Molecular approaches in pig breeding to improve meat quality.

This article reviews the advances in molecular genetics that have led to the identification of genes and markers associated with meat quality in pig. The development of a considerable number of annotated livestock genome sequences represents an incredibly rich source of information that can be used to identify candidate genes responsible for complex traits and quantitative trait loci effects. In pig, the huge amount of information emerging from the study of the genome has helped in the acquisition of new knowledge concerning biological systems and it is opening new opportunities for the genetic selection of this specie. Among the new fields of genomics recently developed, functional genomics and proteomics that allow considering many genes and proteins at the same time are very useful tools for a better understanding of the function and regulation of genes, and how these participate in complex networks controlling the phenotypic characteristics of a trait. In particular, global gene expression profiling at the mRNA and protein level can provide a better understanding of gene regulation that underlies biological functions and physiology related to the delivery of a better pig meat quality. Moreover, the possibility to realize an integrated approach of genomics and proteomics with bioinformatics tools is essential to obtain a complete exploitation of the available molecular genetics information. The development of this knowledge will benefit scientists, industry and breeders considering that the efficiency and accuracy of the traditional pig selection schemes will be improved by the implementation of molecular data into breeding programs.     

Association of corticotropin-releasing hormone gene variation with performance and meat quality traits in commercial pig lines

The porcine corticotropin-releasing hormone(CRH) gene is a functional-positional candidate for quantitative tract loci on porcine chromosome 4 with major effects on growth and carcass composition. In addition, the central role of CRH in the neuroendocrine response to stress implicates the CRH gene as a functional candidate for meat quality. Association of a single nucleotide polymorphism (SNP) in the promoter region of the porcine CRH gene (g.233C > T) with several growth, carcass and meat quality traits was examined using more than 2000 individuals from four commercial lines: German Landrace (LR), Pietrain (Pi), German Large White x German Landrace (F1) and the German commercial fattening pig cross of Pietrain x F1 (PiF1). Significant association of the CRH SNP was found with feed conversion ratio in the PiF1 line, with carcass length in the LR line and with lean content in the F1, LR and Pi lines. Moreover, significant association with meat colour was found in the Pi and LR lines; however, the effects were in opposite directions. The presented results indicate that sequence variation in the porcine CRH gene has no major effect on growth and carcass composition in commercial pig lines, although it may significantly contribute to variation in meat quality. The g.233C>T SNP may be in incomplete linkage disequilibrium with causal mutations and/or exhibit effects in the context of DNA variation at other interacting loci.     

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.     

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.     

Influence of production system in local and conventional pig breeds on stress indicators at slaughter,muscle and meat traits and pork eating quality

Sensory quality of pork is a complex phenotype determined by interactions between genetic and environmental factors. This study aimed at describing the respective influences of breed and production system on the development of pork quality. Plasma stress indicators and Longissimus muscle (LM) composition, physicochemical and sensory quality traits were determined in two contrasted breeds – the conventional Large White (LW, n=40) and the French local Basque (B, n=60). Pigs were reared in either a conventional (C; n=20 per breed), alternative (A; sawdust bedding and outdoor area, n=20 per breed) or extensive system (E; free-range, n=20 B). All the pigs from A and C systems were slaughtered at the same slaughterhouse, whereas B pigs from the E system were slaughtered at a local commercial abattoir. Major breed differences were found for almost all traits under study. LM from B pigs exhibited higher lipid, lower water and collagen concentrations, as well as lower collagen thermal solubility (P<0.001). Although plasma stress indicators at slaughter did not differ between breeds, except lower (P<0.05) lactate levels in B pigs, they exhibited higher LM pH1 and pHu values, and lower meat lightness, hue angle, water (drip, thawing and cooking) losses, glycolytic potential and shear force. Sensory analyses highlighted higher redness, marbling, tenderness, juiciness and flavour scores (P<0.01) of meat from B compared with LW pigs. Within both LW and B breeds, compared with C, the A system did not (P>0.05) influence plasma stress indicators, LM chemical composition and physicochemical or sensory traits of pork. In contrast, within the B pigs, the E system affected the meat quality more. Lower plasma cortisol levels (P<0.05), but higher plasma lactate, creatine kinase and lactate dehydrogenase activities, and more skin lesions (P<0.05), indicating higher muscular activity during pre-slaughter handling, were found in pigs produced in the E compared with the C system. E pigs exhibited higher meat pH1 and pHu values and shear force (P<0.01) and exhibited lower lightness, hue angle and drip and thawing losses (P<0.01) compared with the C pigs, whereas LM lipid, protein or collagen concentrations were not affected. Regarding sensory traits, the E system produced redder meat, but did not impact the eating quality of pork. Altogether, this study demonstrates that differences in meat quality between B and LW breeds can be modulated by extensive pig production system.     

