in breeding programs to improve feed efficiency and optimize RFI selection of rabbits for meat production.

Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array

Introduction: Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic mechanism of glycolytic metabolism in skeletal muscle of pigs remains poorly understood. With a history of more than 400 years and some unique characteristics, the Erhualian pig is called the “giant panda” (very precious) in the world’s pig species by Chinese animal husbandry.

Methods: Here, we performed a genome-wide association study (GWAS) using 1.4M single nucleotide polymorphisms (SNPs) chips for longissimus RG, G6P, LAT, and GP levels in 301 purebred Erhualian pigs.

Results: We found that the average GP value of Erhualian was unusually low (68.09 μmol/g), but the variation was large (10.4–112.7 μmol/g). The SNP-based heritability estimates for the four traits ranged from 0.16–0.32. In total, our GWAS revealed 31 quantitative trait loci (QTLs), including eight for RG, nine for G6P, nine for LAT, five for GP. Of these loci, eight were genome-wide significant (p < 3.8 × 10−7), and six loci were common to two or three traits. Multiple promising candidate genes such as FTO, MINPP1, RIPOR2, SCL8A3, LIFR and SRGAP1 were identified. The genotype combinations of the five GP-associated SNPs also showed significant effect on other meat quality traits.

Discussion: These results not only provide insights into the genetic architecture of GP related traits in Erhualian, but also are useful for pig breeding programs involving this breed.

Transcriptome-based analysis of early post-mortem formation of pale, soft, and exudative (PSE) pork

Pale, soft, and exudative (PSE) meat can cause consumer dissatisfaction and economic losses. This study determined meat quality, glycolytic enzyme activity, and differential gene expression in the longissimus lumborum (LL) and semimembranosus (SM) of normal and PSE pork carcasses. The SM did not result in PSE meat. Hexokinase, lactate dehydrogenase, and pyruvate kinase activities were lower in the SM of PSE carcasses than in the normal carcasses. Functional enrichment analysis revealed that immune, inflammatory, and muscle fibre genes were significantly enriched in PSE pork. More specifically, PPP1R3G and MSS51 may be key genes regulating pork quality in the SM. Meanwhile, the differential expression of PLVAB, ADIPOQ, LEP, MYH4, MYH7, MYL3, MYL6B, FOS, ATF3, and HSPA6 may induce PSE formation in the LL. These results may provide insights into PSE pork formation mechanisms and reveal candidate genes for improving meat quality after validation.

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

Circular RNAs (circRNAs) play a significant regulatory role during skeletal muscle development. To identify circRNAs during postnatal skeletal muscle development in chickens, we constructed 12 cDNA libraries from breast muscle tissues of Chinese Gushi chickens at 6, 14, 22, and 30 weeks and performed RNA sequencing. In total, 2112 circRNAs were identified, and among them 79.92% were derived from exons. CircRNAs are distributed on all chromosomes of chickens, especially chromosomes 1-9 and Z. Bioinformatics analysis showed that each circRNA had an average of 38 miRNA binding sites, 61.32% of which have internal ribosomal entry site (IRES) elements. Furthermore, in total 543 differentially expressed circRNAs (DE-circRNAs) were identified. Functional enrichment analysis revealed that DE-circRNAs source genes are engaged in biological processes and muscle development-related pathways; for example, cell differentiation, sarcomere, and myofibril formation, mTOR signaling pathway, and TGF-β signaling pathway, etc. We also established a competitive endogenous RNA (ceRNA) regulatory network associated with skeletal muscle development. The results in this report indicate that circRNAs can mediate the development of chicken skeletal muscle by means of a complex ceRNA network among circRNAs, miRNAs, genes, and pathways. The findings of this study might help increase the number of known circRNAs in skeletal muscle tissue and offer a worthwhile resource to further investigate the function of circRNAs in chicken skeletal muscle development.

