Genetic Polymorphisms of the CACNA2D1 Gene and Their Association with Carcass and Meat Quality Traits in Cattle

The objective of this study was to identify genetic polymorphisms of the CACNA2D1 gene and to analyze associations between SNPs and carcass and meat quality traits in cattle. Through PCR-RFLP and DNA sequencing methods, a new allelic variant corresponding to the A → G mutation (aspartic to glycine amino acid replacement) of the bovine CACNA2D1 gene was detected. Two alleles and three genotypes (AA, AG, and GG) were defined. Genetic character indicated that the A526745G locus showed moderate polymorphism and was in Hardy–Weinberg equilibrium. Gene-specific SNP marker association analysis showed that the A526745G mutant was significantly associated with carcass weight, dressing percentage, meat percentage, and backfat thickness. The results add new evidence that CACNA2D1 is an important candidate gene for the selection of carcass and meat quality traits in the cattle industry.     

The porcine <Emphasis Type="Italic">TBC1D1</Emphasis> gene: mapping,SNP identification,and association study with meat,carcass and production traits in Italian heavy pigs

TBC1D1 [TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1] is a Rab-GTPase-activating related protein implicated in regulating the trafficking of glucose transporter 4 (GLUT4 or SLC2A4) storage vesicles to the cell surface in response to insulin and AMPK-activating stimuli in skeletal muscle. Mutations in the human and mouse TBC1D1 genes confer risk of obesity or leanness. We identified five single nucleotide polymorphisms (SNPs) in the porcine TBC1D1 gene. One of them (FN677935:g.219G>A) was genotyped either by high resolution melting and PCR-RFLP analyses to study allele frequencies in a few pig breeds and evaluate association with meat production and carcass traits in five groups of sib-tested pigs of Italian Large White and Italian Duroc breeds. The g.219G>A SNP was associated (P < 0.05) with ham weight, back fat thickness and lean cuts content in Italian Large White and with visible intermuscular fat in Italian Duroc pigs.     

New SNP of the porcine Perilipin 2 (<Emphasis Type="Italic">PLIN2</Emphasis>) gene,association with carcass traits and expression analysis in skeletal muscle

PLIN2 (perilipin 2) is a cytosolic protein that promotes the formation and stabilization of the intracellular lipid droplets, organelles involved in the storage of lipid depots. Porcine PLIN2 gene represents a biological and positional candidate for fat deposition, a polygenic trait that affects carcass and meat quality. The aim of the present study was to screen PLIN2 gene for polymorphisms, to evaluate the association with carcass quality traits, and to investigate the gene expression in skeletal muscle. Six new single nucleotide polymorphisms (SNP) were detected by sequencing 32 samples from five pig breeds (Italian Large White, Italian Duroc, Italian Landrace, Belgian Landrace, Pietrain). Two SNP localized in introns, two in the 3′-untranslated region (UTR), and two missense SNP were found in exons. A 3′-UTR mutation (GU461317:g.98G>A), genotyped in 290 Italian Duroc pigs by High Resolution Melting, resulted significantly associated (P < 0.01) with average daily gain, feed conversion ratio, lean cuts and hams weight estimated breeding values. PLIN2 gene expression analysis in skeletal muscle of Italian Large White and Italian Duroc pigs divergent for backfat thickness and visible intermuscular fat showed a trend of higher expression level in pigs with higher intermuscular fat. These results suggest that PLIN2 can be a marker for carcass quality in pigs. Further investigation at both gene and protein level could elucidate its role on fat deposition.     

Association of thyroglobulin gene variants with carcass and meat quality traits in beef cattle

Thyroid hormones play an important role in regulating metabolism and can affect homeostasis of fat deposition. The gene encoding thyroglobulin (TG), producing the precursor for thyroid hormones, has been proposed as a positional and functional candidate gene for a QTL with an effect on fat deposition. In the present study, we identified 6 novel SNPs at the 3′ flanking region of the TG gene. The SNP marker association analysis indicated that the T354C, G392A, A430G and T433G SNP markers were significantly associated with marbling score (P < 0.05). Animals with the new homozygote genotype had higher marbling score than those with the other genotypes. Otherwise, the linkage disequilibrium analysis indicated that these four SNPs were completely linked (r ² = 1). Results from this study suggest that TG gene-specific SNP may be a useful marker for meat quality traits in future marker assisted selection programs in beef cattle.     

