Genetic aspects concerning drip loss and water-holding capacity of porcine meat

Effects of Age on Compounds, Metabolites and Meat Quality in Beijing-You Chicken Breast Meat

The physical properties, free amino acids, and metabolites of Beijing-You chicken (BYC) breast meat aged 90, 120, and 150 days were analyzed to investigate the flavor changes with age. The shear force and intramuscular fat increased from 90 to 120 days significantly. The contents of total free amino acids and essential amino acids decreased from 90 to 120 days significantly. No significant differences were detected between 120 and 150 days. The contents of sweet amino acids, bitter amino acids, and umami amino acids showed no significant differences between different ages. In addition, GC-MS and LC-MS were integrated for metabolite detection in breast meat. A total of 128, 142, and 88 differential metabolites were identified in the comparison groups of 120 d vs. 90 d, 150 d vs. 90 d, and 150 d vs. 120 d. Amino acids and lipids were the main differential metabolites. The pathway analysis showed that arginine biosynthesis, histidine metabolism, purine metabolism, and cysteine and methionine metabolism were the main pathways involved in flavor formation during BYC development. It was also found that the metabolites associated with flavor, such as methionine, cysteine, glucose, anserine, arachidonic acid, and glycerol 1-phosphate, were significantly affected by age.

Reduced water-holding capacity of beef during refrigeration is associated within creased heme oxygenase 1 expression, oxidative stress and ferroptosis

Low molecular weight iron (LMW-Fe)-mediated oxidative stress from heme degradation may reduce beef water-holding capacity (WHC). However, the underlying mechanism of heme degradation is still unknown. In the present study, we assessed the WHC, tissue morphology, reactive oxygen species (ROS), apoptosis, heme oxygenase(HMOX) 1 expression, and ferroptosis characteristics of beef chilled at 4 °C for 6 days. Results showed that water loss increased and WHC decreased during beef storage (P < 0.05). Increased protein and mRNA expression of HMOX1 promoted the decomposition of heme and facilitated the liberation of iron ions (P < 0.05), and excess LMW-Fe was associated with ROS formation, depletion of glutathione, and inhibition of glutathione peroxidase 4 activity (P < 0.05). Muscle tissue showed typical features of ferroptosis, including expression of ferroptosis-related genes, malondialdehyde accumulation, and structural damage to mitochondria (P < 0.05). It was also found that HMOX1 and the heme pathway-mediated ferroptosis were associated with structural changes in myofibrils and reduced WHC in chilled beef.

Expression levels of the filaggrin-2 (FLG2) in relation to drip loss in pigs

Objective

The aim of this study was to investigate the expression level of filaggrin-2 (FLG2) in correlation with drip loss.

Methods

The muscle samples were randomly taken from a local meat supplier. Samples were taken from Longissimus lumborum muscles to evaluate the drip loss (n = 100). Five muscles per group (low and high drip loss) were selected to evaluate FLG2 mRNA and protein expression levels.

Results

mRNA of FLG2 gene was not significantly different in pigs with different levels of drip loss (p>0.05). Statistical analysis revealed that FLG2 protein expression levels were significantly different between the drip loss groups. Western blot revealed that the high drip loss group had higher FLG2 protein expression level than the low drip loss group (p<0.001). Moreover, immunohistochemistry revealed the high signal intensity was on the muscle cell membrane and cytoplasm.

Conclusion

FLG2 protein might play roles in drip loss of pork and will provide the basis for information to improving meat quality traits in pigs.

Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

Water holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

The Effect of Dietary Lycopene Supplementation on Drip Loss during Storage of Lamb Meat by iTRAQ Analysis

This study was designed to investigate the impact of dietary lycopene (antioxidant extracted from tomato) supplementation on postmortem antioxidant capacity, drip loss and protein expression profiles of lamb meat during storage. Thirty male Hu lambs were randomly divided into three treatment groups and housed in individual pens and received 0, 200 or 400 mg·kg⁻¹ lycopene in their diet, respectively. All lambs were slaughtered after 3 months of fattening, and the longissimus thoracis (LT) muscle was collected for analyses. The results indicated that drip loss of LT muscle increased with storage days (P < 0.05). After storage for 7 days, significantly lower drip loss of meat was found in fed the lycopene-supplemented diet (P < 0.05). Dietary lycopene supplementation increased the activity of antioxidant enzymes (total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT)) (P < 0.05) and decreased the thiobarbituric acid reactive substance (TBARS) and carbonyl contents (P < 0.05). During the storage period (days 0, 5 and 7), a number of differentially abundant proteins (DAPs), including oxidases, metabolic enzymes, calcium channels and structural proteins, were identified based on iTRAQ data, with roles predominantly in carbon metabolism, oxidative phosphorylation, cardiac muscle contraction and proteasome pathways, and which contribute to decreased drip loss of lamb meat during storage. It can be concluded that dietary lycopene supplementation increased antioxidant capacity after slaughter, and the decreased drip loss during postmortem storage might occur by changing the expression of proteins related to enzyme activity and cellular structure in lamb muscle.

