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Identification of new polymorphic variants from RNA-seq data is difficult mainly because of the errors arising during bioinformatic analysis. Therefore, new experiments in this area are very profitable for improving new statistical methods. In our study of the porcine brain transcriptome, we have identified 10966 polymorphic variants, among which 7277 were single nucleotide polymorphisms (SNPs). Further, we have calculated allelic ratios for the SNPs identified and estimated that 52% of genes in porcine brain are subjected to allele-specific expression (ASE), a phenomenon in which one allele is preferentially expressed. Our investigation presents the first estimates of ASE in porcine brain. In addition, we have used the results of RNA-seq for the identification of SNPs in putatively imprinted genes. Finally, we have used these SNPs for the verification of the imprinted status of the INPP5f variant 2, LRRTM1 and HM13 genes in pigs by Sanger sequencing. We observed that INPP5f variant 2 is paternally expressed, while HM13 and LRRTM1 are biallelically expressed in porcine brain. We have also confirmed maternal expression of the MEG3 gene in pigs. Our results present how RNA-seq data may be used for imprinting studies without sequencing of parental genomes., (Copyright © 2017 Elsevier B.V. All rights reserved.)

In pig, the histological profile of muscle tissue, especially the proportion of individual fiber types, is one of the main factors affecting meat quality properties. In the present research, RNA sequencing (RNA-seq) by using next generation sequencing method was applied to estimate the whole gene expression profile of Longissimus lumborum muscle of pigs (Large White breed) differing in the percentage of two fiber types (slow-twitch (type I) fibers and fast-twitch glycolytic (type IIB) fibers). The RNA-seq approach allowed us to identify 355 differentially expressed genes (DEGs) indicated as significant (false discovery rate-adjusted P < 0.05) using three types of software: DESeq2, edgeR and baySeq. Detected genes and pathways deregulated in muscle depending on tissue microstructure were associated with: metabolic processes - 158 genes; cellular processes - 122; biological regulation - 62; localization - 51; and 35 genes with developmental processes. The DEGs were included in: PI3K-Akt; FoxO and MAPK signaling pathways, regulation of actin cytoskeleton, lysine degradation and insulin signaling pathway as well as mTOR and Hippo signaling pathways. These results highlight the mainly metabolic pathways related to glucose metabolism and contraction processes of muscle cells. Detection of genes involved in variation of fiber-type distribution will be useful in understanding of the genetic factors affecting muscle structure, metabolic process and indirectly, meat quality traits., (© 2016 Japanese Society of Animal Science.)

The aim of this study was to assess mRNA abundance of calpain 1 (CAPN1) and calpain 3 (CAPN3) in breast muscle of 80 fast-growing (FG) and slow-growing broilers (SG) and relate gene expression in relation to growth and Warner Bratzler (WB) shear force of breast muscle. The expression of CAPN1 and CAPN3 genes was higher in the FG compared to the SG line, but significant results were obtained only for CAPN1. The CAPN1 mRNA level was strongly dependent on line and gender interaction. Lower values of shear force were observed in the FG line, where a higher level of calpain expression was shown. A new panel of housekeeping genes (RPL4 and SDHA) for normalisation of gene expression in muscle tissues could be used in other studies of gene expression in chicken.

