Variation in the IGF2 gene promoter region is associated with intramuscular fat content in porcine skeletal muscle

Strand-Specific RNA Sequencing Reveals Gene Expression Patterns in F1 Chick Breast Muscle and Liver after Hatching

Heterosis refers to the phenomenon where hybrids exhibit superior performance compared to the parental phenotypes and has been widely utilized in crossbreeding programs for animals and crops, yet the molecular mechanisms underlying this phenomenon remain enigmatic. A better understanding of the gene expression patterns in post-hatch chickens is very important for exploring the genetic basis underlying economically important traits in the crossbreeding of chickens. In this study, breast muscle and liver tissues (n = 36) from full-sib F1 birds and their parental pure lines were selected to identify gene expression patterns and differentially expressed genes (DEGs) at 28 days of age by strand-specific RNA sequencing (ssRNA-seq). This study indicates that additivity is the predominant gene expression pattern in the F1 chicken post-hatch breast muscle (80.6% genes with additivity) and liver (94.2% genes with additivity). In breast muscle, Gene Ontology (GO) enrichment analysis revealed that a total of 11 biological process (BP) terms closely associated with growth and development were annotated in the identified DEG sets and non-additive gene sets, including STAT5A, TGFB2, FGF1, IGF2, DMA, FGF16, FGF12, STAC3, GSK3A, and GRB2. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation presented that a total of six growth- and development-related pathways were identified, involving key genes such as SLC27A4, GLUL, TGFB2, COX17, and GSK3A, including the PPAR signaling pathway, TGF-beta signaling pathway, and mTOR signaling pathway. Our results may provide a theoretical basis for crossbreeding in domestic animals.

The variation of insulin like growth factor 2 maker is associated with growth traits in Thai native (Kradon) pigs

OBJECTIVE

This study was conducted to investigate polymorphisms of the melanocortin-4 receptor (MC4R) and insulin like growth factor 2 (IGF2) genes and to evaluate the growth traits affected by such polymorphisms in Thai native (Kradon) pigs.

METHODS

Blood samples and productive data from 91 Kradon pigs were collected. DNA was extracted and quantified, the IGF2 and MC4R genes were amplified, and the polymerase chain reaction (PCR) produces were digested using the PCR-restriction fragment length polymorphism (PCR-RFLP) technique. Genotyping was performed, and the association between genotypes and growth traits on the birth and weaning weights were evaluated.

RESULTS

The IGF2 intron7 g.162G>C variations in Kradon pigs were found in three genotypes: i) GG, ii) GC, and iii) CC. The GG genotype frequency was the highest followed by the GC and CC genotypes. The frequencies of the G and C alleles were 0.703 and 0.297, respectively. The MC4R genotype was found in only one genotype (GG). The IGF2 gene pattern was not associated with birth weight traits, whereas the IGF2 gene pattern was related to the weaning weight trait in Kradon pigs. Pigs with the CC and GC genotypes had higher weaning weights than ones with the GG genotype (p<0.001).

CONCLUSION

Thai native Kradon pigs with the CC and GC genotypes of the IGF2 gene have higher weaning weights than pigs with the GG genotype.

Identification of Meat Quality Determining Marker Genes in Fibroblasts of Bovine Muscle Using Transcriptomic Profiling

In the present study, we comparatively analyzed the transcriptomic profiling of fibroblasts derived from two different muscles, biceps femoris and longissimus dorsi with significant difference in the meat quality and tenderness. EBSeq algorithm was applied to analyze the data, and genes were considered to be significantly differentially expressed if the false discovery rate value was <0.05, the P value was <0.01, and the fold change was >0.585. The results revealed that 253 genes were differentially expressed genes (DEGs) (170 genes were upregulated, and 83 were downregulated) and more than 100 DEGs were probably associated with intramuscular fat deposition, tenderness, and toughness, which are driving the meat quality and were involved in biological processes such as collagen synthesis, cell differentiation, and muscle tissue and fiber development; molecular functions such as chemokine activity and collagen activity; cellular components such as cytoplasm and myofibril; and pathways such as collagen signaling and metabolic pathways. A gene-act network and a co-expression network revealed the close relationship between intramuscular fat deposition and meat tenderness. The expressions of 20 DEGs were validated by real-time PCR, and the results suggested that the DEGs are correlated with RNA-seq data and play crucial roles in muscle growth, development processes, toughness, and tenderness of the meat. Together, the genome-wide transcriptome analysis revealed that various genes are responsible for toughness and tenderness variance in the difference muscles of beef.

