Molecular characterization and association analysis of porcine CA3

Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep

The tail fat of sheep is the most typical deposited fat, and it can be widely used in human daily life, such as diet, cosmetics, and industrial raw materials. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6, 18, and 30 months. A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep. Based on functional analysis, we found that fat-related DEGs were mainly expressed at 6 months of age and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their transregulators. Further, we obtained several fat-related differentially expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Finally, we concluded that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process.

Myogenic regulatory factors are key players in determining muscle mass and meat quality in Jeju native and Berkshire pigs

BACKGROUND

Meat from Jeju native pigs (JNPs) is highly popular among Korean consumers; however, the production efficiency is limited due to the low adult body weight. In contrast, the Berkshire breed, which has a genetic background closely related to Asian native pigs, gains weight more efficiently.

OBJECTIVES

This study focused on the differential expression of genes related to muscle growth in postnatal myogenesis between Berkshire and JNPs, specifically the myogenic regulatory factor (MRF) genes (MyoD, Pax7, Myf5, Myf6 and MyBPH). The MRF family is primarily involved in the proliferation and development of muscle.

METHODS

Qualitative reverse transcription-polymerase chain reaction and western blot analyses revealed that expression of MyoD and Pax7 was significantly higher in Berkshire pigs than in JNPs. In addition, co-expression of MyoD and Pax7 was observed in myotubes formed in cultured C2C12 cells. ToppCluster was used to elucidate the relationship between biological processes of the MRFs and muscle-related signalling pathways.

RESULTS

MyoD and Pax7 are factors essential for the activation of satellite cell during myogenesis. However, the mRNA and protein levels of MyBPH (which is responsible for meat quality, e.g. water content, colour and tenderness) are significantly higher in both 1-day-old piglets and adult JNPs than in Berkshire pigs.

CONCLUSIONS

This study provides a genetic understanding of myogenesis in the postnatal and adult stages of Berkshire pigs and JNPs. Moreover, these results will help identify marker genes related to muscle mass, growth performance and meat quality in indigenous Korean pig breeds.

A genome scan for selection signatures in pigs

Identifying signatures of selection can provide a straightforward insight into the mechanism of artificial selection and further uncover the causal genes related to the phenotypic variation. Based on Illumina Porcine60KSNP chip data, four complementary methods, Long-Range Haplotype (LRH), Tajima’s D, Cross Population Extend Haplotype Homozygosity Test (XPEHH) and F_ST, were implemented in this study to detect the selection signatures in the whole genome of one typical Chinese indigenous breed, Rongchang, one Chinese cultivated breed, Songliao, and two western breeds, Landrace and Yorkshire. False Discovery Rate (FDR) was implemented to control the false positive rates. In our study, a total of 159, 127, 179 and 159 candidate selection regions with average length of 0.80 Mb, 0.73 Mb, 0.78 Mb and 0.73 Mb were identified in Landrace, Rongchang, Songliao and Yorkshire, respectively, that span approximately 128.00 Mb, 92.38 Mb, 130.30 Mb and 115.40 Mb and account for approximately 3.74–5.33% of genome across all autosomes. The selection regions of 11.52 Mb shared by Landrace and Yorkshire were the longest when chosen pairs from the pool of the four breeds were examined. The overlaps between Yorkshire and Songliao, approximately 9.20 Mb, were greater than those of Yorkshire and Rongchang. Meanwhile, the overlaps between Landrace and Songliao were greater than those of Landrace and Rongchang but less than those of Songliao and Ronchang. Bioinformatics analysis showed that the genes/QTLs relevant to fertility, coat color, and ear morphology were found in candidate selection regions. Some genes, such as LEMD3, MC1R, KIT, TRHR etc. that were reported under selection, were confirmed in our study, and this analysis also demonstrated the diversity of breeds.

Variability of mRNA abundance of leukemia inhibitory factor gene (LIF) in porcine ovary, oviduct and uterus tissues

The leukemia inhibitory factor (LIF) gene encodes a pleiotropic cytokine which is produced by the endometrium and plays an important role in implantation and early embryonic development. Because of its function, LIF gene is considered as a candidate gene for litter size in many mammalian species including pig. The aim of present study was to evaluate the expression of LIF gene in the porcine ovary, oviduct and two regions of uterus (corpus uteri, cornu uteri) in prepubertal and pubertal gilts. In order to precise estimation of LIF transcript abundance we evaluated the stability of expression for several candidate housekeeping genes in investigated tissues across different breeds and different stage of oestrus cycle. The geNorm analysis indicated that the most stable reference genes across analyzed tissues were: OAZ1 and RPL27. The analysis conducted separately for each tissue confirmed that the most stable gene was OAZ1 in all tissues expect oviduct (the most stable was RPL27 gene). In prepubertal pigs, the highest level of the LIF expression was obtained in both regions of uterus compare to ovary and oviduct tissues (P < 0.01). A similar trend in LIF expression pattern was observed in follicular phase-the significantly highest transcript level was obtained in cornu uteri, it was about ninefold higher than in ovary (P < 0.05). In luteal stage the highest expression was in corpus uteri. In pig, the high expression in luteal phases suggested that, LIF may be mainly secreted in respond to the increased of progesterone concentration and it can be connected with the preparation of the uterus for implantation.

