A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits

BACKGROUND

Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments.

RESULTS

Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene.

CONCLUSIONS

In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.

Influence of Sex and a High-Fiber Diet on the Gut Microbiome of Alentejano Pigs Raised to Heavy Weights

This study investigates the influence of sex and a dietary transition on the gut microbiota of a local Portuguese pig breed. Three groups of male Alentejano pigs (n = 10 each) were raised between ~40 and 160 kg LW. Group C included pigs that were surgically castrated, while the I group included intact ones; both were fed with commercial diets. The third group, IExp, included intact pigs that were fed commercial diets until ~130 kg, then replaced by an experimental diet based on legumes and agro-industrial by-products between ~130 and 160 kg. Fecal samples were collected two weeks before slaughter. The total DNA was extracted and used for 16S metabarcoding on a MiSeq® System. The dietary transition from a commercial diet to the experimental diet substantially increased and shifted the diversity observed. Complex carbohydrate fermenting bacteria, such as Ruminococcus spp. and Sphaerochaeta spp., were significantly more abundant in IExp (q < 0.05). On the other hand, castrated pigs presented a significantly lower abundance of the potential probiotic, Roseburia spp. and Lachnospiraceae NK4A136 group (q < 0.01), bacteria commonly associated with better gut health and lower body fat composition. Understanding the role of gut microbiota is paramount to ensure a low skatole deposition and consumers' acceptance of pork products from non-castrated male pigs.

Influence of Sex on Meat and Fat Quality from Heavy Alentejano Pigs Finished Outdoors on Commercial and High Fiber Diets

This work aimed to examine the effects of sex on meat and fat quality traits from thirty Portuguese Alentejano (AL) pigs reared in outdoor conditions. These pigs were divided into three groups and fed ad libitum. From ~40 to 130 kg LW, castrated (C group) and intact animals (I and IExp) consumed commercial diets. Until slaughter (~160 kg), C and I pigs remained on commercial diets, and IExp changed to a more sustainable experimental diet with locally produced pulses and byproducts. Samples were collected from the Longissimus lumborum (LL), Psoas major (PM), and dorsal subcutaneous fat (DSF). At ~160 kg, the PM muscle of intact pigs presented lower intramuscular fat content than that of C pigs, while total collagen was higher. Additionally, PM myoglobin was lower and lightness (L*) was higher in intact pigs. Regarding DSF, moisture and total protein contents were higher and total lipids were lower in intact than in castrated pigs, while color parameters were not significantly different. Finally, antioxidant capacity measured in the LL muscle showed an overall lower value in intact pigs. However, lipid oxidation values were not significantly different between the experimental groups and only increased with storage time. Outdoor-reared intact AL pigs produced leaner and less saturated pork and fat compared to castrated ones. Despite the lower antioxidant activity observed in the LL muscles of intact pigs, the lipid oxidative stability of cooked meat was not different among the experimental groups.

Effects of the Mean Weight of Uniform Litters on Sows and Offspring Performance

This study aimed to determine the effects of uniform litters of different mean birth weights on colostrum production of sows and piglets performance. The study involved 98 multiparous sows from a commercial lean genotype and their piglets. Simultaneous farrowing were supervised and the piglets were divided into experimental litters of 12 piglets each of heterogenous litters (HET, CV = 23.8%, n = 20), uniform light litters (ULL, CV = 9.8%, n = 27), uniform average litters (UAL, CV = 8.2%, n = 23) or uniform heavy litters (UHL, CV = 8.6%, n = 28) piglets and allowed to suckle. Piglets were re-weighed at 24 h and 21 d of life and deaths registered. Colostrum intake (CI) of the piglets and sow's colostrum yield (CY) was estimated using two prediction equations. Significant differences (p < 0.001) were observed in the CY of sows being higher in UHL, lower in ULL and intermediary in HET and UAL litters. CY was positively related to litter total weight at birth and litter weight gain in the first 24 h (p < 0.001). The CI differ between litter type being higher in UHL litters and lower in ULL litters. The coefficient of variation of CI in HET litters was higher than in uniform litters, regardless of their type. The mortality rate of piglets until 21 d was globally 9.6% and it was significantly higher in HET than in UAL (p = 0.033) and tended to be higher than in UHL litters (p = 0.052). No differences in piglet survival were observed between uniform litters. Results show the beneficial effect of uniformity in piglet survival and that the mean weight of uniform litter influences colostrum intake and piglet performance.

