Effect of mutation in MC4R gene on carcass quality in Pulawska pig included in conservation breeding programme

In addition to highly productive breeds of pigs, Polish breeders keep local pigs subject to the conservation programme including Pulawska (P) pig. Analysis of records spanning 20 years showed that lean content of P carcass increased from 41.43% in 1983 to 45.68% in 2003, with a simultaneous decrease in fat content. Considering the relatively high rate of changes in these traits, it would be interesting to find out parameters that could serve as a criterion for evaluating the degree of heterozygosity in P pig. The aim of this study was, therefore, to determine the melanocortin receptor gene polymorphism in P pig and its effect on carcass quality. The study involved 66 P fatteners. After slaughter and 24-hour cooling at 4°C, linear measurements of carcasses were taken and dissection was made according to the Walstra and Merkus method. Genotype analysis showed the highest frequency of MC4R A/G and the lowest of MC4R A/A animals. Frequency of the allele MC4R A was only by 15.2 per cent units lower than that of the MC4R G allele. The MC4R A allele showed a significant effect on increasing backfat thickness, especially over the loin and was significantly correlated with a greater fat amount of neck. Animals with the A allele at the MC4R locus were also characterized by a significantly lower amount of lean in this cut. The results obtained for frequency of different genotypes in P pig could serve as reference values for selection-induced changes, thus reflecting the level of genetic variation in the breed

RNA-seq based SNP discovery in gluteus medius muscle of Polish Landrace pigs

BackgroundSingle nucleotide polymorphisms (SNPs) are the well-known molecular markers in genetics and breeding studies applied to veterinary sciences and livestock production. Advancement of next generation sequencing (NGS) provides a high-throughput means of potential putative SNP discovery. The aim of the study was to identify the putative genetic variants in gluteus medius muscle transcriptome of Polish Landrace pigs.MethodsRNA-seq based NGS experiment was performed on Polish Landrace pigs fed with omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) and normal diets. Isolation of total RNA from gluteus medius muscle was performed on low PUFAs (n=6) and High PUFAs dietary group of Polish Landrace pigs. The RNA-seq libraries were constructed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control of raw RNA-seq data was performed using the Trimmomatic and FastQC tools. High QC paired-end RNA-seq data of gluteus medius muscle transcriptome were mapped to the reference genome Sus scrofa v.10.2. Finally, the SNPs discovery was performed using GATK and SAMtools bioinformatics SNPs caller tools.ResultsThe Fastq RNA-seq data generated from two pooled paired-end libraries (151bp) of gluteus medius muscle tissue of Polish Landrace pigs were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Study identified a total of 50.5 million paired-end reads (32.5 million low PUFAs dietary group and 18 million reads high PUFAs dietary group) of gluteus medius muscle transcriptome of Polish Landrace pigs. SNP discovery identified a total of 35436 homozygous and 28644 heterozygous cSNPs in gluteus medius muscle transcriptomes representing both dietary groups of Polish Landrace pig. Moreover, a total of 25187 and 5488 cSNP were identified as synonymous SNPs, and 18005 and 4780 cSNP were identified as nonsynonymous SNPs. Finally, single nucleotide variation (SNV) representing substitutions of all four possibilities (A,T,G,C) were identified ranging 2935 to 3227 SNVs (high PUFAs) and 3528 to 3882 SNVs (low PUFAs) for the heterozygous cSNPs and 2712 to 4058 (high PUFAs) and 4169 to 5692 SNVs (low PUFAs) for the heterozygous SNPs in gluteus medius muscle transcriptomes of Polish Landrace pigs.ConclusionsStudy concluded that identification of cSNPs dataset representing the gluteus medius muscle transcriptome of Polish Landrace pigs fed with a control diet (low) and pigs fed with a PUFAs diet (high) may be helpful to develop a new set of genetic markers specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in genome-wide association studies (GWAS) and to finally implement on marker assisted selection (MAS) and genomics selection (GS) program in active breeding population of Polish Landrace pigs in Poland

RNA-seq based SNP discovery in liver transcriptome of Polish Landrace pigs

Background: RNA-seq technology is most commonly used in quantitative measurement of gene expression levels and identification of non-annotated transcripts. It is also used for the coding SNPs (cSNPs) discoveries in an efficient and cost-effective way. The aim of this study was to identify the putative genetic cSNPs variants in liver transcriptome of Polish Landrace pigs fed with high and low (normal) omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) diets.Methods: RNA-seq based NGS experiment was performed on Polish Landrace pigs fed with high and low PUFAs diets. Total RNA were isolated from liver tissues of low PUFAs (n=6) and high PUFAs dietary group (n=6) of Polish Landrace pigs. The RNA-seq libraries preparations were performed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control (QC) of raw RNA-seq data of liver transcriptome was performed using the Trimmomatic and FastQC tools. The paired-end mapping of the liver transcriptome RNA-seq data (n=12) was performed on the reference genome Sus scrofa v.10.2, followed by cSNPs discovery using GATK and SAMtools bioinformatics SNPs caller tools.Results: Two pooled paired-end libraries of 151bp liver transcriptome of Polish Landrace pigs were generated from MiSeq instrument and subsequent Fastq RNA-seq data were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Our study identified 25.3 million paired-end reads: representing 13,509,248 paired-end reads of high PUFAs dietary group and 11,815,696 paired-end reads of low PUFAs dietary group of Polish Landrace pigs liver transcriptome. The SNP discovery results revealed identification of 25909 homozygous and 23290 heterozygous cSNPs in the liver transcriptome of both dietary groups of Polish Landrace pigs. With regards to same or alternative SNPs alleles encoding amino acids regions, a total of 27141 synonymous cSNP and 5989 non-synonymous cSNPs were identified in liver transcriptome representing high PUFAs dietary group. However, a total of 15128 synonymous cSNPs and 3900 non-synonymous cSNPs were identified in liver transcriptome representing low PUFAs dietary groups of Polish Landrace pigs. The identification of single nucleotide variations (SNVs) representing substitutions of all four possibilities (A,T,G,C) were ranged 2872 to 6868 SNVs (high PUFAs) and 2574 to 3654 SNVs (low PUFAs) in the homozygous cSNPs and 2452 to 2678 SNVs (high PUFAs) and 2094 to 2230 SNVs (low PUFAs) in the heterozygous cSNPs of liver transcriptomes of Polish Landrace pigs, respectively.Conclusions: Study concluded that identification of cSNPs dataset representing the liver transcriptome of Polish Landrace pigs fed with a control diet (low) and pigs fed with a PUFAs diet (high) may be helpful to develop a new set of genetic markers for trait-associated studies (viz., growth and metabolic traits) specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in the genetic improvement of the pig production traits using the genome-wide association studies (GWAS) and to finally implement on marker assisted selection (MAS) and genomics selection (GS) program in active breeding population of Polish Landrace pigs in Poland

