Associations between single nucleotide polymorphisms in 33 candidate genes and meat quality traits in commercial pigs

This study aimed to evaluate the effects of single nucleotide polymorphisms (SNPs) in candidate genes for meat quality using a custom 96‐SNP panel (Illumina Vera Code GoldenGate Assay) on 15 traits collected from 400 commercial pigs. Meat quality measurements included muscle pH, color (L*, a* and b*), drip loss, cooking loss, peak shear force and six sensory traits including appearance (outside and inside), tenderness, juiciness, flavor and overall liking as well as carcass weight and probe yield. Thirty‐five SNPs with minor allele frequencies > 0.10 remained for the multimarker association using the GLM procedure of sas 9.2. Results showed that 20 SNPs were significantly associated with at least one of the traits with either additive or dominance or both effects (P < 0.05). Among these significant SNPs, five of them in ADIPOQ, FTO, TNF, LEPR and AMPD1 had an effect on more than three traits simultaneously; those in MC4R, CAST, DGAT1 and MYF6 had an effect on two traits, while the others were associated with one trait. The results suggest that these markers could be incorporated into commercial pigs for marker‐assisted selection and breeding programs for carcass and meat quality trait improvement.     

Quantitative trait loci analysis of a Duroc commercial population highlights differences in the genetic determination of meat quality traits at two different muscles

We performed a whole‐genome scan with 110 informative microsatellites in a commercial Duroc population for which growth, fatness, carcass and meat quality phenotypes were available. Importantly, meat quality traits were recorded in two different muscles, that is, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), to find out whether these traits are determined by muscle‐specific genetic factors. At the whole‐population level, three genome‐wide QTL were identified for carcass weight (SSC7, 60 cM), meat redness (SSC13, 84 cM) and yellowness (SSC15, 108 cM). Within‐family analyses allowed us to detect genome‐wide significant QTL for muscle loin depth between the 3rd and 4th ribs (SSC15, 54 cM), backfat thickness (BFT) in vivo (SSC10, 58 cM), ham weight (SSC9, 69 cM), carcass weight (SSC7, 60 cM; SSC9, 68 cM), BFT on the last rib (SSC11, 48 cM) and GM redness (SSC8, 85 cM; SSC13, 84 cM). Interestingly, there was low positional concordance between meat quality QTL maps obtained for GM and LTL. As a matter of fact, the three genome‐wide significant QTL for colour traits (SSC8, SSC13 and SSC15) that we detected in our study were all GM specific. This result suggests that QTL effects might be modulated to a certain extent by genetic and environmental factors linked to muscle function and anatomical location.     

丙酸通路基因多态性与猪肉质及胴体性状的关联分析

为了挖掘新的猪肉品质及胴体性状的候选基因,揭示猪肉质及胴体性状的遗传机制,文章将丙酸代谢通路作为候选通路,将通路内基因与猪肉质及胴体性状进行关联分析。实验采用37头三元杂交商品猪作为研究对象,首次针对丙酸通路中7个基因的36个SNP位点利用SNaPshot方法进行基因分型,分别用最小二乘模型及MB-MDR模型与肉质及胴体性状进行关联分析。结果发现,基因PCCB、MUT、MCEE及ACSS2上的4个SNP位点分别与肌内脂肪含量、背膘厚等性状显著相关(P<0.05),ACSS2与猪脂肪含量显著相关;MCEE及MUT与猪的背膘厚显著相关;PCCB基因与脂重显著相关。通过MB-MDR方法检测到多个SNP位点具有互作效应,并与背膘厚、水分含量、脂肪含量显著相关(P<0.05)。另外,丙酸代谢通路中的基因间的互作效应对猪肉品质有显著影响。     

Influence of rearing system,diet and gender on performance,carcass traits and meat quality of Polish Landrace pigs

