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Runs of homozygosity (ROH) are continuous segments of the genome that arose as a result of inbreeding, resulting in the inheritance of identical haplotypes from both parents who shared a common ancestor. In the present study, we performed a detailed characterization and comparison of ROH in four pig breeds, including intensively selected Polish Landrace as well as native unselected animals of Pulawska and two Zlotnicka breeds (White and Spotted). We used a medium-density PorcineSNP60 BeadChip assay (Illumina) and cgaTOH software to detect ROH covering a minimum of 30 adjacent SNPs and maintaining a size over 1 Mb. By analysing ROH distribution and frequency across the genome, we also identified genomic regions with high ROH frequency (so-called "ROH hotspots"). The obtained results showed that the analysed conserved breeds were characterized by a higher ROH span and higher ROH-based inbreeding coefficients (FROH ), which likely result from past population bottlenecks, increasing the overall inbreeding level within these populations. The analysis of ROH distribution across the genomes revealed the presence of both shared and breed-specific ROH hotspots. These hotspots, presumably representing genome regions under selection, overlapped with a variety of genes associated with processes connected with immune system functioning, reproduction, glucose homeostasis and metabolism. The genome regions with ROH hotspots overlapping in all analysed populations, located on SSC4 (51.9-55.9 Mb) and 13 (92.6-97.8 Mb), covered thirty-one different genes, including MMP16, SLC7A13, ATP6V0D2, CNGB3, WWiP1, RiMDN1 and CPNE3. These genes are primarily associated with biological regulation and metabolism, processes that could be responsible for the variety of the selected production and functional features.
Assuntos
Cruzamento , Genoma/genética , Genômica , Reprodução/genética , Animais , Genótipo , Homozigoto , Endogamia , Polônia , Polimorfismo de Nucleotídeo Único/genética , SuínosRESUMO
BACKGROUND: Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals' phenotypic variation. Domestication and subsequent long-time selection have resulted in extensive phenotypic changes in domestic pigs, involving a number of traits, like behavior, body composition, disease resistance, reproduction and coat color. In this study, based on genotypes obtained from PorcineSNP60 Illumina assay we attempt to detect both diversifying and within-breed selection signatures in 530 pigs belonging to four breeds: Polish Landrace, Pulawska, Zlotnicka White and Zlotnicka Spotted, of which the last three are a subject of conservative breeding and substantially represent the native populations. RESULTS: A two largely complementary statistical methods were used for signatures detection, including: pairwise FST and relative extended haplotype homozygosity (REHH) test. Breed-specific diversifying selection signals included several genes involved in processes connected with fertility, growth and metabolism which are potentially responsible for different phenotypes of the studied breeds. The diversifying selection signals also comprised PPARD gene that was previously found to have a large effect on the shape of the external ear in pigs or two genes encoding neuropeptide Y receptors (Y2 and Y5) involved in fat deposition and stress response which are important features differentiating the studied breeds. REHH statistics allowed detecting several within-breed selection signatures overlapping with genes connected with a range of functions including, among others: metabolic pathways, immune system response or implantation and development of the embryo. CONCLUSIONS: The study provides many potential candidate genes with implication for traits selected in the individual breeds and gives strong basis for further studies aiming at identification of sources of variation among the studied pig breeds.
Assuntos
Seleção Genética , Sus scrofa/genética , Animais , Mapeamento Cromossômico , Genótipo , PPAR delta/genética , Fenótipo , Polônia , Polimorfismo de Nucleotídeo Único , Análise de Componente Principal , SuínosRESUMO
The aim of the study was to determine the effect of milk thistle supplementation of fattener pig feeds on physical and chemical properties of pork offal. The experiments were conducted on 60 fatteners (group C-control (30 pigs) and group E-experimental (30 pigs)). The experimental group was supplemented with ground milk thistle (Silybum marianum) at 7 g/kg feed. The offal (tongues, kidneys, hearts, lungs and livers) was analyzed for weight, pH, WHC, water, protein, fat, energy value, fatty acid profile and content of major and trace elements. The present study shows that milk thistle added to fattener pig diets increased pH45 and pH24 values in most of the analyzed offal and significantly (p ≤ 0.01) decreased the weight of heart and lungs and increased the weight of liver and kidneys. Hearts, lungs and kidneys of the experimental group contained more fat and the liver less, than the same offal of the control group. As regards the content of elements, the dietary supplement most often had an effect on the heart and lungs. In general, milk thistle supplemented in fattener diets had modified the physical parameters and chemical composition of the analyzed products.
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The popularity of meat from animals of native breeds is growing all over the world, due to consumer belief regarding its higher quality compared to meat from industrial farm animals. In addition, the living conditions (welfare) are of great importance for consumers. We observed the effect of different ways of keeping and feeding pigs of the same conservative breed on the quality of meat and its health benefits. The aim of the study was to compare the meat quality from pigs of the native Zlotnicka Spotted breed, fattened intensively or extensively (with conventional farm-produced compound feed and acorns). The meat from free-range pigs extensively fed on silage and small amounts of acorns was characterized by a higher content of fat, which acts as a carrier for flavor and juiciness, as well as higher monounsaturated fatty acid (MUFA) content (p ≤ 0.05) and lower atherogenic, thrombogenic, and peroxidability indices (p ≤ 0.05). It may be stated that the meat quality of the native pig breed is significantly dependent on the housing and feeding method. A more beneficial effect on the quality of meat and its dietetic value, as well as its susceptibility to rancidity, can be obtained throughextensive pig feeding with roughage and the addition of acorns.
