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.

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.

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

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

Simple Summary

Due to the negative public opinion and welfare issues related to surgical castration, gradual introduction of alternatives like entire males and immunocastrates is taking place. Despite several economical and welfare advantages that the alternatives offer, numerous issues (i.e., boar taint, meat quality alterations), as well as their interactions with rearing and breeding (genetic) factors remain unanswered. Therefore, the focus of this study was to investigate the possibility of using different commercial sire lines in three male sex categories (entire males, immunocastrates, surgical castrates) and to compare their carcass traits, meat quality and boar taint compounds. A significant effect of terminal sire line and/or male category together with their interaction was observed for most of the investigated carcass and meat quality traits. The observed interaction should be taken into consideration when deciding on the production of a specific male category.

Abstract

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

Simple Summary

A survey was conducted with 5508 consumers from 13 Eastern European countries. 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.

Abstract

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.

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.

Comparação das características de carcaça e qualidade da carne de suínos Black Slavonian em função da duração do período de engorda

O presente estudo aborda a composição da carcaça e da qualidade da carne de suínos provenientes de três fileiras distintas de criação de porcos destinados à produção de kulen Baranjski (IGP). Estas fileiras diferem na raça e no sistema de produção. Na primeira fileira, usaram-se suínos híbridos modernos que foram engordados intensivamente até ao peso vivo 160 kg, em média, atingidos aos 6 meses de idade. Na segunda cadeia produtiva utilizou-se um genótipo cruzado, Duroc x Large White, sendo os suínos criados em instalações com cama de palha espessa, foram abatidos com aproximadamente 180 kg de peso vivo e idade de 12 meses. A última das fileiras produtivas investigada envolveu porcos eslavos pretos (Crna slavonska) alimentados exclusivamente em pastoreio, até chegarem aos 110 kg de peso vivo em média (idade = 12 meses). A composição das carcaças foi apresentada como o peso de carcaça e a proporção do peso dos cortes nobres (kg) principais usados na produção de kulen Baranjski (presunto, pá e lombo) bem como a percentagem relativa de cada um na carcaça inteira. Cada peça foi dissecada nos principais tecidos (músculo, gordura e osso). Os parâmetros avaliados nas carcaças foram todos significativamente afetados pela fileira de produção. Os parâmetros de qualidade na carne foram obtidos 24 horas após o abate, incluindo: pH24; cor de carne (CIE L * a * b *); perda por gotejamento pelo método EZ drip; perda por cozedura e força de cisalhamento Warner-Bratzler. Todos os parâmetros de qualidade da carne diferiam significativamente entre as fileiras investigadas com exceção da força de cisalhamento Warner-Bratzler medida no músculo Longissimus dorsi.

Análise genética de raças suínas autóctones da Croácia através do uso de microssatélites como marcadores

Os suínos Black Slavonian (BS) e Turopolje (TP) são duas raças autóctones da Croácia. No início do presente século foram feitas tentativas para as preservar e reestabelecer, que incluíram o uso de metodologias genéticas para o estudo das características genéticas de ambas as raças. O número de porcas reprodutoras BS aumentou de 237 em 2001 para 1305 no último ano, enquanto que o número de porcas reprodutoras TP aumentou de 45 para 132 no mesmo período. Foram genotipados 20 porcos BS, 20 porcos TP e 20 javalis usando um conjunto de 18 microssatélites. Foi feita uma análise estatística básica em relação ao número de amostras, número de alelos em cada locus, heterozigosidade esperada e observada, FIS e a sua significância estatística FISsign. Nas populações observadas foi detetada uma variedade de loci relativamente elevada. A heterozigosidade média variou entre 0.35 e 0.64. O índice médio de fixação (FST) foi de 0.24. Os valores multilocus do FST indicaram que cerca de 24% da variação genética total era explicada pelas diferenças entre populações e os restantes 78% correspondiam a diferenças entre animais dentro da mesma população. As distâncias genéticas entre populações foram determinadas com o método PCA e verificou-se que as populações estudadas estavam claramente definidas. A análise da estrutura da população indica a ausência de mistura entre as raças analisadas. No entanto foi observada alguma subestruturação na população BS. Os resultados confirmam a utilidade dos microssatélites para estudar a diversidade genética entre as raças suínas autóctones da Croácia mas, para obter resultados mais precisos, será necessário um estudo envolvendo um maior número de animais e outras raças relacionadas.