A porcine gluteus medius muscle genome-wide transcriptome analysis: dietary effects of n-6 and n-3 fatty acids on biological mechanisms

The level of n-6 and n-3 polyunsaturated fatty acids may affect many cellular systems and functions via nuclear receptors or the bioactive lipid regulation of gene expression. The objective of this study was to investigate the changes in the muscle transcriptome and the biological functions regulated by increased consumption of n-3 and n-6 fatty acids in the pig gluteus medius muscle. The transcriptome of the gluteus medius muscle was studied for pigs subjected to either a control diet or a diet supplemented with linseed and rapeseed oil to increase polyunsaturated fatty acid content. Next-generation sequencing (NGS) was used to generate the muscle tissue transcriptome database. The results of the NGS indicate a role of the fatty acids in the regulation of the expression of genes essential for muscle tissue development and functioning. Functional analysis revealed that the identified genes were important for a number of biological processes including protein development, signaling, inflammatory response, membranes, and lipid metabolism. The genes that were expressed specifically in only one of the dietary groups were responsible for many of the same processes listed above, indicating that biological processes were strongly modulated and tended to switch between coherent stages in response to increased levels of n-6 and n-3 fatty acids. Several nuclear receptors regulating transcription showed altered expression, including hepatocyte nuclear factor-4α (HNF4alpha), carbohydrate responsive element binding protein (ChREBP), and nuclear factor κB (NFkappaΒ). We suggest that the identified changes were largely due to regulation of those transcription factors. Our results provide strong evidence that n-6 and n-3 fatty acids regulate fundamental metabolic processes in muscle tissue development and functioning

Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome

The optimal ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) is important for keeping the homeostasis of biological processes and metabolism, yet the underlying biological mechanism is poorly understood. The objective of this study was to identify changes in the pig liver transcriptome induced by a diet enriched with omega-6 and omega-3 fatty acids and to characterize the biological mechanisms related to PUFA metabolism.Polish Landrace pigs (n = 12) were fed diet enriched with linoleic acid (LA, omega-6) and α-linolenic acid (ALA, omega-3) or standard diet as a control. The fatty acid profiling was assayed in order to verify how feeding influenced the fatty acid content in the liver, and subsequently next-generation sequencing (NGS) was used to identify differentially expressed genes (DEG) between transcriptomes between dietary groups. The biological mechanisms and pathway interaction networks were identified using DAVID and Cytoscape tools. Fatty acid profile analysis indicated a higher contribution of PUFAs in the liver for LA- and ALA-enriched diet group, particularly for the omega-3 fatty acid family, but not omega-6. Next-generation sequencing identified 3565 DEG, 1484 of which were induced and 2081 were suppressed by PUFA supplementation. A low ratio of omega-6/omega-3 fatty acids resulted in the modulation of fatty acid metabolism pathways and over-representation of genes involved in energy metabolism, signal transduction, and immune response pathways.In conclusion, a diet enriched with omega-6 and omega-3 fatty acids altered the transcriptomic profile of the pig liver and would influence animal health status.<br/

A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland

Abstract 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, Puławska, Złotnicka White and Złotnicka 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

Additional file 3: of A porcine gluteus medius muscle genome-wide transcriptome analysis: dietary effects of omega-6 and omega-3 fatty acids on biological mechanisms

Additional information for the Cytoscape-ClueGo networks of differentially expressed genes (DEG) identified between pigs fed with the diet supplemented with omega-6 and omega-3 fatty acids versus pigs fed with the control diet. (XLS 46 kb

Credit Growth in Central and Eastern Europe

This thesis focuses on the development of credit to the private sector in the Central and Eastern European (CEE) countries. Although the speed of credit growth in these countries has recently slowed down as the consequence of the global financial crisis, the overall increase in credit to the private sector over the past decades has been immense. As a result, the thesis examines whether this substantial increase in credit is linked to the convergence of the CEE countries towards the equilibrium or whether it represents an excessive credit growth that could threaten the macroeconomic and financial stability in these countries. We estimate the equilibrium credit levels for 11 transition countries by applying a dynamic panel data model. Since in-sample approach may bias the estimation results we perform the estimates out-of-sample using a panel of selected developed EU countries as a benchmark. The difference between the actual and estimated credit-to-GDP ratios serves as a measure of private credit excessiveness. The results indicate a slightly excessive or close to the equilibrium credit-to-GDP ratios in Bulgaria, Estonia, and Latvia prior to the financial crisis. With regard to the significant decline in GDP during the crisis this measure of credit excessiveness in these countries have further increased