Suchergebnisse

Project's idea is a new paradigm of pig production systems and development of sustainable pork chains based on European local pig breeds which are held in less intensive systems, use locally available feeding resources and are adapted to local agro-climatic conditions. Local pig breeds provide products with typical, generally high sensory quality and regional identity searched by consumers. Despite revived interest, these breeds are mainly untapped and often remain endangered. The few successful examples in Europe demonstrate that the best conservation strategy is to ensure breed is self-sustaining resulting from good valorisation of pork products. As their productivity is low, local pork chains can become sustainable only when their genetic potential is benefited, production systems optimised and their products viable on the market. To enhance sustainability of pork chains based on local breeds, it is essential to gain scientific proofs of their genetic singularity, productive potential and product qualities, to develop genetic tools for authentication and breeding, to optimize pig nutrition and management (enhance welfare, use of local feeding resources), to evaluate their environmental impact, to assess consumers' attitudes, acceptability and purchase intentions, and to develop adapted marketing strategies. In addition, project promotes knowledge exchange and building of functional networks among regions esp. by means of creating an 'umbrella' trade mark as exploitation booster. These challenges are addressed by the project and will be presented. Funded by European Union's H2020 RIA program (grant agreement no. 634476).

One of the main objectives in TREASURE project is the genetic characterisation of European autochthonous pig breeds through genetic and genomic tools. The aim of the current pilot study was to evaluate the usefulness of the GeneSeek Genomic Profiler porcine SNP chip to describe genetic diversity of five Mediterranean autochthonous and three commercial pig breeds. 44 animals from Iberian (12), Krskopolje (4), Casertana (5), Cinta Senese (5), Apulo Calabrese (5), Duroc (5), Large White (4) and Landrace (4) breeds were genotyped. All DNA samples were successfully genotyped (call rates ≥0.98). A total of 59,193 SNPs were used in the genetic analyses after QC filtering. Observed (Ho) and expected (He) heterozygosities, FIS statistic and genetic distances (DS and FST) were computed. The overall FST value was 0.15. Ho and Hs values per breed ranged from 0.25 to 0.36 (Ho) and from 0.26 to 0.40 (Hs). Calabrese and Duroc were the breeds with the highest (0.16) and lowest (-0.01) FIS values, respectively. DS and FST genetic distances were very similar. Duroc and Large-White were the closest breeds, since DS and FST were 0.09 and 0.19, respectively and Landrace and Duroc the furthest ones, being DS and FST values equal to 0.22 and 0.34. Distribution of minor allele frequencies (MAF) showed that Iberian is the breed with the highest number of monomorphic SNPs (25.3%) and Landrace and Krskopolje have more alleles at intermediate frequencies. These results provide insights on the genetic diversity and relationships among the investigated breeds. This study will be enlarged to characterize the structure of European autochthonous pig populations using the same SNP chip. Funded by European Union's H2020 RIA program (grant agreement no. 634476).

The Krškopolje pig is the only indigenous Slovenian pig breed being still farmed. The breed is characterised by its rusticity and adaptation to the traditional farming system and has a black coat colour with a white belt across shoulders and forelegs. Despite the limited number of animals, the breed is on the way of becoming more sustainable due to the growing interest for local traditional breeds, in particular for organic farming. The objective of our study (made within project TREASURE) was to characterise the gut microbiota composition in 36 Krškopolje pigs raised by using three different diets: conventional feed, conventional feed supplemented with alfalfa pellets and organic feed supplemented with alfalfa hay. The gut microbiota composition of all pigs at two time points (155 and 228 days-ofage) was determined by resequencing the bacterial 16S gene in an Illumina MiSeq. Bioinformatics analyses were performed by using Qiime's open-reference OTU calling subsampled method following author's recommendations. NMDS and PERMANOVA analyses performed by the Vegan R package showed significant effects of dietary regime, showing that the organic feed produces a differentiation of the gut microbiota composition when compared with the other two diets and the two time points analysed. This pilot study illustrates the power of metagenomic analyses for the identification of effects of diets in the farming conditions of local European pig breeds. Funded by European Union's H2020 RIA program (Grant agreement no. 634476).

The Turopolje pig is a local porcine breed originating from Croatia characterised by its rusticity and adaptation to the traditional outdoor farming system linked to local oak forests. While this once-widespread breed was almost completely replaced by industrial breeds in the second half of the 20th century, there is growing interest on promoting its production in the framework of sustainable porcine production. The objective of our study (made in project TREASURE) was to characterise the gut microbiota composition in 24 Turopolje pigs raised outdoor by using a conventional feed vs a conventional feed supplemented with acorns. The gut microbiota composition of all pigs was determined by re-sequencing the bacterial 16S gene in an Illumina MiSeq device. Bioinformatics analyses were performed by using Qiime's open-reference OTU calling subsampled method following author's recommendations. NMDS and PERMANOVA analyses performed by using the Vegan R package showed significant effects of diet, showing that the acorn supplementation has a relevant impact on gut microbiota, notably by reducing richness and diversity. This result was confirmed in the differential abundance analysis which showed that 152 out of 1,466 OTUs were significantly different between the two groups. Interestingly, the predicted microbiota metabolic functions that were differentially abundant involved fatty acid and amino-acid metabolisms. Funded by European Union's H2020 RIA program (Grant agreement no. 634476).