Association of a polymorphism in exon 3 of the IGF1R gene with growth, body size, slaughter and meat quality traits in Colored Polish Merino sheep

This study aimed to genotype the polymorphism (c.654G > A) in the exon 3 of the insulin-like growth factor 1 receptor gene (IGF1R) and to analyze its association with growth, body size, slaughter and meat quality traits in Colored Polish Merino sheep. In total, 67 traits were analyzed. The IGF1R polymorphism was genotyped using the polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) method. The MIXED procedure of the SAS software was used to assess the genotypic effects of the polymorphism (c.654G > A) on production traits of interest. The IGF1R c.654G > A genotypes were found to have a significant effect on the average daily gain between the 56th and 78th day of life, cold carcass, leg part, leg cut, fore shank, and kidney weights, as well as eye of loin depth, intramuscular fat content, and water-holding capacity of meat. The results suggest that the studied polymorphism may provide useful information for marker-assisted selection for increased meat performance in Colored Polish Merino sheep.

Analysis of FTO and PLIN2 Polymorphisms in Relation to Carcass and Meat Quality Traits in Pigs

The aim of this study was to analyze the association of polymorphisms in alpha-ketoglutarate-dependent dioxygenase (FTO) and perilipin 2 (PLIN2) genes with carcass and meat quality traits in pigs reared in Poland. The research covered 578 sows that belong to the following breeds: Duroc, Hampshire, Polish Landrace, Pietrain, Puławska and Polish Large White. FTO (FM244720:g.400C>G) and PLIN2 (GU461317:g.98G>A) genes variants were determined by means of PCR-RFLP and ACRS-PCR methods respectively. Association between individual genotypes and analyzed traits was calculated by means of GLM procedure for Polish Landrace, Polish Large White and Puławska breeds separately and for all six breeds together in case of FTO gene. The results showed that FTO variants were associated with weight of loin without backfat and skin (WL), loin eye area (AL) and meat percentage (MP) in Polish Large White (P≤0.05), mean backfat thickness from 5 measurements (BFT) and pH measured 45 min after slaughter in m. longissimus dorsi (pH24 ld) as well as with water holding-capacity (WHC) in Puławska breed (P≤0.01). PLIN2 genotypes, however were correlated with WL and height of the loin eye (HL) in Polish Large White and Puławska (P≤0.05), AL in Polish Large White (P≤0.01) as well as luminosity (L*) in Puławska (P≤0.05) pigs. We observed most consistent relationships of PLIN2 SNP with intramuscular fat content (IMF) and WHC. In 3 analyzed breeds GG genotype was connected with highest values of these traits (P≤0.05).

Effects of a Novel p.A41P Mutation in the Swine Myogenic factor 5(MYF5) Gene on Protein Stabilizing, Muscle Fiber Characteristics and Meat Quality

Myogenic factor 5 (MYF5) plays an important role in regulating skeletal muscle fiber characteristics, consequently affecting meat production and quality. We identified a novel p.A41P mutation in exon1 of the porcine MYF5 gene by direct sequencing. The mutation was predicted to be destabilizing in protein structure based on the resultant amino acid substitution. We estimated the significant substitution effect of p.A41P on the energy stabilization of Myf5 protein structure. Then, we demonstrated that the mutation in Yorkshire population significantly affected muscle fiber type I composition (p<0.05), loin-eye area of lean meat content (p<0.05) and filter-fluid uptake of meat quality (p<0.01). Furthermore, dominant effects significantly influenced total muscle fiber number (p<0.05). This study suggests that the novel p.A41P mutation in porcine MYF5 may be a valuable genetic marker to affect the muscle fiber characteristics and consequently improve meat production quality and quantity.

