Association between polymorphisms of the heart fatty acid binding protein gene and intramuscular fat content, fatty acid composition, and meat quality in Berkshire breed

Assessing the relationship between the in silico predicted consequences of 97 missense mutations mapping to 68 genes related to lipid metabolism and their association with porcine fatness traits

In general, the relationship between the predicted functional consequences of missense mutations mapping to genes known to be involved in human diseases and the severity of disease manifestations is weak. In this study, we tested in pigs whether missense single nucleotide polymorphisms (SNPs), predicted to have consequences on the function of genes related to lipid metabolism are associated with lipid phenotypes. Association analysis demonstrated that nine out of 72 nominally associated SNPs were classified as "highly" or "very highly consistent" in silico-predicted functional mutations and did not show association with lipid traits expected to be affected by inactivation of the corresponding gene. Although the lack of endophenotypes and the limited sample size of certain genotypic classes might have limited to some extent the reach of the current study, our data indicate that present-day bioinformatic tools have a modest ability to predict the impact of missense mutations on complex phenotypes.

Correlation of lipoprotein lipase gene polymorphism and mRNA expression with intramuscular fat content in Baicheng-Oil chicken

Lipoprotein lipase (LPL) was often taken as a candidate gene for investigating fat metabolism. However, there are few studies on the effect of LPL on intramuscular fat (IMF) deposition in Baicheng oil chicken (BOC) and Three-yellow Chicken (TYC). In this study, we studied the relationship between polymorphism and messenger RNA (mRNA) expression of LPL with IMF deposition in the chest muscle (CM) and leg muscle (LM) of TYC and BOC. Sixty TYCs and 60 BOCs were raised from 1 d and slaughtered by avascularization at their slaughtering age. IMF contents of the CM and LM in the BOC were markedly higher than those in the TYC. Three genotypes following AA, AB and BB were found by the method of polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). The synonymous mutation C12315T was detected. The content of IMF with the AA genotype was significantly higher than the AB genotype in the LM of TYC. The mRNA expression both of CM and LM in BOC was prominently higher than those in TYC, and there was a positive significant correlation between LM and CM in both BOC and TYC. These results suggested that the SNPs polymorphism and mRNA expression of the LPL gene might be helpful for selective breeding in IMF of the chicken.

Advances of Molecular Markers and Their Application for Body Variables and Carcass Traits in Qinchuan Cattle

This review considers the unique characteristics of Chinese cattle and intramuscular fat content (IMF) as factors influencing meat quality, including tenderness, flavor, and juiciness of meat. Due to its nutritional qualities, meat contributes to a healthy and balanced diet. The intramuscular fat content and eating quality of beef are influenced by many factors, which can generally be divided into on-farm and pre-slaughter factors (breed, sex of cattle, age at slaughter, housing system, diet, and pre-slaughter handling) and postmortem factors (post-slaughter processing, chilling temperature, and packaging). Meat quality traits can also be influenced by the individual genetic background of the animal. Worldwide, the function of genes and genetic polymorphisms that have potential effects on fattening of cattle and beef quality have been investigated. The use of DNA markers is recognized as a powerful and efficient approach to achieve genetic gain for desirable phenotypic characteristics, which is helpful for economic growth. The polymorphisms of the SIRT4, SIRT6, SIRT7, CRTC3, ABHD5, KLF6, H-FABP, and ELOVL6 genes for body and growth characteristics of cattle, and also for beef quality, are considered with the aim of highlighting the significance of beef intramuscular fat content, and that growth, body, and meat quality characteristics are polygenically regulated.

Expression and single-nucleotide polymorphisms of the H-FABP gene in pigs

Heart fatty acid-binding protein (H-FABP) belongs to a family of intracellular fatty acid-binding proteins that are involved in the transport of long-chain fatty acids. Previous studies have indicated that H-FABP is significantly associated with intramuscular fat (IMF) content in pig. In this study, we compared the mRNA and protein expression of H-FABP between Tibetan pig (with high IMF) and Large White pig (with low IMF). The expression of H-FABP at both mRNA and protein levels in the tissues of backfat, longissimus dorsi muscle and liver was found to be significantly higher in TP than in LW. Single-nucleotide polymorphisms (SNPs) in a 2 kb region upstream of the start codon of the gene were screened using Sanger sequencing. We accordingly identified three SNPs (C-1375G, C-314T and T-158G) between the TP and LW populations and genotyped these based on PCR-restriction fragment length polymorphisms (PCF-RFLPs) analysis. The results showed that the C-1375G site might regulate H-FABP gene expression and thus be associated with fat deposition in pigs. Our study provides important data for further investigating the regulatory mechanism of H-FABP for fat deposition in pigs.