Housing of growing rabbits in individual,bicellular and collective cages: growth performance,carcass traits and meat quality

During growth (from 27 to 75 days of age), 384 rabbits were kept in different types of wire-net cages: 72 individual cages (72 rabbits; 10 animals/m²), 48 bicellular cages (96 rabbits; 2 rabbits/cage; 18 animals/m²) and 24 collective cages (216 rabbits; 9 rabbits/cage; 18 animals/m²). The rabbits housed in individual cages showed higher daily weight gain both during the fattening period (from 52 to 75 days of age) and during the whole period of growth (43.0 v. 41.8 and 41.5 g/day; P < 0.05), and they had a higher final live weight at 75 days of age (2678 v. 2619 and 2602 g; P < 0.05) compared with the rabbits in the bicellular and collective cages, respectively. Rabbits in individual cages ingested more feed (133 v. 127 and 126 g/day; P < 0.01), but the feed conversion did not differ significantly among rabbits housed in the three types of cages. At slaughter, the carcass traits and meat quality were weakly affected by the housing system. The transport losses were higher in rabbits kept in individual and bicellular cages compared with those reared in collective cages (3.1% and 2.9% v. 2.2%; P < 0.01). In rabbits kept in individual cages, the hind leg muscle to bone ratio was higher (6.35 v. 6.19 and 5.91; P < 0.05) compared with the bicellular and collective cages, respectively. The pH and colour of the longissimus lumborum did not change with the housing system, while the b* index of the biceps femoris was lower (3.04 and 3.32 v. 4.26; P < 0.001) in the rabbits kept in individual and bicellular cages, respectively, than in those kept in collective cages. In conclusion, the rabbits housed in individual cages showed higher daily growth than rabbits kept in bicellular or collective cages, but they had a similar feed conversion and carcass quality. Differently, neither in vivo performance nor slaughter results differed among the rabbits kept in bicellular cages or in collective cages. The meat colour may be affected by the housing system, but to an extent that is hardly perceivable by the final consumer.     

Expression profiling analysis for genes related to meat quality and carcass traits during postnatal development of backfat in two pig breeds

The competitive equilibrium of fatty acid biosynthesis and oxidation in vivo determines porcine sub-cutaneous fat thickness(SFT) and intramuscular fat(IMF) content.Obese and lean-type pig breeds show obvious differences in adipose deposition;however, the molecular mechanism underlying this phenotypic variation remains unclear.We used pathway-focused oligo microarray studies to examine the expression changes of 140 genes associated with meat quality and carcass traits in backfat at five growth stages(1―5 months) of Landrace(a leaner, Western breed) and Taihu pigs(a fatty, indigenous, Chinese breed).Variance analysis(ANOVA) revealed that differences in the expression of 25 genes in Landrace pigs were significant(FDR adjusted permutation, P<0.05) among 5 growth stages.Gene class test(GCT) indicated that a gene-group was very significant between 2 pig breeds across 5 growth stages(PErmineJ<0.01), which consisted of 23 genes encoding enzymes and regulatory proteins associ-ated with lipid and steroid metabolism.These findings suggest that the distinct differences in fat deposition ability between Landrace and Taihu pigs may closely correlate with the expression changes of these genes.Clustering analysis revealed a very high level of significance(FDR adjusted, P<0.01) for 2 gene expression patterns in Landrace pigs and a high level of significance(FDR adjusted, P<0.05) for 2 gene expression patterns in Taihu pigs.Also, expression patterns of genes were more diversified in Taihu pigs than those in Landrace pigs, which suggests that the regulatory mechanism of micro-effect polygenes in adipocytes may be more complex in Taihu pigs than in Landrace pigs.Based on a dy-namic Bayesian network(DBN) model, gene regulatory networks(GRNs) were reconstructed from time-series data for each pig breed.These two GRNs initially revealed the distinct differences in physiological and biochemical aspects of adipose metabolism between the two pig breeds;from these results, some potential key genes could be identified.Quantitative, real-time RT-PCR(QRT-PCR) was used to verify the microarray data for five modulated genes, and a good correlation between the two measures of expression was observed for both 2 pig breeds at different growth stages(R=0.874±0.071).These results highlight some possible candidate genes for porcine fat characteristics and provide some data on which to base further study of the molecular basis of adipose metabolism.     