Effects of maternal parity on the pork quality traits of progeny

This study aimed to identify the influence of sow parity on the meat quality of progeny. A total of 656 progeny from 196 sows were categorised into three different groups based on parity: stage 1 (gilt), 2 (second to fourth parities), and 3 (over fifth parity). According to the significant differences between the parity stage groups in the multiple meat quality properties (P < 0.05), the parity stage 1 had higher muscle pH and lower drip loss in meat quality traits and showed smaller area composition of type IIb muscle fibres in muscle fibre characteristics than the other older groups. Moreover, the parity stage 1 group had significantly higher springiness, adhesiveness and chewiness (P < 0.001), whereas the stage 3 group showed relatively lower cohesiveness (P < 0.05) in the meat texture properties. The principal component analysis displayed more distance between stage 1 and other two groups than the distance between stage 2 and 3. Therefore, we suggest that maternal parity may affect pork quality in progeny and the younger stage group could have better meat quality than the older group.

Genome-wide association studies, meta-analyses and derived gene network for meat quality and carcass traits in pigs

A large number of quantitative trait loci (QTL) for meat quality and carcass traits has been reported in pigs over the past 20 years. However, few QTL have been validated and the biological meaning of the genes associated to these QTL has been underexploited. In this context, a meta-analysis was performed to compare the significant markers with meta-QTL previously reported in literature. Genome association studies were performed for 12 traits, from which 144 SNPs were found out to be significant (P < 0.05). They were validated in the meta-analysis and used to build the Association Weight Matrix, a matrix framework employed to investigate co-association of pairwise SNP across phenotypes enabling to derive a gene network. A total of 45 genes were selected from the Association Weight Matrix analysis, from which 25 significant transcription factors were identified and used to construct the networks associated to meat quality and carcass traits. These networks allowed the identification of key transcription factors, such as SOX5 and NKX2–5, gene–gene interactions (e.g. ATP5A1, JPH1, DPT and NEDD4) and pathways related to the regulation of adipose tissue metabolism and skeletal muscle development. Validated SNPs and knowledge of key genes driving these important industry traits might assist future strategies in pig breeding.

Elucidating a molecular mechanism that the deterioration of porcine meat quality responds to increased cortisol based on transcriptome sequencing

Stress response is tightly linked to meat quality. The current understanding of the intrinsic mechanism of meat deterioration under stress is limited. Here, male piglets were randomly assigned to cortisol and control groups. Our results showed that when serum cortisol level was significantly increased, the meat color at 1 h postmortem, muscle bundle ratio, apoptosis rate, and gene expression levels of calcium channel and cell apoptosis including SERCA1, IP3R1, BAX, Bcl-2, and Caspase-3, were notably increased. However, the value of drip loss at 24 h postmortem and serum CK were significantly decreased. Additionally, a large number of differentially expressed genes (DEGs) in GC regulation mechanism were screened out using transcriptome sequencing technology. A total of 223 DEGs were found, including 80 up-regulated genes and 143 down-regulated genes. A total of 204 genes were enriched in GO terms, and 140 genes annotated into in KEGG database. Numerous genes were primarily involved in defense, inflammatory and wound responses. This study not only identifies important genes and signalling pathways that may affect the meat quality but also offers a reference for breeding and feeding management to provide consumers with better quality pork products.

Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs

The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein "phosphoglycerate mutase 2" and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes.

Polymorphisms of the porcine cathepsins, growth hormone-releasing hormone and leptin receptor genes and their association with meat quality traits in Ukrainian Large White breed

Cathepsins, growth hormone-releasing hormone (GHRH) and leptin receptor (LEPR) genes have been receiving increasing attention as potential markers for meat quality and pig performance traits. This study investigated the allele variants in four cathepsin genes (CTSB, CTSK, CTSL, CTSS), GHRH and LEPR in pure-bred Ukrainian Large White pigs and evaluated effects of the allele variants on meat quality characteristics. The study was conducted on 72 pigs. Genotyping was performed using PCR-RFLP technique. Meat quality characteristics analysed were intramuscular fat content, tenderness, total water content, ultimate pH, crude protein and ashes. A medium level of heterozygosity values was established for GHRH and LEPR genes which corresponded to very high levels of informativeness indexes. Cathepsins CTSL, CTSB and CTSK had a low level of heterozygosity, and CTSS did not segregate in this breed. Association studies established that intramuscular fat content and tenderness were affected by the allele variance in GHRH and LEPR but not by CTSB and CTSL genes. The GHRH results could be particularly relevant for the production of lean prime cuts as the A allele is associated with both, a lower meat fat content and better tenderness values, which are two attributes highly regarded by consumers. Results of this study suggest that selective breeding towards GHRH/AA genotype would be particularly useful for improving meat quality characteristics in the production systems involving lean Large White lines, which typically have less than 2 % intramuscular fat content.

