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Additional file 15: Figure S1. Sequencing depth obtained for samples analyzed in each one of the two contrasts (AL-T0/AL-T1 and AL-T0/AL-T2). Figure S2. Joint Principal Component Analysis (PCA) clustering of gluteus medius skeletal muscle samples (11 AL-T0, 12 AL-T1 and 12 AL-T2 samples) according to the expression profiles of (A) mRNAs, (B) microRNAs and (C) lincRNAs. Figure S3. Phylogenetically conserved 7mer-8 m predicted binding sites in the 3′- UTR of the pig PDK4 gene for (A) ssc-miR-148a-3p and (B) ssc-miR-493-5p porcine miRNAs. The TargetScan software was used for generating conservation graphs across the investigated mammalian species. Red nucleotides show complementary matching base-pairs between the seed of the mature miRNA and the 3’UTR of the pig PDK4 gene. Figure S4. Gene co-expression module association with meat quality and fatty acids composition traits in the AL-T0/AL-T1 contrast as determined with the WGCNA tool. Figure S5. Gene co-expression module association with meat quality and fatty acids composition traits in the AL-T0/AL-T2 contrast as determined with the WGCNA tool. more...

Negre Mallorquí pig is a native breed from Mallorca, characterized by its high rusticity and adaptation to the Mediterranean climatic conditions. The present chapter presents the history and current status of this breed, its phenotypic characteristics, the particularities of its production system and main products from this Mediterranean native pig breed. Data come from the scarce literature about Porc Negre Mallorquí breed, adding non-published data obtained during the TREASURE project. Reproductive performance was estimated by means of sow age at first parturition, litters per sow per year, piglets alive per litter, piglets birth and weaning weights, percentage of stillborn per litter, death rate percentage from birth to weaning, duration of lactation and farrowing interval. Growth performance was estimated by means of average daily gain and daily feed intake in several production periods. Carcass traits were evaluated by means of age and weight at slaughter, hot carcass weight, carcass yield and back fat thickness in several points. Meat quality traits were evaluated by means of pH at 45 min and 24 h after slaughter, objective colour, intramuscular fat content and fatty acid composition of intramuscular fat and back fat. The current chapter defines a first review about this local pig breed. more...

Sustainable production system: characteristics of animals and products of the Porc Negre Mallorquí The Porc Negre Mallorquí (PNM), recognized as an endangered breed, is the only pig breed native in the Balearic Islands. The formation of this population derives from adaptation process since the arrival of the first inhabitants. Medium size, black hair, drooping ears and “tassels” under the neck, characterize this breed. The current 2018 census identifies 61 farms with 1523 breeding and 3497 fattening pigs. This breed has adapted to Mediterranean agro-climatic conditions, with a diet based on pastures, cereals, legumes, figs, almonds, acorns and Mediterranean bushes, with barley supplements and green peas. Performance depends on available resources, with an average productivity of 14 piglets/sow/year and post-weaning growth of about 400-500 g/day until slaughter (140-160 kg live weight). In the European Union TREASURE project, a lower slaughter yield (~75.1%) and an exceptionally higher fat content (thickness of back fat ~5.5 cm) than those of conventional breeds were confirmed. Significant differences also exist in the quality of the meat, with higher content of fat (~6-8%) and mono-unsaturated fatty acids (~50%) in the loin, a darker colour, and a weaker shearing force. This black pig breed has been consolidated due to the development of the Protected Geographical Indication quality brand for "Sobrassada de Mallorca de Porc Negre" as a main traditional product and local sales of the PNM piglet ("Porcella"), within a sustainable production system. more...

Trabajo presentado a las XVIII Jornadas sobre Producción Animal (AIDA), celebradas en Zaragoza el 7 y 8 de mayo de 2019., AGL2013-48742-C2-1-R; AGL2013-48742-C2-2-R; SEV-2015-0533

