The influence of litter birth weight phenotype on embryonic and placental development at day 30 of gestation in multiparous purebred Large White sows.

The aim of this study was to understand the intrauterine biological processes associated with the low litter birth weight phenotype in pigs. Analyses were conducted on reproductive data from a purebred Large White maternal line to identify sows (>2 parities) with repeatable high or low litter birth weight phenotype (HLBWP or LLBWP). A total of 40 sows were selected (n = 20 HLBWP and n = 20 LLBWP) and bred with semen from purebred Large White boars of proven fertility. Sows were euthanized on day 28-30 of gestation (day 29.5 ± 0.6) and samples of placenta and embryos collected. Total number of embryos (TNE), embryonic weight (EW), embryonic viability, and crown-rump (CRL) measurements were recorded, along with the ovulation rate (OR) and allantochorionic fluid volume (AFV). No significant difference was detected (P > 0.05) in OR, TNE, and number of viable embryos on day 30 of gestation between the two groups. There was no significant difference in EW (LLBWP: 0.80 ± 0.05 g; HLBWP: 0.88 ± 0.04 g, P = 0.18) or CRL (LLBWP: 21.5 ± 0.7 mm; HLBWP: 21.9 ± 0.68 mm, P = 0.46). Placental development represented by the average AFV was significantly lower in the LLBWP compared to HLBWP (LLBWP: 131 ± 9.82 mL; HLBWP: 149 ± 9.39 mL, P = 0.03). In conclusion, placental development may be the main factor causing lower BW of entire litters in LLBWP sows.

Development and validation of a small SNP panel for feed efficiency in beef cattle.

The objective of this study was to develop and validate a customized cost-effective single nucleotide polymorphism (SNP) panel for genetic improvement of feed efficiency in beef cattle. The SNPs identified in previous association studies and through extensive analysis of candidate genomic regions and genes, were screened for their functional impact and allele frequency in Angus and Hereford breeds used as validation candidates for the panel. Association analyses were performed on genotypes of 159 SNPs from new samples of Angus (n = 160), Hereford (n = 329), and Angus-Hereford crossbred (n = 382) cattle using allele substitution and genotypic models in ASReml. Genomic heritabilities were estimated for feed efficiency traits using the full set of SNPs, SNPs associated with at least one of the traits (at P ≤ 0.05 and P < 0.10), as well as the Illumina bovine 50K representing a widely used commercial genotyping panel. A total of 63 SNPs within 43 genes showed association (P ≤ 0.05) with at least one trait. The minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI) and/or RFI adjusted for backfat (RFIf), whereas minor alleles of SNPs within MKI67 gene were associated with increasing effects on RFI and RFIf. Additionally, the minor allele of rs137400016 SNP within CNTFR was associated with increasing average daily gain (ADG). The SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects whereas other SNPs located in SMARCAL1, ANXA2, CACNA1G, and PHYHIPL genes showed additive effects on RFI and RFIf. Gene enrichment analysis indicated that gland development, as well as ion and cation transport are important physiological mechanisms contributing to variation in feed efficiency traits. The study revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTFR, OSMR, and GHR genes. Genomic heritability using the 63 significant (P ≤ 0.05) SNPs was 0.09, 0.09, 0.13, 0.05, 0.05, and 0.07 for ADG, dry matter intake, midpoint metabolic weight, RFI, RFIf, and backfat, respectively. These SNPs contributed to genetic variation in the studied traits and thus can potentially be used or tested to generate cost-effective molecular breeding values for feed efficiency in beef cattle.

Coadministration of the Campylobacter jejuni N-Glycan-Based Vaccine with Probiotics Improves Vaccine Performance in Broiler Chickens.