Effects of DGAT1 gene on meat and carcass fatness quality in Chinese commercial cattle

This study was designed to investigate the candidate single nucleotide polymorphisms (SNPs) in the exon’s region of bovine diacylglycerol O-acyltransferase (DGAT1) gene using bioinformatics and experimental methods. A total of 17 SNPs were screened from public data resources and DNA sequencing. Three SNPs (c.572A>G, c.1241C>T and c.1416T>G) of these candidate SNPs were genotyped by created restriction site-polymerase chain reaction (CRS-PCR) methods. The gene-specific SNP markers and their effects on meat and carcass fatness quality traits were evaluated in Chinese commercial cattle. The c.572A>G and c.1416T>G significantly effected on backfat thickness, longissimus muscle area, marbling score, fat color and Warner-Bratzler shear force. No significant association was detected between the c.1241C>T and measured traits. Results from this study suggested that the SNP markers may be effective for the marker-assisted selection of meat and carcass fatness quality traits, and added new evidence that DGAT1 gene is an important candidate gene for the improvement of meat and carcass fatness quality in beef cattle industry.     

Candidate SNP of CACNA2D1 Gene Associated with Clinical Mastitis and Production Traits in Sahiwal (Bos taurus indicus) and Karan Fries (Bos taurus taurus × Bos taurus indicus)

The present study was conducted to identify polymorphisms in CACNA2D1 gene and their association with clinical mastitis and production traits. Exon 18 and its flanking regions were screened for the presence of SNPs. Statistical analysis was performed to identify association of period of birth, breed, and genotype with mastitis incidence on randomly selected 103 Sahiwal and 102 Karan Fries cattle. PCR-RFLP analysis revealed that g.38819398G?>?A mutation in exon 18 (269?bp amplicon) of CACNA2D1 gene resolved into AA, AG, and GG genotypes in Sahiwal and Karan Fries cattle. Wald chi-square analysis revealed that the period of birth, breed, and genotype were significantly associated with mastitis incidence. GG genotyped cattle were found to be less susceptible to mastitis. Least square analysis revealed that GG and AG genotype animals of G38819398A SNP of CACNA2D1 gene in Sahiwal as well as in Karan Fries cattle were associated with higher average milk yields during 1st, 2nd, and 3rd lactations (P?<?0.01). These observations and their differential association with the incidence of mastitis and production traits can be utilized as an aid to selection for simultaneous improvement of both antagonistic traits; however, validation of results on large number of animals is warranted.     

Identification of three novel SNPs and association with carcass traits in porcine <Emphasis Type="Italic">TNNI1</Emphasis> and <Emphasis Type="Italic">TNNI2</Emphasis>

In this study, two novel SNPs (EU743939:g.5174T>C in intron 4 and EU743939:g.8350C>A in intron 7) in TNNI1 and one SNP (EU696779:g.1167C>T in intron 3) in TNNI2 were identified by PCR–RFLP (PCR restriction fragment length polymorphism) using XbaI, MspI and SmaI restriction enzyme, respectively. The allele frequencies of three novel SNPs were determined in the genetically diverse pig breeds including ten Chinese indigenous pigs and three Western commercial pig breeds. Association analysis of the SNPs with the carcass traits were conducted in a Large White × Meishan F₂ pig population. The linkage of two SNPs (g.5174T>C and g.8350C>A) in TNNI1 gene had significant effect on fat percentage. Besides these, the g.5174T>C polymorphism was also significantly associated with skin percentage (P < 0.05), shoulder fat thickness (P < 0.05) and backfat thickness between sixth and seventh ribs (P < 0.05). The significant effects of g.1167C>T polymorphism in TNNI2 gene on fat percentage (P < 0.01), lean meat percentage (P < 0.05), lion eye area (P < 0.05), thorax–waist backfat thickness (P < 0.01) and average backfat thickness (P < 0.05) were also found.     

A novel association of a polymorphism in the first intron of adiponectin gene with type 2 diabetes, obesity and hypoadiponectinemia in Asian Indians