Forty-eight Polish Landrace pigs (initially 32.43 ± 0.70 kg live weight) were assigned to a 2 × 2 × 2 factorial arrangement in order to assess the effects of the rearing system (outdoor v. indoor), diet (with corn grain silage v. without corn grain silage) and gender (barrows v. gilts) on performance, carcass traits, meat quality and intramuscular collagen (IMC) characteristics. During the trial period of 14 weeks, each group was housed in a pen of 12 m², and the outdoor-reared animals had access to a paddock of 24 m². Pigs were fed a diet computed according to standard requirements and supplied on a basis of 9% of metabolic weight (live weight^0.75). Pigs were slaughtered at 110.69 ± 0.85 kg. The rearing system did not significantly affect growth, hot and cold dressing, meat quality of m. longissimus lumborum or IMC. Outdoor pigs had less (P < 0.05) backfat thickness, slightly higher (P = 0.082) lean percent and a meat with lower pH and fat than the conventional system. In light of these results, alternative pig rearing systems with indoor space and free outdoor access could be an interesting production system for the pigs. Compared with the pigs fed diets with corn grain silage, those fed diets without corn had higher (P < 0.05) lean, ham percentage and IMC content, lower (P < 0.05) neck percentage but similar main tissue components of the ham and meat quality. Compared with the gilts, barrows were fatter and showed a meat with different physico-chemical traits, which was slightly more tender and had similar IMC properties.     

Associations of functional candidate genes derived from gene-expression profiles of prenatal porcine muscle tissue with meat quality and muscle deposition

Ten genes (ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain x (Landrace x Large White), Duroc x (Landrace x Large White) as well as in an experimental F(2) population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human-porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of < or = 0.05; PDGFRA revealed no association reaching the P < or = 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of < 0.003 that correspond to false discovery rates of < 0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical-genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations.     

Association of halothane sensitivity with growth and meat quality in pigs

Previous reports have indicated that a proportion of pigs, homozygous normal for the skeletal muscle ryanodine receptor gene (RYR1), was halothane sensitive, and this was associated with poor meat quality when pigs were handled aggressively. This study was conducted to evaluate halothane sensitivity in RYR1-normal pigs, managed under simulated commercial conditions, to ascertain the association of halothane sensitivity with growth rate and meat quality. A total of 363 pigs across four farrowing groups, from seven Landrace sires and 38 Yorkshire–Landrace F1 dams, were tested at 8 weeks of age for halothane sensitivity using a closed system that delivered 5% halothane at 2 l/min for 3 (group 1) or 2 (groups 2 to 4) min. After 1 min, limb rigidity, limb tremors and abdominal discoloration were evaluated on a binomial scale with 0 indicating no reaction and 1 indicating reaction. Testing was repeated 2 days later. At 10 weeks of age, pigs were moved to finishing pens and not moved again until marketing. Within farrowing group, pigs were harvested in one of two groups, and at marketing were moved a distance of 91 m, weighed, tattooed, loaded and transported a distance of 550 km to a commercial harvest plant. After overnight rest, pigs were harvested and the pH of the loin muscle was measured at 45 min (pH45) after stunning. After an 18-h chill, loin muscle pH (pHu), International Commission on Illumination (CIE) L*, a*, b*, color (1 to 6) and marbling (1 to 10) scores and fluid loss percent were collected. Generalized linear mixed models were used to estimate repeatabilities for response to halothane challenge. Repeatabilities for limb rigidity for the front right and left legs were 0.24 and 0.31, respectively, whereas rear right and left leg repeatabilities were 0.19 and 0.17, respectively. Repeatabilities for front right and left leg tremors were 0.16 and 0.20, respectively. Growth rate was not influenced by any measure of halothane sensitivity. Carcasses from pigs exhibiting limb rigidity tended to have lower pH45 (5.88 v. 5.97; P = 0.06), similar pHu (5.47 v. 5.49; P = 0.32), less pH decline from 45 min to 18 h (−0.40 v. −0.50; P = 0.04) and a tendency for greater fluid loss percent (5.01 v. 4.55; P = 0.08) than carcasses from pigs that did not exhibit limb rigidity during halothane challenge. A proportion of pigs normal for RYR1 did exhibit limb rigidity during halothane gas challenge, and subsequently tended to have lower 45 min pH and greater longissimus muscle fluid loss post harvest.     