The availability of high-throughput whole-genome sequencing (WGS) data illustrating differences among different pig breed genomes opened a new area of genomic research focused on variation caused by single nucleotide polymorphisms (SNP), small scale variation and structural variants which may all contribute to phenotypic variation among pig breeds. In our study (performed within TREASURE project) we re-analysed WGS-based data sets from more than 20 breeds, including commercial and local breeds as well as some wild boar genomes, deposited in publicly available databases. This bioinformatics tool enables discovery of new SNPs, estimation of allele frequencies (genotyping by sequencing) at candidate loci and identification of structural variation in a wide range of pig breeds. The analysis underlined the relevance of structural differences at KIT and MC1R locus involved in colour pattern formation, as well as LEPR locus associated with fatness, fatty acid metabolism and intramuscular fat composition. This approach allows discovery of important genomic differences between commercial breeds and local breeds which are analysed in the frame of the TREASURE project. Extensive mining of publicly available genomic data can together with the newly generated genomic information from local breeds, significantly contribute to the detailed characterisation of animal genetic resources present in local pig breeds. Funded by European Union's H2020 RIA program (grant agreement No. 634476).

The traditional raising system for Iberian pigs includes an open-air fattening period (montanera) where animals have a diet dominated by acorns. This system allows obtaining dry-cured products of unmatched quality. The most usual method for the verification of montanera products relies on assessing the particular backfat fatty acid composition after slaughter. Given that the advances on nutrition science makes feasible to emulate montanera meat products in an industrial farming environment, there is a growing need for the identification of complementary certification approaches. The objective of this study of TREASURE project was to evaluate the potential of gut microbiota composition analyses from faecal samples collected at slaughter as a new discrimination method of the montanera production system. Gut microbiota composition of 131 Iberian pigs (92 montanera and 131 commercial feeds) was determined by re-sequencing the bacterial 16S gene in an Illumina MiSeq device. Bioinformatic analyses were performed using Qiime's subsampled open-reference OTU calling method. NMDS and PERMANOVA analyses performed using the Vegan R package showed significant effects of diet and sampling batch on gut microbiota composition. The microbiota of montanera-raised pigs showed a tendency towards a reduced microbial diversity. Differential abundance analyses performed with the metagenomeSeq R package confirmed these differences by identifying 997 out of 1,703 OTUs whose abundance was significantly different between both systems. Our results suggest that the gut microbiota composition of Iberian pigs sampled at the slaughter could be used as a supplementary certification tool of traditional montanera Iberian pigs. Funded by European Union's H2020 RIA program (grant agreement 634476).

The traditional Iberian pig production system is characterized by a final open-air fattening period (montanera), in which the animals are fed acorns and grass, preceded by a growing period where the feeding is restricted to avoid undesirable weight gain. New growing diets based on olive agro-industrial by-products could be an alternative to avoid this restriction. The objective of the current study (of TREASURE project) was to analyse the effect of two growing alternative diets on the gut microbiota composition from faecal samples collected before and after montanera. Three diets, one incorporating dry olive pulp in the feed (DD), one incorporating olive cake in wet form (WD) and a control diet (CD) were supplied to 45 animals (15 per diet) during the growing period (45 to 95 kg of body weight). The gut microbiota composition of each individual was evaluated at two time points: before transition to montanera (95 kg) and at slaughter (160 kg). Microbiota analyses were performed by re-sequencing the bacterial 16S gene (V3-V4) in an Illumina MiSeq. Bioinformatics analyses were performed by using Qiime's open-reference subsampled OTU calling approach. The effect of diets on microbiota composition and diversity was evaluated using the Vegan package in R. Bray-Curtis distances, NMDS and PERMANOVA analyses showed significant effects on microbiota composition. WD caused an increase in microbiota diversity. In the second sampling point, differences in composition and diversity could be also observed after acorn supplementation. Funded by European Union's H2020 RIA program (Grant agreement no. 634476).

Animal genetic resources are important reservoirs of genetic diversity derived by distinct selection pressures or as result of adaptation to production conditions. The TREASURE project has investigated genetic variability in 20 European autochthonous pig breeds with the aim to describe their singularity, evaluate their adaptation, develop new methodologies for their management and identify DNA markers for breed allocation and meat authentication. Genomic data have been obtained by genotyping candidate gene markers and high density single nucleotide polymorphism arrays in ~48 animals from each breed and by whole genome resequencing. Description of genetic diversity has been obtained using several parameters. Runs of homozygosity and genomic inbreeding measures have been correlated with pedigree inbreeding coefficients. A few breed specific markers have been identified and applied. Genome wide association studies have identified genomic regions affecting unique phenotypes. This project represents one of the few examples of exploitation of genomic information that not only benefits the investigated animal genetic resources but also can provide useful information that could impact commercial populations. Funded by European Union's H2020 RIA program (grant agreement no. 634476).

The study of gut microbiota and its effects on hosts has emerged as an essential component of host homeostasis and global efficiency. Besides host's influence on gut microbiota, major quantitative and qualitative changes may occur in the composition of the intestinal microbiota due to the influence of diet and other environmental factors. In accordance with the TREASURE project global aim of enhancing sustainability of production systems for local pig breeds, the objective of our task was to conduct a pilot characterisation of intestinal microbiota in order to test its usefulness to characterize several local European pig populations and their production systems. This approach has been applied to populations belonging to the following European traditional breeds: Gascon (France), Iberian (Spain), Krskopolje (Slovenia), Mangalitsa (Serbia), Moravka (Serbia) and Turopolje (Croatia). For each breed, faecal samples have been collected along different experiments performed in the TREASURE project targeting the comprehension of a particular traditional production system (e.g. open-air farming), management practice, or the comparison of breeds. In all experiments, the metagenomics technique employed is the resequencing of the bacterial 16S in an Illumina MiSeq system. Overall, the results have shown that the gut microbiota analysis is a promising approach for the characterisation of these local breeds, by allowing a deeper understanding of their production systems and potentially allowing the development of new certification approaches. Preliminary results will be summarized in this communication. Funded by European Union's H2020 RIA program (Grant agreement no. 634476).