Candidate SNPs for meat quality and carcass composition in free-range Iberian pigs

Several genetic markers, previously associated with meat quality traits, have been proposed to be included in Iberian pig breeding programs. However, before being implemented, effects of these candidate SNPs on premium cuts' yield should be evaluated to avoid potential undesirable antagonistic effects. Therefore, the main goals of this study were to evaluate the effects of a set of 26 polymorphisms on premium cuts weights and to corroborate their effects on meat quality in a larger population. Phenotypic data of approximately 1550 Iberian pigs were recorded. The PRKAG3_rs319678464C and PRKAG3_rs1108399077G alleles were associated with an increase of shear force, water losses and color values and a reduction of average daily gain (ADG). The CAST_rs196949783G > A and ADIPOQ_rs3476515794T > G SNPs mainly affected IMF content, with this last SNP being the only one with significant effects on any of the carcass measures, specifically Longissimus thoracis et lumborum (LTL) weight. The ELOVL6_rs3473714672A, FASN_rs331694510A, MTTP_rs335896411C and ACACA_rs340781986C alleles were linked to a higher percentage of oleic acid and monounsaturated FA and a decrease in palmitic, palmitoleic and saturated FA. Besides, suggestive effects were observed between ELOVL6_rs3473714672A > G and ham and shoulder weights, and between MTTP_rs335896411T > C and LTL muscle weight. Finally, the NR6A1_rs326780270T allele was associated with a significant increase in ADG and tended to reduce the ham weight. The SNPs mapped to PRKAG3 (rs319678464G > C), ACACA, FASN and CAST genes could be implemented in breeding programs to improve meat quality traits without undesirable effects on carcass composition. The SNPs mapped to PRKAG3 (rs1108399077G > A) ELOVL6, MTTP and NR6A1 should continue to be tested in a larger number of animals.

Outdoors: Production Performance and Market Value

The current Quality Standard regulating the Iberian pig provides for various differentiated farming systems subject to the type of management implemented and the breed of the pigs. This study attempts to analyse the differences between two of these production systems, i.e., the outdoor and the indoor rearing systems by comparing the main technical and economic factors of six farms, three operating under each system, in order to ascertain the most profitable production system. This analysis is based on the information provided by the farm owners. It also evaluates the impact that the COVID-19 pandemic outbreak had on profitability. The results show that both systems spend the same resources on animal feed, which represents nearly 60% of the expense, with the price of purchase of piglets representing 30-32% of the total; however, there are differences in the cost of labour, which is higher in the outdoor variant. In economic terms, outdoor farms obtained a higher gross margin than indoor farms did. Although their production costs are higher, these are offset with larger incomes due to the higher market price of the pigs at the time of slaughter. Lastly, all the farms under study reveal large financial losses on account of COVID-19, given that there was a general decrease in the revenues due to the decrease in the selling price of the pigs, which seems to be the most determinant factor for the economic profits made by these kinds of farms.

Olive- and Coconut-Oil-Enriched Diets Decreased Secondary Bile Acids and Regulated Metabolic and Transcriptomic Markers of Brain Injury in the Frontal Cortexes of NAFLD Pigs

The objective of this study was to investigate the effect of dietary fatty acid (FA) saturation and carbon chain length on brain bile acid (BA) metabolism and neuronal number in a pig model of pediatric NAFLD. Thirty 20-day-old Iberian pigs, pair-housed in pens, were randomly assigned to receive one of three hypercaloric diets for 10 weeks: (1) lard-enriched (LAR; n = 5 pens), (2) olive-oil-enriched (OLI, n = 5), and (3) coconut-oil-enriched (COC; n = 5). Pig behavior and activity were analyzed throughout the study. All animals were euthanized on week 10 and frontal cortex (FC) samples were collected for immunohistochemistry, metabolomic, and transcriptomic analyses. Data were analyzed by multivariate and univariate statistics. No differences were observed in relative brain weight, neuronal number, or cognitive functioning between diets. Pig activity and FC levels of neuroprotective secondary BAs and betaine decreased in the COC and OLI groups compared with LAR, and paralleled the severity of NAFLD. In addition, OLI-fed pigs showed downregulation of genes involved in neurotransmission, synaptic transmission, and nervous tissue development. Similarly, COC-fed pigs showed upregulation of neurogenesis and myelin repair genes, which caused the accumulation of medium-chain acylcarnitines in brain tissue. In conclusion, our results indicate that secondary BA levels in the FCs of NAFLD pigs are affected by dietary FA composition and are associated with metabolic and transcriptomic markers of brain injury. Dietary interventions that aim to replace saturated FAs by medium-chain or monounsaturated FAs in high-fat hypercaloric diets may have a negative effect on brain health in NAFLD patients.

