A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits.

BACKGROUND: Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments. RESULTS: Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene. CONCLUSIONS: In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.

Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia.

BACKGROUND: The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). RESULTS: The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. CONCLUSIONS: Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.

Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism.

The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations. The analysis of mtDNA showed that haplotypes of the studied pig populations are different from the other European and Chinese haplotypes. BS pigs showed some similarities with Mangalitsa and Duroc breeds. The genetic distances of TP can be explained by high degree of inbreeding during the past century. Despite the European origin of Croatian pig breeds with some impact of Chinese breeds in the past, the results of present study show that genetic diversity is still pronounced within investigated breeds. Furthermore, the genetic diversity is even more pronounced between Croatian breeds and other European and Chinese pig breeds. Thus, conservation of Croatian pig breeds will contribute to overall genetic diversity preservation of pig breeds.

Consumer Preferences for Cured Meat Products from the Autochthonous Black Slavonian Pig.

This study investigated the attitudes of Croatian consumers regarding their preferences for cured meat products from the Black Slavonian Pig. The survey was conducted on a sample of 410 consumers who completed an online survey about their consumption habits, knowledge about the pig breed, and socio-demographic characteristics. In this study, the independent samples t-test and ANOVA were conducted to determine the significant differences between the most important attributes in the purchase of cured Black Slavonian Pig products and the socio-demographic characteristics, consumption, and purchase habits of the respondents. Statistically significant differences were found between the studied intrinsic (color, odor, fat content, and salt content) and extrinsic variables (production method, brand, quality mark, and origin) in relation to the socio-demographic characteristics of the respondents (gender, age, employment status, number of household members, and number of children under 15 in the household) and place of purchase, knowledge about the breed, and frequency of consumption of Black Slavonian Pig meat and products. Principal component analysis (PCA) and cluster analysis (CA) were used to determine the consumer segments. Based on the responses received, three homogeneous consumer segments were identified: intrinsically oriented meat consumers, extrinsically oriented meat consumers, and uninterested meat consumers. The information obtained in the study is important for producers and retailers, as they can use our findings to develop successful marketing tools and different marketing strategies to promote cured Black Slavonian Pig products.

Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data.

Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krskopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products.

Influence of Immunocastration on Slaughter Traits and Boar Taint Compounds in Pigs Originating from Three Different Terminal Sire Lines.

The aim of the research was to investigate the influence of terminal sire line (TSL) and male category (MC) on carcass and meat quality of commercial fatteners. The study was performed on 180 pigs originating from three terminal sire lines: A (Pietrain × Large White), B (pure Pietrain), and C (Pietrain × Duroc × Large White), being assigned to three groups according to MC: immunocastrates (IC, n = 60), surgical castrates (SC, n = 60) and entire males (EM, n = 60). TSL affected most of the carcass and meat quality traits, together with the androstenone concentration. At the same time, MC had a significant effect on fat thickness, ham circumference, drip loss, cooking loss and androstenone and skatole concentrations. A significant interaction effect was observed for carcass length and ham circumference, as well as for most of the measured meat quality traits (except cooking loss, CIE L*, CIE b*, and Warner Bratzler Shear Force (WBSF)). Among the three investigated sire lines, immunocastration was shown to be most beneficial for fatteners sired by the TSL C. However, if deciding to raise EM, fatteners from the TSL B are recommended in terms of carcass and meat quality, although strategies for avoiding boar taint in their carcasses must be taken into consideration.

Genomic Characterization of the Istrian Shorthaired Hound.

Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there is no data on genetic diversity, population structure, and degree of inbreeding that could be used for advanced management and conservation of this breed. Our study aimed to provide a high-resolution population structure of the Istrian shorthaired hound using a 220K HD SNP array, to compare the obtained data with the genealogical records and to place the breed in a broader context of world dog populations. Relatively high population size and low inbreeding coefficient estimated from genealogical data indicate a preserved genetic diversity in this breed. The principle component analysis, the NeighborNet network, and TreeMix were used to determine the genetic relationship between the Istrian shorthaired hound and other breeds. The Istrian shorthaired hound was found to be genetically related to Italian hunting dogs sharing the same branch with the Segugio Italiano a Pelo Raso and Segugio Italiano a Pelo Forte. The ADMIXTURE analysis indicated that the Istrian shorthaired hound could be involved in the development of some other hunting dog breeds. The estimated effective population size (Ne) based on SNP data was similar to Ne calculated from genealogical data indicating the absence of bottlenecks and well-balanced use of breeding animals. The low genomic inbreeding coefficient, together with the higher number of short runs of homozygosity, observed in the Istrian shorthaired hound, confirms the ancient origin of the breed based on historical documents. The analysis of selective sweeps identified genomic regions with the strongest selection signals in the vicinity of the genes associated with cognitive performance and behavior. Genome analysis proved to be a useful tool for estimating population parameters and can be implemented in the conservation plan for this indigenous breed.