Identification of eQTLs associated with lipid metabolism in Longissimus dorsi muscle of pigs with different genetic backgrounds

Intramuscular fat content and its fatty acid composition affect porcine meat quality and its nutritional value. The present work aimed to identify genomic variants regulating the expression in the porcine muscle (Longissimus dorsi) of 45 candidate genes for lipid metabolism and fatty acid composition in three experimental backcrosses based on the Iberian breed. Expression genome-wide association studies (eGWAS) were performed between the muscle gene expression values, measured by real-time quantitative PCR, and the genotypes of 38,426 SNPs distributed along all chromosomes. The eGWAS identified 186 eSNPs located in ten Sus scrofa regions and associated with the expression of ACSM5, ACSS2, ATF3, DGAT2, FOS and IGF2 (FDR < 0.05) genes. Two expression quantitative trait loci (eQTLs) for IGF2 and ACSM5 were classified as cis-acting eQTLs, suggesting a mutation in the same gene affecting its expression. Conversely, ten eQTLs showed trans-regulatory effects on gene expression. When the eGWAS was performed for each backcross independently, only three common trans-eQTL regions were observed, indicating different regulatory mechanisms or allelic frequencies among the breeds. In addition, hotspot regions regulating the expression of several genes were detected. Our results provide new data to better understand the functional regulatory mechanisms of lipid metabolism genes in muscle.

Association of Twelve Candidate Gene Polymorphisms with the Intramuscular Fat Content and Average Backfat Thickness of Chinese Suhuai Pigs

Simple Summary

Appropriate intramuscular fat content (IFC) is the goal of consumers and the direction that breeders must pursue. However, it is difficult to improve the IFC but not average backfat thickness (ABT) by traditional breeding methods, and pigs must be slaughtered to accurately measure IFC. Marker-assisted selection (MAS) provides an economic and efficient method to improve the IFC in pigs. Our research indicated that the FABP3 (rs1110770079) single nucleotide polymorphism (SNP) could be a candidate gene associated with IFC (but not ABT), and IFC could be improved by selecting the individuals with a favorable genotype (GG) of FABP3 (rs1110770079) SNP for pig breeding.

Abstract

The present study aimed to identify the molecular markers for genes that influence intramuscular fat content (IFC), but not average backfat thickness (ABT). A total of 330 Suhuai pigs were slaughtered, and measurements of IFC and ABT were obtained. Phenotypic and genetic correlations between IFC and ABT were calculated. Thirteen single nucleotide polymorphisms (SNPs) among 12 candidate genes for IFC were analyzed, including FABP3, LIPE, IGF1, IGF2, LEP, LEPR, MC4R, PHKG1, RETN, RYR1, SCD, and UBE3C. Associations of the evaluated SNPs with IFCIFC and ABT were performed. Our results showed that the means of IFC and ABT were 1.99 ± 0.03 % and 26.68 ± 0.28 mm, respectively. The coefficients of variation (CVs) of IFC and ABT were 31.21% and 19.36%, respectively. The phenotypic and genetic correlations between IFC and ABT were moderate. Only the FABP3 (rs1110770079) was associated with IFC (p < 0.05) but not with ABT. Besides, there was a tendency for associations of RYR1 (rs344435545) and SCD (rs80912566) with IFC (p < 0.1). Our results indicated that the FABP3 (rs1110770079) SNP could be used as a marker to improve IFC without changing ABT in the Suhuai pig breeding system.

Analysis of porcine IGF2 gene expression in adipose tissue and its effect on fatty acid composition