Isolation, Genotyping, and Mouse Virulence Characterization of Toxoplasma gondii From Free Ranging Iberian Pigs

The present study aimed to isolate and perform molecular and phenotypic characterization of Toxoplasma gondii strains infecting Iberian pigs bred under semi-free conditions and destined for human consumption. Blood and heart tissue samples from 361 fattening pigs from 10 various herds selected in the main areas of Iberian pig production were collected at a slaughterhouse; the sera were tested for anti-T. gondii antibodies using a commercial indirect ELISA kit, and a mouse bioassay was carried out using heart muscle of seropositive individual representatives from each geographical location. Seventy-nine (21.9%) of the 361 animals tested positive for anti-T. gondii antibodies according to the serology test. Fifteen samples of myocardial tissue were subjected to bioassay and 5 isolates (TgPigSp1 to TgPigSp5) were obtained. The isolates were characterized by using 11 PCR-RFLP genetic markers; three isolates had a ToxoDB #3 genotype (3/5) and two isolates had a ToxoDB #2 genotype (2/5). The TgPigSp1 and TgPigSp4 isolates were selected for virulence in mice characterization as instances of each different RFLP-genotype found. The TgPigSp1 isolate (#2 genotype) was virulent in mice with notable cumulative mortality (87.5%) and morbidity rates (100%); the TgPigSp4 (#3) was nonvirulent and triggered mild clinical signs in 42.1% of seropositive mice. Infection dynamics and organ distribution of both isolates were analyzed; the data revealed significant differences, including substantially higher parasite load in the lung during the acute phase of infection, in mice infected with TgPigSp1 than in the case of TgPigSp4 (median parasite load 7.6 vs. 0 zoites/mg, respectively; p < 0.05). Furthermore, degrees of severity of detected histopathological lesions appeared to be related to higher parasite burdens. Taking into account the unexpectedly high mortality rate and parasite load associated with the clonal genotype III, which is traditionally considered nonvirulent in mice, the need for further investigation and characterization of the T. gondii strains circulating in any host in Europe is emphasized.

Environmental and Management Factors Affecting the Time Budgets of Free-Ranging Iberian Pigs Reared in Spain

Simple Summary

Understanding the natural behaviour of pigs in free-range conditions facilitates the interpretation of their behaviour in intensive conditions. The present study aims to study behavioural indicators of activity in the domestic pig, reared free-range and under two feeding regimes, with some help from humans with concentrates and without help, just eating natural resources. Results confirmed that exploratory behaviour was an important behaviour for pigs, but the same animals that dedicated 50% of their time to this activity when they were not fed by humans reduced this activity to 17.8% when they were fed with concentrates. In addition, few social contacts between animals were seen in extensive conditions, with a higher incidence of negative rather than positive social behaviour. It was concluded that: (1) the need for exploring the surroundings in natural environments is of less importance for pigs when they are fed by humans, and (2) bathing areas in outdoor conditions are important for pigs in the event of warm conditions. Overall, it is concluded that natural behaviour of pigs in free-range conditions, such as a reduced foraging behaviour when pigs are fed with concentrates, should be considered when interpreting behavioural needs in intensive conditions.

Abstract

Understanding the natural behaviour of pigs in free-range conditions facilitates interpretation of their behaviour in intensive conditions. Studying six different farms over two years at different seasons, with climatic and management variations, allowed for a general description of Iberian pig behaviour and which factors have an influence on it. The main activity found was resting (56.5% of the time observed), followed by exploratory behaviour. However, this exploratory behaviour was higher when animals were fed only with natural resources than when fed with concentrates (50% versus 17.8%, respectively). In addition, pigs used bathing areas in summer that were not visited in winter. Negative social behaviour was seen more frequently than positive social behaviour, accounting, in total, for 1% of the total activity of animals. Pigs situated at the centre of the groups tended to remain more relaxed, while the peripheral animals remained more alert and vigilant. Our results indicate that foraging behaviour accounts for a significant proportion of pigs’ active time, but this proportion is much more reduced when pigs are fed concentrates. Therefore, behavioural needs in pigs reared in intensive conditions should consider that exploratory behaviour is reduced when pigs are fed with concentrates.

Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs

One of the most important determinants of meat quality is the intramuscular fat (IMF) content. The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the present study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for their IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq allowed identifying ∼10,000 of the 25,878 annotated genes in the analyzed samples. In addition to this, 42.46% of the identified transcripts corresponded to newly predicted isoforms. Differential expression analyses revealed a total of 221 DE annotated genes and 116 DE new isoforms. Functional analyses identified an enrichment of overexpressed genes involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC, and ADIPOQ) in animals with a higher content of IMF and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB, and SEMA4D) in the animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. Co-expression networks analyses revealed six long non-coding RNAs (lncRNAs) (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, and ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1, and CIDEC. Analyses of the regulatory impact factors (RIFs) revealed 301 transcriptionally regulatory factors involved in expression differences, with five of them involved in adipogenesis (ARID5B, CREB1, VDR, ATF6, and SP1) and other three taking part of myogenesis and development of skeletal muscle (ATF3, KLF11, and MYF6). The results obtained provide relevant insights about the genetic mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors for further identification of polymorphisms susceptible of being incorporated in a selection program.

Extent of third-order linkage disequilibrium in a composite line of Iberian pigs

BACKGROUND

Previous studies on linkage disequilibrium have investigated second order linkage disequilibrium in animal and plant populations. The objective of this paper was to investigate the genome-wide levels of third order linkage disequilibrium in a composite line founded by admixture of four Iberian pig strains. A model for the generation of third order linkage disequilibrium by population admixture is proposed. A computer Expectation-Maximization algorithm is developed and applied to the estimation of third order linkage disequilibrium at inter- and intra-chromosomal level using 26,347 SNPs typed in 306 sows. The relationship of third order linkage disequilibrium with physical distance was investigated over 35 million triplets in SSC12. Basic and normalized estimates of inter and intra-chromosomal third order linkage disequilibrium are reported.

RESULTS

Genome-wide analyses revealed that third order linkage disequilibrium is rather common among linked loci in this Iberian pig line. It is shown that population admixture of multiple populations may explain the observed levels of third order linkage disequilibrium although it could be generated by genetic drift. Third order linkage disequilibrium decreases rapidly up to 4 Mb and then declines slowly. The short distances between consecutive markers explain the maintenance of the observed third order linkage disequilibria levels when using a model incorporating the break-up of disequilibrium by recombination. Genome-wide testing also revealed that only 3.6% of the normalized estimates were different from 1, - 1, 0, or from a not well-defined situation in which there is only one possible value for the third order linkage disequilibrium parameter, given allele frequencies and pairwise linkage disequilibria parameters.

CONCLUSIONS

Third order linkage disequilibrium is common among linked markers in the analyzed pig line and may have been generated by population admixture of multiple populations or by genetic drift. As with second order linkage disequilibrium, the absolute value of the third order linkage disequilibrium decreases with physical distance. Normalization of third order linkage disequilibrium should be avoided for closely linked bi-allelic loci.

Maternal undernutrition and offspring sex determine birth-weight, postnatal development and meat characteristics in traditional swine breeds

Background

The aim of this study was to determine how maternal undernutrition during pregnancy and offspring birth-weight can affect the postnatal development of offspring under farm conditions, which may lead to consequences in its meat and carcass quality. The current study involved a total of 80 litters from Iberian sows fed a diet fulfilling daily requirements (n = 47; control) or providing 70% daily requirements (n = 33; underfed) from d 38 to d 90 of gestation when fetal tissue development begins. After birth, piglets born live were classified as low birth-weight (LBW; < 1 kg) and normal birth-weight (NBW; ≥1 kg). During the growing phase, 240 control and 230 underfed pigs (50% males and females) distributed by BW category and sex were studied until the slaughter.

Results

At birth and weaning, there were significant differences in all morphological measures and weight between NBW and LBW piglets as expected (P < 0.0005), but few effects of the gestational feed restriction. During the growing phase, NBW pigs continued with higher weight than LBW pigs on all the days of evaluation (P < 0.05), even though control-LBW-females and LBW-males showed a catch-up growth. However, underfed pigs showed slower growth and higher feed conversion ratio than control pigs (P < 0.0001) at 215 days old. Moreover, the average daily weight gain (ADWG) for the overall period was greater for NBW, male and control pigs than for their LBW, female and underfed pigs (P < 0.0001, P< 0.0005 and P< 0.05, respectively) and NBW pigs were slaughtered at a younger age than LBW pigs (P < 0.0001). After slaughtering, control pigs also had higher carcass yield and backfat depth than underfed pigs (P < 0.0005) and the maternal nutritional effect caused main changes in the polar lipid fraction of liver and loin. The fatty acid composition of loin in control pigs had higher C18:1n-9 and n-3 FA concentrations, as well as lower ∑n-6/∑n-3 ratio, than in underfed pigs (P < 0.005).