Proteomic analysis of goat Longissimus dorsi muscles with different drip loss values related to meat quality traits

Longissimus dorsi muscles from 3 goat species were assigned to high and low drip loss groups. Physio-chemical properties, sarcomere length, and proteome profiles were investigated. The high drip loss group had lower pH, higher brightness, and higher shear force values, and shorter sarcomere lengths than the low drip loss group. 22 differential proteins were identified between high and low loss groups. α-Enolase, NADH dehydrogenase, pyruvate dehydrogenase E1, HSP27, superoxide dismutase, peroxiredoxin-2, myosin, and the myosin light chain were among these proteins, which were metabolic enzymes, stress response factors, and structural proteins that affected glycolysis, oxidation, and muscle contraction. Drip loss was probably produced via proteins involved in glycolysis, oxidation, and muscle contraction.

Comparative Proteomic Profiling of Divergent Phenotypes for Water Holding Capacity across the Post Mortem Ageing Period in Porcine Muscle Exudate

Two dimensional Difference Gel Electrophoresis (2-D DIGE) and mass spectrometry were applied to investigate the changes in metabolic proteins that occur over a seven day (day 1, 3 and 7) post mortem ageing period in porcine centrifugal exudate from divergent meat quality phenotypes. The objectives of the research were to enhance our understanding of the phenotype (water holding capacity) and search for biomarkers of this economically significant pork quality attribute. Major changes in protein abundance across nine phenotype-by-time conditions were observed. Proteomic patterns were dominated by post mortem ageing timepoint. Using a machine learning algorithm (l1-regularized logistic regression), a model was derived with the ability to discriminate between high drip and low drip phenotypes using a subset of 25 proteins with an accuracy of 63%. Models discriminating between divergent phenotypes with accuracy of 72% and 73% were also derived comparing respectively, high drip plus intermediate phenotype (considered as one phenotype) versus low drip and comparing low drip plus intermediate phenotype (considered as one phenotype) versus high drip. In all comparisons, the general classes of discriminatory proteins identified include metabolic enzymes, stress response, transport and structural proteins. In this research we have enhanced our understanding of the protein related processes underpinning this phenotype and provided strong data to work toward development of protein biomarkers for water holding capacity.

Association of eight EST-derived SNPs with carcass and meat quality traits in pigs

The identification of genetic markers associated with important economic traits is fundamental to improving the productivity and quality of livestock. In this investigation, we searched for 177 expressed sequence tags (ESTs) putatively involved in meat quality from the available pig EST database, and detected eight single nucleotide polymorphisms (SNPs) in eight ESTs. We investigated the associations of these SNPs with 18 carcass and meat quality traits in a Landrace × Lantang F2 resource population (n = 257). Association analysis revealed that seven SNPs (except E42) were associated with some of the carcass- and meat quality-related traits. Particularly, significant associations of three SNPs (E53, E82, and E36) with backfat thickness traits were observed. Further, the genetic effects of E53 on four live backfat thickness traits were validated in an independent population (n = 221). More investigations about E53 sequence characteristics were performed, i.e., radiation hybrid (RH) mapping, 3'-RACE, and screening analysis of the positive BAC clones. Our research identified the genetic effects of eight EST-derived SNPs on carcass and meat quality traits, and suggested that E53 may be a useful marker for live backfat thickness traits in pig breeding programs.