H-FABP and LEPR gene expression profile in skeletal muscles and liver during ontogenesis in various breeds of pigs

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.

Transcriptional profiling during foetal skeletal muscle development of Piau and Yorkshire-Landrace cross-bred pigs

Skeletal muscle development is a complex process involving the coordinated expression of thousands of genes. The aim of this study was to identify differentially expressed genes in longissimus dorsi (LD) muscle of pigs at 40 and 70 days (d) of gestation (developmental stages encompassing primary and secondary fibre formation) in Yorkshire-Landrace (YL) cross-bred pigs and Piau pigs (a naturalized Brazilian breed), which are two breed types that differ in muscularity. Foetuses were obtained from gilts at each gestational age (n = 3 YL; n = 4 Piau), and transcriptional profiling was performed using the Pigoligoarray microarray containing 20 400 oligonucleotides. A total of 486 oligonucleotides were differentially expressed (fold change (FC) ≥ 1.5; false discovery rate (FDR) ≤ 0.05) between 40 and 70 d gestation in either YL or Piau pigs, and a total of 1300 oligonucleotides were differentially expressed (FC ≥ 1.5; FDR ≤ 0.05) between YL and Piau pigs at either age. Gene ontology annotation and pathway analyses determined functional classifications for differentially expressed genes and revealed breed type-specific developmental expression patterns. Thirteen genes were selected for confirmation by qRT-PCR analyses, and expression patterns for most of these genes were confirmed, providing further insight into the roles of these genes in pig muscle development. This study revealed both developmental and breed type-specific patterns of gene expression in foetal pig skeletal muscle, including genes not previously associated with myogenesis. This information will contribute to future pig genetic improvement efforts.

Novel porcine housekeeping genes for real-time RT-PCR experiments normalization in adipose tissue: assessment of leptin mRNA quantity in different pig breeds

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 90 mRNA 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.

The expression pattern of myogenic regulatory factors MyoD, Myf6 and Pax7 in postnatal porcine skeletal muscles

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. gracilisP<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.

Relationship between proteome changes of Longissimus muscle and intramuscular fat content in finishing pigs fed conjugated linoleic acid

The present experiment was conducted to determine proteome changes in Longissimus muscle of finishing pigs fed conjugated linoleic acid (CLA), in association with alteration of intramuscular fat content. Previously, seventy-two Duroc × Landrace × Large White gilts (approximately 60 kg) had been fed maize–soyabean meal-based diets with 0, 12·5 and 25 g CLA/kg diet. The CLA contained 369·1 mg/g cis-9, trans-11 CLA, 374·6 mg/g trans-10, cis-12 CLA and 53·7 mg/g other isomers. Six pigs per treatment were slaughtered when they reached a body weight of approximately 100 kg. Data published from a previous experiment demonstrated that supplementation with 12·5 or 25 g CLA/kg diet increased intramuscular fat content (P < 0·05). The present study investigated the proteome changes in Longissimus muscle of control and pigs supplemented with 25 g CLA/kg diet. CLA significantly influenced the abundance of proteins related to energy metabolism, fatty acid oxidation and synthesis, amino acid metabolism, defence, transport and other miscellaneous processes (P < 0·05). The increase in intramuscular fat content was positively correlated with the increased abundance of carbonic anhydrase 3 and aspartate aminotransferase (P < 0·05). We suggest that the proteome changes in Longissimus muscle contributed to greater intramuscular lipid content in CLA-supplemented pigs.

Molecular characterization and association analysis of FBXO40 with partial hematological indexes in pig

F-box proteins are quite significant ubiquitin-proteasome pathway regulators in eukaryotic cells. FBXO40, a member of this large family, alters its expression pattern in muscle atrophy. Here we isolated most of the verified porcine FBXO40 coding sequence (CDS) (2258 bp) and assigned it to the porcine chromosome 13q4.1-4.6 by using the INRA-Minnesota porcine radiation hybrid panel, and we also explored the tissue expression distributions, which is relatively high in longissimus dorsi muscle, heart, low in kidney, small intestine, brain, hypophysis, lymphonode, thymus, spleen, large intestine, ovary, stomach, and undetectable in testis, liver, uterus and thyroid gland. Inferring phylogenetic tree was constructed to study the evolutionary implications. Moreover, a HindII (HincII)-RFLP (A/C) polymorphism in 3'-untranslated region (3'-UTR) of porcine FBXO40 gene was demonstrated by sequencing and PCR-restriction fragment length polymorphism (PCR-RFLP) analysis. Statistical analysis result of this polymorphism showed that the allele A was predominant in all detected indigenous breeds, but C in western introduced commercial breeds. The SNP was further analyzed in our experimental pig population including Tongcheng, Landrace, Large White, and crossbreds of Large White × (Landrace × Tongcheng) and Landrace × (Large White × Tongcheng). The association analysis results indicated that the A/C base substitution was associate with some hematological indexes, the hemoglobin concentration (P < 0.0001), mean corpuscular volume hemoglobin concentration (P = 0.0002) and mean corpuscular volume (P = 0.0138).