Comparison of Growth Performance and Meat Quality Traits of Commercial Cross-Bred Pigs versus the Large Black Pig Breed

The meat quality of different pig breeds is associated with their different muscle tissue physiological processes, which involves a large variety of genes related with muscle fat and energy metabolism. Understanding the differences of biological processes of muscle after slaughter is helpful to reveal the meat quality development of different breeds. Therefore, eight native Large Black pigs (BP), with high fat content in meat, and seven cross-bred commercial pigs (CP), which had a high feed efficiency with high lean meat, were used to investigate the differences in their meat quality and RNA transcriptomes. The average daily gain (ADG) and hot carcass weight (HCW) of CP were higher than BP, but the back-fat thickness of BP was higher than CP (p < 0.05). The CP had higher a* (redness) but lower h (hue angle) than BP (p < 0.05). The metmyoglobin (MMb) percentage of CP was higher (p < 0.05) than BP. The fat content and oxygen consumption of longissimus dorsi (LD) muscles in BP were higher (p < 0.05) than CP. BP had higher monounsaturated fatty acids (MUFA) content, but CP had higher polyunsaturated fatty acids (PUFA) content (p < 0.05). The RNA-seq data highlighted 201 genes differentially expressed between the two groups (corrected false discovery rate (FDR) p < 0.05), with 75 up-regulated and 126 down-regulated genes in BP compared with CP using the fold change (FC). The real-time PCR was used to validate the results of RNA-seq for eight genes, and the genes related to lipid and energy metabolism were highly expressed in BP (p < 0.05). Based on the results, BP had superior intramuscular fat content to CP, while the growth performance of CP was better, and the transcriptomic differences between these two groups of pigs may cause the meat quality and growth performance variance.

Differences in the Loin Tenderness of Iberian Pigs Explained through Dissimilarities in Their Transcriptome Expression Profile

Simple Summary

The Iberian pig is the most representative autochthonous breed of the Mediterranean region with unique genetic and phenotypic characteristics. The breed has been successfully preserved by its high-quality meat and high-priced products. Tenderness is one of the most relevant meat quality traits, and meat tenderization is influenced by genetic and environmental effects such as pre-slaughter handling and post-mortem conditions. Tenderness could be included in Iberian pig breeding programs, mainly focused on the improvement of premium-cuts percentage, in order to avoid the meat quality decline. A better biological understanding of this trait is needed. In the current study, we analyze the transcriptome of pigs divergent for Warner–Bratzler shear force through RNA-seq technique for the identification, characterization and quantification of candidate genes involved in biological pathways, networks and functions affecting meat tenderness.

Abstract

Tenderness is one of the most important meat quality traits and it can be measured through shear force with the Warner–Bratzler test. In the current study, we use the RNA-seq technique to analyze the transcriptome of Longissimus dorsi (LD) muscle in two groups of Iberian pigs (Tough and Tender) divergent for shear force breeding values. We identified 200 annotated differentially expressed genes (DEGs) and 245 newly predicted isoforms. The RNAseq expression results of 10 genes were validated with quantitative PCR (qPCR). Functional analyses showed an enrichment of DE genes in biological processes related to proteolysis (CTSC, RHOD, MYH8, ACTC1, GADD45B, CASQ2, CHRNA9 and ANKRD1), skeletal muscle tissue development (ANKRD1, DMD, FOS and MSTN), lipid metabolism (FABP3 and PPARGC1A) and collagen metabolism (COL14A1). The upstream analysis revealed a total of 11 transcription regulatory factors that could regulate the expression of some DEGs. Among them, IGF1, VGLL3 and PPARG can be highlighted since they regulate the expression of genes involved in biological pathways that could affect tenderness. The experiment revealed a set of candidate genes and regulatory factors suggestive to search polymorphisms that could be incorporated in a breeding program for improving meat tenderness.

Transcriptional Regulatory Network Analysis to Reveal the Key Genes Involved in Skeletal Muscle Injury

Skeletal muscle is among the three major muscle types, and skeletal muscle injury (SMI) can elevate the risk of dependency and falls. This study is designed to explore the key genes involved in SMI and skeletal muscle regeneration. Microarray data set GSE81096, which included 11 injured skeletal muscle stem cell samples and 12 noninjured skeletal muscle stem cell samples, was from Gene Expression Omnibus. The differentially expressed genes (DEGs) between injured and noninjured samples were screened by R package limma, and then were performed with enrichment analysis based on the Database for Annotation, Visualization, and Integrated Discovery. Followed by protein-protein interaction (PPI), transcriptional regulatory analyses were conducted using Cytoscape software. A total of 1018 DEGs were screened from the injured samples, among which four upregulated genes and nine downregulated genes were predicted as transcription factors. Besides, four modules were identified from the PPI network. In the transcriptional regulatory network, E2F1, E2F4, JUNB, FOS, and MEF2C had higher degrees. Moreover, E2F4 and FOS might function in SMI separately through targeting E2F1 and JUNB. E2F1, E2F4, JUNB, FOS, and MEF2C might be involved in SMI and skeletal muscle regeneration.

Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds

Circular RNA (circRNA) and long non-coding RNA (lncRNA) are known to participate in adipogenesis and myogenic differentiation, but their impact on porcine muscle traits is not well understood. We compared their expressional profiles in the longissimus dorsi muscle of Chinese Huainan pigs (HN, the fat type) and Western commercial Duroc×(Landrace×Yorkshire) (DLY, the thin type) pigs, and 854 mRNAs, 233 lncRNAs, and 66 circRNAs (p < 0.05 and ｜log₂FoldChange｜>1) were found to be differentially expressed. The differentially expressed mRNA and circRNA parental genes were enriched in the Wnt signaling pathway (adipogenesis), the transition between fast and slow fibers (myogenic differentiation), and alanine, aspartate and glutamate metabolism (pork flavor). The potential lncRNAs/circRNAs-miRNAs-mRNAs regulatory networks shared MYOD1, PPARD, miR-423-5p and miR-874, which were associated with skeletal muscle muscular proliferation, differentiation/regeneration and adipogenesis. Taken together, these differentially expressed non-coding RNAs may be involved in the molecular basis of muscle traits, acting as the competing endogenous RNA (ceRNA) for miRNAs.

Identification of common regulators of genes in co-expression networks affecting muscle and meat properties

Understanding the genetic contributions behind skeletal muscle composition and metabolism is of great interest in medicine and agriculture. Attempts to dissect these complex traits combine genome-wide genotyping, expression data analyses and network analyses. Weighted gene co-expression network analysis (WGCNA) groups genes into modules based on patterns of co-expression, which can be linked to phenotypes by correlation analysis of trait values and the module eigengenes, i.e. the first principal component of a given module. Network hub genes and regulators of the genes in the modules are likely to play an important role in the emergence of respective traits. In order to detect common regulators of genes in modules showing association with meat quality traits, we identified eQTL for each of these genes, including the highly connected hub genes. Additionally, the module eigengene values were used for association analyses in order to derive a joint eQTL for the respective module. Thereby major sites of orchestrated regulation of genes within trait-associated modules were detected as hotspots of eQTL of many genes of a module and of its eigengene. These sites harbor likely common regulators of genes in the modules. We exemplarily showed the consistent impact of candidate common regulators on the expression of members of respective modules by RNAi knockdown experiments. In fact, Cxcr7 was identified and validated as a regulator of genes in a module, which is involved in the function of defense response in muscle cells. Zfp36l2 was confirmed as a regulator of genes of a module related to cell death or apoptosis pathways. The integration of eQTL in module networks enabled to interpret the differentially-regulated genes from a systems perspective. By integrating genome-wide genomic and transcriptomic data, employing co-expression and eQTL analyses, the study revealed likely regulators that are involved in the fine-tuning and synchronization of genes with trait-associated expression.

Correlated mRNAs and miRNAs from co-expression and regulatory networks affect porcine muscle and finally meat properties

Background

Physiological processes aiding the conversion of muscle to meat involve many genes associated with muscle structure and metabolic processes. MicroRNAs regulate networks of genes to orchestrate cellular functions, in turn regulating phenotypes.

Results

We applied weighted gene co-expression network analysis to identify co-expression modules that correlated to meat quality phenotypes and were highly enriched for genes involved in glucose metabolism, response to wounding, mitochondrial ribosome, mitochondrion, and extracellular matrix. Negative correlation of miRNA with mRNA and target prediction were used to select transcripts out of the modules of trait-associated mRNAs to further identify those genes that are correlated with post mortem traits.