A Whole Genome Association Study on Meat Quality Traits Using High Density SNP Chips in a Cross between Korean Native Pig and Landrace

A whole genome association (WGA) study was performed to detect significant polymorphisms for meat quality traits in an F₂ cross population (N = 478) that were generated with Korean native pig sires and Landrace dams in National Livestock Research Institute, Songwhan, Korea. The animals were genotyped using Illumina porcine 60k SNP beadchips, in which a set of 46,865 SNPs were available for the WGA analyses on ten carcass quality traits; live weight, crude protein, crude lipids, crude ash, water holding capacity, drip loss, shear force, CIE L, CIE a and CIE b. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model, after adjusting for sex, sire and slaughter stage as fixed effects. With the significant SNPs for each trait (p<0.001), a stepwise regression procedure was applied to determine the best set of SNPs with the additive and/or dominance effects. A total of 106 SNPs, or quantitative trait loci (QTL) were detected, and about 32 to 66% of the total phenotypic variation was explained by the significant SNPs for each trait. The QTL were identified in most porcine chromosomes (SSCs), in which majority of the QTL were detected in SSCs 1, 2, 12, 13, 14 and 16. Several QTL clusters were identified on SSCs 12, 16 and 17, and a cluster of QTL influencing crude protein, crude lipid, drip loss, shear force, CIE a and CIE b were located between 20 and 29 Mb of SSC12. A pleiotropic QTL for drip loss, CIE L and CIE b was also detected on SSC16. These QTL need to be validated in commercial pig populations for genetic improvement in meat quality via marker-assisted selection.

2D DIGE proteomic analysis of early post mortem muscle exudate highlights the importance of the stress response for improved water-holding capacity of fresh pork meat

Variation in water-holding capacity (WHC), which presents a major economic burden to the swine industry, is considered to be underpinned by variation at a molecular and biochemical level. High-resolution 2D DIGE followed by MS analysis and Western blot were used to unravel the proteome of muscle exudate, collected following centrifugation, in the pH 4-7 range. A first 2DE-based protein map of this substrate was produced where 89 spots were successfully characterised. Two phenotypes divergent for WHC plus one intermediate were compared with a view to deciphering the biochemical processes impacting on variation in WHC. Twenty spots were observed to be altered across the phenotypes. Of these, 14 represented sixteen proteins including metabolic enzymes, stress response proteins and structural proteins. Triosephosphate isomerase and transferrin showed a major difference between the two extreme phenotypes, and may have potential as biological markers for WHC prediction. Several members of the HSPs family were highlighted. This proteomic study makes an important contribution towards a more detailed molecular view of the processes behind WHC and will provide a valuable resource for future investigations.

SNPs detection in DHPS-WDR83 overlapping genes mapping on porcine chromosome 2 in a QTL region for meat pH

Background

The pH is an important parameter influencing technological quality of pig meat, a trait affected by environmental and genetic factors. Several quantitative trait loci associated to meat pH are described on PigQTL database but only two genes influencing this parameter have been so far detected: Ryanodine receptor 1 and Protein kinase, AMP-activated, gamma 3 non-catalytic subunit. To search for genes influencing meat pH we analyzed genomic regions with quantitative effect on this trait in order to detect SNPs to use for an association study.

Results

The expressed sequences mapping on porcine chromosomes 1, 2, 3 in regions associated to pork pH were searched in silico to find SNPs. 356 out of 617 detected SNPs were used to genotype Italian Large White pigs and to perform an association analysis with meat pH values recorded in semimembranosus muscle at about 1 hour (pH1) and 24 hours (pHu) post mortem.

The results of the analysis showed that 5 markers mapping on chromosomes 1 or 3 were associated with pH1 and 10 markers mapping on chromosomes 1 or 2 were associated with pHu. After False Discovery Rate correction only one SNP mapping on chromosome 2 was confirmed to be associated to pHu. This polymorphism was located in the 3’UTR of two partly overlapping genes, Deoxyhypusine synthase (DHPS) and WD repeat domain 83 (WDR83). The overlapping of the 3’UTRs allows the co-regulation of mRNAs stability by a cis-natural antisense transcript method of regulation. DHPS catalyzes the first step in hypusine formation, a unique amino acid formed by the posttranslational modification of the protein eukaryotic translation initiation factor 5A in a specific lysine residue. WDR83 has an important role in the modulation of a cascade of genes involved in cellular hypoxia defense by intensifying the glycolytic pathway and, theoretically, the meat pH value.

Conclusions

The involvement of the SNP detected in the DHPS/WDR83 genes on meat pH phenotypic variability and their functional role are suggestive of molecular and biological processes related to glycolysis increase during post-mortem phase. This finding, after validation, can be applied to identify new biomarkers to be used to improve pig meat quality.

