Association of the polymorphism in the 5'-noncoding region of the bovine growth hormone receptor gene with meat production traits in Polish Black-and-White cattle

Single and combined effects of polymorphisms in the 5'-noncoding region of the bovine growth hormone receptor (GHR) gene on the traits related to meat production were examined in Polish Black-and-White (BW; Friesian) cattle. Four single nucleotide polymorphisms (SNPs) located in the P1 promoter region were analysed. One-hundred and fifty young bulls were included in the study. The traits analysed were daily weight gain, feed intake and conversion, and carcass parameters. Individual SNPs had no effect on growth rates, feed consumption and conversion but showed marked effect on carcass composition traits. The (-/-) genotype at RFLP-AluI appeared favorable for weight of carcass, carcass dressing percentage, and weight of lean in valuable cuts. Animals with the RFLP-NsiI (+/+) genotype seemed better for most of the carcass parameters. In addition, statistically significant associations were found between combined GHR genotypes and feed consumption, carcass weight and dimensions.     

Effect of polymorphisms in candidate genes on carcass and meat quality traits in double muscled Piemontese cattle

The aim of this study was to investigate the association between 10 candidate genes and carcass weight and conformation, carcass daily gain, and meat quality (pH, color, cooking loss, drip loss and shear force) in 990 double-muscled Piemontese young bulls. Animals were genotyped at each of the following genes: growth hormone, growth hormone receptor, pro-opiomelanocortin, pro-opiomelanocortin class 1 homeobox 1, melanocortin-4 receptor, corticotrophin-releasing hormone, diacylglycerol O-acyltransferase-1, thyroglobulin, carboxypeptidase E and gamma-3 regulatory subunit of the AMP-activated protein kinase. All the investigated SNPs had additive effects which were relevant for at least one of the traits. Relevant associations between the investigated SNPs and carcass weight, carcass daily gain and carcass conformation were detected, whereas associations of SNPs with meat quality were moderate. Results confirmed some of previously reported associations, but diverged for others. Validation in other cattle breeds is required to use these SNPs in gene-assisted selection programs for enhancement of carcass traits and meat quality.     

Polymorphism and expression of the porcine Tenascin C gene associated with meat and carcass quality

The research aimed to screen for polymorphism, expression of Tenascin C (TNC) and association with meat and carcass quality traits. Three single nucleotide polymorphisms were detected. In a Duroc×Pietrain F2 cross (DuPi) population, g.44488C>T was associated with meat color and ham weight; g.68794A>G was associated with pH at 24h post mortem in ham (pH24(H)) and muscle area but g.68841C>T was not statistically associated. Genotyping in a commercial Pietrain (Pi) population showed that g.44488C>T was associated with pH24(H), whereas g.68794A>G was associated with conductivity at 45 min post mortem in loin and backfat thickness. Diplotypes showed significant effects on pH24(H) in both populations. The expression was associated with pH at 45 min post mortem in loin and cooking loss. TNC was significantly higher in animals with higher muscle pH. Linkage analysis revealed four trans-regulated eQTL on four autosomes. These results suggest that TNC could be a potential candidate gene for meat quality traits in pigs.     

Associations between single nucleotide polymorphisms in multiple candidate genes and carcass and meat quality traits in a commercial Angus-cross population

The aim of this study was to evaluate the effects of 28 single nucleotide polymorphisms (SNP) in 10 candidate genes previously shown to be associated with quality traits in pigs and cattle. The data set comprised 28 traits recorded on a commercial population of 536 Aberdeen Angus-cross beef cattle. Among the traits, 20 were carcass and sirloin quality related, one mechanical measure of tenderness, and the remaining seven were taste panel assessed sensory traits. The candidate genes studied included growth hormone (GH) and pro-opiomelanocortin (POMC). Association analysis showed that 13 of the 28 SNPs were significantly associated with at least one of the traits. Some of these were novel (POMC and mechanical tenderness), whilst others confirmed previous results (GH and eye muscle length).     