Conclusions

Porcine muscle co-expression transcript networks that correlated to post mortem traits were identified. The integration of miRNA and mRNA expression analyses, as well as network analysis, enabled us to interpret the differentially-regulated genes from a systems perspective. Linking co-expression networks of transcripts and hierarchically organized pairs of miRNAs and mRNAs to meat properties yields new insight into several biological pathways underlying phenotype differences. These pathways may also be diagnostic for many myopathies, which are accompanied by deficient nutrient and oxygen supply of muscle fibers.

Associations between muscle gene expression pattern and technological and sensory meat traits highlight new biomarkers for pork quality assessment

Meat quality (MQ) results from complex phenomenon and despite improved knowledge on MQ development, its variability remains high. The identification of biomarkers and the further development of rapid tests would thus be helpful to evaluate MQ in pork industries. Using transcriptomics, the present study aimed at identifying biomarkers of eight pork quality traits: ultimate pH, drip loss, lightness, redness, hue angle, intramuscular fat, shear force and tenderness, based on an experimental design inducing a high variability in MQ. Associations between microarray gene expression and pork traits (n=50 pigs) highlighted numerous potential biomarkers of MQ. Using quantitative RT-PCR, 113 transcript-trait correlations including 40 of these genes were confirmed (P<0.05, |r|≤0.73), out of which 60 were validated (P<0.05, |r|≤0.68) on complementary experimental data (n=50). Multiple regression models including 3 to 5 genes explained up to 59% of MQ trait variability. Moreover, functional analysis of correlated-trait genes provided information on the biological phenomena underlying MQ.

Meat from wild boar (Sus scrofa L.): a review

Wild boar is a species that is utilised for food and sport hunting throughout the world. Recent increases in natural populations and the potential of farming wild boars have stimulated interest in this species as a meat producer. Compared to domestic pigs, wild boars present a higher degree of carcass fatness and larger loin areas, more slow-twitch oxidative (I) and fast-twitch oxidative glycolytic (IIA) and less fast-twitch glycolytic (IIB) muscle fibres, and darker, less tender and leaner meat. Differences in diets might contribute to differences in cooked meat flavour and fatty acid composition between wild boars and domestic pigs. Higher α-tocopherol concentrations in wild boar might extend its meat shelf-life. Mechanical massaging of muscles, vacuum package ageing and addition of marinates have been attempted to tenderise wild boar meat. Further research on hunting protocols for wild boar, and value-added products from its meat, are needed.

Head-only followed by cardiac arrest electrical stunning is an effective alternative to head-only electrical stunning in pigs

Many small slaughter facilities use head-only electrical stunning to render swine unconscious and insensible to pain before slaughter. Head-only electrical stunning is a reversible procedure that is optimally effective for approximately 15 s after stun completion. In many small North American slaughter plants, the authors have observed hoist speeds that are too slow to achieve a short enough stun-to-bleed interval to maintain insensibility through exsanguination. Unlike many European plants, there is no separate high-speed hoist for pigs and exsanguination on the floor is not condoned. As a result, a 2-stage stunning method was proposed where head-only stunning for 3 s was immediately followed by application of the same stunning wand to the cardiac region of the animal for 3 s while lying in lateral recumbancy. A paired-comparison study was conducted on 89 pigs in a small slaughter facility to compare the head-only method applied for 6 s with the head/heart method. The objective was to evaluate signs of return to sensibility, stun-to-bleed time, blood lactate concentration, muscle pH, drip loss, and fresh meat color to validate the head/heart electrical stunning method for small slaughter plants. Incidence of corneal reflex was not different (P > 0.05) between head/heart (93.8%) and head only (85%) stunning. Nose twitching was more common (P < 0.05) in head only (26.5%) than head/heart (5%) stunning. Head/heart stunning eliminated rhythmic breathing, natural blinking, eye tracking to moving objects, and righting reflex, which were all observed in head-only stunned pigs. Eye tracking to moving objects was observed in 40.8% of head-only stunned pigs. Blood lactate was not different (P > 0.05) between stunning methods (head only: 8.8 ± 0.7 mmol/L, head/heart: 7.8 ± 0.7 mmol/L). Stun-to-bleed time did not differ (P > 0.05; head only: 32 ± 1 s, head/heart: 33 ± 1 s). Mean time to loss of heartbeat with the head-only method was 121 ± 5 s. No heartbeat was observed with the head/heart method. Longissimus thoracis pH, color, and drip loss were not different (P > 0.05) between stunning methods. This study determined that the head/heart electrical stunning method reduces the incidence of signs of return to sensibility without significant effects on meat quality, plant operation speed, or blood lactate concentration. In addition, the head/heart method requires no capital investment for plants that are currently using the head-only method.