A genetical genomics approach reveals new candidates and confirms known candidate genes for drip loss in a porcine resource population

In this study lean meat water-holding capacity (WHC) of a Duroc × Pietrain (DuPi) resource population with corresponding genotypes and transcriptomes was investigated using genetical genomics. WHC was characterized by drip loss measured in M. longissimus dorsi. The 60K Illumina SNP chips identified genotypes of 169 F2 DuPi animals. Whole-genome transcriptomes of muscle samples were available for 132 F2 animals using the Affymetrix 24K GeneChip® Porcine Genome Array. Performing genome-wide association studies of transcriptional profiles, which are correlated with phenotypes, allows elucidation of cis- and trans-regulation. Expression levels of 1,228 genes were significantly correlated with drip loss and were further analyzed for enrichment of functional annotation groups as defined by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. A hypergeometric gene set enrichment test was performed and revealed glycolysis/glyconeogenesis, pentose phosphate pathway, and pyruvate metabolism as the most promising pathways. For 267 selected transcripts, expression quantitative trait loci (eQTL) analysis was performed and revealed a total of 1,541 significant associations. Because of positional accordance of the gene underlying transcript and the eQTL location, it was possible to identify eight eQTL that can be assumed to be cis-regulated. Comparing the results of gene set enrichment and the eQTL detection tests, molecular networks and potential candidate genes, which seemed to play key roles in the expression of WHC, were detected. The α-1-microglobulin/bikunin precursor (AMBP) gene was assumed to be cis-regulated and was part of the glycolysis pathway. This approach supports the identification of trait-associated SNPs and the further biological understanding of complex traits.

Molecular characterization, expression analysis and association study with meat quality traits of porcine TTID gene

Titin immunoglobulin domain protein (TTID) is localized to the Z-line and binds to alpha-actinin, gamma-filamin. It plays an indispensable role in stabilization and anchorage of thin filaments. In this study, the full-length cDNA sequence was isolated by the reverse transcription-polymerase chain reaction (RT-PCR) and the rapid amplification of cDNA ends (RACE). The TTID sequence was deposited into the Genbank under the accession no. DQ157551. The deduced protein of 499 amino acids showed 93 % identity to the corresponding human and rat sequence. Semi-quantitative RT-PCR revealed porcine TTID gene was expressed highest level in skeletal muscle, at second-highest level in the heart, but only low expression in the fat was detected. Bioinformatics analysis shows the molecular weight of the TTID protein is 55.747 kD with a PI of 9.26. It contains the protein function site of two potential Ig-like domain profiles, six N-myristoylation sites, six potential Casein kinase II phosphorylation sites, eight protein kinase C phosphorylation sites, three N-glycosylation sites, a tyrosine kinase phosphorylation site and a cell attachment sequence site. No putative base substitution was detected in the coding region by comparing sequences of Large White, Landrace and Meishan pig breeds. A T978C single nucleotide polymorphism in the intron 6 of porcine TTID gene was detected by a HinfI PCR-restriction fragment length polymorphism. Study showed allele frequency differences among four purebreds. Association of the genotypes with meat quality traits showed that different genotypes of porcine TTID gene were significantly associated with meat pH (m.Biceps Femoris) (P < 0.05), meat color value (m.longissimus Dorsi) (P < 0.05) and Water Moisture (m.longissimus Dorsi) (P < 0.05).

Mapeamento de QTL nos cromossomos 1, 2, 3, 12, 14, 15 e X em suínos: características de carcaça e qualidade de carne

A realização do presente estudo teve como objetivo mapear Quantitative Trait Loci (QTL) de carcaça e qualidade de carne em uma população F2 de suínos desenvolvida pelo cruzamento de dois reprodutores da raça brasileira Piau com 18 fêmeas comerciais (Landrace x Large White x Pietrain). O mapa de ligação para essa população foi construído após a genotipagem de 684 animais para 35 marcadores microssatélites. Os dados foram analisados pelo mapeamento por intervalo usando-se sexo, lote e genótipo halotano como efeitos fixos e peso de carcaça ao abate, peso da carcaça direita e idade ao abate como covariáveis. Um total de 18 QTLs foi encontrado; os QTLs para maior espessura de toucinho na região da copa, na linha dorsolombar, e a perda por cozimento foram significativos em nível de 5% genômico. A característica espessura de toucinho foi essencialmente associada aos alelos da raça Piau, conhecido como porco tipo banha. As informações dos QTLs significativos encontrados servem para futuros estudos de mapeamento fino para identificação de genes a serem usados em conjunto com os métodos tradicionais de seleção, para melhorar a eficiência dos programas de melhoramento, assim como prover informação acerca da fisiologia envolvida no desenvolvimento das características quantitativas dos suínos.

