Finishing season and feeding resources influence the quality of products from extensive-system Gascon pigs. Part 2: muscle traits and sensory quality of dry-cured ham.

The quality of pork products from local breeds in extensive systems depends, among other things, on pig production. In particular, the variability in climatic conditions and feeding resources may influence the properties of tissues at slaughter and the quality of pork and processed products. The present study (part 2) was part of a larger project that assessed the influence of the finishing season and feeding resources on carcass and tissue traits and the quality of meat and dry-cured ham from Gascon pigs in an extensive system. Following the specifications of the Protected Designation of Origin "Noir de Bigorre", castrated Gascon males were reared on rangelands (grassland and forest areas) and received a supplementary diet from 5 to 6 months of age until slaughter at a minimum of 12 months and ca. 170 kg BW. Three finishing seasons were considered: Winter (n = 18), Spring (n = 22) and Autumn (n = 23). To estimate the specific effects of season on quality traits and avoid bias due to effects of genes known to influence these traits, polymorphisms in the RYR1, PRKAG3, MC4R and LEPR genes were included in the analysis models. Compared to Winter pigs, Spring and Autumn pigs had higher ultimate pH in the semimembranosus and gluteus medius (GM) muscles, lower meat lightness (P < 0.05) and tended to have higher GM intramuscular fat (IMF) content (P < 0.10). They also had higher GM contents of saturated, monounsaturated and polyunsaturated fatty acids (FAs) than Winter pigs (P < 0.05). Spring pigs had the lowest n-6:n-3 polyunsaturated FA ratio and the highest GM α-tocopherol content (P < 0.001), indicating pig grazing. The finishing season did not influence the processing yield of dry-cured hams (24-month process). Within each seasonal group, ten hams selected for genetic variability and IMF content were analyzed by a trained sensory panel. The season did not modify the appearance or odor, but influenced texture and taste. Hams from Winter and Spring pigs had higher tenderness and melting fat scores than hams from Autumn pigs (P < 0.01). Hams from Spring pigs had higher taste intensity and salty taste (P < 0.01) but lower positive tastes (e.g. fruits, forest) than hams from the other groups. Overall, finishing season had moderate effects on ham sensory traits. Furthermore, our results reveal high redness, tenderness, taste and odor intensity, and low rancid flavor of hams from Gascon pigs produced in an extensive system.

Finishing season and feeding resources influence the quality of products from extensive-system Gascon pigs. Part 1: Carcass traits and quality of fresh loin.

Consumers perceive pork products from local breeds reared in extensive systems positively because of their specific quality properties and regional identity. The sensory, nutritional and technological qualities of these products depend, among other things, on pig production, especially its climatic conditions and the availability of feed resources, which can influence traits of muscle and fat tissue. The present study (part 1) was part of a larger project that assessed the influence of the finishing season and feeding resources on carcass and tissue traits and the quality of meat and dry-cured ham from Gascon pigs in an extensive system. Following the specifications of the Protected Designation of Origin "Noir de Bigorre", castrated Gascon males were reared on rangelands (grassland and forest areas) and received a supplementary diet from 5 to 6 months of age until slaughter at a minimum of 12 months of age and ca. 170 kg live weight. Three finishing seasons were considered as follows: Winter (n = 18), Spring (n = 22) and Autumn (n = 23). To estimate specific effects of season on productive and quality traits and avoid bias due to effects of genes known to influence these traits, polymorphisms in the RYR1, PRKAG3, MC4R and LEPR genes were included in the analysis models. The finishing season did not influence growth rate. Compared to Winter pigs, Spring and Autumn pigs had slightly lower carcass fatness (P < 0.05), higher ultimate pH and redder and darker color of the Longissimus muscle (LM) (P < 0.01). Loin drip loss was low overall, but was higher for Spring pigs, whereas cooking loss and shear force were similar among seasons. Spring pigs tended to have the lowest LM lipid content, whereas LM myoglobin content remained unaffected. Autumn pigs had lower potential of lipid oxidation in LM than Winter and Spring pigs (P < 0.01), but muscle metabolic traits assessed via glycolytic and oxidative enzyme activities did not differ among seasons. The finishing season modified the backfat fatty acid (FA) profile, with a lower polyunsaturated FA percentage in Autumn pigs than Winter or Spring pigs (P < 0.001), even though the saturated and monounsaturated FA percentages did not differ. In particular, Spring pigs had the lowest n-6:n-3 and C18:2:C18:3 ratios (P < 0.001), as a result of grazing. Overall, Spring and Autumn finishing seasons seem more favorable to technological and sensory pork attributes, with an additional positive effect of Spring finishing on pork nutritional value.