Source attribution studies report that the consumption of contaminated poultry is the primary source for acquiring human campylobacteriosis. Oral administration of an engineered Escherichia coli strain expressing the Campylobacter jejuni N-glycan reduces bacterial colonization in specific-pathogen-free leghorn chickens, but only a fraction of birds respond to vaccination. Optimization of the vaccine for commercial broiler chickens has great potential to prevent the entry of the pathogen into the food chain. Here, we tested the same vaccination approach in broiler chickens and observed similar efficacies in pathogen load reduction, stimulation of the host IgY response, the lack of C. jejuni resistance development, uniformity in microbial gut composition, and the bimodal response to treatment. Gut microbiota analysis of leghorn and broiler vaccine responders identified one member of Clostridiales cluster XIVa, Anaerosporobacter mobilis, that was significantly more abundant in responder birds. In broiler chickens, coadministration of the live vaccine with A. mobilis or Lactobacillus reuteri, a commonly used probiotic, resulted in increased vaccine efficacy, antibody responses, and weight gain. To investigate whether the responder-nonresponder effect was due to the selection of a C. jejuni "supercolonizer mutant" with altered phase-variable genes, we analyzed all poly(G)-containing loci of the input strain compared to nonresponder colony isolates and found no evidence of phase state selection. However, untargeted nuclear magnetic resonance (NMR)-based metabolomics identified a potential biomarker negatively correlated with C. jejuni colonization levels that is possibly linked to increased microbial diversity in this subgroup. The comprehensive methods used to examine the bimodality of the vaccine response provide several opportunities to improve the C. jejuni vaccine and the efficacy of any vaccination strategy.IMPORTANCECampylobacter jejuni is a common cause of human diarrheal disease worldwide and is listed by the World Health Organization as a high-priority pathogen. C. jejuni infection typically occurs through the ingestion of contaminated chicken meat, so many efforts are targeted at reducing C. jejuni levels at the source. We previously developed a vaccine that reduces C. jejuni levels in egg-laying chickens. In this study, we improved vaccine performance in meat birds by supplementing the vaccine with probiotics. In addition, we demonstrated that C. jejuni colonization levels in chickens are negatively correlated with the abundance of clostridia, another group of common gut microbes. We describe new methods for vaccine optimization that will assist in improving the C. jejuni vaccine and other vaccines under development.

Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks.

Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, PED outbreaks have become a source of problems in pig producing countries all over the world, causing large economic losses for pig producers. Although the infection in adults is not fatal, in naïve suckling piglets mortality is close to 100%. In this study, we investigated genome-wide differences between dead and recovered suckling piglets from commercial farms after PED outbreaks. Samples from 262 animals (156 dead and 106 recovered) belonging to several commercial lines were collected from five different farms in three different countries (USA, Canada and Germany) and genotyped with the porcine 80K SNP chip. Mean Fst value was calculated in 1-Mb non-overlapping windows between dead and recovered individuals, and the results were normalized to find differences within the comparison. Seven windows with high divergence between dead and recovered were detected-five on chromosome 2, one on chromosome 4 and one on chromosome 15-in total encompassing 152 genes. Several of these genes are either under- or overexpressed in many virus infections, including Coronaviridae (such as SARS-CoV). A total of 32 genes are included in one or more Gene Ontology terms that can be related to PED development, such as Golgi apparatus, as well as mechanisms generally linked to resilience or diarrhea development (cell proliferation, ion transport, ATPase activity). Taken together this information provides a first genomic picture of PEDV resilience in suckling piglets.

Estimation of genetic parameters for traits associated with reproduction, lactation, and efficiency in sows.