Association and expression quantitative trait loci (eQTL) analysis of porcine AMBP, GC and PPP1R3B genes with meat quality traits

The aim of this research was to screen polymorphism and to perform association study of porcine AMBP (alpha-1-microglobulin/bikunin precursor), GC (group-specific component protein) and PPP1R3B (protein phosphatase 1, regulatory (inhibitor) subunit 3B) genes with meat quality traits as well as to unravel the transcriptional regulation of these genes by expression QTL (eQTL) study. For this purpose, Duroc × Pietrain F2 resource population (DuPi; n = 313) and a commercial breed Pietrain (Pi; n = 110) were used for association and only DuPi for expression and eQTL study. A SNP was identified in the genes AMBP (g.22229C>T), GC (g.398C>T) and PPP1R3B (c.479A>G), respectively. In DuPi SNP of AMBP was associated (P < 0.05) with meat colour, pH(1L), pH(24L), pH(24H) and conductivity(24L); SNP of GC showed tendency to association (P < 0.10) with pH24H, conductivity(1L) and thawing loss, and SNP of PPP1R3B was associated (P < 0.05) with meat colour, pH(1L), pH(24L), pH(24H) and shear force. In Pi SNPs of AMBP and GC was associated with pH(24H) and PPP1R3B SNP was associated with pH(24L). The mRNA levels in Longissimus dorsi muscle tissue of these three genes were evaluated by using qRT-PCR to identify association between gene expression and meat quality traits as well as to analyse eQTL. The mRNA expression of PPP1R3B associated with pH(24L) (P < 0.05). Expression of these three genes was higher in animals with low pH of muscle. Linkage analysis using QTL Express revealed ten trans-regulated eQTL on seven porcine autosomes. Suggestive eQTL [P < 0.05, CW (chromosome-wide)] were found for PPP1R3B on SSC3 and 13. These results revealed that genetic variation and gene expression of these genes are associated with the meat quality traits. These three genes could influence meat quality and could be potential positional, physiological and functional candidate gene for meat quality traits in pigs. However, the analysis of eQTL also suggested that we need to consider additional genes encoding for transcription factors (TF), via fine-mapping underlying the eQTL peaks, in order to understand interaction among these genes.

Epistatic QTL pairs associated with meat quality and carcass composition traits in a porcine Duroc × Pietrain population

Background

Quantitative trait loci (QTL) analyses in pig have revealed numerous individual QTL affecting growth, carcass composition, reproduction and meat quality, indicating a complex genetic architecture. In general, statistical QTL models consider only additive and dominance effects and identification of epistatic effects in livestock is not yet widespread. The aim of this study was to identify and characterize epistatic effects between common and novel QTL regions for carcass composition and meat quality traits in pig.

Methods

Five hundred and eighty five F₂ pigs from a Duroc × Pietrain resource population were genotyped using 131 genetic markers (microsatellites and SNP) spread over the 18 pig autosomes. Phenotypic information for 26 carcass composition and meat quality traits was available for all F₂ animals. Linkage analysis was performed in a two-step procedure using a maximum likelihood approach implemented in the QxPak program.

Results

A number of interacting QTL was observed for different traits, leading to the identification of a variety of networks among chromosomal regions throughout the porcine genome. We distinguished 17 epistatic QTL pairs for carcass composition and 39 for meat quality traits. These interacting QTL pairs explained up to 8% of the phenotypic variance.

Conclusions

Our findings demonstrate the significance of epistasis in pigs. We have revealed evidence for epistatic relationships between different chromosomal regions, confirmed known QTL loci and connected regions reported in other studies. Considering interactions between loci allowed us to identify several novel QTL and trait-specific relationships of loci within and across chromosomes.