Effects of aging on fat deposition and meat quality in Sheldrake duck

Sheldrake is a duck breed widely used for its meat and eggs. In this study, the quantities of abdominal fat, sebum, intramuscular fat and liver fat, meat quality (pH, cooking loss, drip loss, and shear force), and expression and activity of several enzymes at different ages were determined. The results showed that the fat content increased (P < 0.05) during the aging process (90 d, 180 d, 270 d, and 360 d). Fatty acid synthase (FAS) and malic enzyme (ME) were chosen to represent the activity of lipid biosynthesis in Sheldrake ducks. The quantitative real-time PCR and enzymic activity data showed that the expression of both FAS and ME were generally up-regulated along with aging. Based on these results, the individual ducks were selected at 180 d and 360 d for analyzing the changes of serum lipid levels and related enzymic activities in liver. The contents of triglycerides (TG), total cholesterol (TCH), high-density lipoprotein (HDL), and low-density lipoprotein (LDL) in serum were found not significantly different (P > 0.05). However, we thought that the variation of TG/HDL (P < 0.05) might explain the increased fat deposition. Moreover, the activities of lipoprotein lipase (LPL) and hepatic lipase (HL) were both detected significantly up-regulated at 360 d (P < 0.05). The meat quality results of breast muscles indicated that pH, cooking loss, drip loss, and shear force values could all be affected by aging. Considering these results, we concluded that the best quality of Sheldrake duck meat occurs between 180 d and 270 d. These results might provide useful information for Sheldrake cultivation and research on lipid metabolism.

Association of single nucleotide polymorphisms in fat metabolism candidate genes with fatty acid profiles of muscle and subcutaneous fat in heavy pigs

Dietary and organoleptic qualities of pork products are largely influenced by the profiles of fatty acids (FAs) of meat and fat. The objective of this work was to investigate the potential associations between FA profile in subcutaneous adipose (back fat and leg fat) and muscular (longissimus dorsi and biceps femoris) tissues in heavy pigs (n = 129, 9-month-old) with single nucleotide polymorphisms (SNPs) in six candidate genes involved in fat metabolism: Stearoyl-CoA desaturase (SCD), Diacylglycerol acyltransferase 1 and 2 (DGAT1 &DGAT2), Microsomal Triglyceride Transfer Protein (MTTP), Fatty Acid Synthase (FASN) and Heart- fatty acid binding protein (H-FABP). Preliminary results suggest a putative association between MTTP, DGAT2 and FASN and the FA content in both fat and meat, whereas between DGAT1, SCD and H-FABP the association was found in adipose tissue only. However, the effect of the analyzed genes, needs to be verified in a larger and better characterized pig population to support the hypothesized associations with FA content.

miR-17-5p Regulates Differential Expression of NCOA3 in Pig Intramuscular and Subcutaneous Adipose Tissue

Fat distribution affects economic value in pork production. Intramuscular adipose tissue (IMAT) improves meat quality, whereas subcutaneous adipose tissue (SCAT) is usually regarded as waste. In the present study, we analyzed IMAT/SCAT (I/S) ratios in each pig. Individuals selected from a population of 1200 Suhuai pigs were divided into two cohorts; those with high I/S ratios and those with low I/S ratios, and correlations between nuclear Receptor Co-activator 3 (NCOA3), a critical gene involved in regulating fat accumulation, and fat distribution were investigated. The ratio of IMAT NCOA3 to SCAT NCOA3 expression levels (NCOA3_I/NCOA3_S) was higher in the high I/S group compared with the low I/S group. The NCOA3 expression level in fat tissue was positively correlated with fat deposition. miR-17-5p was identified as a putative regulator of NCOA3 based on bioinformatics prediction analysis followed by gene expression analysis. The miR-17-5p_I/miR-17-5p_S ratio was negatively correlated with the NCOA3_I/NCOA3_S ratio. The predicted relationship between miR-17-5p and NCOA3 was further verified by dual luciferase activity assays, qPCR, and western blots. Overexpression of miR-17-5p in intramuscular preadipocytes inhibited NCOA3 expression and reduced preadipocyte differentiation. FABP4 and PPARG expression were also significantly decreased, as was triglyceride content. Meanwhile, knockdown of miR-17-5p significantly increased NCOA3 expression and promoted intramuscular preadipocyte differentiation. Based on these results, we propose that differential expression of NCOA3 in pig intramuscular and subcutaneous adipose tissue is regulated by miR-17-5p.

Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba)

Despite the fact that squab is consumed throughout the world because of its high nutritional value and appreciated sensory attributes, aspects related to its characterization, and in particular genetic issues, have rarely been studied. In this study, meat traits in terms of pH, water-holding capacity, intramuscular fat content, and fatty acid profile of the breast muscle of squabs from two meat pigeon breeds were determined. Breed-specific differences were detected in fat-related traits of intramuscular fat content and fatty acid composition. RNA-Sequencing was applied to compare the transcriptomes of muscle and liver tissues between squabs of two breeds to identify candidate genes associated with the differences in the capacity of fat deposition. A total of 27 differentially expressed genes assigned to pathways of lipid metabolism were identified, of which, six genes belonged to the peroxisome proliferator-activated receptor signaling pathway along with four other genes. Our results confirmed in part previous reports in livestock and provided also a number of genes which had not been related to fat deposition so far. These genes can serve as a basis for further investigations to screen markers closely associated with intramuscular fat content and fatty acid composition in squabs. The data from this study were deposited in the National Center for Biotechnology Information (NCBI)’s Sequence Read Archive under the accession numbers SRX1680021 and SRX1680022. This is the first transcriptome analysis of the muscle and liver tissue in Columba using next generation sequencing technology. Data provided here are of potential value to dissect functional genes influencing fat deposition in squabs.

Effect of a c-MYC Gene Polymorphism (g.3350G>C) on Meat Quality Traits in Berkshire

c-MYC (v-myelocytomatosis viral oncogene homologue) is a transcription factor that plays important role in many biological process including cell growth and differentiation, such as myogenesis and adipogenesis. In this study, we aimed to detect MYC gene polymorphisms, their genotype frequencies and to determine associations between these polymorphisms and meat quality traits in Berkshire pigs. We identified a single nucleotide polymorphism (SNP) in intron 2 of MYC gene by Sanger sequencing, i.e., g.3350G>C (rs321898326), that is only found in Berkshire pigs, but not in other breeds including Duroc, Landrace, and Yorkshire pigs that were used in this study. Genotypes of total 378 Berkshire pigs (138 sows and 240 boars) were determined using Hha I restriction enzyme digestion after polymerase chain reaction. Observed allele frequencies of GG, GC, and CC genotypes were 0.399, 0.508, and 0.093 respectively. Statistical analysis indicated that the g.3350G>C polymorphism was significantly associated with pH45min and cooking loss (p<0.05), suggesting that g.3350G>C SNP can be used for pre-selection of pH45min and cooking loss traits in Berkshire pigs.

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

BACKGROUND

Natural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand. However, most of the studies have been performed using trained sensory panel analysis without investigating the underlying genetic factors. Here we investigate the relationship between genomic composition and this phenotypic trait by scanning for signatures of positive selection in whole-genome sequencing data.

RESULTS

We generated genomes of 10 Berkshire pigs at a total of 100.6 coverage depth, using the Illumina Hiseq2000 platform. Along with the genomes of 11 Landrace and 13 Yorkshire pigs, we identified genomic variants of 18.9 million SNVs and 3.4 million Indels in the mapped regions. We identified several associated genes related to lipid metabolism, intramuscular fatty acid deposition, and muscle fiber type which attribute to pork quality (TG, FABP1, AKIRIN2, GLP2R, TGFBR3, JPH3, ICAM2, and ERN1) by applying between population statistical tests (XP-EHH and XP-CLR). A statistical enrichment test was also conducted to detect breed specific genetic variation. In addition, de novo short sequence read assembly strategy identified several candidate genes (SLC25A14, IGF1, PI4KA, CACNA1A) as also contributing to lipid metabolism.