Increased milk production due to high litter size, coupled with low feed intake, results in excessive mobilization of sow body reserves during lactation, which can have detrimental effects on future reproductive performance. A possibility to prevent this is to improve sow lactation performance genetically, along with other traits of interest. The aim of this study was to estimate breed-specific genetic parameters (by parity, between parities, and across parities) for traits associated with lactation and reproduction in Yorkshire and Landrace sows. Performance data were available for 2,107 sows with 1 to 3 parities (3,424 farrowings total). Sow back fat, loin depth and BW at farrowing, sow feed intake (SFI), and body weight loss (BWL) during lactation showed moderate heritabilities (0.21 to 0.37) in both breeds, whereas back fat loss (BFL), loin depth loss (LDL), and litter weight gain (LWG) showed low heritabilities (0.12 to 0.18). Among the efficiency traits, sow lactation efficiency showed extremely low heritability (near zero) in Yorkshire sows but a slightly higher (0.05) estimate in Landrace sows, whereas sow residual feed intake (SRFI) and energy balance traits showed moderate heritabilities in both breeds. Genetic correlations indicated that SFI during lactation had strong negative genetic correlations with body resource mobilization traits (BWL, BFL, and LDL; -0.35 to -0.70), and tissue mobilization traits in turn had strong positive genetic correlations with LWG (+0.24 to +0.54; < 0.05). However, SFI did not have a significant genetic correlation with LWG. These genetic correlations suggest that SFI during lactation is predominantly used for reducing sow body tissue losses, rather than for milk production. Estimates of genetic correlations for the same trait measured in parities 1 and 2 ranged from 0.64 to 0.98, which suggests that first and later parities should be treated as genetically different for some traits. Genetic correlations estimated between traits in parities 1 and 2 indicated that BWF and BWL measured in parity 1 can be used as indicator traits for SFI and SRFI measured in parities 1 and 2. In conclusion, traits associated with lactation in sows have a sizable genetic component and show potential for genetic improvement.

Genetic analysis of reproductive traits and antibody response in a PRRS outbreak herd.

Porcine reproductive and respiratory syndrome (PRRS) is the most economically significant disease impacting pig production in North America, Europe, and Asia, causing reproductive losses such as increased rates of stillbirth and mummified piglets. The objective of this study was to explore the genetic basis of host response to the PRRS virus (PRRSV) in a commercial multiplier sow herd before and after a PRRS outbreak, using antibody response and reproductive traits. Reproductive data comprising number born alive (NBA), number alive at 24 h (NA24), number stillborn (NSB), number born mummified (NBM), proportion born dead (PBD), number born dead (NBD), number weaned (NW), and number of mortalities through weaning (MW) of 5,227 litters from 1,967 purebred Landrace sows were used along with a pedigree comprising 2,995 pigs. The PRRS outbreak date was estimated from rolling averages of farrowing traits and was used to split the data into a pre-PRRS phase and a PRRS phase. All 641 sows in the herd during the outbreak were blood sampled 46 d after the estimated outbreak date and were tested for anti-PRRSV IgG using ELISA (sample-to-positive [S/P] ratio). Genetic parameters of traits were estimated separately for the pre-PRRS and PRRS phase data sets. Sows were genotyped using the PorcineSNP60 BeadChip, and genome-wide association studies (GWAS) were performed using method Bayes B. Heritability estimates for reproductive traits ranged from 0.01 (NBM) to 0.12 (NSB) and from 0.01 (MW) to 0.12 (NBD) for the pre-PRRS and PRRS phases, respectively. S/P ratio had heritability (0.45) and strong genetic correlations with most traits, ranging from -0.72 (NBM) to 0.73 (NBA). In the pre-PRRS phase, regions associated with NSB and PBD explained 1.6% and 3% of the genetic variance, respectively. In the PRRS phase, regions associated with NBD, NSB, and S/P ratio explained 0.8%, 11%, and 50.6% of the genetic variance, respectively. For S/P ratio, 2 regions on SSC 7 (SSC7) separated by 100 Mb explained 40% of the genetic variation, including a region encompassing the major histocompatibility complex, which explained 25% of the genetic variance. These results indicate a significant genomic component associated with PRRSV antibody response and NSB in this data set. Also, the high heritability and genetic correlation estimates for S/P ratio during the PRRS phase suggest that S/P ratio could be used as an indicator of the impact of PRRS on reproductive traits.