Molecular characterization of five porcine candidate genes for drip loss in pork

Drip loss is the loss of fluid from a piece of meat without mechanical force and represents an important meat quality trait. Previous work revealed a quantitative trait locus (QTL) for drip loss in pork in an experimental Duroc x Pietrain (DUPI) F2 family on SSC 5. Based on functional data indicating their possible involvement in water holding capacity and their expression in skeletal muscle, we selected five positional candidates (ACO2, ADSL, CBY1, KCNJ4, PLA2AG6) out of 130 predicted genes in the QTL interval for further analysis. We performed a mutation analysis of all coding exons and discovered 204 polymorphisms. We genotyped 39 single nucleotide polymorphisms (SNPs) in 192 Pietrain pigs with extreme drip loss phenotypes and detected a possible association with drip loss for one non-coding SNP in the ADSL gene (ss107793818, p(raw) = 0.021). Correspondingly, ADSL diplotypes were associated with drip loss and pH1 of M. longissimus dorsi. However, after correction for multiple testing, none of the tested SNPs were significantly associated with drip loss. One possible explanation for these results is that one of the QTL-alleles from the experimental DUPI family may be fixed or nearly fixed in the tested Pietrain population.

Identification of suitable reference genes for gene expression analysis of pork meat quality and analysis of candidate genes associated with the trait drip loss

The aim of this study was to identify a set of stably expressed endogenous control genes for quantitative PCR analysis of mRNA expression in the porcine LTL muscle and to subsequently perform expression analysis of potential candidate genes associated with drip loss. Expression stability of seven commonly used reference genes was examined in n=60 pigs from three independent populations of different genetic backgrounds. The genes examined were: ACTB, ATP5G1, B2M, GPX1, RPL4, TBP and YWHAZ. GeNorm analysis of expression stability identified B2M, RPL4 and TBP as consistently stable in each breed examined. Analysis of meat samples divergent for water holding capacity identified positive and negative associations between drip loss and gene expression using B2M, RPL4 and TBP as endogenous controls. Specifically, expression of COL1A1 increased significantly with increasing drip loss while expression of CAST decreased significantly with increasing drip loss. This study therefore indicates the use of B2M, RPL4 and TBP as suitable endogenous controls for gene expression analysis of the porcine LTL muscle. Further study is recommended to identify the detailed roles of COL1A1 and CAST with respect to the development of drip loss.

Functional genomics and genetical genomics approaches towards elucidating networks of genes affecting meat performance in pigs

The benefit of functional genomics is to identify key pathways and functional networks of genes and candidate genes underlying the genetic control of phenotypes. Genetical genomics, i.e. the integration of genetic analysis and expression phenotypes, has the potential to uncover regulatory networks controlling the coordinated expression of genes and to map variation on the level of DNA affecting the mRNA expression. Here we illustrate our own attempts to apply functional genomics and genetical genomics approaches in order to identify functional networks of genes relevant to traits related to meat performance. Expression data of 74 M longissimus dorsi samples obtained using Affymetrix GeneChips were correlated with drip loss and principal components (PCs) with high loadings of meat quality traits. Functional annotation analyses revealed that differences in water holding capacity, early pH decline and ultimate pH were related to the ubiquitin-proteasome system, mitochondrial metabolic pathways and muscle structural aspects. In particular, 1279 genes were correlated with drip loss (P <or= 0.001; q <or= 0.004). Negatively correlated transcripts were enriched in functional categories like extracellular matrix receptor interaction and Ca-signalling. Transcripts with a positive correlation represented oxidative phosphorylation, mitochondrial pathways and transporter activity. A linkage analysis revealed 897 expression QTL (eQTL) with 104 eQTL mapping in QTL regions for water holding capacity including 8 cis eQTL. The reduction of the multi-dimensional data sets of meat performance traits into lower dimensions of PC and the genetical genomics approach of eQTL analysis proved to be appropriate means to detect relevant biological pathways and to experimentally prioritize candidate genes.

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 x 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.

Expression profiling of muscle reveals transcripts differentially expressed in muscle that affect water-holding capacity of pork

To identify biological processes as well as molecular markers for drip loss, a parameter for water holding capacity of meat, the M. longissimus dorsi transcriptomes of six divergent sib pairs were analyzed using Affymetrix Porcine Genome Array. Functional categories of differentially regulated transcripts were determined by single-gene analysis and gene set analysis. The transcripts being up-regulated at high drip loss belong to groups of genes functionally categorized as genes of membrane proteins, signal transduction, cell communication, response to stimulus, and cytoskeleton. Among genes down-regulated with high drip loss, functional groups of oxidoreductase activity, lipid metabolism, and electron transport were identified. Differential regulation of the abundance of transcripts of these biological networks in live muscle affect mortem biochemical processes of meat maturation. Knowledge of this functional link is indicative for the identification of candidate genes for improvement of meat quality.