Association of polymorphisms at DGAT1, leptin, SCD1, CAPN1 and CAST genes with color,marbling and water holding capacity in meat from beef cattle populations in Sweden

The objective of this study was to investigate the associations of single nucleotide polymorphisms (SNPs) at five candidate genes with meat pH, color, marbling and water holding capacity (WHC) in young bulls from five beef breeds (n = 243) in Sweden. The UASMS2 polymorphism at the leptin gene and the SNPs at the Stearoyl-CoA desaturase 1 gene (SCD1.878) and μ-calpain gene (CAPN1:c.947) were associated with variation in meat color traits after 6 days of exposure to air. The K232A polymorphism at the diacylglycerol O-acyltransferase 1 (DGAT1) gene and the CAPN1:c.947 SNP were associated with level of beef marbling. There was no association between the SNP at the calpastatin gene (CAST:c.155) and meat quality traits, nor was there any association of the tested SNPs with WHC traits and pH value.     

Characterization of porcine SKIP gene in skeletal muscle development: Polymorphisms, association analysis, expression and regulation of cell growth in C2C12 cells

Skeletal muscle and kidney-enriched inositol phosphatase (SKIP) was identified as a 5'-inositol phosphatase that hydrolyzes phosphatidylinositol (3,4,5)-triphosphate (PI(3,4,5)P3) to PI(3,4)P2 and negatively regulates insulin-induced phosphatidylinositol 3-kinase signaling in skeletal muscle. In this study, two new single nucleotide polymorphisms (SNPs) in porcine SKIP introns 1 and 6 were detected. The C1092T locus in intron 1 showed significant associations with some meat traits, whereas the A17G locus in intron 6 showed significant associations with some carcass traits. Expression analysis showed that porcine SKIP is upregulated at d 65 of gestation and Meishan fetuses have higher and prolonged expression of SKIP compared to Large White at d 100 of gestation. Ectopic expression of porcine SKIP decreased insulin-induced cell proliferation and promoted serum starvation-induced cell cycle arrest in G0/G1 phase in C2C12. Our results suggest that SKIP plays a negative regulatory role in skeletal muscle development partly by preventing cell proliferation.     

EFFECT OF I199V POLYMORPHISM ON PRKAG3 GENE ON CARCASS AND MEAT QUALITY TRAITS IN SLOVENIAN COMMERCIAL PIGS

The effect of I199V polymorphism at the PRKAG3 gene on carcass and meat quality of commercial pigs was studied independently from PRKAG3 200Q or RYR1 "n" allele, known to decrease meat quality, i.e., animals were genotyped for RYR1 R615C, PRKAG3 I199V and R200Q substitutions, and only pigs without 200Q and "n" were retained for the analysis of carcass and meat quality traits ( n =  274). Genotype frequencies were 12.0, 57.7 and 30.3% for I/I, I/V and V/V, respectively. The I199V polymorphism affected significantly fat thickness and drip loss and tended to affect ultimate pH. Interestingly, I/V were the fattest and significantly different from V/V, with I/I pigs being intermediate. The ultimate pH of I/I was higher than the one of I/V or V/V pigs. Regarding drip loss, significant difference was detected between I/I and V/V pigs. The heterozygous I/V pigs were intermediate with differences to I/I or V/V tending toward significance.

PRACTICAL APPLICATIONS

Our results provide new evidence about the significant effect of second polymorphism on the PRKAG3 gene (I199V) on carcass and meat quality. Because of low frequencies of I/I genotype in the majority of modern pig breeds, the available literature data for genotype I/I are scarce. Our results confirm a beneficial impact of 199I allele for pork quality, but indicate possible adverse impact for carcass leanness. It would be worthwhile rechecking the interesting position of heterozygous I/V pigs, which turned out to be the fattest. We expect the results to be useful for breeders in search of the compromise between carcass and meat quality.     

Effects of variation in porcine MYOD1 gene on muscle fiber characteristics, lean meat production, and meat quality traits

Three single nucleotide polymorphisms (SNPs) in the porcine MYOD1 gene were used for association analysis and haplotype construction to evaluate the effects of their substitution. Four hundred and three pigs of Yorkshire and Berkshire breeds were used. The mRNA expression levels of MYOD1 were examined. The g.489C>T and g.1264C>A SNPs were significantly associated with several muscle fiber characteristics, the loin eye area, and lightness. Particularly, animals having hetero-genotypes of both sites showed good performance both in lean meat production and meat quality traits. The results of haplotype substitution were similar to the associations of individual SNPs. Moreover, the 2 SNPs had significant effects on mRNA expression. Therefore, the g.489C>T and g.1264C>A SNPs in MYOD1 may be meaningful DNA markers that can be used for improving important porcine economic traits.     

