Suchergebnisse

The interest for traditional genetic resources, here comprised local pig breeds, has been increased in the last decades. Yet, at the time being, majority of local pig breeds still need to be supported with subsidies to ensure their conservation. However, the best strategy is if breeds could reach self-sustainability which is possible by an efficient marketing strategy of their products. The majority of studied breeds in project TREASURE are untapped, so the ambition is to develop an "umbrella" collective trademark that would gather together all breeds and that would create added values for their products. Major socio-economic aspects related to the implementation of the collective trademark include rights, responsibilities and expected added value for end-users. Based on the results obtained by an internal survey conducted in TREASURE, we have identified the main features of the collaborative trademark: 1) it should attract end-users such as farmers, breeders associations and meat processors; 2) it should be developed and promoted by an operational committee of end-users, under the coordination and supervision of TREASURE Consortium; 3) it should emphasize local pig genetic resources as the key common point, considering also production systems and nutrition; 4) it should explore possible collaboration or conflict with existing EU protected products (PDO, PGI, TSG) in order to optimally promote local products. An overview of intellectual property rights (IPR) in the context of pork value chains existing in the European Union is presented and prospects for TREASURE trademark analysed.

Artificial selection may cause an increasing of homozygosity in circumscribed regions of the genome and lead to allele drift. This is particularly important for selection nuclei of pure breeds. In this work we analysed the genome of the Italian Large White (ILW) and Italian Duroc (ID) breeds, that are purposely selected for the heavy pig breeding industry, to identify regions of high homozygosity. A total of 1,953 Italian Large White and 460 Italian Duroc pigs were genotyped with the Illumina PorcineSNP60 BeadChip. Filtering was performed to remove poor quality single nucleotide polymorphisms (SNPs) having call rate<0.9 that were then imputed whereas no other filter was applied. The Runs of Homozygosity (ROH) analyses were performed with the sliding window-based option of the Plink 1.9 software, allowing a minimum of 30 SNP to define a ROH. Then, for each SNP, the percentage of the number of animals that have a ROH containing the SNP was calculated and the top 0.994 percentile of the SNPs empirical distribution was considered. The analyses of the ILW detected four regions, three on porcine chromosome (SSC) 1 and one region on SSC14, with size from ~1 to 5 Mb and with maximum peak of shared regions of 70% on SSC1. The analysis of the ID pigs showed several SNPs shared by more than the 50% of the animals, particularly two regions on SSC9 and SSC15, with maximum peak of 95% on SSC15. The detected regions contained genes involved in functions such as DNA repair and biosynthesis of cellular amino acid. The possible effects of these regions and the genes included in relation to production traits still need to be analysed. Partially funded by European Union's H2020 RIA program (grant agreement no. 634476).

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).

Next generation sequencing applied in pigs have recently produced re-sequenced pig genome data from different individuals belonging to a large variety of breeds. The availability of these large datasets is opening new opportunities to mine public nucleotide archives and identify mutations that could putatively affect economic relevant traits. Moreover, resequencing data from pooled pig DNA could provide cost-effective whole genome information from a large number of animals. In this study, we mined 110 individual pig genomes retrieved from the European Nucleotide Archive and from proprietary datasets generated from pigs of 28 different breeds. This dataset was integrated from 8 pooled whole genome resequencing datasets generated from 35 individuals each from 8 distinct commercial or autochthonous breeds (Italian Large White, Italian Duroc, Italian Landrace, Apulo Calabrese, Cinta Senese, Casertana, Mora Romagnola, Nero Siciliano), respectively. Individual and pooled pig genome datasets were searched for polymorphisms in 135 annotated candidate genes, including 25 genes involved in androsterone and skatole biochemical related pathways. Short reads from these genomes were aligned using bowtie to a customized reference sequence generated from the reference pig genome, including sequence of selected genes (with depth ranging from 4 to 40X for each genome). A total of 100k variants were identified (2.3% in coding regions with about 500 missense mutations and a few other potential functional mutations). About 15% of these numbers refers to genes encoding enzymes involved in the androsterone and skatole biochemical pathways. This study provided an overview of the variability in targeted gene regions potentially involved in determining boar taint in pigs. Partially funded by European Union's H2020 RIA program (grant agreement no. 634476). Abstract reflects the authors' view. European Union Agency is not responsible for any use that may be made of the information it contains.

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).

International audience ; Traditional pig productions systems, relying mainly on local pig breeds and outdoor rearing, have been poorly investigated so far in terms of environmental impacts. The few existing studies did not account for possible sequestration of carbon and emissions consecutive to grazing. Twenty-five farms of Gascon breed in France (FR), 8 with Mora Romagnola breed in Italy (IT), and 15 of Krškopolje breed in Slovenia (SI) were evaluated while accounting for the emissions from pasture intake and the potential for carbon sequestration. Pig production system in SI presented the lowest impacts per kg of live weight, due to better feed conversion ratio caused by indoor production and due to lower impacts of feeds – most diets were based on grains, vegetables, tubers and roots produced on farm. Among the systems, acidification potential (AP) was 13% higher in IT than the average for FR and SI, due to higher dietary crude protein content (+9% than the average), while the eutrophication potential (EP) was 27% higher in FR system than the average, as a result of higher phosphorus content of feeds (+28% than the average). When the potential of carbon sequestration was taken into account, the GWP impact was reduced 4% on average. Conversely, when accounting for the emissions from pasture intake the GWP was increased by 2%, mainly when a high digestible grass was considered. The use of high digestible grass provided lower AP and EP impacts than low digestible grass. The large variability between farms in terms of environmental impacts suggests that the margins for improvement of local breeds' production rely on improvement of feed composition and supply, and origin of feed ingredients. There is a great need for better estimation of digestibility of grasses and of carbon sequestration, in order to reduce the uncertainties associated with the environmental impacts evaluated of outdoor pigs' systems. Funded by European Union's H2020 RIA program (grant agreement no. 634476).