Identification of three novel SNPs and association with carcass traits in porcine TNNI1 and TNNI2

In this study, two novel SNPs (EU743939:g.5174T>C in intron 4 and EU743939:g.8350C>A in intron 7) in TNNI1 and one SNP (EU696779:g.1167C>T in intron 3) in TNNI2 were identified by PCR-RFLP (PCR restriction fragment length polymorphism) using XbaI, MspI and SmaI restriction enzyme, respectively. The allele frequencies of three novel SNPs were determined in the genetically diverse pig breeds including ten Chinese indigenous pigs and three Western commercial pig breeds. Association analysis of the SNPs with the carcass traits were conducted in a Large White × Meishan F(2) pig population. The linkage of two SNPs (g.5174T>C and g.8350C>A) in TNNI1 gene had significant effect on fat percentage. Besides these, the g.5174T>C polymorphism was also significantly associated with skin percentage (P < 0.05), shoulder fat thickness (P < 0.05) and backfat thickness between sixth and seventh ribs (P < 0.05). The significant effects of g.1167C>T polymorphism in TNNI2 gene on fat percentage (P < 0.01), lean meat percentage (P < 0.05), lion eye area (P < 0.05), thorax-waist backfat thickness (P < 0.01) and average backfat thickness (P < 0.05) were also found.

Genome-wide identification of quantitative trait loci for pork temperature, pH decline, and glycolytic potential in a large-scale White Duroc x Chinese Erhualian resource population

The pH values and temperatures at 45 min, and 3, 9, 15, and 24 h postmortem in the LM and semimembranosus muscle (SM) and glycolytic potential in LM were measured in 1,030 F(2) animals from a White Duroc x Erhualian resource population. A whole genome scan was performed with 183 microsatellites covering 19 porcine chromosomes to detect QTL for traits measured. A total of 73 QTL have been identified, including 1% genome-wise significant QTL for 24-h pH in LM and SM on SSC 15, and for glycolytic potential, total glycogen, and residual glycogen on SSC3, 6, and 7. Six 5% genome-wise significant QTL were detected for 9-h pH in SM on SSC3, pH decline from 3/9 h to 24 h in SM on SSC7, glycolytic potential on SSC1, and total glycogen on SSC1 and 6. This study confirmed QTL previously identified for pH except those on SSC1, 11, 12, and X, and found 11 new 5% genome-wise significant QTL for glycogen-related traits. This is the first time to report QTL for pH development during post-slaughter and for glycolytic potential at 5% genome-wise significance level. In addition, the observed different QTL for pH and pH decline at different times show that causal genes for pH postmortem play distinct roles at specific stages, in specific muscles, or both. These results provide a starting point for fine mapping of QTL for the traits measured and improve the understanding of the genetic basis of pH metabolism after slaughter.

Single nucleotide polymorphisms in several porcine cathepsin genes are associated with growth, carcass, and production traits in Italian Large White pigs