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds.

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states.

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

Genetic determinism of boar taint and relationship with growth traits, meat quality and lesions.

Breeding entire males is an alternative to surgical castration to improve their welfare. However, entire males may have a major quality defect called boar taint. Boar taint is partly due to the presence of androstenone in fat. In this study, we estimated the genetic parameters between androstenone and production traits to evaluate the consequences of selection against boar taint for traits of interest. We focused on growth traits, meat quality, lesions, hormone levels and computerised tomography measurements in purebred Piétrain (P) or Piétrain cross Large White (X) entire males. The number of measured animals varied from 670 P and 734 X for hormones concentrations to 553 P and 645 X for computerised tomography measurements. Skin lesions were measured on live pigs shortly after mixing, at the end of the fattening period, and on carcasses. Heritabilities of traits measured by tomography ranged from low to high: femur density (P: 0.34, X: 0.69), loin eye area (P: 0.53, X: 0.88) and loin eye density (P: 0.12, X: 0.18). The mean number of lesions at each stage was lower in purebred pigs than in crossbreds (entering the fattening stage 4.01 in P and 4.68 in X; before slaughter 3.72 in P and 4.22 in X; on carcass 4.50 in P and 4.96 in X). We also observed a decrease in the average number of lesions between the two stages in live pigs. We found high genetic correlations between stages in purebred pigs (0.74 to 0.76) but low correlations (-0.30 to 0.29) in crossbred pigs. Selection aiming to decrease fat androstenone is feasible (h2 = 0.57 in P and h2 = 0.71 in X). It would have overall positive effects on meat production and quality traits. Selection aiming to reduce plasma oestradiol would strongly reduce the level of fat androstenone (rg = 0.89 in P and rg = 0.84 in X). Selection against oestradiol is easier and less invasive since it would only require a blood sample rather than a fat biopsy in live animals.

Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip.

Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

Towards the quantitative characterisation of piglets' robustness to weaning: a modelling approach.

Weaning is a critical transition phase in swine production in which piglets must cope with different stressors that may affect their health. During this period, the prophylactic use of antibiotics is still frequent to limit piglet morbidity, which raises both economic and public health concerns such as the appearance of antimicrobial-resistant microbes. With the interest of developing tools for assisting health and management decisions around weaning, it is key to provide robustness indexes that inform on the animals' capacity to endure the challenges associated with weaning. This work aimed at developing a modelling approach for facilitating the quantification of piglet resilience to weaning. A total of 325 Large White pigs weaned at 28 days of age were monitored and further housed and fed conventionally during the post-weaning period without antibiotic administration. Body weight and diarrhoea scores were recorded before and after weaning, and blood was sampled at weaning and 1 week later for collecting haematological data. A dynamic model was constructed based on the Gompertz-Makeham law to describe live weight trajectories during the first 75 days after weaning, following the rationale that the animal response is partitioned in two time windows (a perturbation and a recovery window). Model calibration was performed for each animal. Our results show that the transition time between the two time windows, as well as the weight trajectories are characteristic for each individual. The model captured the weight dynamics of animals at different degrees of perturbation, with an average coefficient of determination of 0.99, and a concordance correlation coefficient of 0.99. The utility of the model is that it provides biologically meaningful parameters that inform on the amplitude and length of perturbation, and the rate of animal recovery. Our rationale is that the dynamics of weight inform on the capability of the animal to cope with the weaning disturbance. Indeed, there were significant correlations between model parameters and individual diarrhoea scores and haematological traits. Overall, the parameters of our model can be useful for constructing weaning robustness indexes by using exclusively the growth curves. We foresee that this modelling approach will provide a step forward in the quantitative characterisation of robustness.

Dissecting total genetic variance into additive and dominance components of purebred and crossbred pig traits.