CONCLUSIONS

Results revealed several candidate genes involved in Berkshire meat quality; most of these genes are involved in lipid metabolism and intramuscular fat deposition. These results can provide a basis for future research on the genomic characteristics of Berkshire pigs.

Polymorphism of fat metabolism genes as candidate markers for meat quality and production traits in heavy pigs

High meat quality is required for dry-cured ham production, which quality depends on meat fat quantity and composition. The aim was to study the polymorphisms of six genes involved in fat metabolism, namely, Stearoyl-CoA desaturase (SCD), Diacylglycerol acyltransferase 1 and 2 (DGAT1 &DGAT2), Microsomal triglyceride transfer protein (MTTP), Fatty acid synthase (FASN) and Heart fatty acid binding protein (H-FABP) in two traditional (Large White or Duroc × (Landrace × Large White)) and two industrial hybrids (Goland and Danbred), which are used for dry-cured ham production. Significant associations of SCD and MTTP were found with carcass weight. DGAT2 was associated with back fat thickness and L* fat colour (objective white colour score). Several genes (DGAT2, MTTP &FASN) were associated with weight loss during salting, first step in dry-cured ham production, affecting final yield. Finally, MTTP was associated with shear force. Our findings suggest that the SCD, DGAT2, MTTP and FASN polymorphisms are associated with quality of heavy pig meat products.

A Candidate Single Nucleotide Polymorphism in the 3' Untranslated Region of Stearoyl-CoA Desaturase Gene for Fatness Quality and the Gene Expression in Berkshire Pigs

Fatness qualities in pigs measured by the amount of fat deposition and composition of fatty acids (FAs) in pork have considerable effect on current breeding goals. The stearoyl-CoA desaturase (SCD) gene plays a crucial role in the conversion of saturated FAs into monounsaturated FAs (MUFAs), and hence, is among the candidate genes responsible for pig fatness traits. Here, we identified a single nucleotide polymorphism (SNP, c.*2041T>C) in the 3′ untranslated region by direct sequencing focused on coding and regulatory regions of porcine SCD. According to the association analysis using a hundred of Berkshire pigs, the SNP was significantly associated with FA composition (MUFAs and polyunsaturated FAs [PUFAs]), polyunsaturated to saturated (P:S) FA ratio, n-6:n-3 FA ratio, and extent of fat deposition such as intramuscular fat and marbling (p<0.05). In addition, the SNP showed a significant effect on the SCD mRNA expression levels (p = 0.041). Based on our results, we suggest that the SCD c.*2041T>C SNP plays a role in the gene regulation and affects the fatness qualities in Berkshire pigs.

Novel variation in the FABP3 promoter and its association with fatness traits in pigs

This study examines associations between SNPs in the promoter region of the fatty acid binding protein 3 (FABP3) gene and fatness traits in pure bred Large White (n=98), Duroc (n=99) and Pietrain (n=98) populations. In the Large White breed, SNP g.-634 C>A was associated a 27% increase in IMF (%) in the heterozygote (CA) and a 38% increase in the homozygote (CC) relative to the (AA) genotype in the M. semimembranosus (SM) muscle (P=0.02). While the associations observed in this breed were suggestive of significance in both the SM and in the M. longissimus thoracis et lumborum (LTL) (P=0.08), these associations no longer attained significance at thresholds adjusted for multiple testing. In conclusion, SNPs in the FABP3 promoter may contribute to IMF without influencing carcass fatness traits in pigs, however further confirmation of these associations in larger independent populations would be essential before their incorporation into breeding programmes.

Transcript level of the porcine ME1 gene is affected by SNP in its 3'UTR, which is also associated with subcutaneous fat thickness