To identify DNA markers associated with performance, carcass, and meat production traits including muscle postmortem cathepsin activity, several porcine genes encoding for lysosomal proteinases (cathepsin B, CTSB; cathepsin D, CTSD; cathepsin F, CTSF; cathepsin H, CTSH; cathepsin L, CTSL; and cathepsin Z, CTSZ) and for a cathepsin inhibitor (cystatin B) were investigated. Single nucleotide polymorphisms were identified in CTSD, CTSH, CTSL, and CTSZ genes with a combination of in silico expressed sequence tag database mining and single-strand conformation polymorphism analysis. Sequencing and PCR-RFLP protocols were used to validate the identified polymorphisms. Allele frequencies at these loci were investigated in Italian Large White, Landrace, Duroc, Piétrain, Belgian Landrace, Hampshire, and Meishan breeds. Genotyping CTSD and CTSH markers made it possible to genetically map these genes to SSC 2 and 7, respectively. Markers in CTSD, CTSH, CTSL, and CTSZ genes, together with mutations we previously reported in cystatin B, CTSB, and CTSF genes, were genotyped in an Italian Large White sib-tested population (272 or 482 animals). For these animals, meat quality traits (cathepsin B activity, pH measured at 2 h postmortem, pH measured at 24 h postmortem, glycogen, lactate, and glycolytic potential of semimembranosus muscle) and EBV for ADG, lean cuts (LC), backfat thickness (BFT), ham weight (HW), and feed:gain ratio (FGR) were determined. Analyzed markers did not show any association with muscle cathepsin B activity. Thus, it could be possible that different genes, other than these investigated candidates, affect this trait, which is correlated with the excessive softness defect of dry-cured hams. The results of association analysis confirmed the effects we already reported in another study for CTSF on ADG (P = 0.008), LC (P = 0.001), and BFT (P = 0.02). Moreover, CTSD was associated with ADG, LC (P < 0.0001), BFT, HW, and FGR (P < 0.001); CTSH was associated with FGR (P = 0.026); and CTSZ was associated with ADG (P = 0.006), LC (P = 0.01), HW (P = 0.024), and FGR (P = 0.029). The biochemical and physiological functions of the lysosomal proteinases, together with the results obtained in our investigation, suggest that the cathepsin gene family might play important roles affecting economic traits in pigs.

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.

Investigation of candidate genes for glycolytic potential of porcine skeletal muscle: Association with meat quality and production traits in Italian Large White pigs

The objective of this study was to investigate the association of DNA markers in candidate genes for glycolytic potential on meat quality parameters (pH(1), pH(u), glycogen and lactate content and glycolytic potential of semimembranosus muscle) and estimated breeding values (EBVs) for average daily gain, lean cuts, back fat thickness, ham weight, and feed:gain ratio in 272 Italian Large White pigs. Three mutations in the PRKAG3 gene (T30N, G52S and I199V) were investigated as well as single nucleotide polymorphisms in two other skeletal muscle genes (PGAM2 and PKM2) involved in the glycolytic pathway. Association analysis with the PRKAG3 markers showed significant results (P<0.05) only for pH(1) (I199V, with significant additive effect) and lactate content (T30N), confirming, at least in part, the effects of this gene on meat quality traits. Significant association (P<0.05) was also observed for PGAM2 and ham weight EBV with significant additive and dominance effects. PKM2 was associated with average daily gain, lean cuts (P<0.001), back fat thickness and feed:gain ratio (P<0.05), with significant additive and/or dominance effects on these traits. PKM2 encodes for a key enzyme of the muscle glycolytic pathway and maps on porcine chromosome 7 where other studies have reported important QTL for the same traits. These data might suggest an important function of this gene in the mechanisms that produce the observed effects. The results will be important to evaluate the inclusion of some of these DNA polymorphisms in marker assisted selection programs.

Identification of differentially expressed genes in distinct skeletal muscles in cattle using cDNA microarray

The 788-gene microarray was manufactured using selected elements from three different cDNA libraries in order to identify molecular processes that determine phenotypic characteristics between loin (M. longissimus thoracis) and round (M. semimembranosus) muscles. Microarray analyses identified 24 differentially expressed genes between the two muscles investigated. Five of the genes were verified by quantitative RT-PCR and three of them were mapped on bovine chromosomes using 5,000 rad bovine radiation hybrid (RH) panel. The map locations indicated that they were mapped in the same chromosomal regions where IMF and growth QTLs were located, suggesting that they are most possible positional candidate genes for the traits.

Quantitative trait loci mapping for meat quality and muscle fiber traits in a Japanese wild boar x Large White intercross