Transcriptomic Profiling of Subcutaneous Backfat in Castrated and Intact Alentejano Pigs Finished Outdoors with Commercial and Fiber-Rich Diets

In this work, we studied the backfat transcriptome of surgically castrated (C), intact (I) and intact fed an experimental diet (IE) outdoor-reared male Alentejano (AL) pigs. The experimental diet was a high-fiber diet with locally produced legumes and by-products associated with a boar taint reduction effect. At slaughter (~160 kg), backfat samples were collected for total RNA sequencing. Intact pigs presented leaner carcasses, more total collagen, and more unsaturated intramuscular fat content than C animals. A total of 2726 differentially expressed genes (DEGs, |log2 FC|> 0.58, q < 0.05) were identified between C and I with overexpressed genes related to muscular activity (MYH1, ACTA1) or collagen metabolism (COL1A1, COL1A2) in I pigs. Between C and IE, 1639 DEGs of genes involved in lipidic metabolism (LEP, ME1, FABP4, ELOVL6) were overexpressed in C. Finally, only 28 DEGs were determined between I and IE. Clustering results indicated a drastic influence of the testis in the transcriptome of subcutaneous fat of AL pigs, while the diet had a marginal effect. Diet can reduce stress by increasing satiety in animals, and could have induced an increase of skatole degradation due to the higher expression of the CYP2A19 gene in the IE group.

Outdoor Finishing of Intact Male Portuguese Alentejano Pigs on a Sustainable High-Fiber Diet: Impacts on Blood, Growth, Carcass, Meat Quality and Boar Taint Compounds

This trial evaluated the effect of sex on the blood, growth, carcass, meat quality, and boar taint compounds in male Alentejano (AL) pigs (n = 30). From ~40 to 130 kg LW, castrated (C) and intact pigs (I and IExp groups) were fed commercial diets ad libitum. Between ~130 and 160 kg (slaughter), C and I pigs continued on commercial diets, while IExp were fed an experimental diet containing locally produced pulses and by-products aimed at reducing boar taint. At ~160 kg, blood urea levels were higher in IExp than C pigs, triacylglycerols were lower in both intact groups, and cortisol was lower in IExp. IExp pigs exhibited faster growth, improved feed conversion ratio, carcass higher commercial yield and leaner meat than C pigs. The loin intramuscular fat in intact pigs was lower, less saturated and more polyunsaturated, while total collagen was higher. Fat androstenone content was higher in intact pigs and skatole content was similar across treatments, although they were below threshold values for consumer detection. Finally, although boar taint compounds were low in intact AL pigs raised outdoors, adding pulses and by-products to the experimental diet did not result in a reduction in fat skatole content compared to pigs fed the commercial diet.

Prediction of fatty acid composition in intact and minced fat of European autochthonous pigs breeds by near infrared spectroscopy

The fatty acids profile has been playing a decisive role in recent years, thanks to technological, sensory and health demands from producers and consumers. The application of NIRS technique on fat tissues, could lead to more efficient, practical, and economical in the quality control. The study aim was to assess the accuracy of Fourier Transformed Near Infrared Spectroscopy technique to determine fatty acids composition in fat of 12 European local pig breeds. A total of 439 spectra of backfat were collected both in intact and minced tissue and then were analyzed using gas chromatographic analysis. Predictive equations were developed using the 80% of samples for the calibration, followed by full cross validation, and the remaining 20% for the external validation test. NIRS analysis of minced samples allowed a better response for fatty acid families, n6 PUFA, it is promising both for n3 PUFA quantification and for the screening (high, low value) of the major fatty acids. Intact fat prediction, although with a lower predictive ability, seems suitable for PUFA and n6 PUFA while for other families allows only a discrimination between high and low values.

Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Simple Summary

Screening and interpretation of differentially expressed genes and associated biological pathways was conducted among experimental groups with divergent phenotypes providing valuable information about the metabolic events occurring and identification of candidate genes with major regulation roles. This comparative transcriptomic analysis includes the first RNA-seq analysis of the Longissimus lumborum muscle tissue from two Portuguese autochthonous pig breeds with different genetic backgrounds, Alentejano and Bísaro. Moreover, a complementary candidate gene approach was employed to analyse, by real time qPCR, the expression profile of relevant genes involved in lipid metabolism, and therefore with potential impacts on meat composition. This study contributes to explaining the biological basis of phenotypical differences occurring between breeds, particularly the ones related to meat quality traits that affect consumer interest.

Abstract

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

Effect of litter birth weight standardization before first suckling on colostrum intake, passive immunization, pre-weaning survival, and growth of the piglets

Within-litter variation in birth weight is a relevant factor in pig production. This study aimed at comparing pre-weaning mortality, colostrum intake (CI), passive immunization, and growth of piglets from litters of uniform (UN) or heterogeneous (HET) birth weights. The study included 52 multiparous sows (Large White × Landrace) and their litters. Two types of litters were constituted based on birth weight, namely: UN or HET, the control group, using piglets from two to three sows farrowing approximately at the same time. At birth, piglets were weighed, identified, and placed in a box under an IR lamp. At the end of farrowing, piglets were re-weighed and allotted to groups UN or HET (12 per litter) with average weights of 1394 and 1390 g, respectively, and allowed to suckle (time 0). They were re-weighed 24 h later to estimate CI and sows' colostrum yield. At time 0, the average intra-litter CV (%) in weight of experimental litters were 9.3 ± 0.8 (SEM) and 27.8 ± 0.7 in groups UN and HET, respectively (P < 0.001). At 2 days of age, blood samples were taken from the piglets of 11 litters five UN and six HET) and serum Immunoglobulin G (IgG) contents were determined. Mean CI/piglet/litter was similar in both groups, that is, 415 ± 13 in UN and 395 ± 13 g in HET (P = 0.28), but was less variable in UN litters (CV = 22.4 ± 2 vs 36.0 ± 2%, P < 0.001). The IgG levels at 2 days of age were higher in piglets from UN litters (22.5 ± 0.8 vs 18.4 ± 0.7 g/l; P < 0.001) but the CV of IgG levels was not different between litter type (P= 0.46). Mortality up to 21 days of age was lower in UN litters (6.4 vs 11.9%, P = 0.03). The BW at 21 days was not different between litter type (P = 0.25) but it was less variable among piglets from UN litters (CV: 17.1 ± 1.3 vs 25.7 ± 1.3%; P = 0.01). Results reveal that CI is less variable and mortality is lower in piglets from litters of UN birth weight. The results infer that genetic improvement to decrease variation in birth weight within-litter could have a positive effect on homogeneous CI and thus contribute to reducing piglet mortality.

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a “One Health” perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a “One Health” perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.

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.

Physical Activity Effects on Blood Parameters, Growth, Carcass, and Meat and Fat Composition of Portuguese Alentejano Pigs

Simple Summary

Outdoor farming systems are associated with health, animal welfare, sustainability, and food security, making them highly desirable for consumers. In this trial, it was possible to confirm that pig physical activity, a major factor in the traditional and extensive production systems of the Alentejano pig, influences animal welfare and the results of biochemical and zootechnical parameters. In this perspective, breeding pig breeds that perform spontaneous physical activity has greater advantages for producers, as pigs can reach the same slaughter weight in less time and with lower feed costs than animals reared in individual pens. Based on these results, the negative impacts that system intensification (with the consequent reduction in the vital space of each animal and the physical activity performed) may have on animal welfare, animal performance and on the quality of the meat obtained, should be considered.