IGF2:g.3072G>A polymorphism has been described as the causal mutation of a maternally imprinted QTL for muscle growth and fat deposition in pigs. The objective of the current work was to study the association between the IGF2:g.3072G>A polymorphism and the IGF2 gene expression and its effect on fatty acid composition in adipose tissue in different pig genetic backgrounds. A cis-eQTL region associated with the IGF2 mRNA expression in adipose tissue was identified in an eGWAS with 355 animals. The IGF2 gene was located in this genomic interval and IGF2g.3072G>A was the most significant SNP, explaining a 25% of the gene expression variance. Significant associations between IGF2:g.3072G>A polymorphism and oleic (C18:1(n-9); p-value = 4.18x10^-07), hexadecanoic (C16:1(n-9); p-value = 4.04x10^-07), linoleic (C18:2(n-6); p-value = 6.44x10^-09), α-linoleic (C18:3(n-3); p-value = 3.30x10^-06), arachidonic (C20:4(n-6); p-value = 9.82x10^-08) FAs and the MUFA/PUFA ratio (p-value = 2.51x10^-9) measured in backfat were identified. Animals carrying the A allele showed an increase in IGF2 gene expression and higher PUFA and lower MUFA content. However, in additional studies was observed that there could be other proximal genetic variants affecting FA composition in adipose tissue. Finally, no differences in the IGF2 gene expression in adipose tissue were found between heterozygous animals classified according to the IGF2:g.3072G>A allele inherited from the father (A^PG^M or A^MG^P). However, pyrosequencing analysis revealed that there is imprinting of the IGF2 gene in muscle and adipose tissues, with stronger differences among the paternally and maternally inherited alleles in muscle. Our results suggested that IGF2:g.3072G>A polymorphism plays an important role in the regulation of IGF2 gene expression and can be involved in the fatty acid composition in adipose tissue. In both cases, further studies are still needed to deepen the mechanism of regulation of IGF2 gene expression in adipose tissue and the IGF2 role in FA composition.

Intrinsic High Aerobic Capacity in Male Rats Protects Against Diet-Induced Insulin Resistance

Low aerobic capacity increases the risk for insulin resistance but the mechanisms are unknown. In this study, we tested susceptibility to acute (3-day) high-fat, high-sucrose diet (HFD)-induced insulin resistance in male rats selectively bred for divergent intrinsic aerobic capacity, that is, high-capacity running (HCR) and low-capacity running (LCR) rats. We employed hyperinsulinemic-euglycemic clamps, tracers, and transcriptome sequencing of skeletal muscle to test whether divergence in aerobic capacity impacted insulin resistance through systemic and tissue-specific metabolic adaptations. An HFD evoked decreased insulin sensitivity and insulin signaling in muscle and liver in LCR rats, whereas HCR rats were protected. An HFD led to increased glucose transport in skeletal muscle (twofold) of HCR rats while increasing glucose transport into adipose depots of the LCR rats (twofold). Skeletal muscle transcriptome revealed robust differences in the gene profile of HCR vs LCR on low-fat diet and HFD conditions, including robust differences in specific genes involved in lipid metabolism, adipogenesis, and differentiation. HCR transcriptional adaptations to an acute HFD were more robust than for LCR and included genes driving mitochondrial energy metabolism. In conclusion, intrinsic aerobic capacity robustly impacts systemic and skeletal muscle adaptations to HFD-induced alterations in insulin resistance, an effect that is likely driven by baseline differences in oxidative capacity, gene expression profile, and transcriptional adaptations to an HFD.

Variability of the IGF2 locus in the Suino Nero Lucano pig population and its effects on meat quality

The aim of this study was to analyse the polymorphisms in the two promoter regions, P1 and P2, of the porcine Insulin-like Growth Factor 2 (IGF2) gene and to investigate the effect of IGF2 genotypes on meat quality traits in the Italian autochthonous Suino Nero Lucano pig. Three polymorphic sites were analysed and only two of the eight potential haplotypes were observed in the Suino Nero Lucano pig population: A haplotype (–366A – –225G – –182C), and B haplotype (–366G – –225C – –182T). Muscle mass and meat quality characteristics were analysed in 30 castrated pigs (10 for each of the three IGF2 genotypes: A/A, A/B, and B/B). According to the results, B/B animals, at the same carcass weight, showed the highest Longissimus lumborum and Psoas weight (P < 0.05), whereas A/A animals showed a higher intramuscular fat percentage and lower Warner–Bratzler shear force, drip loss, and polyunsaturated fatty acids content. Meat from B/B animals showed also a higher L* value and myoglobin and deoxymyoglobin percentage compared with meat from A/A ones (P < 0.05).