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.

Genetic and phenotypic parameters for carcass and meat quality traits in commercial crossbred pigs.

Pork quality and carcass characteristics are now being integrated into swine breeding objectives because of their economic value. Understanding the genetic basis for these traits is necessary for this to be accomplished. The objective of this study was to estimate phenotypic and genetic parameters for carcass and meat quality traits in 2 Canadian swine populations. Data from a genomic selection study aimed at improving meat quality with a mating system involving hybrid Landrace × Large White and Duroc pigs were used to estimate heritabilities and phenotypic and genetic correlations among them. Data on 2,100 commercial crossbred pigs for meat quality and carcass traits were recorded with pedigrees compromising 9,439 animals over 15 generations. Significant fixed effects (company, sex, and slaughter batch), covariates (cold carcass weight and slaughter age), and random additive and common litter effects were fitted in the models. A series of pairwise bivariate analyses were implemented in ASReml to estimate phenotypic and genetic parameters. Heritability estimates (±SE) for carcass traits were moderate to high and ranged from 0.22 ± 0.08 for longissimus dorsi muscle area to 0.63 ± 0.04 for trimmed ham weight, except for firmness, which was low. Heritability estimates (±SE) for meat quality traits varied from 0.10 ± 0.04 to 0.39 ± 0.06 for the Minolta b* of ham quadriceps femoris muscle and shear force, respectively. Generally, most of the genetic correlations were significant (P < 0.05) and ranged from low (0.18 ± 0.07) to high (-0.97 ± 0.35). There were high negative genetic correlations between drip loss with pH and shear force and a positive correlation with cooking loss. Genetic correlations between carcass weight (both hot and cold) with carcass marbling were highly positive. It was concluded that selection for increasing primal and subprimal cut weights with better pork quality may be possible. Furthermore, the use of pH is confirmed as an indicator for pork water-holding capacity and cooking loss. The heritabilities of carcass and pork quality traits indicated that they can be improved using traditional breeding methods and genomic selection, respectively. The estimated genetic parameters for carcass and meat quality traits can be incorporated into the breeding programs that emphasize product quality in these Canadian swine populations.

Influence of on-farm production practices on sensory and technological quality characteristics of pork loin.

Quality of pork from pigs raised either traditionally (outdoor access or bedded settings with no sub-therapeutic antibiotics or growth promotants in feed) or conventionally (commercial indoor) was evaluated. Pork loins (m. longissimus thoracis et lumborum, LTL) from four hundred pigs from either traditional or conventional production systems (n=200) fed commercially formulated diets ad libitum were harvested at slaughter. Intramuscular crude fat content and lean color (L* and b*) values were significantly decreased in conventional pork loins. LTL from conventionally-raised pig carcasses showed increased (P<0.05) mean pH, moisture content and reduced cooking loss and shear force values and had increased tenderness and juiciness scores compared to those from traditionally-raised pig carcasses. Results indicated that pork from conventionally raised pigs was superior to that from traditionally raised pigs in terms of tenderness and juiciness, suggesting that consumers may value pork from traditionally raised pigs on the basis of factors other than eating quality and appearance.

Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle.