Attitudes and Beliefs of Eastern European Consumers Towards Animal Welfare.

The aim of this exploratory work, because of the existing bias on the size of the sample and some of the sociodemographic characteristics of the participants, was to investigate the Eastern European consumers' beliefs and attitudes toward animal welfare, to perform a cross-country segmentation analysis and to observe possible differences with their Western European counterparts. For this purpose, a survey was conducted with 5508 consumers from 13 Eastern European countries (Bosnia and Herzegovina, Bulgaria, Czech Republic, Croatia, North Macedonia, Hungary, Moldova, Poland, Romania, Serbia, Slovakia, Slovenia, and Ukraine) using a questionnaire with nine statements about consumers beliefs regarding animal welfare (aspects of management, ethical issues about animals, and consequences of animal welfare on meat quality and price), one statement about the willingness to pay more for meat produced under better welfare conditions, and four statements regarding attitudes toward animal welfare. Differences between countries were detected for all the statements. Moreover, three clusters of consumers were identified: one with consumers indifferent towards animal welfare; one with consumers concerned about animal welfare, but they believe it is difficult to achieve; and one with consumers concerned about animal welfare, and they believe it is possible to achieve it.

Exploratory Survey on European Consumer and Stakeholder Attitudes towards Alternatives for Surgical Castration of Piglets.

Surgical castration of piglets without pain relief is still common practice in many countries. Possible alternatives for surgical castration are application of pain relief or anaesthesia or production of boars (entire males) and immunocastrates. Each of these alternatives faces advantages and disadvantages which may result in different citizen attitudes and consumers acceptability. Understanding which practice is acceptable to whom and why may further stimulate implementation. Consumer (n = 3251) and stakeholder (n = 1027) attitudes towards surgical castration without pain relief, surgical castration with anaesthesia, immunocastration, and production of boars were surveyed from April to June 2020 via an online questionnaire in 16 countries (>175 respondents per country). Surgical castration without pain relief was separated from each of the alternatives due to animal welfare and showed the lowest acceptability (32%). Within the alternatives, a further partitioning between the alternatives was based on perceived quality and food safety, with an acceptance of 85% for applying anaesthesia, 71% for immunocastration, and 49% for boar production. Differences depending on professional involvement and familiarity with agriculture could be observed, mainly for the acceptance of surgical castration without anaesthesia, immunocastration, and boars. Castration with anaesthesia was highly accepted by all types of respondents.

Erratum: Aluwé, M. et al. Exploratory Survey on European Consumer and Stakeholder Attitudes towards Alternatives for Surgical Castration of Piglets. Animals 2020, 10, 1758.

The authors wish to make the following corrections to this paper [...].

The impact of frozen storage duration on physical, chemical and microbiological properties of pork.

The aim of the present study was to evaluate the effect of frozen storage duration (3, 6, 9, 12, 15, 18 months) on physical, chemical and microbial properties of pork in three cuts (loin, ham, and belly rib). During frozen storage, significant alterations in physical and chemical parameters were observed through the increase of the total exudate, pH and lightness (L*), and a decrease of shear force and yellowness (b*). Water content in ham samples decreased, while protein content increased. The lipid oxidation (TBA) values in loin and ham samples increased for up to fifteen months of frozen storage, after which they decreased. The proportion of saturated fatty acids in frozen samples was significantly higher than in fresh meat. The total amount of Enterobacteriaceae, S. aureus and Pseudomonas spp. decreased during frozen storage, indicating that freezing may reduce the number of bacteria found in meat. Frozen pork microflora did not change after eighteen months of storage.

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, Krskopolje (Krskopoljski), 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.