Conclusions

In brief, results showed that the effects of maternal nutritional restriction appeared and increased with offspring age, causing worse developmental patterns for underfed pigs than for control pigs.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0240-6) contains supplementary material, which is available to authorized users.

Molecular typing of Streptococcus suis isolates from Iberian pigs: a comparison with isolates from common intensively-reared commercial pig breeds

The Iberian pig (IP) is a traditional Spanish breed variety of the domestic pig (Sus scrofa domesticus) with high economic importance because of the value of the dry-cured products in national and international markets. The genetic characteristics of tonsillar and clinical Streptococcus suis isolates from the IP maintained under extensive or intensive management conditions were investigated. S. suis isolates from IP pigs were compared with S. suis isolates from intensively-farmed pigs of common breeds (CBP). S. suis was isolated from 48.4% of the IP tonsils examined, indicating wide distribution among IP pigs. Serotypes 1 (9.4%), 2 (8.6%) and 9 (7%) were the most commonly found, although a high percentage of S. suis isolates were not typeable by coagglutination testing. No significant differences in carrier rates or serotype diversity were observed between management systems, indicating that intensive farming does not influence S. suis colonisation. Both pulsed-field gel electrophoresis and multiple-locus variable number tandem repeat analysis showed a serotype-based distribution of S. suis IP isolates. Serotypes 1 and 2 S. suis isolates were grouped in the same cluster, whereas isolates of serotypes 9 and 7 were assigned to another cluster. All clinical and most tonsillar serotype 2 IP isolates were assigned to sequence type 1 (ST1) and exhibited the virulence genotype mrp+/epf+/sly+, indicating a high distribution of this genetic lineage among IP as well as a population of serotype 2 common to IPs and CBPs. The only clinical isolate of serotype 9 from IP was assigned to ST123, a sequence type associated with clinical isolates in CBPs in Spain.

The genetic background affects composition, oxidative stability and quality traits of Iberian dry-cured hams: purebred Iberian versus reciprocal Iberian × Duroc crossbred pigs

This study examined the physico-chemical characteristics, oxidative stability and sensory properties of Iberian cry-cured hams as affected by the genetic background of the pigs: purebred Iberian (PBI) pigs vs reciprocal cross-bred Iberian × Duroc pigs (IB × D pigs: Iberian dams × Duroc sires; D × IB pigs: Duroc dams × Iberian sires). Samples from PBI pigs contained significantly higher amounts of IMF, monounsaturated fatty acids, heme pigments and iron than those from crossbred pigs. The extent of lipid and protein oxidation was significantly larger in dry-cured hams of crossbred pigs than in those from PBI pigs. Dry-cured hams from PBI pigs were defined by positive sensory properties (i.e. redness, brightness and juiciness) while hams from crossbred pigs were ascribed to negative ones (i.e. hardness, bitterness and sourness). Hams from PBI pigs displayed a superior quality than those from crossbred pigs. The position of the dam or the sire in reciprocal Iberian × Duroc crosses had no effect on the quality of Iberian hams.

Effect of production system on physical-chemical, antioxidant and fatty acids composition of Longissimus dorsi and Serratus ventralis muscles from Iberian pig

The effect of three production systems of Iberian pigs namely Montanera (free-range system and feeding based on acorns and grass), Recebo (free-range system and nutrition based in combination of acorns, grass and mixed feeds) and Intensive (confinement with mixed feeds) on some quality traits of Longissimus dorsi (LD) and Serratus ventralis (SV) muscles were studied. Muscles from pigs raised in the Montanera system showed significantly higher CIE L(∗), a(∗) and b(∗) values and higher haem pigment content than those from Intensive system. Similarly, muscles from pigs raised in the Montanera system had significantly higher contents of α and γ-tocopherol and phenolic compounds contents and higher lipophilic and hydrophilic activity antioxidant than those from pigs raised in the Intensive system. Fatty acids profiles from Montanera pigs had significantly higher monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids and lower saturated fatty acids (SFA) than those from pigs raised in the Intensive system. In relation to muscle effect, LD showed lower intramuscular fat (IMF), α-tocopherol, phenolic compounds, lipid oxidation and PUFA, but higher MUFA than SV.