The partition of the total genetic variance into its additive and non-additive components can differ from trait to trait, and between purebred and crossbred populations. A quantification of these genetic variance components will determine the extent to which it would be of interest to account for dominance in genomic evaluations or to establish mate allocation strategies along different populations and traits. This study aims at assessing the contribution of the additive and dominance genomic variances to the phenotype expression of several purebred Piétrain and crossbred (Piétrain × Large White) pig performances. A total of 636 purebred and 720 crossbred male piglets were phenotyped for 22 traits that can be classified into six groups of traits: growth rate and feed efficiency, carcass composition, meat quality, behaviour, boar taint and puberty. Additive and dominance variances estimated in univariate genotypic models, including additive and dominance genotypic effects, and a genomic inbreeding covariate allowed to retrieve the additive and dominance single nucleotide polymorphism variances for purebred and crossbred performances. These estimated variances were used, together with the allelic frequencies of the parental populations, to obtain additive and dominance variances in terms of genetic breeding values and dominance deviations. Estimates of the Piétrain and Large White allelic contributions to the crossbred variance were of about the same magnitude in all the traits. Estimates of additive genetic variances were similar regardless of the inclusion of dominance. Some traits showed relevant amount of dominance genetic variance with respect to phenotypic variance in both populations (i.e. growth rate 8%, feed conversion ratio 9% to 12%, backfat thickness 14% to 12%, purebreds-crossbreds). Other traits showed higher amount in crossbreds (i.e. ham cut 8% to 13%, loin 7% to 16%, pH semimembranosus 13% to 18%, pH longissimus dorsi 9% to 14%, androstenone 5% to 13% and estradiol 6% to 11%, purebreds-crossbreds). It was not encountered a clear common pattern of dominance expression between groups of analysed traits and between populations. These estimates give initial hints regarding which traits could benefit from accounting for dominance for example to improve genomic estimated breeding value accuracy in genetic evaluations or to boost the total genetic value of progeny by means of assortative mating.

Immunome differences between porcine ileal and jejunal Peyer's patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues.

The epithelium of the intestinal mucosa and the gut-associated lymphoid tissues (GALT) constitute an essential physical and immunological barrier against pathogens. In order to study the specificities of the GALT transcriptome in pigs, we compared the transcriptome profiles of jejunal and ileal Peyer's patches (PPs), mesenteric lymph nodes (MLNs) and peripheral blood (PB) of four male piglets by RNA-Seq. We identified 1,103 differentially expressed (DE) genes between ileal PPs (IPPs) and jejunal PPs (JPPs), and six times more DE genes between PPs and MLNs. The master regulator genes FOXP3, GATA3, STAT4, TBX21 and RORC were less expressed in IPPs compared to JPPs, whereas the transcription factor BCL6 was found more expressed in IPPs. In comparison between IPPs and JPPs, our analyses revealed predominant differential expression related to the differentiation of T cells into Th1, Th2, Th17 and iTreg in JPPs. Our results were consistent with previous reports regarding a higher T/B cells ratio in JPPs compared to IPPs. We found antisense transcription for respectively 24%, 22% and 14% of the transcripts detected in MLNs, PPs and PB, and significant positive correlations between PB and GALT transcriptomes. Allele-specific expression analyses revealed both shared and tissue-specific cis-genetic control of gene expression.

Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis.

BACKGROUND: Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity. The objective of this work was to study the genetic architecture of variation in gene expression in the blood of healthy young pigs using two approaches: an expression genome-wide association study (eGWAS) and allele-specific expression (ASE) analysis. RESULTS: The blood transcriptomes of 60-day-old Large White pigs were analyzed by expression microarrays for eGWAS (242 animals) and by RNA-Seq for ASE analysis (38 animals). Using eGWAS, the expression levels of 1901 genes were found to be associated with expression quantitative trait loci (eQTLs). We recovered 2839 local and 1752 distant associations (Single Nucleotide Polymorphism or SNP located less or more than 1 Mb from expression probe, respectively). ASE analyses confirmed the extensive cis-regulation of gene transcription in blood, and revealed allelic imbalance in 2286 SNPs, which affected 763 genes. eQTLs and ASE-genes were widely distributed on all chromosomes. By analyzing mutually overlapping eGWAS results, we were able to describe putative regulatory networks, which were further refined using ASE data. At the functional level, genes with genetically controlled expression that were detected by eGWAS and/or ASE analyses were significantly enriched in biological processes related to RNA processing and immune function. Indeed, numerous distant and local regulatory relationships were detected within the major histocompatibility complex region on chromosome 7, revealing ASE for most class I and II genes. CONCLUSIONS: This study represents, to the best of our knowledge, the first genome-wide map of the genetic control of gene expression in porcine peripheral blood. These results represent an interesting resource for the identification of genetic markers and blood biomarkers associated with variations in immunity traits in pigs, as well as any other complex traits for which blood is an appropriate surrogate tissue.

