Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings cause inheritance of haplotypes that are identical by ...descent (IBD) and result in homozygous stretches along the genome of the offspring. Size and position of regions of homozygosity (ROHs) are expected to correlate with genomic features such as GC content and recombination rate, but also direction of selection. Thus, ROHs should be non-randomly distributed across the genome. Therefore, demographic history may not fully predict the effects of inbreeding. The porcine genome has a relatively heterogeneous distribution of recombination rate, making Sus scrofa an excellent model to study the influence of both recombination landscape and demography on genomic variation. This study utilizes next-generation sequencing data for the analysis of genomic ROH patterns, using a comparative sliding window approach. We present an in-depth study of genomic variation based on three different parameters: nucleotide diversity outside ROHs, the number of ROHs in the genome, and the average ROH size. We identified an abundance of ROHs in all genomes of multiple pigs from commercial breeds and wild populations from Eurasia. Size and number of ROHs are in agreement with known demography of the populations, with population bottlenecks highly increasing ROH occurrence. Nucleotide diversity outside ROHs is high in populations derived from a large ancient population, regardless of current population size. In addition, we show an unequal genomic ROH distribution, with strong correlations of ROH size and abundance with recombination rate and GC content. Global gene content does not correlate with ROH frequency, but some ROH hotspots do contain positive selected genes in commercial lines and wild populations. This study highlights the importance of the influence of demography and recombination on homozygosity in the genome to understand the effects of inbreeding.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The EU is supporting measures that stimulate enhanced value-added products in order to conserve local and threatened livestock breeds. Several Traditional Pork Products (TPP) and Innovative ...Traditional Pork Products (ITPP) with health innovations from four untapped pig breeds in Spain (Porc Negre Mallorquí), Croatia (Turopolje), Italy (Cinta Senese) and Slovenia (Krškopolje) were analysed. Consumers' “Non-hypothetical” willingness to pay (WTP) and hedonic evaluation were investigated. An integrated experimental approach using two Non-Hypothetical Discrete Choice Experiment (NH-DCE) was carried out before and after a hedonic evaluation test. Results showed that the health innovative products (ITPP) received similar and even lower WTP than the “control” products (TPP) from the untapped pig breeds. The TPP outperformed products enriched with healthy ingredients or with reduced undesirable compounds. The potential demand for traditional and “unaltered” product from the rustic pig breeds could contribute to their conservation. A market niche exists, where consumers appreciate these high-quality products and where no “add-ons” are required to enhance their uptake.
•Traditional pork products may help thriving the untapped and threatened EU pig breeds.•Innovative pork products from local breeds do not outperform the traditional ones.•Consumers appreciate the pork products from local breeds with no healthy “add-ons”.•Non-hypothetical choice scenarios revealed potential demand for traditional pig products.•Preferences patterns are built on consumer's health beliefs and their hedonic evaluation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The aim of the study was to ascertain the acceptability of Traditional (T) and Innovative (IT) pork products by European consumers considering also the influence of the sensory properties. The tests ...were performed in Barcelona, Bologna, Toulouse and Zagreb, with products from autochthonous pig breeds Porc Negre Mallorquí (patties), Cinta Senese (dry-fermented sausages), Gascon-Noir de Bigorre (dry-cured hams) and Turopolje (dry-cured hams), respectively. The methodological approach relied on the expectancy-disconfirmation model and the assimilation theory (blind, expected and informed tests). All consumers had a similar behaviour: higher expectations of T and IT differentiating them significantly from the remaining products, except in Barcelona test, because consumers in this city were not acquainted with the production system. Innovation in T products focusing on healthy and process innovation highlighted the need to provide information about the breed and the production system, but we can conclude that the sensory quality had a significant role on the preferences of consumers.
•The acceptability of different traditional pork products from autochthonous pig breeds of Europe was evaluated by standart commom protocol.•Expectations on traditional and innovative pork products with respect to standard and premium controls were higher when consumers were acquainted with the local production system.•Sensory quality had a relevant role on the preferences of consumers
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The purine contents of animal foods are becoming widely concerned because excess intake of purine increases the risk of hyperuricemia and gout. In this study, we investigated the impacts of breed, ...tissue and sex on pork purine content and its correlations with multiple meat quality traits. Among six pig breeds, the average value of total purine contents (TP) in longissimus lumborum muscle was lowest in Chinese Laiwu pigs (114.2 mg/100 g) while highest in Chinese Bamaxiang mini pigs (139.3 mg/100 g). Considerable variations in TP were observed within most breeds, as well as among twelve pork organs with the range from 7 to 245 mg/100 g. However, no significant differences in TP were found between barrows and gilts. Intriguingly, lower purine content in meat was significantly associated with higher ultimate pH, better meat color and more abundant intramuscular fat content and marbling. The results thus suggest that the selection of low-purine pig species is available, which may simultaneously improve other meat quality traits.
•Purine contents varied significantly among pig breeds, tissues but not sex.•Purine content has significant correlations with some meat quality traits.•Meat with abundant marbling and bright red has relatively lower purine content.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
The transcriptional initiation of genes is closely bound to the functions of cis-regulatory elements, including promoters, typical enhancers (TEs), and recently-identified super-enhancers (SEs). In ...this study, we identified these cis-regulatory elements in the livers of two Chinese (Meishan and Enshi Black) and two Western (Duroc and Large White) pig breeds using ChIP-seq data, then explored their similarities and differences. In addition, we analyzed the conservation of SEs among different tissues and species (pig, human, and mouse). We observed that SEs were more significantly enriched by transcriptional initiation regions, TF binding sites, and SNPs than other cis-elements. Western breeds included fewer SEs in number, while more growth-related QTLs were associated with these SEs. Additionally, the SEs were highly tissue-specific, and were conserved in the liver among humans, pigs, and mice. We concluded that intense selection could concentrate functional SEs; thus, SEs could be applied as effective detection regions in genomic selection breeding.
