Local pig breeds: Nutritional requirements, innovative practices and local feeding resources as challenges in project TREASURE

TREASURE is a research and innovation project of European Union’s Horizon 2020 programme which is devoted to traditional genetic resources in pig production with aim to improve their potentials for enhanced use. Studying and improving management of local pig breeds in their production systems is one of the challenges in which we address their performances and nutrition with special attention on locally available feeding resources and innovative practices aiming to improved welfare. For that purpose 15 experiments on 12 breeds were designed in the project, which are hereafter shortly presented. Their concepts and main objectives with some highlights on already available results are described. © 2017, University of Zagreb. All rights reserved

Survey of Demographic and Phenotypic Data of Local Pig Breeds of Treasure Project

Local genetic resources represent an important reservoir of biodiversity in the animal sector. Sustainable use of these resources can be an important source of income for farmers taking advantage of the peculiar characteristics of their products

Diversity across Major and Candidate Genes in European Local Pig Breeds

In the frame of the European TREASURE* project, the genetic characterization of 20 local pig breeds is being performed with genetic and genomic tools. The objectives are the study of genetic diversity in these populations and the identification of useful markers for authentication, traceability, conservation and breeding programs. In first place, a candidate gene approach has been applied and the most relevant genes and mutations associated with pig productive, meat quality, reproductive and disease resistance traits have been prioritized and analyzed. Two OpenArray® chips of 32 and 16 SNPs were designed and genotyped in 48 animals from each one of 20 breeds included in the project (Alentejana, Apulo Calabrese, Basque, Bísaro, Black Majorcan, Black Sicilian, Black Slavonian, Casertana, Cinta Senese, Gascon, Iberian, Krskopolje, Lithuanian indigenous wattle, Mangalitsa, Mora Romagnola, Moravka, Old Lithuanian White, Sarda, Schwäbisch Hällisches, Turopolje). Forty SNPs located in 34 genes were successfully genotyped (MC1R, TYRP1, NR6A, PCK1, RYR1, IGF2, MC4R, PHKG1, SCD, GBP5, TAS2R39, TAS2R4, MUC4, ESR1, CYP2E1, LEP, CAST, MTTP, CYB5A, FTO, PPARGC1A, CAPN1, PPARD, CTSL, LEPR, PRKAG3, ACACA, KIT, ACSL4, ADIPOQ, FASN, AHR, FUT1, MSTN). Results provide relevant information regarding genetic diversity and segregation of SNPs responsible for specific production and quality traits. Coat color and morphological trait-genes, showing low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for breeding programs. For instance, we observed predominance of unfavorable alleles for disease resistance and boar taint genes in most breeds, and segregation of many genes involved in meat quality, fatness and growth. These results joint with ongoing genomic assays, will provide essential information regarding genetic diversity, structure, selective signatures and biological processes responsible for specific production and quality traits

Diversity across Major and Candidate Genes in European Local Pig Breeds

In the frame of the European TREASURE* project, the genetic characterization of 20 local pig breeds is being performed with genetic and genomic tools. The objectives are the study of genetic diversity in these populations and the identification of useful markers for authentication, traceability, conservation and breeding programs. In first place, a candidate gene approach has been applied and the most relevant genes and mutations associated with pig productive, meat quality, reproductive and disease resistance traits have been prioritized and analyzed. Two OpenArray® chips of 32 and 16 SNPs were designed and genotyped in 48 animals from each one of 20 breeds included in the project (Alentejana, Apulo Calabrese, Basque, Bísaro, Black Majorcan, Black Sicilian, Black Slavonian, Casertana, Cinta Senese, Gascon, Iberian, Krskopolje, Lithuanian indigenous wattle, Mangalitsa, Mora Romagnola, Moravka, Old Lithuanian White, Sarda, Schwäbisch Hällisches, Turopolje). Forty SNPs located in 34 genes were successfully genotyped (MC1R, TYRP1, NR6A, PCK1, RYR1, IGF2, MC4R, PHKG1, SCD, GBP5, TAS2R39, TAS2R4, MUC4, ESR1, CYP2E1, LEP, CAST, MTTP, CYB5A, FTO, PPARGC1A, CAPN1, PPARD, CTSL, LEPR, PRKAG3, ACACA, KIT, ACSL4, ADIPOQ, FASN, AHR, FUT1, MSTN). Results provide relevant information regarding genetic diversity and segregation of SNPs responsible for specific production and quality traits. Coat color and morphological trait-genes, showing low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for breeding programs. For instance, we observed predominance of unfavorable alleles for disease resistance and boar taint genes in most breeds, and segregation of many genes involved in meat quality, fatness and growth. These results joint with ongoing genomic assays, will provide essential information regarding genetic diversity, structure, selective signatures and biological processes responsible for specific production and quality traits

Association between the pig genome and its gut microbiota composition

The gut microbiota has been evolving with its host along the time creating a symbiotic relationship. In this study, we assess the role of the host genome in the modulation of the microbiota composition in pigs. Gut microbiota compositions were estimated through sequencing the V3-V4 region of the 16S rRNA gene from rectal contents of 285 pigs. A total of 1,261 operational taxonomic units were obtained and grouped in 18 phyla and 101 genera. Firmicutes (45.36%) and Bacteroidetes (37.47%) were the two major phyla obtained, whereas at genus level Prevotella (7.03%) and Treponema (6.29%) were the most abundant. Pigs were also genotyped with a high-throughput method for 45,508 single nucleotide polymorphisms that covered the entire pig genome. Subsequently, genome-wide association studies were made among the genotypes of these pigs and their gut microbiota composition. A total of 52 single-nucleotide polymorphisms distributed in 17 regions along the pig genome were associated with the relative abundance of six genera; Akkermansia, CF231, Phascolarctobacterium, Prevotella, SMB53, and Streptococcus. Our results suggest 39 candidate genes that may be modulating the microbiota composition and manifest the association between host genome and gut microbiota in pigs.info:eu-repo/semantics/publishedVersio

Potential use of near-infrared spectroscopy to predict fatty acid profile of meat from different european autochthonous pig breeds

Autochthonous pig breeds provide products of differentiated quality, among which quality control is difficult to perform and insufficient for current market requirements. The present research evaluates the predictive ability of near?infrared (NIR) spectroscopy, combined with chemometric methods as a rapid and affordable tool to assure traceability and quality control. Thus, NIR technology was assessed for intact and minced muscle Longissimus thoracis et lumborum samples collected from 12 European autochthonous pig breeds for the quantification of lipid content and fatty acid composition. Different tests were performed using different numbers of samples for calibration and validation. The best predictive ability was found using minced presentation and set with 80% of the samples for the calibration and the remaining 20% for the external validation test for the following traits: lipid content and saturated and polyunsaturated fatty acids, which attained both the highest determination coefficients (0.89, 0.61, and 0.65, respectively) and the lowest root mean square errors in external validation (0.62, 1.82, and 1.36, respectively). Lower predictive ability was observed for intact muscles. These results could contribute to improve the management of autochthonous breeds and to ensure quality of their products by traditional meat industry chains.FE1B-06B2-126F | Jos? Pedro Pinto de Ara?joN/

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-S(T) 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

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

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 429. 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 system