Three generations of a swine family produced by crossing a Japanese wild boar and three Large White female pigs were used to map QTL for various production traits. Here we report the results of QTL analyses for skeletal muscle fiber composition and meat quality traits based on phenotypic data of 353 F(2) animals and genotypic data of 225 markers covering almost the entire pig genome for all of the F(2) animals as well as their F(1) parents and F(0) grandparents. The results of a genome scan using least squares regression interval mapping provided evidence that QTL (<1% genome-wise error rate) affected the proportion of the number of type IIA muscle fibers on SSC2, the number of type IIB on SSC14, the relative area (RA) of type I on SSCX, the RA of type IIA on SSC6, the RA of type IIB on SSC6 and SSC14, the Minolta a* values of loin on SSC4 and SSC6, the Minolta b* value of loin on SSC15, and the hematin content of the LM on SSC6. Quantitative trait loci (<5% genome-wise error rate) were found for the number of type I on SSC1, SSC14, and SSCX, for the number of type IIA on SSC14, for the number of type IIB on SSC2, for the RA of type IIA on SSC2, for the Minolta b* value of loin on SSC3, for the pH of loin on SSC15, and for the i.m. fat content on SSC15. Twenty-four QTL were detected for 11 traits at the 5% genome-wise level. Some traits were associated with each other, so the 24 QTL were located on 11 genomic regions. In five QTL located on SSC2, SSC6, and SSC14, each wild boar allele had the effect of increasing types I and IIA muscle fibers and decreasing type IIB muscle fibers. These effects are expected to improve meat quality.

SNaPshot Minisequencing and a Panel of Candidate Genes for Complex Routine Testing of Meat Performance Traits in Pigs

The aim of the study was to introduce a convenient method for identification of differences among individual animals in genes supposed to influence meat performance in pigs. The set of seven candidate genes (IGF2, FOS, MC4R, DGAT1, MYF4, MYF, and MC3R) was used. To determine the genotypes, multiplex polymerase chain reaction (PCR) and minisequencing using SNaPshot system (Applied Biosystems; Forster City, CA, USA) were applied. The efficiency of this gene panel for routine testing in pigs was verified in the Black Pied Prestice pig breed by the statistical general linear model. The results showed that both the method and the gene panel are convenient for meat quality testing and offer reproducible results.

Genetic architecture of fast- and slow-twitch skeletal muscle weight in 200-day-old mice of the C57BL/6J and DBA/2J lineage

The aim of the study was to explore the genetic architecture influencing weight of fast- and slow-twitch skeletal muscles. The weights of the slow-twitch soleus, the mixed gastrocnemius, the fast-twitch tibialis anterior (TA), and extensor digitorum longus (EDL) muscles were 11-34% greater (P < 0.001) in 200-day-old C57BL/6J (B6) than in DBA/2J (D2) mice. Male muscles were 13-28% larger than female (P < 1 x 10(-5), no strain by sex interaction). The sex-related difference in muscle weight, however, varied significantly among the 23 derivative BXD recombinant inbred (RI) strains (strain by sex interaction for soleus, P < 0.01; TA, P < 1 x 10(-4); EDL, not significant; and gastrocnemius, P < 0.001). Quantitative trait loci (QTL) affecting muscle weight were mapped in an F2 intercross of B6 and D2 mice (B6D2F2) and BXD RIs. A total of 10 autosomal, muscle-specific, but not muscle-type-specific, QTL, explaining a total of 5.4, 7.7, 22.9, and 8.6% of phenotypic variance for soleus, TA, EDL, and gastrocnemius muscles, respectively, were found across chromosomes 1 (Chr 1), 2, 3 (female-specific), 5 (two), 6, 7, 8, and 9 in B6D2F2 mice. The QTL on Chr 8 for EDL and the female-specific QTL on Chr 3 for gastrocnemius muscles were statistically significant, but the remaining QTL were at the suggestive level of statistical significance. Ten QTL on Chr 1, 2, 4, 5, 7, 8, 14, 17 (two), and 19 were identified in BXD RIs. Half of the QTL in BXD RIs had pleiotropic effects and were at the suggestive level of significance (except for the significant QTL for gastrocnemius muscle on Chr 17). The B6D2F2 nominated QTL on Chr 8 for EDL weight was validated in BXD RIs (P < 0.03). Support intervals for the QTL on Chr 1 and 5 overlapped between B6D2F2 and BXD RIs. An epistatic interaction between markers on Chr 1 and 17 affected gastrocnemius weight in BXD RIs. The interaction was not, however, validated in the B6D2F2 population. Our results indicate that the differences in muscle weight in the B6 and D2 segregating populations were the outcome of a polygenic system, with each factor contributing a small amount to the phenotypic variance and the genetic architecture affecting muscle weight was muscle specific, but not muscle-type specific, and in some instances sex specific.