[Background]: The molecular basis of compensatory growth in monogastric animals has not yet been fully explored. Herewith, in this study we aim to determine changes in the pig skeletal muscle transcriptome profile during compensatory growth following a feed restriction period. A RNA-Seq experiment was performed with a total of 24 females belonging to a Duroc commercial line. Half of the animals received either a restricted (RE) or ad libitum (AL) diet during the first fattening period (60–125 d of age). After that, all gilts were fed ad libitum for a further ~30 d until the age of ~155 d, when animals were slaughtered and samples of gluteus medius muscle were harvested to perform RNA-Seq analyses and intramuscular fat content determination., [Results]: During the period following food restriction, RE animals re-fed ad libitum displayed compensatory growth, showed better feed conversion rate and tended to deposit more subcutaneous fat than AL fed animals. Animals were slaughtered in the phase of accelerated growth, when RE animals had not completely compensated the performance of AL group, showing lower live and carcass weights. At intramuscular level, RE gilts showed a higher content of polyunsaturated fatty acids during the compensatory growth phase. The comparison of RE and AL expression profiles allowed the identification of 86 (ǀlog2Fold-Changeǀ > 1, padj, [Conclusions]: Animals re-fed after a restriction period exhibited a less oxidative metabolic profile and catabolic processes in muscle than animals fed ad libitum. The downregulation of autophagy observed in the skeletal muscle of pigs undergoing compensatory growth may constitute a mechanism to increase muscle mass thus ensuring an accelerated growth rate. These results reveal that the downregulation of AMPK Signaling plays an important role in compensatory growth in pigs., The study was funded by grants AGL2013–48742-C2–1-R and AGL2013–48742-C2–2-R, awarded by the Spanish Ministry of Economy and Competitivity (MINECO). We also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016–2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics (CRAG). Maria Ballester is financially supported by a Ramon y Cajal contract (RYC-2013-12573) from the Spanish Ministry of Economy and Competitiveness. Tainã Figueiredo Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education of the Federal Government of Brazil. Rayner Gonzalez-Prendes was funded with a FPU Ph.D. grant from the Spanish Ministry of Education (FPU12/00860). Thanks also to the CERCA Programme of the Generalitat de Catalunya. more...

Objectives: Metabolic programming of the offspring following maternal overfeeding during gestation may be mediated by epigenetic changes in adipose tissue, the mechanisms of which remain to be elucidated. No studies have been reported on the pharmacological reversibility of such processes early in life. In this context, our aims were: (1) to study the effects of maternal overfeeding on the metabolic and epigenetic programming of adipose tissue; and (2) to test the potential of postnatal metformin treatment to reverse these changes. Methods: We studied male and female piglets born to commercial production sows (Sus scrofa domesticus) who were fed during gestation with a standard diet (control feeding piglets: CF piglets; n=16), or a hypercaloric diet (piglets from overfed sows: OF piglets; n=16). Piglets received treatment with metformin or vehicle (1:1) during lactation, and were sacrificed at weaning (28 days). At sacrifice, weight was assessed and metabolic markers in serum were analyzed: glucose, insulin, fructosamine, C-reactive protein (CRP), lipids and adiponectin. Visceral adipose tissue hypertrophy (size of the adipocytes), inflammation (gene expression of TNFA, IL6 and CCL2) and DNA methylation levels of adipogenesis genes (NDN and DLK1) were studied. Results: OF piglets showed a worse metabolic profile (higher weight, increased levels of fructosamine and CRP, and lower HOMA-β and adiponectin) together with an inflammatory phenotype in visceral adipose tissue (higher expression of CCL2) and adipocyte hypertrophy (increased area, perimeter and diameter), all p more...

International audience; TREASURE project aims to develop sustainable pork chains based on European local pig breeds. The Porc Negre Mallorquí (Majorcan Black Pig, MBP) is an untapped pig breed from Mallorca, in the Balearic Islands, included in the project due its high rusticity, adaptation to the environment and meat quality differentiation. Particularities of MBP are mostly unknown out from Mallorca, with only one representative meat product, the ‘sobrassada de Mallorca de Porc Negre’, a fat-rich cured sausage owning a PGI trademark. Carcass, meat and fat quality of MBP was evaluated, according to a standardised toolbox of parameters. The toolbox aimed for a harmonised knowledge of untapped breeds, made from the contribution of researcher’s expertise and the literature. The mean values and standard deviation for carcass traits (n=29) were: 156.8±11.8 kg for live weight, 125.3±12.9 kg for carcass weight, 75.1±3.2% for carcass dressing, 88.7±3.7 cm for carcass length and 55.2±10.1 mm for ZP fat. The most remarkable results for the meat quality parameters toolbox (n=58) were an ultimate pH of 5.58±0.12 and electrical conductivity of 6.99±3.44 mS, a lightness value (L*) of 44.10±3.59, a drip loss of 1.49±1.46%, a shear force of 3.46±1.07 kg, and an intramuscular fat (IMF) content of 6.11±3.09%. The maximum value of IMF was 19%, a hint of the wide variability within this untapped breed, representing a disadvantage for the product standardisation in case of fresh meat, but not for ‘sobrassada’, mainly made of grounded ham, shoulder and loin. The results for the major fatty acid (FA) groups in back fat (n=48) samples were 41.00±1.42% of saturated FA, 51.27±1.64% monounsaturated FA and 6.88±0.71% polyunsaturated FA. ‘Sobrassada’ includes 40-50% of back fat, thus the FA composition is critical for product quality. The FA composition, with a high proportion of MUFA and low of PUFA contributes to an optimal technological quality of MBP back fat. Funded by European Union’s H2020 RIA program (grant agreement no. 634476). more...