Abstract

This study evaluated the effects of physical activity on blood, growth, carcass, and meat quality of finishing Alentejano (AL) pigs. Pigs, reared from ~87 to 160 kg in individual pens (no exercise area, NE group, n = 9) or in an outdoor park (with exercise area, WE group, n = 9), were fed commercial diets (85% ad libitum). WE pigs were in a park (~400 m²) with a feeding area separated from the drinking area with an automatic waterer, forcing pigs to walk at least 800 m daily. Blood samples were obtained during the trial (weeks 2, 11, and 18) and at slaughter. The left-side carcass was submitted to commercial cuts, and samples from loin, tenderloin, and dorsal subcutaneous fat (DSF) were analyzed. Plasma urea in WE pigs was higher in weeks 2 and 11, while cholesterol, LDL-cholesterol, cholesterol to HDL-cholesterol and LDL- to HDL-cholesterol ratios, and cortisol were lower in weeks 11 and 18. Final weight and average daily gain were higher and feed conversion ratio lower in WE pigs. DSF thickness and carcass weight were higher in WE pigs, leading to higher carcass yield. Finally, loin and tenderloin from WE pigs presented higher total protein content. These data show that allowing physical activity affects metabolism, growth, and carcass and meat quality of AL pigs.

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Background

Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (H_P) and fixation index (F_ST)] and group-based F_ST approaches, which compare groups of breeds defined according to external traits and use/specialization/type.

Results

We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars.

Conclusions

Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these 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.

Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds

When compared to modern lean-type breeds, Portuguese local Alentejano (AL) and Bísaro (BI) pig breeds present a high potential for subcutaneous and intramuscular fat (IMF) deposition which contributes for better meat quality. The aim of this work was to explore the genome function to better understand the underlying physiological mechanisms associated with body fat accretion. Dorsal subcutaneous fat samples were collected at slaughter from adult animals (n = 4 for each breed) with ~150 kg body weight. Total RNA was obtained and sequenced for transcriptome analysis using DESeq2. A total of 458 differentially expressed (DE) genes (q-value < 0.05) were identified, with 263 overexpressed in AL and 195 in BI. Key genes involved in de novo fatty acid biosynthesis, elongation and desaturation were upregulated in AL such as ACLY, FASN, ME1, ELOVL6 and SCD. A functional enrichment analysis of the DE genes was performed using Ingenuity Pathway Analysis. Cholesterol synthesis is suggested to be higher in AL via SREBF2, SCAP and PPARG, while lipolytic activity may be more active in BI through GH and AMPK signalling. Increased signalling of CD40 together with the predicted activation of INSIG1 and INSIG2 in BI suggests that this breed is more sensitive to insulin whereas the AL is less sensitive like the Iberian breed.

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 F_ST 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.

Modelling Nutritional Requirements of Growing Pigs from Local Breeds Using InraPorc

Models such as InraPorc enable the growth of pigs to be simulated and their nutrient requirements to be determined. However, so far, these models have not been applied to local breeds. We used InraPorc to determine the nutrient requirements of growing pigs from local breeds (H2020 European Union project TREASURE). Data on feed composition, allowance and intake, and body weight (BW) were obtained from literature reports or experiments conducted within the project. Data were used in InraPorc to calibrate 16 growth and intake profiles from nine breeds (Alentejana, Basque, Bísara, Apulo Calabrese, Cinta Senese, Iberian, Krškopolje pig, Mangalitsa, and Moravka), with one to three profiles per breed depending on the experimental conditions or data source. On the 40-100 kg BW range, mean protein deposition (PDm) was low for all breeds (below 116 g/d vs. over 130 g/d in conventional breeds). The age of pigs at 40 kg BW (110 to 206 days) denoted different types of feeding management in addition to genetic differences. The PDm and the lysine requirements were the highest in breeds with the highest average daily gain. In all breeds, a small proportion of total body energy retention was dedicated to protein, with the greatest proportion of energy retention in the form of lipids. Despite some methodological limitations, this study provides initial insights into the nutrient requirements of some local breeds.

Diversity across major and candidate genes in European local pig breeds

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.