DLK1--(Drosophila like element 1) is a paternally expressed gene, associated with the callipyge phenotype in sheep. In a present study we designed a new real-time PCR alleleic discrimination assay for genotyping of a silent C/T mutation (c.639C>T) in DLK1 gene in swine. The DLK1 c.639C>T mutation was highly polymorphic in all breeds analyzed and C allele was predominant in Landrace and Duroc while T allele was more frequent in Pietrain and Puławska breed. Moreover, we analyzed mRNA expression of DLK1 and adjacent genes--MEG3 and PEG11 in muscles of swines of different breeds raised in Poland. We did not observe significantly different expression of DLK1, MEG3 or PEG11 mRNA in any of analyzed breeds. We also attempted to assess the effect of DLK1 (c.639C>T) on the expression of genes in callipyge locus but did not find significant differences between animals with alternate genotypes (C/C and T/T homozygotes)., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Contents In recent years, intensive attention has been put on improving reproductive performance of pigs. Several experiments aimed to identify markers associated with prolificacy, but this issue still remains open. In our study, we investigated associations between polymorphisms in IGF2, GNAS and MC4 R genes with reproductive traits of Polish Landrace and Large White pigs. We did not find any significant associations for g. GNAS314T > 324C, IGF2 intron3-g.3072G > A or g. MC4R 1426G > A in Polish Landrace and Large White pigs. In the case of IGF2 intron3-g.3072G > A, this information is of great importance, because this marker is widely implemented in pigs breeding and previous experiments suggested its role in prolificacy of pigs. We also investigated expression of IGF2 gene and showed that this gene is monoallelically expressed in reproductive organs (ovary and cornus uteri). [ABSTRACT FROM AUTHOR]

Abstract: The main function of adipose tissue is energy storage and production of various cytokines and hormones, such as leptin. Leptin is a protein hormone synthesized and secreted by adipose tissue. The expression of leptin is strongly dependent on growth and luteinizing hormones, which play an important role in the brain-pituitary axis. The concentration of leptin in blood plasma increases with age and obesity and is associated with the level of leptin mRNA in adipose tissue. Selection of appropriate internal control gene (ICG) for normalization of quantitative PCR data for genes of interest is critical for interpretation of results. The estimation of leptin mRNA is important in the research on regulation of feed intake and metabolic and energy balance. Therefore, the objective of this study was to evaluate the stability of mRNA expression for a number of candidate housekeeping genes in the porcine backfat tissue across different breeds. In our study we used a freeware computer program (geNorm) to evaluate the most stable among eight ICG genes (β-actin, hypoxanthine phosphoribosyltransferase 1, TATA binding protein, glyceraldehyde-3-phosphate dehydrogenase, ornithine decarboxylase antizyme 1, 60S ribosomal protein L27, 40S ribosomal protein S29, eukaryotic elongation factor (1) in 90mRNA samples of backfat tissue. In the study we used three breeds differing in muscling: Polish Large White (n=30), Polish Landrace (n =30) and Pietrain (n =30). The results showed that the three most stable genes were ornithine decarboxylase antizyme 1 (OAZ1), 60S ribosomal protein L27 (RPL27) and β-actin (M =0.579, 0.602 and 0.607, respectively). In order to evaluate the abundance of leptin mRNA, the two most stable genes were used. The highest level of mRNA expression was obtained for PL and the lowest for Pietrain pigs. These results confirmed previous studies which showed that pigs with lean carcass were characterized by a lower level of leptin transcript compared to pigs with large fat deposit. Moreover, we analyzed relationship between C3469T Lep polymorphism and level of leptin mRNA, but did not find significant associations. Our study provides a new panel of housekeeping genes for normalization of the expression of a gene of interest in adipose tissue. [Copyright &y& Elsevier]

Abstract: The MyoD, Myf6 genes, which belong to the family of muscle regulatory factors (MRFs) play a major role in muscle growth and development. Therefore, they are considered as candidate genes for meat production traits in pigs. These basic helix-loop-helix (bHLH) transcription factors regulate myogenesis: they initiate the formation of muscle fibres and regulate the transcription of muscle specific genes. The paired-box transcription factor Pax7 plays critical roles during fetal development and this protein is essential for renewal and maintenance of muscle stem cells. In particular, expression of Pax7 and MyoD is correlated with presence of active satellite cells, important in hyperplastic and hypertrophic growth in skeletal muscle. The objective of the study was to investigate the level of expression of MyoD, Myf6 and Pax7 genes in porcine skeletal muscles (m. semimembranosus, m. biceps femoris, m. gracilis) in breeds differing in muscularity. Moreover, we investigated expression profile of these genes during ontogenesis in Polish Large White (PLW) and Pietrain pigs in the largest ham muscle (m. semimembranosus). Analysis of several ham muscles showed higher expression of MyoD in the Polish Landrace (PL) breed than in Pietrain and PLW pigs (m. semimembranosus P <0.001; m. biceps femoris P <0.05 and P <0.01, respectively; m. gracilis P <0.01). The level of Pax7 transcript depended on type of muscle and breed. The highest expression was in m. gracilis in Pietrain and the lowest in Polish Landrace. Our results indicate that MyoD and Pax7 genes had higher expression levels in the early stages of development in both investigated breeds. The total expression profile of MyoD and Pax7 genes suggests that higher muscularity in Pietrain pigs is associated with the presence of a greater number of active satellite stem cells compared to other breeds. The expression level of Myf6 gene does not indicate significant differences between muscles, ages and breeds. [Copyright &y& Elsevier]