Pork quality depends on multiple factors, including fatty acid composition in muscle and fat tissues. The ME1 gene is a strong candidate for fat accumulation, as it encodes the malic enzyme, which is required for fatty acid synthesis. We identified seven new polymorphisms in 3'UTR of the ME1 gene and moreover confirmed the presence of 4 polymorphisms detected previously. Interestingly, the studied Duroc pigs were monomorphic at all these polymorphic sites, while in 3 other breeds (Pietrain, Polish Landrace and Polish Large White), the polymorphisms were unevenly distributed. One of the novel SNPs (c.*488A>G) was found in the Polish Large White and the Polish Landrace only, and the association studies revealed that it was significantly associated with backfat thickness and average daily weight gain in the Polish Landrace (N = 207) and the Polish Large White (N = 157). This SNP was differently associated with ME1 transcript level in muscle and backfat. The in silico analysis of another novel SNP (c.*548C>T) indicated that it is located within a binding sequence conserved among vertebrates for the miR-30 family in 3'UTR of the ME1. It was shown that in the longissimus muscle, but not in adipose tissue, CT gilts compared with CC ones had significantly lower levels of the ME1 transcript. This polymorphism, however, was not associated with production traits. Additionally, we observed that transcript level of the ME1 was significantly higher in subcutaneous fat than in the longissimus muscle, as well as both investigated tissues of the Polish Landrace when compared to the other breeds. However, no association was found between this polymorphism and fatty acid profiles. We conclude that the ME1 gene polymorphism (c.*488A>G) is a potential marker for porcine backfat thickness.

Genetic polymorphisms, growth performance, hematological parameters, serum enzymes, and reproductive characteristics in phenotypically normal Landrace boars produced by somatic cell nuclear transfer

Understanding the performances of cloned pigs and their offspring is critical to evaluate the practical applications of somatic cell nuclear transfer. In this study, genetic polymorphism, growth performance, hematological parameters, and reproduction characteristics of cloned Landrace boars were compared with those of controls. In addition, the growth performance of clone offspring was also evaluated. A total of 479 reconstructed embryos were transferred to five recipient pigs and resulted in the delivery of 14 piglets (overall cloning of 2.9%) from two litters. Analyses of microsatellite markers and polymorphisms of the specific genes confirmed that the 14 clones were genetically identical to the nuclear donor and maintained the desirable genotypes. Growth performance of five healthy, phenotypically normal cloned boars from one litter and eight of their male offspring did not differ from age, breed, and management-matched controls. Although some significant differences were observed between cloned and control boars in hematological and serum enzymes, most of these parameters were within the normal range. Cloned boars had less (P < 0.05) normal sperm in the ejaculated boars than in control boars (71.4% vs. 77.9%, respectively), but sperm production (ejaculate volume, sperm concentration, and total sperm) did not differ between these groups. In addition, use of frozen-thawed semen from cloned boars for insemination produced results that seemed comparable to a control. In conclusion, the present study reported that somatic cell nuclear transfer is effective in reproducing preferred genetic traits and has potential applications to conserve elite bloodlines in a routine pig breeding program.

A novel single nucleotide polymorphism in exon 7 of LPL gene and its association with carcass traits and visceral fat deposition in yak (Bos grunniens) steers

Lipoprotein lipase (LPL) is considered as a key enzyme in the lipid deposition and metabolism in tissues. It is assumed to be a major candidate gene for genetic markers in lipid deposition. Therefore, the polymorphisms of the LPL gene and associations with carcass traits and viscera fat content were examined in 398 individuals from five yak (Bos grunniens) breeds using PCR-SSCP analysis and DNA sequencing. A novel nucleotide polymorphism (SNP)-C→T (nt19913) was identified located in exon 7 in the coding region of the LPL gene, which replacement was responsible for a Phe-to-Ser substitution at amino acid. Two alleles (A and B) and three genotypes designed as AA, AB and BB were detected in the PCR products. The frequencies of allele A were 0.7928, 0.7421, 0.7357, 0.6900 and 0.7083 for Tianzhu white yak (WY), Gannan yak (GY), Qinghai-Plateau yak (PY), Xinjiang yak (XY) and Datong yak (DY), respectively. The SNP loci was in Hardy-Weinberg equilibrium in five yak populations (P>0.05). Polymorphism of LPL gene was shown to be associated with carcass traits and lipid deposition. Least squares analysis revealed that there was a significant effect on live-weight (LW) (P<0.01), average daily weight gain (ADG) and carcass weight (P<0.05). Individuals with genotype BB had lower mean values than those with genotype AA and AB for loin eye area and viscera fat weight (% of LW) in 25-36 months (P<0.05). The results indicated that LPL gene is a strong candidate gene that affects carcass traits and fat deposition in yak.