Partial molecular characterization, expression pattern, polymorphism and association analysis of porcine SKP2 gene

As a component of E3 ubiquitin protein ligases called SCFs, SKP2 protein belongs to a member of FBLs protein which is the biggest eukaryotic subfamily of F-BOX proteins with 12 members. In this study, we cloned and sequenced partial cDNA, intron 1 and intron 6 of porcine SKP2 gene. The partial cDNA is 1,402 bp long and has an open reading frame of 1,272 bp which encodes 424 putative amino acids. The deduced protein comprises a conserved F-BOX domain at position from the 90th to 140th amino acid. The phylogenetic tree indicated that porcine SKP2 has the closest genetic relationship with bovine SKP2 than other selected animal species. Quantitative RT-PCR analysis displayed that the tissue expression level of porcine SKP2 fluctuated remarkably in a large range, and it expressed in thymus with the highest level and in longissimus dorsi muscle with the lowest level. Two SNPs were identified, meanwhile, further polymorphism analysis with Cfr42I showed that AA genotype was in dominance absolutely among four kinds of unrelated Chinese indigenous miniature and one introduced Landrace pig breeds. In addition, association analysis with immune traits and blood parameters revealed that the SNP Cfr42I in intron 1 was significantly associated with red cell distribution width of neonate piglets at 0 day (P = 0.027).

Board-invited review: the biology and regulation of preadipocytes and adipocytes in meat animals

The quality and value of the carcass in domestic meat animals are reflected in its protein and fat content. Preadipocytes and adipocytes are important in establishing the overall fatness of a carcass, as well as being the main contributors to the marbling component needed for consumer preference of meat products. Although some fat accumulation is essential, any excess fat that is deposited into adipose depots other than the marbling fraction is energetically unfavorable and reduces efficiency of production. Hence, this review is focused on current knowledge about the biology and regulation of the important cells of adipose tissue: preadipocytes and adipocytes.

Regulation of pH in the mammalian central nervous system under normal and pathological conditions: facts and hypotheses

The maintenance of pH homeostasis in the CNS is of key importance for proper execution and regulation of neurotransmission, and deviations from this homeostasis are a crucial factor in the mechanism underlying a spectrum of pathological conditions. The first few sections of the review are devoted to the brain operating under normal conditions. The article commences with an overview of how extrinsic factors modelling the brain at work: neurotransmitters, depolarising stimuli (potassium and voltage changes) and cyclic nucleotides as major signal transducing vehicles affect pH in the CNS. Further, consequences of pH alterations on the major aspects of CNS function and metabolism are outlined. Next, the major cellular events involved in the transport, sequestration, metabolic production and buffering of protons that are common to all the mammalian cells, including the CNS cells. Since CNS function reflects tight interaction between astrocytes and neurons, the pH regulatory events pertinent to either cell type are discussed: overwhelming evidence implicates astrocytes as a key player in pH homeostasis in the brain. The different classes of membrane proteins involved in proton shuttling are listed and their mechanisms of action are given. These include: the Na+/H+ exchanger, different classes of bicarbonate transporters acting in a sodium-dependent- or -independent mode, monocarboxylic acid transporters and the vacuolar-type proton ATPase. A separate section is devoted to carbonic anhydrase, which is represented by multiple isoenzymes capable of pH buffering both in the cell interior and in the extracellular space. Next, impairment of pH regulation and compensatory responses occurring in brain affected by different pathologies: hypoxia/ischemia, epilepsy, hyperammonemic encephalopathies, cerebral tumours and HIV will be described. The review is limited to facts and plausible hypotheses pertaining to phenomena directly involved in pH regulation: changes in pH that accompany metabolic stress but have no distinct implications for the pH regulatory mechanisms are not dealt with. In most cases, the vast body of knowledge derived from in vitro studies remains to be verified in in vivo settings.

Associations of functional candidate genes derived from gene-expression profiles of prenatal porcine muscle tissue with meat quality and muscle deposition

Ten genes (ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain x (Landrace x Large White), Duroc x (Landrace x Large White) as well as in an experimental F(2) population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human-porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of < or = 0.05; PDGFRA revealed no association reaching the P < or = 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of < 0.003 that correspond to false discovery rates of < 0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical-genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations.