BackgroundIdentification 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, Puławska, Złotnicka White and Złotnicka Spotted, of which the last three are a subject of conservative breeding and substantially represent the native populations.ResultsA 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0681-0) contains supplementary material, which is available to authorized users.
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 Złotnicka 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.
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 Puławska 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.
Native breeds of farm animals, despite their unique characteristics and adaptability to diverse and often adverse environmental conditions, are at risk due to their lower profitability and corresponding declining use. According to FAO data, there are currently around 8800 livestock breeds in the world (http://www.fao.org/dad-is/en/ update: 09.11.2019), of which 17% have been assessed to be endangered. The objective of the study was to develop a model for estimating the risk status of Polish native breeds. The proposed new model is based on 3 factors: demographic, genetic, and socio-economic. The last factor is composed of 6 elements: geographical concentration, demographic trend over the last 5 years, cultural value of a breed, parentage control, ex situ conservation and anthropogenic factors. Using the factors and elements above, among the examined 30 breeds of cattle, horses, pigs, sheep and goats, 1 was assessed as being critically endangered; 24 were determined to be endangered and in need of conservation; 5 were less endangered, but in need of constant monitoring. Out of 35 populations of poultry 29 were assessed as endangered as they were being kept in only single public collections. Six flocks of ducks were given a critical risk status, due to a very low number of females.
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