O porco Ribatejano: Renascimento de uma população autóctone? Primeiros dados de crescimento e de carcaça

No âmbito do projeto TREASURE e com o objectivo de avaliar o desempenho produtivo do porco Ribatejano, resultante do cruzamento entre porcos Alentejanos (AL) e Bísaros (BI), 10 machos castrados de cada um dos genótipos AL, BI, ALxBI e BIxAL, foram estudados. Os animais foram criados em sistema tradicional e alimentados com rações comerciais ad libitum, tendo sido abatidos a ~65 kg de peso vivo (PV). Os dados obtidos mostraram que os suínos BI, ALxBI e BIxAL atingiram o peso de abate mais rapidamente (P

Primeiros resultados reprodutivos e produtivos do porco Ribatejano

Este trabalho pretendeu estudar comparativamente, parâmetros reprodutivos e produtivos das raças suínas Bísara (BI) e Alentejana (AL) utilizadas em cruzamento recíproco para a obtenção do porco Ribatejano. Nove porcas e marrãs AL e seis marrãs BI foram cobertas por varrascos BI e AL, respetivamente. Registaram-se as datas de cobrição e parto e os tamanhos da ninhada ao parto e aos 28 dias. As fêmeas AL apresentaram uma gestação mais curta (111±0,4d vs 113,7±0,5d; P=0,002). As fêmeas BI apresentaram ninhadas maiores quer em nascidos totais (11,0±1,0 vs 6,7±0,8; P=0,004), quer em nascidos vivos (10,0±1,0 vs 6,7±0,8; P=0,026). A mortalidade até ao desmame não foi diferente entre genótipos (P=0,255) apresentando uma taxa média de 12%. Aos 28d as ninhadas das fêmeas BI permaneciam maiores (8,5±0,8 vs 6,1±0,6; P=0,032). Em 4 marrãs de cada genótipo foram acompanhados o parto e a lactação até aos 28d, pesando-se os leitões ao nascimento, às 24h e aos 28d. O parto teve uma duração média de 97±22min, não sendo diferente entre genótipos (P=0,253). Quando comparados com os leitões ALBI (ALxBI), os leitões BIAL (BIxAL) pesavam mais ao nascimento (1402±46g vs 1209±36g; P=0,002). A ingestão de colostro por kg de peso vivo nas primeiras 24h foi similar entre genótipos (P=0,735), apresentando um valor de 289±15g para os leitões ALBI e de 281±19g para os leitões BIAL. O ganho médio diário até aos 28 dias e o peso dos leitões a essa idade não foi diferente entre genótipos (P=0.161 e P=0.091), e apresentaram valores médios de 195±6g e 6761±181g, respetivamente. O peso da ninhada aos 28 dias tendeu a ser maior (P=0,058) em ninhadas ALBI (56,6±4,0kg) quando comparadas com as ninhadas BIAL (43,2±4,0kg). Estes resultados, obtidos no âmbito do projeto europeu Treasure são, aparentemente, os primeiros registos acerca deste cruzamento e poderão ser usados no futuro como referência para estudos e para criadores que equacionem fazer este cruzamento para uma utilização comercial.

IX Simposio Internacional del Cerdo Mediterráneo

Bienvenidos al IX Simposio Internacional del cerdo mediterráneo. Es un placer dar la bienvenida a todos los colegas y participantes en Portalegre-Portugal. Veintisiete años después del primer simposio en Ajaccio-Córcega esperamos tener un simposio fructífero y desafiante en el que los enfoques de apertura de la discusión y la innovación, sobre la producción porcina en sistemas abiertos o silvopastoriles, conduzcan a mejorar y actualizar nuestra comprensión actual.