Genetic relationships between measures of sexual development, boar taint, health, and aggressiveness in pigs.

Breeding intact boars is a promising alternative to surgical castration of piglets. Genetic selection should enable farmers to solve problems due to boar taint and aggressiveness while taking into account potential consequences on other traits of interest. The aim of the study was to estimate genetic relations between sexual development, boar taint, health, and aggressiveness. About 1,600 Pietrain (purebred) or Pietrain × Large White (crossbred) boars were raised in a testing station. Blood samples were collected at about 105 kg BW for measuring sex hormones (testosterone and estradiol) and indicators of the inflammatory status (C-reactive protein [CRP], pig major acute-phase protein [pigMAP], and blood formula). Animals were slaughtered 9 d later and measured for boar taint compounds present in fat (androstenone and skatole) and skin lesions on carcass, an indicator of aggressiveness. For both genetic types, heritability was moderate for sex hormones (from 0.17 to 0.29) and skatole (0.24 for purebred and 0.37 for crossbred) and high for androstenone (0.63 and 0.70 for purebred and crossbred, respectively). Genetic correlations between sex hormones and boar taint compounds were moderate to high (from 0.31 to 0.95). Heritability was moderate for CRP (0.24 and 0.46 for purebred and crossbred, respectively) and very low for pigMAP (0.06 and 0.05 for purebred and crossbred, respectively. Numbers of leukocytes had moderate to high heritabilities according to the genetic type (from 0.21 to 0.52). Heritability of skin lesions was moderate for both genetic types (0.31). Genetic correlations were negative between sex hormones and inflammatory measures (from -0.46 to -0.05), positive between testosterone and number of lesions (0.43 and 0.53 for purebred and crossbred, respectively), and low between androstenone and lesions (-0.06 and -0.17 for purebred and crossbred, respectively). Overall, both breeds of pigs had very similar estimations of heritabilities, but estimates of genetic correlations were different for some pairs of traits. It would be possible to select boars based on their plasma concentration of sex hormones to decrease boar taint and aggressiveness without important consequences on the immune response. However, because of the strong links between boar taint and reproductive function, the possible consequences on the reproductive performance should be evaluated.

Phenotypic prediction based on metabolomic data for growing pigs from three main European breeds.

Predicting phenotypes is a statistical and biotechnical challenge, both in medicine (predicting an illness) and animal breeding (predicting the carcass economical value on a young living animal). High-throughput fine phenotyping is possible using metabolomics, which describes the global metabolic status of an individual, and is the closest to the terminal phenotype. The purpose of this work was to quantify the prediction power of metabolomic profiles for commonly used production phenotypes from a single blood sample from growing pigs. Several statistical approaches were investigated and compared on the basis of cross validation: raw data vs. signal preprocessing (wavelet transformation), with a single-feature selection method. The best results in terms of prediction accuracy were obtained when data were preprocessed using wavelet transformations on the Daubechies basis. The phenotypes related to meat quality were not well predicted because the blood sample was taken some time before slaughter, and slaughter is known to have a strong influence on these traits. By contrast, phenotypes of potential economic interest (e.g., lean meat percentage and ADFI) were well predicted (R(2) = 0.7; P < 0.0001) using metabolomic data.

Genetic variability, structure and assignment of Spanish and French pig populations based on a large sampling.

The Spanish and French pig populations share the common practice of quasi systematic paternity control of pure breed and composite line males. Ten microsatellite markers are in common between Spain and France controls, among the 17 markers used in France and the 13 used in Spain. After the adjustment of allele sizes, it is possible to merge the two datasets and to obtain a set of 5791 animals, including the vast majority of the males in the Duroc, Landrace, Large White and Piétrain French and Spanish breeds. Twelve French composite lines are also available. The genetic diversity analysis of these pig populations is presented, as well as the assignment of an individual to its breed. The effects of heterogeneous sampling across time and of relatedness among animals are also assessed. Consistent with the results of the previous studies, we found that different populations from the same breed clearly clustered together. In addition, all populations of this study, whether purebred or composite, are quite well differentiated from the other ones. As a result, we note that the 10 microsatellites commonly used for paternity control ensure a powerful detection of the breed of origin, with the power of detection being 95-99%. The detection of the exact population within breed is more difficult, but the power exceeds 70% for most of the populations. Practical implications include, for instance, the detection of outlier animals, crosses and admixture events.