Comparação das características de carcaça e qualidade da carne de suínos Black Slavonian em função da duração do período de engorda

O objetivo deste estudo foi analisar a possibilidade de encurtar o período de engorda do porco Black Slavonian sem deteriorar a qualidade da carne. A pesquisa foi realizada em 30 porcos Black Slavonian divididos em dois grupos iguais, A e B, de acordo com a duração do período de engorda: 18 e 12 meses, respetivamente. Os porcos foram criados em sistema extensivo (pastagens, bosques). Durante o ano, os porcos foram alimentados com uma mistura de cereais (50% de milho, 30% de cevada, 10% de aveia, 10% de soja) que foi suplementada com alfafa durante o período de crescimento vegetal; durante o inverno, os porcos foram alimentados com feno de alfafa. No final do período de engorda, os porcos foram abatidos num matadouro comercial. Foram obtidos dados de carcaça e qualidade da carne: peso da carcaça, comprimento da carcaça, espessura muscular e de gordura subcutânea dorsal, bem como comprimento e circunferência do presunto, pH45 dos músculos semimembranoso e longissimus dorsi, cor da carne (CIE L * a * b *) e perda por gotejamento pelo método EZ drip. Os porcos do grupo B apresentaram carcaças significativamente mais leves e mais curtas, caracterizadas por uma gordura subcutânea dorsal menos espessa que os porcos do grupo A. O comprimento e a circunferência do presunto não foram afetados pela duração do período de engorda. Por outro lado, os resultados mostraram que o encurtamento do período de engorda deteriorou significativamente alguns traços importantes da qualidade da carne, sobretudo a perda por gotejamento e os valores CIE L* da carne no grupo B. A carne dos porcos deste grupo também se apresentou menos tenra do que a carne dos porcos do grupo A, como mostrado por valores de força de cisalhamento WB (N) significativamente maiores.

Differences in carcass traits, meat quality and chemical composition between the pigs of different CAST genotype

The study was carried out on 89 Pig Improvement Co. (PIC) pig carcasses, with the aim to investigate the differences between three CAST loci in carcass and meat-quality traits, as well as chemical composition of longissimus dorsi (LD) muscle. The differences among genotypes at CAST/HinfI locus were significant in all carcass traits measured, where AB genotype exhibited preferable values in carcass lengths, ham length, muscle thickness, loin eye area, fat thickness and fat area. Among meat-quality traits analysed, genotypes at CAST/HinfI locus differed in pH45 in SM muscle, both pH24 in semimembranosus (SM) and LD muscles, as well as luminosity; genotypes at CAST/MspI differed in pH24 and EC24 measured at LD muscle and in red colour intensity, level of yellowness and hue angle; while genotypes at CAST/RsaI differed in pH45 and EC45 in SM muscle, pH24 in LD muscle, paleness and redness, as well as in shear force and calpain activity. EF genotype at this locus exhibited the highest pH values and the lowest CIE L*, with more pronounced red colour, but also highest shear force and lowest calpain activity values. Furthermore, significant differences in chemical composition of LD muscle were found only among genotypes at CAST/RsaI loci, where FF genotype had the lowest intramuscular fat and the highest relative share of protein.

Modeling of pig growth by S-function – least absolute deviation approach for parameter estimation

Abstract. The aim of this study was to determine a mathematical model which can be used to describe the growth of the pig. The study was conducted on 60 pigs (30 barrows and 30 gilts) in the interval between the age of 49 and 215 days. All animals were weighed at 49th day after birth. For the purpose of growth measurements pigs were weighted every 7th day during the experiment. Every 21th day four pigs were selected for the slaughter according to average live weight. By applying the generalised logistic function, the growth of live weight and tissues were described. Thereby optimal parameters in the model were estimated on the basis of measurement data by means of the robust least absolute deviations principle. The prediction of optimum slaughter age/weight, on the basis of such model represent a contribution of this paper to the practice.