International audience ; Traditional pig productions systems, relying mainly on local pig breeds and outdoor rearing, have been poorly investigated so far in terms of environmental impacts. The few existing studies did not account for possible sequestration of carbon and emissions consecutive to grazing. Twenty-five farms of Gascon breed in France (FR), 8 with Mora Romagnola breed in Italy (IT), and 15 of Krškopolje breed in Slovenia (SI) were evaluated while accounting for the emissions from pasture intake and the potential for carbon sequestration. Pig production system in SI presented the lowest impacts per kg of live weight, due to better feed conversion ratio caused by indoor production and due to lower impacts of feeds – most diets were based on grains, vegetables, tubers and roots produced on farm. Among the systems, acidification potential (AP) was 13% higher in IT than the average for FR and SI, due to higher dietary crude protein content (+9% than the average), while the eutrophication potential (EP) was 27% higher in FR system than the average, as a result of higher phosphorus content of feeds (+28% than the average). When the potential of carbon sequestration was taken into account, the GWP impact was reduced 4% on average. Conversely, when accounting for the emissions from pasture intake the GWP was increased by 2%, mainly when a high digestible grass was considered. The use of high digestible grass provided lower AP and EP impacts than low digestible grass. The large variability between farms in terms of environmental impacts suggests that the margins for improvement of local breeds' production rely on improvement of feed composition and supply, and origin of feed ingredients. There is a great need for better estimation of digestibility of grasses and of carbon sequestration, in order to reduce the uncertainties associated with the environmental impacts evaluated of outdoor pigs' systems. Funded by European Union's H2020 RIA program (grant agreement no. 634476).

This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 634476

Traditional pig productions systems, relying mainly on local pig breeds and outdoor rearing, have been poorly investigated so far in terms of environmental impacts. The few existing studies did not account for possible sequestration of carbon and emissions consecutive to grazing. Twentyfive farms of Gascon breed in France (FR), 8 with Mora Romagnola breed in Italy (IT), and 15 of Krškopolje breed in Slovenia (SI) were evaluated while accounting for the emissions from pasture intake and the potential for carbon sequestration. Pig production system in SI presented the lowest impacts per kg of live weight, due to better feed conversion ratio caused by indoor production and due to lower impacts of feeds – most diets were based on grains, vegetables, tubers and roots produced on farm. Among the systems, acidification potential (AP) was 13% higher in IT than the average for FR and SI, due to higher dietary crude protein content (+9% than the average), while the eutrophication potential (EP) was 27% higher in FR system than the average, as a result of higher phosphorus content of feeds (+28% than the average). When the potential of carbon sequestration was taken into account, the GWP impact was reduced 4% on average. Conversely, when accounting for the emissions from pasture intake the GWP was increased by 2%, mainly when a high digestible grass was considered. The use of high digestible grass provided lower AP and EP impacts than low digestible grass. The large variability between farms in terms of environmental impacts suggests that the margins for improvement of local breeds' production rely on improvement of feed composition and supply, and origin of feed ingredients. There is a great need for better estimation of digestibility of grasses and of carbon sequestration, in order to reduce the uncertainties associated with the environmental impacts evaluated of outdoor pigs' systems. 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).

Traditional pig productions systems, relying mainly on local pig breeds and outdoor rearing, have been poorly investigated so far in terms of environmental impacts. The few existing studies did not account for possible sequestration of carbon and emissions consecutive to grazing. Twenty-five farms of Gascon breed in France (FR), 8 with Mora Romagnola breed in Italy (IT), and 15 of Krškopolje breed in Slovenia (SI) were evaluated while accounting for the emissions from pasture intake and the potential for carbon sequestration. Pig production system in SI presented the lowest impacts per kg of live weight, due to better feed conversion ratio caused by indoor production and due to lower impacts of feeds – most diets were based on grains, vegetables, tubers and roots produced on farm. Among the systems, acidification potential (AP) was 13% higher in IT than the average for FR and SI, due to higher dietary crude protein content (+9% than the average), while the eutrophication potential (EP) was 27% higher in FR system than the average, as a result of higher phosphorus content of feeds (+28% than the average). When the potential of carbon sequestration was taken into account, the GWP impact was reduced 4% on average. Conversely, when accounting for the emissions from pasture intake the GWP was increased by 2%, mainly when a high digestible grass was considered. The use of high digestible grass provided lower AP and EP impacts than low digestible grass. The large variability between farms in terms of environmental impacts suggests that the margins for improvement of local breeds' production rely on improvement of feed composition and supply, and origin of feed ingredients. There is a great need for better estimation of digestibility of grasses and of carbon sequestration, in order to reduce the uncertainties associated with the environmental impacts evaluated of outdoor pigs' systems. 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).