Comparison between the three porcine RN genotypes for growth,carcass composition and meat quality traits

A three-step experimental design has been carried out to add evidence about the existence of the RN gene, with two segregating alleles RN^- and rn⁺, having major effects on meat quality in pigs, to estimate its effects on production traits and to map the RN locus. In the present article, the experimental population and sampling procedures are described and discussed, and effects of the three RN genotypes on growth and carcass traits are presented. The RN genotype had no major effect on growth performance and killing out percentage. Variables pertaining to carcass tissue composition showed that the RN^- allele is associated with leaner carcasses (about 1 s.d. effect without dominance for back fat thickness, 0.5 s.d. effect with dominance for weights of joints). Muscle glycolytic potential (GP) was considerably higher in RN^- carriers, with a maximum of a 6.85 s.d. effect for the live longissimus muscle GP. Physico-chemical characteristics of meat were also influenced by the RN genotype in a dominant way, ultimate pH differing by about 2 s.d. between homozygous genotypes and meat colour by about 1 s.d. Technological quality was also affected, with a 1 s.d. decrease in technological yield for RN^- carriers. The RN genotype had a more limited effect on eating quality. On the whole, the identity between the acid meat condition and the RN^- allele effect is clearly demonstrated (higher muscle GP, lower ultimate pH, paler meat and lower protein content), and the unfavourable relationship between GP and carcass lean to fat ratio is confirmed.     

Malic enzyme 1 genotype is associated with backfat thickness and meat quality traits in pigs

Malic enzyme 1 (ME1) is a part of the tricarboxylate shuttle that provides NADPH and acetyl-CoA required in fatty acid biosynthesis. The pig ME1 locus maps on the proximal end of chromosome 1, where a quantitative trait loci (QTL) affecting fat deposition has been previously described. We amplified fragments of 1457 and 1459 bp that corresponded to the complete coding region and the 3'-untranslated region (UTR), respectively, of the pig ME1 gene. The sequences of these two fragments in pigs from three breeds (Landrace, Large White and Piétrain) contained five single nucleotide polymorphisms (SNP) in the 3'-UTR: C1706T, G1762T, A1807C, C1857A and T1880A. Three haplotypes were found in two generations of a selected Landrace population: H1 (C1706 G1762 A1807 C1857 A1880), H2 (C1706 G1762 A1807 C1857 T1880) and H3 (T1706 T1762 C1807 A1857 T1880). Using Bayesian association analyses, significant associations (highest posterior density at 95%) between ME1 genotype and backfat (BF) thickness at 171 days and muscular pH were found in a Landrace population.     

From phenotyping towards breeding strategies: using in vivo indicator traits and genetic markers to improve meat quality in an endangered pig breed

In endangered and local pig breeds of small population sizes, production has to focus on alternative niche markets with an emphasis on specific product and meat quality traits to achieve economic competiveness. For designing breeding strategies on meat quality, an adequate performance testing scheme focussing on phenotyped selection candidates is required. For the endangered German pig breed ‘Bunte Bentheimer’ (BB), no breeding program has been designed until now, and no performance testing scheme has been implemented. For local breeds, mainly reared in small-scale production systems, a performance test based on in vivo indicator traits might be a promising alternative in order to increase genetic gain for meat quality traits. Hence, the main objective of this study was to design and evaluate breeding strategies for the improvement of meat quality within the BB breed using in vivo indicator traits and genetic markers. The in vivo indicator trait was backfat thickness measured by ultrasound (BF_iv), and genetic markers were allele variants at the ryanodine receptor 1 (RYR1) locus. In total, 1116 records of production and meat quality traits were collected, including 613 in vivo ultrasound measurements and 713 carcass and meat quality records. Additionally, 700 pigs were genotyped at the RYR1 locus. Data were used (1) to estimate genetic (co)variance components for production and meat quality traits, (2) to estimate allele substitution effects at the RYR1 locus using a selective genotyping approach and (3) to evaluate breeding strategies on meat quality by combining results from quantitative-genetic and molecular-genetic approaches. Heritability for the production trait BF_iv was 0.27, and 0.48 for backfat thickness measured on carcass. Estimated heritabilities for meat quality traits ranged from 0.14 for meat brightness to 0.78 for the intramuscular fat content (IMF). Genetic correlations between BF_iv and IMF were higher than estimates based on carcass backfat measurements (0.39 v. 0.25). The presence of the unfavorable n allele was associated with increased electric conductivity, paler meat and higher drip loss. The allele substitution effect on IMF was unfavorable, indicating lower IMF when the n allele is present. A breeding strategy including the phenotype (BF_iv) combined with genetic marker information at the RYR1 locus from the selection candidate, resulted in a 20% increase in accuracy and selection response when compared with a breeding strategy without genetic marker information.     

