Structural differences among pig genomes illustrate genetic uniqueness of breeds

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)

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.info:eu-repo/semantics/acceptedVersio

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

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 Profler (GGP) 70K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population diferentiation and structure, genetic distances, linkage disequilibrium and efective 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 efective 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 FST outlier tests. Candidate genes that may underlie diferences in adaptation to specifc environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.FE1B-06B2-126F | José Pedro Pinto de AraújoN/

Potential sensitivity of pork production situations aiming at high-quality products to the use of entire male pigs as an alternative to surgical castrates

The perspective of a possible ban on surgical castration of male pigs in the EU is a real challenge for pork production systems aiming at (very) high-quality products. Information was collected from a total of 272 situations in 16 European countries, including 170 situations related to EU protected designations (Database of Origin & Registration (DOOR) database) and 102 other situations related to high-quality products or differentiated production systems, in order to evaluate their potential sensitivity to the use of entire male pigs along four dimensions: BT-Inc, likelihood of increased levels of boar taint compounds compared with conventional production of entire males; BT-Per, extent to which (some of) the associated pork product(s) are susceptible to perception of boar taint by consumers; FatQQ, likelihood that the quality of (some of) the related products is decreased due to the lower fat quantity and quality in entire males; Manag, increased likelihood of animal management and welfare problems compared with conventional production of entire males. Situations corresponding to EU protected designations (DOOR situations) were on average more sensitive to entire male production but 11% of the non-DOOR situations were highly potentially sensitive, whereas one-third of the DOOR situations had low potential sensitivity. In total, 37% of the situations where castration is not formally specified as mandatory exhibited high potential sensitivity to entire male production. Three main patterns of situations were identified via ascending hierarchical clustering. A first pattern including 31% of the DOOR situations and 74% of the other ones, had potentially no increased risk compared with conventional production of entire males. A second pattern including 28% of the DOOR situations and 16% of the other ones had a high, moderate and low potential sensitivity for FatQQ, BT-Inc and Manag, respectively. The third pattern including 41% of the DOOR situations and 11% of the other situations had high potential sensitivity for BT-Inc and FatQQ, associated with moderate to high sensitivity for Manag. The approach used to evaluate the sensitivity to entire male pig production from the limited information collected for this study has many limitations. More precise approaches using more specific information are needed to evaluate the actual sensitivity of individual situations to the use of entire male pigs. Still, the present study provides a first global insight on the capacity of European production systems aiming at high-quality products to use entire male pigs as an alternative to surgical castration

UV light causes structural changes in microplastics exposed in bio-solids

Bio-solids (biological sludge) from wastewater treatment plants are a significant source of the emission of microplastics (MPs) into the environment. Weakening the structure of MPs before they enter the environment may accelerate their degradation and reduce the environmental exposure time. Therefore, we studied the effect of UV-A and UV-C, applied at 70 °C, on three types of MPs, polypropylene (PP), polyethylene (PE), and polyethylene terephthalate (PET), that are commonly found in sewage sludge, using three shapes (fibers, lines, granules). The MPs were exposed to UV radiation in bio-solid suspensions, and to air and water as control. The structural changes in and degradation of the MPs were investigated using Attenuated Total Reflectance–Fourier Transform Infrared Spectrometry (ATR-FTIR) and surface morphology was performed with SEM analysis. UV exposure led to the emergence of carbonyl and hydroxyl groups in all of the PP samples. In PE and PET, these groups were formed only in the bio-solid suspensions. The presence of carbonyl and hydroxyl groups increased with an increasing exposure time. Overall, UV radiation had the greatest impact on the MPs in the bio-solids suspension. Due to the surface-to-volume ratio of the tested samples, which influences the degradation rate, the fibers were more degraded than the other two plastic shapes. UV-A was slightly more effective at degrading the MPs than UV-C. These findings show that ultraviolet radiation in combination with an elevated temperature affects the structure of polymers in wastewater bio-solids, which can accelerate their degradation