Adiponectin is an adipose tissue specific protein that is decreased in subjects with obesity and type 2 diabetes. The objective of the present study was to examine whether variants in the regulatory regions of the adiponectin gene contribute to type 2 diabetes in Asian Indians. The study comprised of 2,000 normal glucose tolerant (NGT) and 2,000 type 2 diabetic, unrelated subjects randomly selected from the Chennai Urban Rural Epidemiology Study (CURES), in southern India. Fasting serum adiponectin levels were measured by radioimmunoassay. We identified two proximal promoter SNPs (−11377C→G and −11282T→C), one intronic SNP (+10211T→G) and one exonic SNP (+45T→G) by SSCP and direct sequencing in a pilot study (n = 500). The +10211T→G SNP alone was genotyped using PCR-RFLP in 4,000 study subjects. Logistic regression analysis revealed that subjects with TG genotype of +10211T→G had significantly higher risk for diabetes compared to TT genotype [Odds ratio 1.28; 95% Confidence Interval (CI) 1.07–1.54; P = 0.008]. However, no association with diabetes was observed with GG genotype (P = 0.22). Stratification of the study subjects based on BMI showed that the odds ratio for obesity for the TG genotype was 1.53 (95%CI 1.3–1.8; P < 10⁻⁷) and that for GG genotype, 2.10 (95% CI 1.3–3.3; P = 0.002). Among NGT subjects, the mean serum adiponectin levels were significantly lower among the GG (P = 0.007) and TG (P = 0.001) genotypes compared to TT genotype. Among Asian Indians there is an association of +10211T→G polymorphism in the first intron of the adiponectin gene with type 2 diabetes, obesity and hypoadiponectinemia.     

Molecular characterization of the porcine <Emphasis Type="Italic">JHDM1A</Emphasis> gene associated with average daily gain: evaluation its role in skeletal muscle development and growth

JHDM1A, a member of the JHDM (JmjC-domain-containing histone demethylase) family, plays an central role in gene silencing, cell cycle, cell growth and cancer development through histone H3K36 demethylation modification. Here reported the cloning, expression, chromosomal location and association analysis with growth traits of porcine JHDM1A gene. Sequence analysis showed that the porcine JHDM1A gene encodes 1,162 amino acids and contains JmjC, F-box, and CXXC zinc-finger domains, which coding sequence and deduced protein shares 91 and 99% similarity with human JHDM1A, respectively. Spatio-Temporal expression analysis indicated that the mRNA expression of porcine JHDM1A had significantly higher levels in the middle (65 days) and later (90 days) period’s embryo skeletal muscle than that of 33 days, and showed a ubiquitously expression but with the highest abundance in kidney, lung and liver of an adult pig. Radiation hybrid mapping and the following linkage mapping data indicate that JHDM1A maps to 2p17 region of pig chromosome 2 (SSC2). Allele frequency differences were detected in different pig breeds and an association study was performed with a SNP within 3′UTR. The results showed that there is a tendency for allele frequencies to differ between the fast growth breeds (Yorkshire) and slow growth pig breeds (Qingping pigs, Yushan Black pigs, Erhualian pigs and Dahuabai pigs). The association analysis using a Berkshire × Yorkshire F₂ population indicated that the C224G polymorphism had a highly significant association with average daily gain on test (P < 0.01), a trend association with average back fat thickness (P < 0.07), and significant associations (P < 0.01) on percent of average drip loss, Fiber Type II Ratio, muscle shear force and average lactate content in μmol/g. This study provides the first evidence that JHDM1A is differentially expressed in porcine embryonic skeletal muscle and associated with meat growth and quality traits.     

Effects of genetic variability of the carpine homeobox transcription factor <Emphasis Type="Italic">HESX1</Emphasis> gene on performance traits

HESX1 plays a key role in the development of the forebrain and pituitary gland and produces potential effects on performance traits. The objective of this study was to detect and assess the associations of the possible polymorphisms of six loci within HESX1 gene with performance traits in Chinese 1,119 goats. Only one novel SNP (NM_001494116:g.307049A > G) locating on IVS1 + 348A > G was identified and detected by HaeIII forced-RFLP-PCR. The frequencies of allele “G” varied from 0.025 to 0.245 in analyzed populations with the Hardy–Weinberg equilibrium (P > 0.05). Genotypic and allelic frequencies were found to be significantly different in four breeds (χ² = 147.674, df = 6, P < 0.001; χ² = 157.250, df = 3, P < 0.001, respectively), implying that the distribution of genotypic and allelic frequencies of goat HESX1 gene was significantly associated with different goat utilities (cashmere, meat and dairy). Association analysis results revealed no significant effects of caprine HESX1 gene on body sizes in XNSN population (P > 0.05) and cashmere traits in IMWC population (P > 0.05). Significant statistical of HESX1 gene with body weight was found (*P < 0.05). The genotype AA showed significantly higher body weight than those of AG in 2-year-old age (*P < 0.05), while the AA genotype was senior to AG genotype in 4-year-old body weight trait (*P < 0.05). These suggestions indicated that the HESX1 gene has significant effect on goat body weight depending on ages, which is accordance with the function repressor of the HESX1.     