Abstract The ACTN3 gene codes for α-actinin-3, a protein localized in the Z -line in the skeletal muscle. Actinin-3 is critical in anchoring the myofibrillar actin filaments and plays a key role in muscle contraction. ACTN3 (α-actinin-3) cross-links glycogen phosphorylase (GP), which is the key enzyme catalysing glycogen metabolism. The aim of present study was to establish the expression level of the ACTN3 gene (for both isoforms separately and together in the gene expression analysis) in the gluteus medius muscle in order to verify if the α-actinin-3 gene can be related to training intensity in Arabian horses. A structural analysis of the ACTN3 gene was performed simultaneously to identify polymorphisms that can be related to racing performance traits. Our results showed the significant decrease (p < 0.05) of ACTN3 expression in the skeletal muscle of Arabian horses during the training periods preparing for flat-racing, and this decrease differed by the intensity of the exercises. The highest mRNA abundance measured for all ACTN3 genes was detected in the muscle of untrained horses, while the lowest expression was identified at the end of the racing season when horses had fully adapted to the physical effort. This gene expression profile was confirmed for both ACTN3 isoforms. The analysis of the ACTN3 sequence allowed us to identify 14 polymorphisms, which were localized in the promoter region, the 5′UTR (7 SNPs), exons (2 SNPs) and introns (5 SNPs). Two of them, a novel c.2334C>T - splice variant and the g.1104G>A polymorphism in the promoter region, were proposed as the causative mutations that might affect gene expression. The presented gene expression analyses indicated the significant role of the ACTN3 gene in adaptation to physiological effort in horses. Due to previous reports and our findings, further studies should be conducted to verify the usage of the ACTN3 gene as a potential genetic marker for determining exercise performance in Arabian horses and other horse breeds. Highlights • Equine ACTN3 gene expression was evaluated in skeletal muscle during exercise. • The results show the exercise-induced modification of ACTN3 expression. • Intensive physiological effort affected the decrease of the ACTN3 transcript levels. • Several polymorphisms were identified in ACTN3 locus in Arabian horses. [ABSTRACT FROM AUTHOR]

Abstract: The genes coding for H-FABP (heart acid-binding protein) and LEPR (leptin receptor) are considered to be candidates for lipid metabolism and thus affect fat deposition in pigs. The aim of our study was to assess the amount of H-FABP and LEPR transcript in the skeletal muscles (m. longissimus dorsi, m. semimembranosus) and liver of pigs of various ages. The experiments were carried out on 5 popular breeds of swine raised in Poland which exhibit different levels of fat tissue. Furthermore, we examined the effect of H-FABP and LEPR genotypes (HinfI, HpaII, and HaeIII for H-FABP and HpaII for LEPR) on the expression abundance of these genes. We confirmed a statistically significant relationship between the breed (P < .001), type of tissue (LEPR P < .001; H-FABP P < .01), and age of the animal (P < .05) on the abundance of mRNA transcript of both genes. In all breeds, the expression of the leptin receptor gene increased significantly (P < .01) with age in muscle tissue, whereas this relationship was not observed in liver tissue. However, the expression of the H-FABP gene in muscles did not change with age or breed, although in the liver expression levels were high in young (60 and 90 d) pigs. In conclusion, H-FABP and LEPR genes are strongly related to the development and function of fat tissue in pigs. [Copyright &y& Elsevier]