Analysis of public single nucleotide polymorphisms in commercial pig populations

More than 5500 pig single nucleotide polymorphisms (SNPs) were recently identified and deposited in the public domain. To test the usefulness of these public SNPs, 109 SNPs were analysed for polymorphism within six commercial pig populations. A functional polymerase chain reaction (PCR) assay was obtained for 103 SNPs and it was possible to validate c. 59% by PCR-restriction fragment length polymorphism. Furthermore, polymorphism was found using a relatively limited number of genomic DNA samples, indicating that these polymorphisms are segregating at a useful frequency in these populations. The high percentage of validated markers demonstrates the utility of these public pig SNPs to identify loci responsible for economically important traits in commercial pig populations.     

Influence of cage or pen housing on carcass traits and meat quality of rabbit

Carcass traits and meat quality of rabbits reared in conventional cages (0.385 m2), small pens (0.662 m2) or large pens (4.052 m2) at a similar stock density of 15 rabbits/m2 were compared (n = 30 per group). Pens contained an elevated platform. Slaughter weight (SW; P < 0.01) and cold carcass weight (P < 0.05) decreased in the order of Cage < Small pen < Large pen groups. SW and cold carcass weight were 7% lower in rabbits housed in large pens than in cages. Dressing out and meat-to-bone ratio were not influenced by the housing system. Percentage of fat deposits was highest in caged rabbits (+0.15 point for scapular fat and +0.26 point for perirenal fat compared to rabbits reared in large pens P < 0.05). Rabbits housed in large pens had a bigger proportion of hind part (+1 point), and meat colour was shifted towards greater a* values (P < 0.01) compared to caged rabbits. Water holding capacity and shear test parameters in longissimus lumborum muscle, lipid content and shear test parameters of abductor cruralis cranialis, biceps femoris and semitendinosus muscles were not affected by the housing system. Tibia and femur bone moment of inertia increased in the order of Cage < Small pen < Large pen groups (P < 0.05), whereas elastic modulus, which is a measure of intrinsic stiffness, was highest in caged rabbits. This study showed that large pen housing altered carcass traits independently and increased meat redness and fracture resistance of tibia and femur.     

Parent-of-origin effects cause genetic variation in pig performance traits

In order to assess the relative importance of genomic imprinting for the genetic variation of traits economically relevant for pork production, a data set containing 21 209 records from Large White pigs was analysed. A total of 33 traits for growth, carcass composition and meat quality were investigated. All traits were recorded between 1997 and 2006 at a test station in Switzerland and the pedigree included 15 747 ancestors. A model with two genetic effects for each animal was applied: the first corresponds to a paternal and the second to a maternal expression pattern of imprinted genes. The imprinting variance was estimated as the sum of both corresponding genetic variances per animal minus twice the covariance. The null hypothesis of no imprinting was tested by a restricted maximum likelihood ratio test with two degrees of freedom. Genomic imprinting significantly contributed to the genetic variance of 19 traits. The proportion of the total additive genetic variance that could be attributed to genomic imprinting was of the order between 5% and 19%.     