Genetic variants in IL15 promoter affect transcription activity and intramuscular fat deposition in longissimus dorsi muscle of pigs

Intramuscular fat (IMF) content is a key aspect of pork quality. Elucidation of intramuscular adipocyte regulation mechanisms is important for improving IMF content. Intramuscular adipocytes are dispersed among muscle fibers, so they are inclined to be affected by muscle-derived factors. Interleukin-15 is a major muscle-secreted factor. In this study, the genetic and physiological impacts of IL15 on adipogenesis is investigated. The promoter region of IL15 was scanned by comparative sequencing using two DNA pools of high- and low-IMF individuals. Two SNPs, c.-342C>T (ss2137497757) and c.-334G>A (ss2137497756) (the translation start site is designated as +1), were identified with reverse allele distribution in these two groups. Genotyping by allele-specific PCR revealed that the two SNPs were completely linked. The IMF content of TA/TA individuals was lower than that for CG/CG ones, whereas the IL15 expression level was higher in T-A/T-A individuals. Luciferase assaying also revealed that the T-A haplotype promoter had higher transcription activity. Meanwhile, the effect of interleukin-15 on adipocyte differentiation was further assessed in vitro. Results showed that interleukin-15 suppressed preadipocyte proliferation in a dose-dependent manner. The cell cycle of preadipocytes was arrested, and apoptosis was induced. Oil Red O staining and triglyceride quantification indicated that adipocyte differentiation was also inhibited by interleukin-15. The mRNA levels of PPARG and FABP4 decreased markably upon interleukin-15 treatment. Taken together, we identified two completely linked SNPs in the porcine IL15 promoter region that could alter IL15 transcription activity. As interleukin-15 can inhibit porcine adipocyte differentiation, these promoter mutations could affect IMF deposition by producing differential levels of muscle-derived interleukin-15.

The Relationship of Insulin-Like Growth Factor 2 to Fetal Growth and Adiposity

Insulin-like growth factor 2 (IGF-2) is necessary for adequate human growth. Overexpression of the IGF2 gene is associated with fetal overgrowth and may play a role in the intrauterine programming of adipose tissue. As obesity in children is a major public health problem associated with early onset of comorbid metabolic diseases, identifying early life markers of obesity may serve as useful tool for counseling and implementation of preventive efforts before obesity develops. The relationship between IGF-2 and body composition is an emerging field of study and existing data are conflicting. In this review, we discuss the IGF2 gene and its function, highlight the proposed mechanisms for the effects of IGF-2 on adiposity, and examine the current literature studying the relationships between IGF-2 levels, changes within the IGF2 gene, weight, and adiposity. With additional study, IGF-2 may emerge as a useful marker of future obesity risk in infants.

The association of NR1H3 gene with lipid deposition in the pig

Background

Nuclear receptor subfamily 1, group H, member 3 (NR1H3, an alias for Liver X receptor α, LXRα) is a member of the LXR nuclear receptor super family and is an important regulator of lipid and fatty acid accumulation in the liver, adipose and skeletal muscle.

Methods

In this study, single-nucleotide polymorphisms (SNPs) from six populations of pig (Sus scrofa) were screened by PCR-sequencing and genotyped, and its association with backfat thickness was analyzed in a population of New Huai line (NHP, n = 117). In addition, quantitative real-time PCR and western blot were used to measure expression of NR1H3 in the liver tissue, backfat and longissimus dorsi muscle of DSP (n = 10), TP (n = 10) and YY (n = 10) pigs.

Results

Three SNPs (exon2-C105T, exon2-G106C, and exon5-A201C) were screened and exon5-A201C was identified; the genotype frequencies were significantly different between indigenous and introduced breeds. The CC genotype was associated with higher backfat thickness than the AA and AC genotypes in the NYP. NR1H3 mRNA and protein expression were higher in the liver and longissimus dorsi of DSP and TP than in those of YY. This increased NR1H3 expression might be associated with higher lipid deposition. NR1H3 expression in the backfat of YY was not lower than that in DSP or TP, which might because NR1H3 has an alternative regulatory function for lipid metabolism in the subcutaneous fat of pigs.

Conclusions

Our results suggest that allele A of the exon5-A201C in NR1H3 may promote a reduction in backfat thickness, and differences in NR1H3 expression may be associated with differences in lipid deposition capacity among pigs.