The candidate gene approach was used to identify genes associated with residual feed intake (RFI) in beef steers. The approach uses prior knowledge of gene functions to predict their biological role in the variation observed in a trait. It is suited to identify genes associated with complex traits where each gene has a relatively small effect. First, positional candidate genes were identified within the genomic positions of previously reported QTL associated with component traits related to RFI such as dry matter intake (DMI), growth, feed conversion ratio (FCR), average daily gain (ADG), and energy balance. Secondly, the positional candidate genes were prioritized into functional candidate genes according to their biological functions and their relationship with the biological processes associated with RFI including carbohydrate, fat and protein metabolism, thermoregulation, immunity and muscle activity. Single nucleotide polymorphisms (SNPs) located within the functional candidate genes were identified using mRNA sequences and prioritized into functional classes such as non-synonymous (nsSNP), synonymous (sSNP) or intronic SNP. A total of 117 nsSNP were considered as functional SNP and genotyped in steers at the University of Alberta ranch in Kinsella. Multiple marker association analysis in ASReml was performed using RFI data obtained from 531 beef steers. Twenty-five SNP were significantly associated with RFI (P < 0.05) accounting for 19.7% of the phenotypic variation. Using SIFT program to predict the effect of the SNP on the function of the corresponding protein, 3 of the 25 SNP were predicted to cause a significant effect on protein function (P < 0.05). One of the 3 SNP was located in the GHR gene and was also associated with a significant effect on the tertiary structure of the GHR protein (P < 0.05) as modeled using SWISSModel software. Least square means for each genotype were estimated and an over-dominance effect was observed for the SNP located in the GHR, CAST, ACAD11 and UGT3A1 genes. In addition, 2 other SNP showed a dominance effect and 3 genes had an additive effect. Gene network analysis performed in Ingenuity pathway analysis (IPA) software (Ingenuity Systems, www.ingenuity.com) indicated that the significant genes were involved in biological pathways such as lipid, protein and energy metabolism, electron transport and membrane signaling. The genes in this study, if validated in other beef cattle populations, may be useful for marker assisted selection for feed efficiency.

Correlations between fat depot traits and fatty acid composition in abdominal subcutaneous adipose tissue and longissimus muscle: results from a White Duroc × Erhualian intercross F2 population.

The aim of this study was to quantify the partial correlation coefficients (r(p)) between fat depot traits (FDT) and the fatty acid composition of abdominal subcutaneous adipose tissue and LM intramuscular fat in 639 F(2) pigs derived from a White Duroc × Chinese Erhualian cross. Fat depot traits are classified into 2 groups: 1 is adipose tissues (abdominal subcutaneous adipose tissue weight, mesenteric adipose tissue weight, perirenal adipose tissue weight, and backfat thickness at 4 locations); the other is LM [intramuscular fat content (IMF) and marbling score]. Correlations of FDT within classification groups were markedly greater (P < 0.001) than those observed between the 2 groups (r(p) = 0.62 vs. 0.26), indicating variability in fat content of muscle is relatively independent of amount of carcass fat. In general, fatter pigs had greater (P < 0.05) proportions of SFA and MUFA, and less PUFA, than leaner pigs. However, the relationships of individual fatty acids with FDT varied. We found that the amounts of some fatty acids regarded as neutral (e.g., stearic acid) or beneficial (e.g., palmitoleic acid and linolenic acid) for human health were associated with smaller amount of adipose tissues, or merely with greater IMF (P < 0.05). Therefore, we conclude that increasing the proportions of these neutral or healthy fatty acids can be achieved without reducing the IMF of LM, which is positively related to eating quality.

A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei).

Bioinformatics and re-sequencing approaches were used for the discovery of sequence polymorphisms in Litopenaeus vannamei. A total of 1221 putative single nucleotide polymorphisms (SNPs) were identified in a pool of individuals from various commercial populations. A set of 211 SNPs were selected for further molecular validation and 88% showed variation in 637 samples representing three commercial breeding lines. An association analysis was performed between these markers and several traits of economic importance for shrimp producers including resistance to three major viral diseases. A small number of SNPs showed associations with test weekly gain, grow-out survival and resistance to Taura Syndrome Virus. Very low levels of linkage disequilibrium were revealed between most SNP pairs, with only 11% of SNPs showing an r(2)-value above 0.10 with at least one other SNP. Comparison of allele frequencies showed small changes over three generations of the breeding programme in one of the commercial breeding populations. This unique SNP resource has the potential to catalyse future studies of genetic dissection of complex traits, tracing relationships in breeding programmes, and monitoring genetic diversity in commercial and wild populations of L. vannamei.