Meat quality and carcass traits in relation to HGD-BstXI and HGD-HaeIII PCR–RFLP polymorphism in Chinese red cattle

We investigated the effect of homogentisate 1, 2 dioxygenase (HGD) gene on meat quality and carcass traits in 287 Chinese red cattle. The PCR–SSCP method was used to identify polymorphism of the HGD gene in the exon 1 and intron 1. Two polymorphisms were detected in intron 1 and two restriction sites for endonuclease HGD-BstXI and HGD-HaeIII have also been found. The HGD-BstXI genotypes showed significant effects on cooking loss, drip loss, net meat weight, carcass weight, and eye muscle area (P < 0.05). The HGD-HaeIII genotypes significant affected cooking loss, muscle fibre diameter, shear force, drip loss, and carcass yield ratio (P < 0.05). Moreover, we found significant effects of diplotypes on cooking loss, muscle fibre diameter, shear force, drip loss, net meat weight, carcass weight, and eye muscle area (P < 0.05).     

Association of ZYX polymorphisms with carcass and meat quality traits in commercial pigs

Zyxin (ZYX) is one of the proteins in focal adhesions along the actin fibers playing a role in actin organization and signal transduction. By radiation hybrid and genetic mapping we assigned ZYX to porcine chromosome 18 in the area of quantitative traits loci for carcass and meat quality and muscle fiber traits and hence considered ZYX a functional positional candidate gene. Analysis of a newly detected SNPs (c.+279 C>T, c.+399 A>G, c.+522 A>G) in pigs from different commercial breeds (Pietrain [Pi], German Landrace [LR], German Large White × German Landrace [F1] and PiF1) revealed a significant association with carcass traits (including: side- and backfat thickness, loin weight and carcass lean content) and meat quality traits (including: pH, color and drip loss). However, the lack of consistent association across all pig populations in this study indicates that the association of the SNPs may be depending on causal mutations in linkage disequilibrium and/or interactions with other loci.     

Characterization of porcine SKIP gene in skeletal muscle development: Polymorphisms,association analysis,expression and regulation of cell growth in C2C12 cells

Skeletal muscle and kidney-enriched inositol phosphatase (SKIP) was identified as a 5′-inositol phosphatase that hydrolyzes phosphatidylinositol (3,4,5)-triphosphate (PI(3,4,5)P3) to PI(3,4)P2 and negatively regulates insulin-induced phosphatidylinositol 3-kinase signaling in skeletal muscle. In this study, two new single nucleotide polymorphisms (SNPs) in porcine SKIP introns 1 and 6 were detected. The C1092T locus in intron 1 showed significant associations with some meat traits, whereas the A17G locus in intron 6 showed significant associations with some carcass traits. Expression analysis showed that porcine SKIP is upregulated at d 65 of gestation and Meishan fetuses have higher and prolonged expression of SKIP compared to Large White at d 100 of gestation. Ectopic expression of porcine SKIP decreased insulin-induced cell proliferation and promoted serum starvation-induced cell cycle arrest in G0/G1 phase in C2C12. Our results suggest that SKIP plays a negative regulatory role in skeletal muscle development partly by preventing cell proliferation.     

An independent validation association study of carcass quality,shear force,intramuscular fat percentage and omega-3 polyunsaturated fatty acid content with gene markers in Australian lamb

Previous association studies revealed several single nucleotide polymorphisms (SNPs) that explained the observed phenotypic variation for meat tenderness and long-chain omega-3 polyunsaturated fatty acid (PUFA) content of Australian lamb. To confirm the validity of these associated SNPs at predicting meat tenderness and omega-3 PUFA content, an independent validation study was designed. The OvineSNP50 genotypes of these animals were used to impute the 192 SNP Meat Quality Research (MQR) panel genotypes on nearly 6200 animals from the Cooperative Research Centre for Sheep Industry Innovation Information Nucleus Flock and Sheep Genomics Falkiner Memorial Field Station flock. Association analysis revealed numerous SNP from the 192 SNP MQR panel that were associated with carcass quality – fat depth at the C-site and eye muscle depth; shear force at day 1 and day 5 after slaughter (SF1 and SF5); and omega-3 PUFA content at P < 0.01. However, 1 SNP was independently validated for SF5 (i.e. CAST_101781475). The magnitude of the effect of each significant SNP and the relative allele frequencies across Merino-, Maternal- and Terminal-sired progeny was determined. The independently validated SNP for SF5 and the associated SNP with omega-3 PUFA content will accelerate efforts to improve these phenotypic traits in Australian lamb.     