Genome-wide association studies for seven production traits highlight genomic regions useful to dissect dry-cured ham quality and production traits in Duroc heavy pigs

Protected designation of origin dry-cured hams are obtained from heavy pigs (slaughtered at about 160 kg of live weight). A specific breeding program designed to improve meat quality for this production has included as key traits the level of intermuscular fat between the leg muscles and ham weight loss during the seasoning period together with a balance between fat and lean cuts. In this study we carried out genome-wide association studies for seven traits used in the genetic merit of Italian Duroc heavy pigs, five related to meat and carcass quality traits (visible intermuscular fat, ham weight loss at first salting, backfat thickness, ham weight and lean cuts), and two related to performance and efficiency traits (average daily gain and feed : gain ratio). A total of 573 performance-tested pigs were genotyped with the Illumina PorcineSNP60 BeadChip and genome-wide association analyses were carried out using the Bayes B approach with the 1 Mb window option of GenSel and random residuals for each of the seven traits. Detected windows were supported by independent single nucleotide polymorphism analyses with a linear mixed model (LMM) approach on the same animals for the same traits. A total of 30 windows identifying different quantitative trait loci (QTL) were detected and among those, 27 were confirmed by LMM in one of these traits. Among the confirmed windows, three QTL were reported for visible intermuscular fat, seven for ham weight loss at first salting and five and four for backfat thickness and lean cut, respectively. A total of eight QTL were detected for the other production traits. No overlapping QTL were reported except for one window on porcine chromosome 10 between lean cuts and ham weight that contained the CACNB2 gene that has been already associated with loin marbling score in other Duroc pigs. Several regions contained genes that have been already associated with production traits in other pig breeds, including Duroc lines, related to fat deposition or muscle structure. This work reports, for the first time, genome-wide association study results for several traits in Italian Duroc heavy pigs. These results will be useful to dissect the genetic basis for dry-cured ham production traits that determine the total genetic merit index of Italian Duroc pigs.     

Associations between newly discovered polymorphisms in the Bos taurusgrowth hormone receptor gene and performance traits in Holstein–Friesian dairy cattle

Variations in the growth hormone receptor (GHR) gene sequence are associated with performance traits in cattle. For example, the single nucleotide polymorphism (SNP) F279Y in transmembrane exon 8 has a strong association with milk yield. In this study, 32 previously unreported, putative novel SNPs (31 in the 5′ non‐coding region) were identified by resequencing ～19 kb of the GHR gene in genomic DNA from 22 cattle of multiple breeds. A population of 848 Holstein–Friesian AI sires was subsequently genotyped for the 32 putative novel SNPs and seven published SNPs (including F279Y, one in exon 1A promoter and five in exon 10). Associations between each segregating SNP and genetic merit for performance were quantified in the 848 Holstein–Friesians using weighted animal linear mixed models. Six of the published SNPs and seven of the novel SNPs were associated with at least one of the traits – milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score, calving interval, survival and growth and size traits. Even when the allelic substitution effect (P < 0.001) of F279Y was accounted for, the allelic substitution effect of one of the novel SNPs (GHR4.2) in the 5′ non‐coding region of GHR was associated with a lactation milk yield of 37.46 kg (P < 0.001). GHR4.2 and F279Y were not in linkage disequilibrium (r² = 0.00, D’ = 0.04) in the 848 Holstein–Friesians, indicating that their association with milk yield was independent.     