Copy number variation (CNV) is an important class of genetic variations widely associated with the porcine genome, but little is known about the characteristics of CNVs in foreign and indigenous pig ...breeds. We performed a genome-wide comparison of CNVs between Anhui indigenous pig (AHIP) and Western commercial pig (WECP) breeds based on data from the Porcine 80K SNP BeadChip. After analysis using the PennCNV software, we detected 3863 and 7546 CNVs in the AHIP and WECP populations, respectively. We obtained 225 (loss: 178, gain: 47) and 379 (loss: 293, gain: 86) copy number variation regions (CNVRs) randomly distributed across the autosomes of the AHIP and WECP populations, accounting for 10.90% and 22.57% of the porcine autosomal genome, respectively. Functional enrichment analysis of genes in the CNVRs identified genes related to immunity (
,
,
,
,
,
) and meat quality (
,
) in the WECP population; these genes were a loss event in the WECP population. This study provides important information on CNV differences between foreign and indigenous pig breeds, making it possible to provide a reference for future improvement of these breeds and their production performance.
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•A comprehensive analysis was conducted to characteristic aroma of five pork breeds.•Identified 8 key characteristic aroma compounds of five pork breeds.•14 aroma markers were ...proposed to define the aroma boundaries of five pork breeds.•Elucidated the relationship between various pork varieties and aroma components.
To clarify the characteristic aroma compounds and flavor discrepancies of five Chinese typical pig species, headspace-solid phase microextraction gas chromatography–olfactometry-mass spectrometry (HS-SPME/GC-O-MS), electronic nose (E-nose), aroma recombination and omission experiments were used to analyze the characteristic aroma and boundary of five boiled pork. A total of 38 volatile compounds were identified, of which 14 were identified as important odorants with odor-activity values (OAVs) greater than 1. Aroma recombination and omission experiments revealed 8 key characteristic aroma compounds, which significantly contributed to the overall aroma. Sensory evaluation of the recombination model with the 8 aroma compounds scored 3.0 to 4.0 out of 5 points. 12 potential markers were identified to distinguish by principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), including (E)-2-octenal, 3-ethyl-2-methyl-1,3-hexadiene, (E)-2-heptenal, 2-pentylfuran, cyclooctanol, 1-heptanol, sec-butylamine, D-limonene, N-vinylformamide, 2,3-octanedione, 2-ethylfuran and 3-pentanamine. Alongside benzaldehyde and pentanal, the combinations and fluctuations of these 14 aroma markers were proposed to constitute the aroma boundaries of different pork breeds. The aroma-active substances were able to effectively differentiate different breeds.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Pork is a favorite type of meat with a large share in the structure of consumption worlwide, including China and Russia. Pork production in China and Russia has been constantly growing over the last ...years. This type of meat remains to be in high demand due to its sensory properties despite consumer attitude to pork fat content. This review presents the short history of pig farming in China and Russia, as well as the modern trends in the development of this industry. The data on the pork production and consumption in two countries over the last years are compared. Characteristics that consumers consider important when buying pork and negative factors influencing consumer choice are described. Consumer properties of meat products from pork depend on keeping conditions and feeding of animals. Meat composition and functional properties depend greatly on pig breed. Information about pig breeds that are raised in China (depending on a region) and Russia, as well as indicators of productivity of pigs of certain breeds, are presented.
Background:
The use of breed-informative genetic markers, specifically coding Single Nucleotide Polymorphisms (SNPs), is crucial for breed traceability, authentication of meat and dairy products, and ...the preservation and improvement of pig breeds. By identifying breed informative markers, we aimed to gain insights into the genetic mechanisms that influence production traits, enabling informed decisions in animal management and promoting sustainable pig production to meet the growing demand for animal products.
Methods:
Our dataset consists of 300 coding SNPs genotyped from three Italian commercial pig populations: Landrace, Yorkshire, and Duroc. Firstly, we analyzed the genetic diversity among the populations. Then, we applied a discriminant analysis of principal components to identify the most informative SNPs for discriminating between these populations. Lastly, we conducted a functional enrichment analysis to identify the most enriched pathways related to the genetic variation observed in the pig populations.
Results:
The alpha diversity indexes revealed a high genetic diversity within the three breeds. The higher proportion of observed heterozygosity than expected revealed an excess of heterozygotes in the populations that was supported by negative values of the fixation index (F
IS
) and deviations from the Hardy-Weinberg equilibrium. The Euclidean distance, the pairwise F
ST
, and the pairwise Nei’s G
ST
genetic distances revealed that Yorkshire and Landrace breeds are genetically the closest, with distance values of 2.242, 0.029, and 0.033, respectively. Conversely, Landrace and Duroc breeds showed the highest genetic divergence, with distance values of 2.815, 0.048, and 0.052, respectively. We identified 28 significant SNPs that are related to phenotypic traits and these SNPs were able to differentiate between the pig breeds with high accuracy. The Functional Enrichment Analysis of the informative SNPs highlighted biological functions related to DNA packaging, chromatin integrity, and the preparation of DNA into higher-order structures.
Conclusion:
Our study sheds light on the genetic underpinnings of phenotypic variation among three Italian pig breeds, offering potential insights into the mechanisms driving breed differentiation. By prioritizing breed-specific coding SNPs, our approach enables a more focused analysis of specific genomic regions relevant to the research question compared to analyzing the entire genome.
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