Titin-cap (TCAP) polymorphisms associated with marbling score of beef

Marbling score (MS) is the major qualitative trait that affects carcass quality in beef cattle. In this study, we examined the association between genetic polymorphisms of the titin-cap gene (TCAP) and carcass traits in Korean native cattle (also known as Hanwoo). By direct DNA sequencing in 24 unrelated Korean cattle, we identified five sequence variants in 1.2kb of TCAP. Among them, four common polymorphic sites were selected for genotyping in the beef cattle (n=437). Pair-wise linkage analysis with four polymorphisms showed strong linkage disequilibrium (LD), and three major haplotypes (freq.>0.1) were constructed. Statistical analysis revealed that polymorphisms in intron1 (g.346G>A) and exon2 (g.592-597CTGCAG[Leu-Gln]insdel) showed significant association with marbling score (P(cor.)=0.003 and 0.02, respectively). One haplotype, ht2[C-G-G-del], also showed significant association with MS (P(cor.)=0.0004). Our findings suggest that polymorphisms in TCAP might be among the important genetic factors involved in carcass quality in beef cattle.     

Carcass characteristics and meat quality of male and female foals

This research was conducted to characterize the carcass traits and meat quality of 16-month and 24-month old foals (33 males and 23 females) reared in two different livestock production systems. The carcass parameters assessed were conformation, degree of fatness, morphology, weight and carcass meat colour. The physicochemical characteristics and sensory profile of the M. longissimus dorsi (LD) were determined at 4 days of ageing. The carcass parameters and meat quality traits differed little between colts and fillies. There were significant differences between production systems. Carcasses were characterized by B conformation, 3 of fatness and high dressing percentages (>63%). Foal meat had a high myoglobin content and there were differences between the production systems in the flavour, juiciness, flourness and greasiness of the LD.     

Assessment of GH1, CAPN1 and CAST polymorphisms as markers of carcass and meat traits in Bos indicus and Bos taurus–Bos indicus cross beef cattle

The objective of this study was to investigate the effects of bovine GH1, CAPN1 and CAST gene polymorphisms on carcass and meat traits in Nellore and Nellore x Bos taurus beef cattle. Three hundred animals were genotyped for GH1/MspI (TC/G in intron 3), CAPN316 (AF_252504.2:g.5709C > G) and CAST/RsaI (AY_008267.1:g282C > G) and phenotyped for rib eye area, backfat thickness, intramuscular fat, shear force (SF), and myofibrillar fragmentation index (MFI). No significant associations were observed between the GH1/MspI and CAST/RsaI polymorphisms and phenotypes, although the relation between the CAST/RsaI genotypes and meat tenderness evaluated by MFI approached significant. The fact that the CAPN316 polymorphism did not show adequate segregation in Nellore cattle confirms the difficulty of using this marker in breeding programs of different Bos indicus breeds. However, the positive results of the association analysis obtained for Nellore x B. taurus crosses contributed to the validation of previous findings.     

Mutations in calpastatin and μ-calpain are associated with meat tenderness,flavor and juiciness in Hanwoo (Korean cattle): Molecular modeling of the effects of substitutions in the calpastatin/μ-calpain complex

The objective of this study was to evaluate the effects of seven single nucleotide polymorphisms (SNPs) in Calpain 1 and Calpastatin genes previously associated with meat tenderness attributes in other cattle breeds in Korean Hanwoo cattle. The Hanwoo resource population was used to study association of 7 SNPs with beef tenderness, flavor, juiciness, intramuscular fat and shear force. In this association study, CAST:c.182A > G (+ 0.14, P = 0.04) and CAST:c.1985G > C (− 0.12, P = 0.02) had significant effects on juiciness, but no effects on other traits. In contrast, CAPN1:c.1589G > A was associated with meat tenderness (P = 0.01) and juiciness (P = 0.04). The CAPN1:c.1589G > A (Val530Ile) SNP marker displayed significant effect on the meat tenderness score which is strongly supported by molecular modeling of the CAPN1:c.1589G > A (Val530Ile) variant that inhibits CAST protein from binding more strongly than the wild-type protein, which may explain its effect on meat tenderness.     

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.