The adiponectin (ADIPOQ) locus is a positional and functional candidate gene for 2 porcine chromosome 13 (SSC13) QTL influencing cholesterol (CHOL) and low-density lipoprotein (LDL) concentrations in 190-d-old pigs. By sequencing 2.37 kb of the pig ADIPOQ cDNA, we have identified 1 c.*1512G > T 3′ untranslated region polymorphism that has been genotyped in a Duroc pig commercial population with records for serum lipid levels at 45 and 190 d of age. Statistical analysis of the data have revealed significant associations between the ADIPOQ genotype and CHOL (P = 0.0040) and LDL (P = 0.0011) concentrations at 190 d but not at 45 d. In family 3, most of the SSC13 QTL effects on LDL levels at 190 d were explained by the ADIPOQ genotype. We also found an association with triglyceride levels at 45 d (P = 0.0060) but not at 190 d. Measurement of allelic mRNA imbalance demonstrated that the G and T alleles are expressed at very similar levels in muscle and fat tissues, indicating that the c.*1512G > T polymorphism does not affect transcript abundance. As a whole, results obtained in the current work as well as previous data gathered in humans and pigs provide evidence that the magnitude of associations between blood lipid phenotypes and candidate loci genotypes may vary depending on the age of the individual, therefore suggesting the existence of dynamic genotype × environment interactions changing on a temporal scale., This work has been funded by grants AGL2007-66707-C02, AGL2010-22208-C02-01, and AGL2010-22208-C02-02 (Ministerio de Ciencia e Innovación) and CSD 2007-00036 (Ministerio de Ciencia e Innovación, Consolider Ingenio 2010 Program). D. Gallardo and C. Melo were funded with fellowships from the Universitat Autònoma de Barcelona and the Instituto Agronómico Mediterráneo, respectively. A. Zidi received a contractual grant under the framework of CSD 2007-00036. more...

National audience

Sustainable production system: characteristics of animals and products of the Porc Negre Mallorquí The Porc Negre Mallorquí (PNM), recognized as an endangered breed, is the only pig breed native in the Balearic Islands. The formation of this population derives from adaptation process since the arrival of the first inhabitants. Medium size, black hair, drooping ears and “tassels” under the neck, characterize this breed. The current 2018 census identifies 61 farms with 1523 breeding and 3497 fattening pigs. This breed has adapted to Mediterranean agro-climatic conditions, with a diet based on pastures, cereals, legumes, figs, almonds, acorns and Mediterranean bushes, with barley supplements and green peas. Performance depends on available resources, with an average productivity of 14 piglets/sow/year and post-weaning growth of about 400-500 g/day until slaughter (140-160 kg live weight). In the European Union TREASURE project, a lower slaughter yield (~75.1%) and an exceptionally higher fat content (thickness of back fat ~5.5 cm) than those of conventional breeds were confirmed. Significant differences also exist in the quality of the meat, with higher content of fat (~6-8%) and mono-unsaturated fatty acids (~50%) in the loin, a darker colour, and a weaker shearing force. This black pig breed has been consolidated due to the development of the Protected Geographical Indication quality brand for "Sobrassada de Mallorca de Porc Negre" as a main traditional product and local sales of the PNM piglet ("Porcella"), within a sustainable production system. more...

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. more...