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The aim of the study was to determine technological and consumption quality of some offal components obtained from Pulawska and Polish Landrace fattening pigs, and to analyse the eating quality of the offal products. The study material consisted of 100 fattening pigs: Pulawska (PUL) and 50 Polish Landrace (PL) pigs. The offal components were analysed for physical traits, chemical composition and energy value. Offal products were made from the offal and their physical, chemical and organoleptic parameters were evaluated. Our study showed that breed had a significant effect (p ≤ 0.05) on pH45 of the tongue, heart (PUL > PL), lungs and kidneys (PUL < PL), and on the fat content of the tongue, heart (PUL > PL), liver and kidneys (PUL < PL). A highly significant effect of breed (p ≤ 0.01) was observed for protein content of the lungs, liver (PUL < PL) and kidneys (PUL > PL), for collagen content of the kidneys (PUL < PL) and liver (PUL < PL), and for energy value (p ≤ 0.01) of the heart (PUL > PL) and liver (PUL < PL). Moreover, our results indicate that the organoleptic quality of the evaluated offal products was higher for Pulawska than Polish Landrace pigs, in particular with regard to consistency (p < 0.05) and flavour (p < 0.01) of the liver sausage.
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In recent years, pig producers have struggled with the problem of low intramuscular fat levels in pork, which impacts palatability and ultimately meat quality. Reduced levels of intramuscular fat are likely the result of breeding objectives aimed at increasing lean meat content. In this study, three mutations within candidate genes for fat content (SCD, ACACA, and FASN) were selected, based on RNA-seq results and the relationship between polymorphisms in genes related to lipid metabolism, fattening and slaughter characteristics, as well as pork quality, including IMF level, were evaluated to identify selection markers. Moreover, their impact on gene expression was also examined. The PCR-RFLP (polymerase cha- in reaction - restriction fragments length) method was used to establish genotypes and effect sizes of potential genetic markers were estimated using a GLM model. It was identified that a FASN missense variant was positively associated with the expression level of this gene, which suggested its linkage with a mutation having a regulatory function. The association study indicated that the FASN missense variant may play a role in the determination of feed conversion and meat colour. In turn, a mutation in the ACACA gene showed a relationship with IMF content in the Pulawska breed where the differences reached as much as 20%. We suggest considering all three mutations in further studies based on different pig populations due to the crucial role of SCD, ACACA, and FASN genes in lipid metabolism.
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Numerous studies have been conducted to explain the biological functions and mechanism of ghrelin (GHRL) action in animals. However, the exact role of ghrelin in the regulation of growth and development in pigs is still unclear. The ghrelin gene is considered to be a good candidate marker for the identification of economically important traits in pig production such as feed intake, growth or carcass quality. The objectives of the present study were to investigate the regulatory regions and coding sequence of the porcine GHRL gene and determine the effect of polymorphisms at the ghrelin gene locus on selected fattening traits. Data were obtained from 346 gilts (pure breeds: Landrace, 188; Duroc, 74; Pietrain, 84). The PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) method was used to detect polymorphisms within GHRL. Three polymorphisms were found, one in the promoter region (c.-93A>G) and two in the 3'UTR sequence (g.4428T>C; g.4486C>T). A significant (p ≤ 0.01) additive effect on daily gain (negative) and age at slaughter (positive) was obtained at the locus c.-93A>G. However, the most promising mutation was at the locus g.4486C > T, which is associated with total feed intake. Overall, the described GHRL polymorphisms may be useful as molecular markers in pig selection but future studies are required.
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Over the decades, pig breeding objectives have focused on improving the meat content in the carcass without taking into consideration the more effective fattening indicators that affect feed conversion. At present, pig growth traits associated particularly with animal feeding have become crucial due to their economic significance. This is especially evident in countries where pigs are maintained on large farms. The present study indicates that pituitary differentially expressed genes (DEGs) are activated in response to variable feed conversion (FC) in pigs. The experiment included two native Polish breeds: Pulawska and Zlotnicka White (ZW). The whole pituitary transcriptome was sequenced using next-generation sequencing (NGS) technology. The RNA-seq method identified over 500 and 300 DEGs in the pituitaries of the ZW and the Pulawska pig populations, respectively, that were associated with hormonal regulation, notch signaling, and Wnt pathways. Lower FC in the ZW pigs favoured increased fat content in the body and significantly higher prolactin expression. The obtained results indicate that low FC values in pigs are related to slower growth or increased fat content, which suggests various pituitary responses. Therefore, the identified candidate genes were not directly associated with feed conversion values but with other factors. However, the present study delivers new insights into pituitary regulation in pigs.