Effect of slaughter age on foal carcass traits and meat quality

Meat has played a crucial role in human evolution and is an important component of a healthy and well-balanced diet due to its nutritional richness. Recent studies have shown that horsemeat may be considered as an alternative to other meat (such as beef or pork), and it may have a positive effect on human health from a nutritional point of view. This research was conducted to characterize the carcass measurement, meat quality (chemical composition, colour characteristics and textural traits) and nutritional value (fatty acid and amino acid composition) of foals slaughtered at 8 and 11 months of age (8 and 11 m groups). For this study, a total of 21 foals (10 and 11 animals from the 8 and 11-m groups, respectively) were used. The results obtained showed a positive influence on carcass characteristics with an increase in slaughter age, because 11 m animals had slightly higher values of live (275 v. 247 kg) and carcass weights (148 v. 133 kg), length of leg (72.86 v. 69.85 cm) and carcass (100.41 v. 96.30 cm) and perimeter of leg (97.68 v. 89.22 cm) compared with animals from the 8-m group. Regarding meat quality, only Fe-haeme and cholesterol content in chemical composition and luminosity (L*) in colour parameters showed significant differences. Foals from the 8-m group had the highest content of cholesterol (0.47 v. 0.28 mg/100 g of meat) and luminosity values (39.66 v. 37.88) and the lowest content of ash (1.20% v. 1.40%). In fatty acids content, only five out of 23 fatty acids showed differences between the two groups. However, an interesting change in the fatty acid profile occurred with an increase in the slaughter age. Foals from the 8-m group had the highest values of α-linolenic acid and n-3 fatty acids and the lowest values of linoleic and n-6 fatty acids, which is an interesting fact from a health point of view. Finally, slaughter age had no statistical influence on textural properties or amino acid content. As a main conclusion, animals slaughtered at 8 months of age had higher nutritional quality meat (with higher content of n-3 fatty acids) than meat from foals slaughtered at 11 months of age. The slaughter of animals at 8 months of age also reduced production costs because they ate a smaller amount of commercial fodder.     

Pig identification and meat traceability by multiallelic amplification fragments with multiple single nucleotide polymorphisms

Compared with conventional identification methods, DNA-based genetic approaches such as single nucleotide polymorphisms (SNPs) and satellites are much more reliable for pig identification and meat traceability. In this study, multiallelic amplification fragments with multiple SNPs, incorporating the advantages of both SNPs and microsatellites, were explored for the first time for pig identification and meat traceability. Primer pairs for multiallelic fragments and their optimal SNPs were successfully selected and used for identification of individuals from Suzhong and Duroc populations. Meanwhile, the combined panel of the above mentioned primer pairs together with their optimal SNPs for Suzhong and/or Duroc pigs were validated for identification of the hybrids (Suzhong×Duroc). Therefore, we have successfully selected multiallelic amplification fragments with multiple SNPs to identify pigs and their meat samples from Suzhong, Duroc or their hybrids. Our study demonstrates that our method is more powerful for pig identification or meat traceability than SNPs or microsatellites.     

Effect of dietary protein level on carcass traits and meat properties of Cinta Senese pigs

The aim of this study was to test the effect of various dietary protein contents (CP) on the carcass traits and the meat quality of Cinta Senese pigs. A total of 60 Cinta Senese pigs were equally distributed in four dietary groups that were balanced for sex (barrows and gilts) and live weight. The animals in the groups were fed one of four diets (80CP, 100CP, 130CP and 160CP) containing different CP contents (80, 100, 130 and 160 g/kg, respectively). The diets were administered to the pigs during the entire growing–fattening period in a controlled dose of 90 g/kg W^0.75, to a maximum of 2.5 kg/day per animal. The duration of the trial was ~250 days, ending when the animals reached the target slaughter weight of 145 kg. The 80CP diet produced fatter carcasses than did the other diets; no differences in carcass composition were found among the animals fed the other three diets (total lean cuts: 57.4%, 61.4%, 60.8% and 61.3% for 80CP, 100CP, 130CP and 160CP diet, respectively). The sample joint composition confirmed the highest fatness and the lowest meatiness of pigs fed 80CP. This same pattern was evident for the composition of the muscle (Longissimus lumborum) containing the largest amount of i.m. fat, and the lowest protein content in the 80CP group. Moreover, the 80CP diet resulted in the lightest and yellowest meat with the highest cooking loss. A principal component analysis of the physical and chemical traits of the meat revealed three first factors that explained 56% of the total variance. Among them, only the intersection of Factor1, which combined mainly lower pH at 24 h postmortem and higher drip loss, cooking loss, lightness and yellowness, with Factor2, which associated higher toughness, higher protein and lower fat content, graphically appeared to discriminate the 80CP diet from the other ones. In conclusion, a diet with 80 g/kg of CP content was inadequate for this local breed, while, in consideration of the cost of protein feed and the need to reduce N pollution, the 100CP diet would be an optimal compromise for the growth–fattening of Cinta Senese pigs.