Potential sensitivity of pork production situations aiming at high-quality products to the use of entire male pigs as an alternative to surgical castrates

The perspective of a possible ban on surgical castration of male pigs in the EU is a real challenge for pork production systems aiming at (very) high-quality products. Information was collected from a total of 272 situations in 16 European countries, including 170 situations related to EU protected designations (Database of Origin & Registration (DOOR) database) and 102 other situations related to high-quality products or differentiated production systems, in order to evaluate their potential sensitivity to the use of entire male pigs along four dimensions: BT-Inc, likelihood of increased levels of boar taint compounds compared with conventional production of entire males; BT-Per, extent to which (some of) the associated pork product(s) are susceptible to perception of boar taint by consumers; FatQQ, likelihood that the quality of (some of) the related products is decreased due to the lower fat quantity and quality in entire males; Manag, increased likelihood of animal management and welfare problems compared with conventional production of entire males. Situations corresponding to EU protected designations (DOOR situations) were on average more sensitive to entire male production but 11% of the non-DOOR situations were highly potentially sensitive, whereas one-third of the DOOR situations had low potential sensitivity. In total, 37% of the situations where castration is not formally specified as mandatory exhibited high potential sensitivity to entire male production. Three main patterns of situations were identified via ascending hierarchical clustering. A first pattern including 31% of the DOOR situations and 74% of the other ones, had potentially no increased risk compared with conventional production of entire males. A second pattern including 28% of the DOOR situations and 16% of the other ones had a high, moderate and low potential sensitivity for FatQQ, BT-Inc and Manag, respectively. The third pattern including 41% of the DOOR situations and 11% of the other situations had high potential sensitivity for BT-Inc and FatQQ, associated with moderate to high sensitivity for Manag. The approach used to evaluate the sensitivity to entire male pig production from the limited information collected for this study has many limitations. More precise approaches using more specific information are needed to evaluate the actual sensitivity of individual situations to the use of entire male pigs. Still, the present study provides a first global insight on the capacity of European production systems aiming at high-quality products to use entire male pigs as an alternative to surgical castration

Properties and aromatic profile of dry-fermented sausages produced from Krškopolje pigs reared under organic and conventional rearing regime

Krškopolje pig, the only Slovenian autochtonous breed is still relatively untapped, with almost no information available on the effect of rearing conditions or its aptitude for processing and meat product quality. In the present study, dry-fermented sausages were produced from Krškopolje pigs that were fed similar diets (with regard to ingredients, energy and protein content) but reared in either conventional (CON) or organic conditions (ECO). Sausage weight losses at the end of processing were recorded and their final pH, chemical composition (moisture, fat and protein content, proteolysis index, fat and protein oxidation, fatty acid and free fatty acid profile) were determined in addition to measurements of instrumental texture, sensory evaluation and volatile profile analysis. Compared with CON, ECO dry-fermented sausages had lower processing losses, lower pH, higher moisture, salt and thiobarbituric acid reactive substances content, less saturated fat and less free fatty acids. Volatile profile analysis showed that ECO dry-fermented sausages exhibited higher concentrations of compounds arising from lipid autooxidation and lower levels of volatile compounds resulting from microbial lipid β-oxidation, amino acid degradation and spices. Panellists perceived ECO dry-fermented sausages as saltier and less colour intensive, while both rheological and sensory analysis indicated that ECO sausages had softer texture than CON. The present results indicate that rearing of Krškopolje pigs according to organic standards induced differences in meat and fat properties which affected the quality of dry-fermented sausages, most distinctly in terms of softer texture and different volatile profile.The research has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 634476 (Project acronym TREASURE). The content of this paper reflects only the authors’ view and Research Executive Agency is not responsible for any use that may be made of the information it contains. Authors also acknowledge the financial support of the Slovenian Research Agency (grants P4-0133 and V4-1417) and the Ministry of Agriculture, Food and Forestry (V4-1417), from AGL2015-64673-R (MINEICO, Spain) and FEDER funds.Peer reviewe