Transient Hepatic Overexpression of Insulin-Like Growth Factor 2 Induces Free Cholesterol and Lipid Droplet Formation

Although insulin-like growth factor 2 (IGF2) has been reported to be overexpressed in steatosis and steatohepatitis, a causal role of IGF2 in steatosis development remains elusive. Aim of our study was to decipher the role of IGF2 in steatosis development. Hydrodynamic gene delivery of an Igf2 plasmid used for transient Igf2 overexpression employing codon-optimized plasmid DNA resulted in a strong induction of hepatic Igf2 expression. The exogenously delivered Igf2 had no influence on endogenous Igf2 expression. The downstream kinase AKT was activated in Igf2 animals. Decreased ALT levels mirrored the cytoprotective effect of IGF2. Serum cholesterol was increased and sulfo-phospho-vanillin colorimetric assay confirmed lipid accumulation in Igf2-livers while no signs of inflammation were observed. Interestingly, hepatic cholesterol and phospholipids, determined by thin layer chromatography, and free cholesterol by filipin staining, were specifically increased. Lipid droplet (LD) size was not changed, but their number was significantly elevated. Furthermore, free cholesterol, which can be stored in LDs and has been reported to be critical for steatosis progression, was elevated in Igf2 overexpressing mice. Accordingly, Hmgcr/HmgCoAR was upregulated. To have a closer look at de novo lipid synthesis we investigated expression of the lipogenic transcription factor SREBF1 and its target genes. SREBF1 was induced and also SREBF1 target genes were slightly upregulated. Interestingly, the expression of Cpt1a, which is responsible for mitochondrial fatty acid oxidation, was induced. Hepatic IGF2 expression induces a fatty liver, characterized by increased cholesterol and phospholipids leading to accumulation of LDs. We therefore suggest a causal role for IGF2 in hepatic lipid accumulation.

Genome-wide study on intramuscular fat in Italian Large White pig breed using the PorcineSNP60 BeadChip

Genome-wide association study results are presented for intramuscular fat in Italian Large White pig breed. A total of 886 individuals were genotyped with PorcineSNP60 BeadChip. After quality control performed with plink software and in R environment, 49 208 markers remained for the association analysis. The genome-wide association studies was conducted using linear mixed model implemented in GenABEL. We detected seven new SNPs of genes till now not found associated to intramuscular fat (IMF). Three markers map in a wide intergenic region rich of QTL linked to fat traits, one map 388 kb upstream the gene SDK1, one map inside PPP3CA gene, one inside SCPEP1 gene and the last is not mapped in the porcine genome yet. Associations here presented indicate a moderate effect of these genes on IMF. In particular, PPP3CA, that is involved in the oxidative metabolism of skeletal muscle, could be considerated as an interesting candidate gene for IMF content in pigs. However, further studies are needed to clarify the role of these genes on the physiological processes involved in IMF regulation. These results may be useful to control this trait that is important in terms of nutritional, technological and organoleptic characteristics of fresh meat and processed products.

Putative regulatory factors associated with intramuscular fat content

Intramuscular fat (IMF) content is related to insulin resistance, which is an important prediction factor for disorders, such as cardiovascular disease, obesity and type 2 diabetes in human. At the same time, it is an economically important trait, which influences the sensorial and nutritional value of meat. The deposition of IMF is influenced by many factors such as sex, age, nutrition, and genetics. In this study Nellore steers (Bos taurus indicus subspecies) were used to better understand the molecular mechanisms involved in IMF content. This was accomplished by identifying differentially expressed genes (DEG), biological pathways and putative regulatory factors. Animals included in this study had extreme genomic estimated breeding value (GEBV) for IMF. RNA-seq analysis, gene set enrichment analysis (GSEA) and co-expression network methods, such as partial correlation coefficient with information theory (PCIT), regulatory impact factor (RIF) and phenotypic impact factor (PIF) were utilized to better understand intramuscular adipogenesis. A total of 16,101 genes were analyzed in both groups (high (H) and low (L) GEBV) and 77 DEG (FDR 10%) were identified between the two groups. Pathway Studio software identified 13 significantly over-represented pathways, functional classes and small molecule signaling pathways within the DEG list. PCIT analyses identified genes with a difference in the number of gene-gene correlations between H and L group and detected putative regulatory factors involved in IMF content. Candidate genes identified by PCIT include: ANKRD26, HOXC5 and PPAPDC2. RIF and PIF analyses identified several candidate genes: GLI2 and IGF2 (RIF1), MPC1 and UBL5 (RIF2) and a host of small RNAs, including miR-1281 (PIF). These findings contribute to a better understanding of the molecular mechanisms that underlie fat content and energy balance in muscle and provide important information for the production of healthier beef for human consumption.