Investigation of candidate genes for meat quality in dry-cured ham production: the porcine cathepsin B (CTSB) and cystatin B (CSTB) genes

Excessive softness is a serious defect of dry cured hams which seems related to high activity of lysosomal cysteine proteinases, such as cathepsin B, in fresh pork muscles a few days after slaughtering. As it has been shown that cathepsin B activity has a moderate heritability in Italian Large White pigs we started a candidate gene approach to identify the gene(s) that affect(s) this parameter. Here, we studied two candidate genes: cathepsin B (CTSB) and cystatin B (CSTB). We amplified and sequenced porcine DNA fragments for these two genes that were used to identify polymorphisms by SSCP and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Four and two alleles were detected at the CTSB and CSTB loci, respectively. Sequencing of the CSTB alleles showed a missense mutation that changes a codon for aspartic acid into a codon for asparagine in exon 3 of the gene. Allele frequencies for the two loci differed among the pig breeds studied (Large White, Landrace, Duroc, Belgian Landrace, Hampshire, Piétrain, Meishan, Cinta Senese, Casertana, Calabrese and Nero di Sicilia). Linkage, somatic cell hybrid panel and radiation hybrid panel analyses assigned CTSB to porcine chromosome (Sscr) 14 and CSTB to Sscr 13. The markers identified at the CTSB and CSTB loci were used in association studies with several traits of economic importance including parameters that may indicate the suitability of pig meat to produce dry-cured hams. Significant associations were observed between CTSB and back-fat thickness and between CSTB and average daily gain. In this study, cathepsin B activity was not associated with the polymorphisms identified at the CTSB and CSTB loci.     

The Asp298Asn missense mutation in the porcine melanocortin-4 receptor ( MC4R) gene can be used to affect growth and carcass traits without an effect on meat quality

A promising tool to improve daily gain in pigs is the missense mutation (Asp298Asn) in the melanocortin-4 receptor (MC4R) gene, especially in the Belgian pig industry where the slow-growing Piétrain breed is very frequently used as the sire breed. The MC4R is expressed in the appetite-regulating region of the brain where it regulates feed intake and energy balance. The mutation has been associated with differences in fatness, daily gain and feed intake. However, less information on the correlated effects on meat quality is available. In order to evaluate the influence of the MC4R mutation on carcass and meat quality parameters, a total of 1155 pigs of a four-way cross were slaughtered at an average live weight of 109 kg, and data about daily live-weight gain, carcass and meat quality were collected. Allelic frequencies were 0.69 for the G-allele (298Asp variant or well-conserved variant) and 0.31 for the A-allele (298Asn variant or the mutated variant). Barrows and gilts were almost equally distributed in this population with, respectively, 49.9% and 50.1%. Moreover, independent of this mutation, the relationship between average daily gain (ADG) and carcass on the one hand and meat quality traits on the other hand was evaluated in this population. A significant positive influence of the MC4R mutation on ADG (P < 0.001) was found, accompanied by a higher fat thickness (P < 0.05) and a lower carcass lean meat content (P < 0.01), whereas muscle thickness and carcass conformation traits were not affected. The effects on meat quality traits were not significant, except for a lower shear force (P = 0.054) and a higher intramuscular fat content (P = 0.052) in AA animals. In the longissimus, pH and pork quality meter (PQM) values were not influenced, and effects on drip loss and colour were not apparent. Residual correlation coefficients between ADG and carcass lean meat content on the one hand and meat quality traits on the other hand were generally very low (|r|>0.1). Higher ADG, higher carcass fat thickness and lower carcass lean meat content were correlated with slightly lower shear force values (|r|～0.1, P < 0.05). In conclusion, in the studied population, the Asp298Asn mutation in the MC4R gene was associated with improved daily gain, higher carcass fatness and almost no effect on meat quality traits.