Encuesta de datos demográficos y fenotípicos de razas locales de cerdos del proyecto TREASURE

Este trabajo presenta los resultados de una encuesta de datos demográficos y fenotípicos de 20 razas locales de cerdos en estudio en el proyecto H2020 TREASURE y incluí información de: parámetros demográficos, características morfológicas principales, parámetros reproductivos, informaciones adicionales a nivel de los efectivos (ex. Temperamento, instalaciones, prácticas de cubrición), orígenes y desarrollo de las razas. Casi todas las razas (18 de 20) tienen libro genealógico, aunque su fecha de inicio varía mucho (de 1980 a 2006). El número de hembras reproductoras varía de 24 (Moravka) a más de 200 mil cabezas (Ibérico). La relación macho/hembra varía mucho con los valores más altos verificados en las razas italianas muy probablemente debido a una política diferente relativamente al registro de animales. Casi todas las razas tienen programas de conservación, aunque pocas están interesadas en otras técnicas de conservación y sólo en menos que 5 razas los datos relativos a número de efectivos y de coeficiente de consanguinidad están fácilmente disponibles. Los valores medios para números de pezones, tamaño de camada y lechones destetados son de 12, 8 y 6, respectivamente con un grande potencial para mejora. El escenario descrito es altamente diversificado y esta colecta de datos representa el punto de partida para una marca colectiva debajo del parasol del proyecto TREASURE.

Influence of outdoor rearing and oleic acid supplementation on lipid characteristics of muscle and adipose tissues from obese Alentejano pigs

Data evaluating the effect of oleic-acid-enriched diets and outdoor rearing (with access to pasture) on the quality of Alentejano (AL) pork and fat are limited. The aim of this work was to study the effects of feeding low (LO) or high oleic acid (HO) diets to AL pigs reared in individual pens (IND) or outdoors (OUT) with access to pasture. Biceps femoris and dorsal subcutaneous fat (DSF) samples were collected to analyse chemical composition and lipids fatty acid (FA) profile. The expression of seven genes involved in lipogenesis, lipolysis and FA transport, as well as two transcription factors were also evaluated in the muscle. B. femoris and DSF presented lower lipid content in OUT-reared than in IND-reared pigs. Two genes involved in lipogenesis, ACACA and FASN, were under-expressed in B. femoris from OUT-reared pigs, while two involved in lipolysis, LPL and HSL were over-expressed. HO diet also significantly reduced FASN expression. Both rearing system and diet affected the FA profile of tissues, particularly DSF. Overall, OUT-reared pigs presented lower n6 to n3 FA ratios in all tissues, and lower monounsaturated (MUFA) and higher polyunsaturated fatty acids (PUFA) content in DSF. When compared to LO-fed ones, HO-fed pigs presented higher oleic acid proportions in all tissues, and lower SFA, higher MUFA and PUFA levels, as well as lower saturation, atherogenic and thrombogenic indexes in DSF. This study shows that rearing system and oleic acid supplementation have complementary effects and influence the nutritional quality of pork and DSF.

How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes

The coexistence of wild boars and domestic pigs across Eurasia makes it feasible to conduct comparative genetic or genomic analyses for addressing how genetically different a domestic species is from its wild ancestor. To test whether there are differences in patterns of genetic variability between wild and domestic pigs at immunity-related genes and to detect outlier loci putatively under selection that may underlie differences in immune responses, here we analyzed 54 single-nucleotide polymorphisms (SNPs) of 19 immunity-related candidate genes on 11 autosomes in three pairs of wild boar and domestic pig populations from China, Iberian Peninsula, and Hungary. Our results showed no statistically significant differences in allele frequency and heterozygosity across SNPs between three pairs of wild and domestic populations. This observation was more likely due to the widespread and long-lasting gene flow between wild boars and domestic pigs across Eurasia. In addition, we detected eight coding SNPs from six genes as outliers being under selection consistently by three outlier tests (BayeScan2.1, FDIST2, and Arlequin3.5). Among four non-synonymous outlier SNPs, one from TLR4 gene was identified as being subject to positive (diversifying) selection and three each from CD36, IFNW1, and IL1B genes were suggested as under balancing selection. All of these four non-synonymous variants were predicted as being benign by PolyPhen-2. Our results were supported by other independent lines of evidence for positive selection or balancing selection acting on these four immune genes (CD36, IFNW1, IL1B, and TLR4). Our study showed an example applying a candidate gene approach to identify functionally important mutations (i.e., outlier loci) in wild and domestic pigs for subsequent functional experiments.