IGF2 methylation is associated with lipid profile in obese children

AIM

Our aim was to investigate the relationships between the degree of IGF2 methylation and the metabolic status in obese children and adolescents.

SUBJECTS AND METHODS

Eighty-five obese subjects aged 11.6 ± 2.1 years were studied. Anthropometry, metabolic parameters, blood pressure and body composition were assessed. DNA methylation analysis was performed by restriction enzyme digestion assay. The study population was subdivided into two groups according to the percentage of IGF2 cytidine-guanosine (CpG) island methylation.

RESULTS

Twenty-two subjects showed intermediate methylation (a percentage of CpG site methylation comprised between 10 and 60%), 56 were hypomethylated (percentage of methylation lower than 10%), and only 1 showed a high rate of hypermethylation (percentage of methylation above 60%). Children with intermediate methylation showed significantly higher levels of triglycerides (107.6 ± 41.99 vs. 76.6 ± 30.18 mg/dl, p < 0.005) and a higher triglyceride/high-density lipoprotein-cholesterol ratio (2.23 ± 0.98 vs. 1.79 ± 0.98, p < 0.02) compared with hypomethylated children.

CONCLUSIONS

These preliminary findings show for the first time a relationship between IGF2 methylation pattern and lipid profile in obese children. Although the correlation does not imply causation, if our findings are confirmed in further studies, IGF2 methylation might represent an epigenetic marker of metabolic risk.

SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle

Insulin-like growth factor 2 (IGF2) is a potent cell growth and differentiation factor and is implicated in mammals' growth and development. The objective of this study was to evaluate the effects of the mutations in the bovine IGF2 with growth traits in Chinese Qinchuan cattle. Four single nucleotide polymorphisms (SNPs) were detected of the bovine IGF2 by DNA pool sequencing and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. We also investigated haplotype structure and linkage disequilibrium (LD) coefficients for four SNPs in 817 individuals representing two main cattle breeds from China. The result of haplotype analysis showed eight different haplotypes and 27 combined genotypes within the study population. The statistical analyses indicated that the four SNPs, combined genotypes and haplotypes are associated with the withers height, body length, chest breadth, chest depth and body weight in Qinchuan cattle population (P < 0.05 or <0.01). The mutant-type variants and mutant haplotype (Hap 8: ATGG; likely to be the beneficial QTN allele) was superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to wild-type homozygote. Our results provide evidence that polymorphisms in the IGF2 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.

Investigation of four candidate genes (IGF2, JHDM1A, COPB1 and TEF1) for growth rate and backfat thickness traits on SSC2q in Large White pigs

As important quantitative traits, the growth rate and backfat thickness are controlled by multiple genes. The aim of this investigation was to evaluate the effect of the single and multiple SNPs of four candidate genes (IGF2, JHDM1A, COPB1 and TEF-1) on growth rate and backfat thickness. The four candidate genes were mapped on the p arm of SSC 2, and there are several QTLs, such as average daily gain, backfat thickness, an imprinted QTLs affecting muscle mass and fat deposition have been reported in this region. The polymorphisms of these genes were detected using PCR-RFLP methods, mixed procedure was used to analyze the single marker association with the growth and backfat thickness traits, and the gene-gene combination was investigated using multiple-markers analysis. The single marker association analysis indicated that the IGF2 intron-3 g.3072G > A and the substitution g.93G > A of TEF-1 gene were significantly associated with the age at 100 kg (P < 0.05). The JHDM1A 3′UTR g.224C > G, the c.3096C > T polymorphism of COPB1 gene and the substitution g.93G > A of TEF-1 gene were all significantly associated with the backfat at the shoulder (P < 0.05), backfat at the last rib, backfat at the lumbar, and the average backfat thickness, respectively. The multiple-markers analysis indicated that IGF2 and TEF-1 integrated gene networks for the age at 100 kg. Therefore, we can suggest that the polymorphism of IGF2 and TEF-1 gene could be used in marker-assisted selection for the age at 100 kg in Large White pigs.

Assessment of association between variants and haplotypes of the IGF2 gene in beef cattle

Insulin-like growth factor 2 (IGF2) is a fetal growth and differentiation factor that plays an important role in muscle growth and in myoblast proliferation and differentiation. The aim of this study was to examine the association of the IGF2 polymorphism with growth traits in beef cattle breed. Four single nucleotide polymorphisms (SNPs: 1-4) were identified in the bovine IGF2 by sequencing pooled DNA samples (Pool-Seq) and forced polymerase chain reaction-restriction fragment length polymorphism (Forced PCR-RFLP) methods. The result of haplotype analysis of four SNPs showed that eight haplotypes and eighteen combined genotypes were revealed, and the linkage disequilibrium and evolutionary relationship were assessed in 1522 individuals representing four purebred cattle breeds from China. The statistical analyses indicated that the 4 SNPs and 18 combined genotypes or haplotypes are associated with the body weight at 18 and 24 months in Jiaxian cattle population (P<0.05 or P<0.01). Our results provide evidence that polymorphisms in the IGF2 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.

Association and expression analysis of porcine HNF1A gene related to meat and carcass quality traits

The aim of this study was to investigate the association and expression of HNF1A gene as a candidate gene for meat and carcass quality traits in pigs. Statistical analysis revealed that the g.8260 A>G polymorphism significantly associated with pH 24(H), meat percentage and muscle area in the F₂ Duroc × Pietrain (DuPi, n=313) and with pH 24(L), fat area and backfat thickness in the Pietrain (Pi, n=110) population. HNF1A mRNA and protein expressions were higher (p<0.05) in animals with the low post-mortem muscle pH 24(L). The promoter methylation profiling suggested that methylation was not involved on HNF1A expression regulation (p>0.05) in animal with divergent muscle pH. In conclusion, polymorphism in porcine HNF1A gene could be used as a candidate marker to improve the meat and carcass quality traits, with the consideration of breed-specific effect.

SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig

Background

The PRKAG3 gene encodes the γ3 subunit of adenosine monophosphate activated protein kinase (AMPK), a protein that plays a key role in energy metabolism in skeletal muscle. Non-synonymous single nucleotide polymorphisms (SNPs) in this gene such as I199V are associated with important pork quality traits. The objective of this study was to investigate the relationship between gene expression of the PRKAG3 gene, SNP variation in the PRKAG3 promoter and meat quality phenotypes in pork.

Results

PRKAG3 gene expression was found to correlate with a number of traits relating to glycolytic potential (GP) and intramuscular fat (IMF) in three phenotypically diverse F1 crosses comprising of 31 Large White, 23 Duroc and 32 Pietrain sire breeds. The majority of associations were observed in the Large White cross. There was a significant association between genotype at the g.-311A>G locus and PRKAG3 gene expression in the Large White cross. In the same population, ten novel SNPs were identified within a 1.3 kb region spanning the promoter and from this three major haplotypes were inferred. Two tagging SNPs (g.-995A>G and g.-311A>G) characterised the haplotypes within the promoter region being studied. These two SNPs were subsequently genotyped in larger populations consisting of Large White (n = 98), Duroc (n = 99) and Pietrain (n = 98) purebreds. Four major haplotypes including promoter SNP’s g.-995A>G and g.-311A>G and I199V were inferred. In the Large White breed, HAP1 was associated with IMF% in the M. longissmus thoracis et lumborum (LTL) and driploss%. HAP2 was associated with IMFL% GP-influenced traits pH at 24 hr in LTL (pHULT), pH at 45 min in LTL (pH₄₅LT) and pH at 45 min in the M. semimembranosus muscle (pH₄₅SM). HAP3 was associated with driploss%, pHULT pH₄₅LT and b* Minolta. In the Duroc breed, associations were observed between HAP1 and driploss% and pHUSM. No associations were observed with the remaining haplotypes (HAP2, HAP3 and HAP4) in the Duroc breed. The Pietrain breed was monomorphic in the promoter region. The I199V locus was associated with several GP-influenced traits across all three breeds and IMF% in the Large White and Pietrain breed. No significant difference in promoter function was observed for the three main promoter haplotypes when tested in vitro.

Conclusion

Gene expression levels of the porcine PRKAG3 are associated with meat quality phenotypes relating to glycolytic potential and IMF% in the Large White breed, while SNP variation in the promoter region of the gene is associated with PRKAG3 gene expression and meat quality phenotypes.