Genes located on a SSC17 meat quality QTL region are associated with growth in outbred pig populations.

The objective of this study was to evaluate the effect of markers developed in eight genes, located in a previously detected meat quality QTL region on SSC17, on growth, fat and meat quality traits collected in commercial pig populations of different genetic backgrounds. The genes had been previously mapped to SSC17 as part of a fine-mapping effort. Association analyses were conducted between each marker and the available phenotypic traits. Results showed that three genes (CTSZ, CSTF1 and C20orf43) were significantly associated with the growth traits. In addition, CTSZ also impacted on meat colour, with the less favourable genotype for growth being associated with darker meat. The differences observed between genotypes were substantial and may be of economic importance to pig producers. These markers may be useful for selecting for faster growth or improved meat quality.

Detailed characterization of the porcine MC4R gene in relation to fatness and growth.

In contrast to the human MC4R gene, where multiple variants have been described, several of which are associated with appetite and obesity, few MC4R variants have been reported in the pig. The most interesting polymorphism reported to date in the pig is p.Asp298Asn, which is significantly associated with variation in growth and fatness traits in most breeds and crosses. However, some reports have seemingly failed to confirm this association. The discrepancy of p.Asp298Asn associations in some pig populations suggested that further discovery of SNPs in MC4R would be useful. Utilizing the recently released pig genome sequence information, we obtained the whole MC4R genome sequence and detected five additional SNPs, a variable (CA)(n) repeat and a C indel in the ISU Berkshire x Yorkshire pig resource family. Linkage disequilibrium (LD) analysis revealed that the additional five SNPs were not in strong LD with p.Asp298Asn, but single marker association analysis indicated that they were significantly (P < 0.05) associated with fatness measures and very highly significantly (P < 0.0001) associated with average daily gain on test (ADGTEST). Three major haplotypes were identified and the subsequent association analyses suggested that the two non-synonymous SNPs had different effects, e.g. p.Arg236His influenced back fat and growth on test while p.Asp298Asn was primarily associated with variation in growth rate in this population. An interaction effect between these two SNPs was found for ADGTEST, which may partly explain some of the previous discrepancies reported for MC4R in different pig populations. Examination of the p.Arg236His polymorphism in populations where the effect of p.Asp298Asn is limited is warranted.

Characterization of the porcine KIT ligand gene: expression analysis, genomic structure, polymorphism detection and association with coat colour traits.

Kit ligand (KITLG) is the ligand for the type III receptor tyrosine kinase KIT. Studies of the KIT/KITLG pathway in a number of mammalian species have shown that it is important for the development of stem cell populations in haematopoietic tissues, germ cells in reproductive organs and the embryonic migrating melanoblasts that give rise to melanocytes. Consequently, mutations in the pathway may result in a range of defects including anaemia, sterility and de-pigmentation. The cDNA sequence of the porcine KITLG gene has been reported previously, and is an attractive candidate locus for moderating coat colour in pigs. In this paper we report the gene structure and physical mapping of the porcine gene. We also report the identification of polymorphisms in the gene, one of which was used to confirm linkage to chromosome 5. Preliminary RNA expression studies using a panel of tissues have shown that in addition to the known variant lacking exon 6, there is alternative splicing of exon 4. However, little evidence was found for the KITLG gene being linked to variation in colour in a Meishan x Large White cross.

Relationships between carcass quality parameters and genetic types.

It is important for the meat industry, including pig farmers and breeding companies, to know the composition of the carcass including the proportions of the different commercial cuts when making decisions on the type of pigs to be produced and marketed. Carcass composition is influenced significantly by the genotype of the animals. The aim of this work was to characterise carcasses from five different pig genotypes, by means of the quantification and comparison of their physical composition. Carcasses from 500 gilts from five different genetic types were studied. These lines were based on the following breeds: Large White, Landrace, Duroc, Piétrain and a Meishan synthetic population developed from a cross with a Large White based line. Measurements were taken in the carcasses directly with a ruler and with the Fat-O-Meat'er. The carcasses were cut following the European reference method and the four main joints were dissected. Carcasses from the Piétrain based line, which was halothane negative, presented the highest killing-out (83.34%) and were the shortest (81.81cm). The Piétrain based line was also the leanest and the Meishan based line the fattest. The highest proportion of ham (270.9g/kg) and the lowest proportion of belly (97.97g/kg) were found in the Piétrain line. The proportion of lean in all of the dissected cuts was higher in carcasses from this line while the Meishan line presented the highest proportions of intermuscular fat in all of the pieces. Carcasses came from the Piétrain line received the highest conformation scores and they were leaner and with better ham yield.

Associations of DNA markers with meat quality traits in pigs with emphasis on drip loss.

Phenotypic information on 1155 market pigs for several pig meat quality traits, was collected. Genotypes on 12 DNA markers, including RYR1 and PRKAG3 I199V, were also obtained on all pigs to investigate the relationship between genetic markers and meat quality. The RYR1 gene had the highest impact on meat quality, however, several other markers showed significant effects on one or more traits. Animals heterozygous at the RYR1 locus were significantly inferior in almost all meat quality traits, except ultimate pH value, initial conductivity and redness of the meat. Drip loss from case-ready meat (measured from 1 to 7 days post-mortem) was 43% higher for heterozygotes than animals of the stress resistant genotype. The homozygous genotype II at position I199V of the PRKAG3 locus also resulted in less drip loss than genotypes IV and VV, regardless of the method and time of measurement. Furthermore, the favourable genotype related to higher ultimate pH and darker meat. Both loci significantly affected the intercept, linear and quadratic terms of fitted drip loss development curves. The favourable genotypes showed a lower drip loss after one day of measurement and a slower increase and a more linear development over time. Whilst the RYR1 and PRKAG3 markers influenced numerous meat quality traits, some of the other markers were also found to have significant effects on one or two meat quality traits. Markers at MC4R and HMGA1 loci significantly affected drip loss, whereas LDHA, CAST (Hpy188I) and ATP2A1 influenced pH value. In addition, the marker ATP2A1 was associated with variation in intramuscular fat content in M. longissimus dorsi. GLUT4 affected temperature 45min post-mortem and several markers (MC4R, LDHA, GLUT4, HMGA1, CAST (Hpy188I and PvuII)) influenced one or two of the different colour measurements. The markers at MC4R, CKM, AGRP, PRKAG3, and HMGA1 loci were tested for their interactions with RYR1 regarding drip loss. Only AGRP showed a significant interaction, but this was based on only a few animals with the homozygous genotype for one allele. Our results suggest that genetic markers provide a useful tool to improve meat quality in pigs independently from RYR1, especially the mutation I199V in the PRKAG3 gene.

Stress neuroendocrine profiles in five pig breeding lines and the relationship with carcass composition.

Stress neuroendocrine systems (hypothalamic-pituitary-adrenal axis and sympathetic nervous system) were studied in 100 female pigs from each of the five main genetic lines used in Europe for pork production: Piétrain, Large White, Landrace, Duroc and Meishan. Levels of cortisol and catecholamines were measured in urine collected at the farm, after transportation to the slaughterhouse and the next morning before slaughter. With the exception of the Piétrain line that showed intermediate levels of cortisol despite its extreme leanness, a significant positive relationship was found between basal cortisol levels and fatness, both across and within (except in Piétrain and Duroc) lines. Basal cortisol levels were 2.46-fold higher in Meishan (20.46 ng/mg creatinine) than in Large White pigs (8.30 ng/mg creatinine), the two extreme breeds. Post-transportation levels were highest but proportional to basal levels, suggesting that the adrenal reactivity to adrenocorticotropic hormone is a major source of variability between lines. Levels of catecholamines were less variable between lines but correlated also with fatness, partlyviapartial correlations with cortisol levels. In serum collected at exsanguination, creatine kinase activity was correlated with muscularity across the five breeds. However, this was due to a much larger activity than expected in Piétrain pigs, although all animals were negative for the allele of the ryanodine receptor gene responsible for stress sensitivity. Serum glucose levels were inversely related to fatness. These data show that the differences between breeds or lines can be utilised by cross-breeding and that this can lead to changes in stress hormones and in turn to some degree of changes in carcass traits.

A polymorphism in the 5'-untranslated region of the porcine cholecystokinin type a receptor gene affects feed intake and growth.

The location and utilization of quantitative trait loci (QTL) and candidate genes with significant effects on economically important traits are becoming increasingly important in livestock breeding programs. The porcine cholecystokinin type A receptor (CCKAR) is a candidate gene for performance traits, due to its known role in the physiological control of feed intake, satiety, and obesity. We investigated the association of CCKAR polymorphisms with feeding, growth, and efficiency traits in an F2 population derived from a cross between Meishan and Large White founder animals and in lines of Large White pigs that had been divergently selected on the basis of lean growth efficiency traits. In the F2 population, CCKAR genotype was significantly associated with daily feed intake and average daily gain. The effects of the polymorphisms were then assessed in a larger-scale analysis of segregating commercial lines. A newly discovered single-nucleotide polymorphism (SNP) within the 5'-untranslated region (5'-UTR) had highly significant effects on feed intake, average daily gain, and days to 110 kg, which were not seen for a previously reported SNP within the CCKAR gene. Furthermore, we provide evidence that the novel SNP disrupts the binding of the YY1 transcription factor, which raises the possibility that it is the causal variant. The 5'-UTR SNP could be utilized as a molecular genetic test for increased feed intake, faster lean growth, and reduced days to market weight in segregating commercial lines.

Quantitative trait loci associated with AutoFOM grading characteristics, carcass cuts and chemical body composition during growth of Sus scrofa.

A three-generation full-sib resource family was constructed by crossing two commercial pig lines. Genotypes for 37 molecular markers covering chromosomes SSC1, SSC6, SSC7 and SSC13 were obtained for 315 F2 animals of 49 families and their parents and grandparents. Phenotypic records of traits including carcass characteristics measured by the AutoFOM grading system, dissected carcass cuts and meat quality characteristics were recorded at 140 kg slaughter weight. Furthermore, phenotypic records on live animals were obtained for chemical composition of the empty body, protein and lipid accretion (determined by the deuterium dilution technique), daily gain and feed intake during the course of growth from 30 to 140 kg body weight. Quantitative trait loci (QTL) detection was conducted using least-squares regression interval mapping. Highest significance at the 0.1% chromosome-wise level was obtained for five QTL: AutoFOM belly weight on SSC1; ham lean-meat weight, percentage of fat of primal cuts and daily feed intake between 60 and 90 kg live weight on SSC6; and loin lean-meat weight on SSC13. QTL affecting daily gain and protein accretion were found on SSC1 in the same region. QTL for protein and lipid content of empty body at 60 kg liveweight were located close to the ryanodine receptor 1 (RYR1) locus on SSC6. On SSC13, significant QTL for protein accretion and feed conversion ratio were detected during growth from 60 to 90 kg. In general, additive genetic effects of alleles originating from the Piétrain line were associated with lower fatness and larger muscularity as well as lower daily gain and lower protein accretion rates. Most of the QTL for carcass characteristics were found on SSC6 and were estimated after adjustment for the RYR1 gene. QTL for carcass traits, fatness and growth on SSC7 reported in the literature, mainly detected in crosses of commercial lines x obese breeds, were not obtained in the present study using crosses of only commercial lines, suggesting that these QTL are not segregating in the analysed commercial lines.