Genetic association of <Emphasis Type="Italic">Phosphodiesterase 1B</Emphasis> (PDE1B) with carcass traits in Korean cattle

Quantitative trait loci for fat deposition and carcass traits have been identified in the vicinity of the gene encoding phosphodiesterase 1B (PDE1B) on bovine chromosome 5. Therefore, the PDE1B gene can be considered as a positional and functional candidate gene for carcass traits in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the PDE1B gene and to evaluate their associations with carcass traits in Korean cattle. Eight SNPs, g.440T>G, g.17122A>G, g.17507A>C, g.17575A>G, g.17607T>C, g.17609C>A, g.17692C>T, and g.17707C>G, were identified in the region ranged from exon 1 to intron 6. Five of them were used for association analysis because of their availability of restriction fragment length polymorphisms. As a result, g.17122A>G in intron 3 was significantly associated with backfat thickness (BFT), and g.17507A>C in exon 5 was associated with longissimus dorsi muscle area (LMA, P < 0.05). Animals with the AG genotype of g.17122 had thicker BFT than those with the AA genotype. Animals with the AA or AC genotype of g.17507A>C had larger LMA than those with the CC genotype. We suggested the PDE1B gene as a candidate gene for carcass traits of beef cattle. Fine mapping would be required for application to marker-assisted selection.     

Molecular characterization and expression patterns of <Emphasis Type="Italic">Lbx1</Emphasis> in porcine skeletal muscle

Ladybird-like genes were recently identified in mammals. The first member characterized, Lbx1, is expressed in developing skeletal muscle and the nervous system. However, little is known about the porcine Lbx1 gene. In the present study, we cloned and characterized Lbx1 from porcine muscle. RT-PCR analyses showed that Lbx1 was highly expressed in porcine skeletal muscle tissues. And we provide the first evidence that Lbx1 has a certain regulated expression pattern during the postnatal period of the porcine skeletal muscle development. Lbx1 gene expressed at higher levels in biceps femoris muscles compared with masseter, semitendinosus and longissimus dorsi muscles in Meishan pigs. Phylogenetic tree was constructed by aligning the amino acid sequences of different species. Moreover, single nucleotide polymorphism (SNP) scanning in the Lbx1 genomic fragment identified two mutations, g.752A>G and g.−1559C>G. Association analysis in our experimental pig populations showed that the mutation of g.752A>G was significantly associated with loin muscle area (P < 0.05) and internal fat rate (P < 0.05). Our results suggest that the Lbx1 gene might be a candidate gene of carcass traits and provide useful information for further studies on its roles in porcine skeletal muscle.     

Cloning,chromosomal localization,SNP detection and association analysis of the porcine IRS-1 gene

Insulin receptor substrate-1(IRS-1) gene is one member of the Insulin receptor substrate (IRS) gene family, which plays an important role in mediating the growth of skeletal muscle and the molecular metabolism of type 2 diabetes. Here, we cloned a 3,573 bp fragment of the partial CDS sequence of porcine IRS-1 gene by in silicon cloning strategy and RT-PCR method. The porcine IRS-1 gene was assigned to SSC15q25 by using IMpRH. Sequencing of PCR products from Duroc and Tibetan pig breeds identified one SNP in exon 1 of porcine IRS-1 gene (C3257A polymorphisms). Association analysis of genotypes with the growth traits, anatomy traits, meat quality traits and physiological biochemical indexes traits showed that different genotypes at locus 3,257 of IRS-1 have significant differences in carcass straight length in pigs (P = 0.0102 < 0.05).     

Molecular characterization,chromosomal location,alternative splicing and polymorphism of porcine <Emphasis Type="Italic">GFAT1</Emphasis> gene

Glutamine: fructose-6-phosphate amidotransferase (GFAT) is the rate-limiting enzyme of the hexosamine synthesis pathway, which plays important roles in insulin resistance and glucose toxicity. GFAT1 is one of the two isoenzymes of GFAT. In the present study, we cloned cDNA sequence of the porcine GFAT1 gene and identified a GFAT1 splice variant (designed GFAT1-L) that contains a 54 bp insertion within the coding region. Nested RT–PCR revealed that GFAT1 was ubiquitously expressed in all tested tissues, but GFAT1-L was only expressed in skeletal muscle and heart, not in liver, spleen, lung, kidney, small intestine, stomach and fat tissue, suggested that GFAT1-L was selectively expressed in striate muscle in pig. Using both the somatic cell hybrid panel and radiation hybrid panel, the GFAT1 gene was mapped to porcine chromosome 3q21-q27, in which several significant QTLs for carcass traits were found. Among the SNPs we found in porcine GFAT1 gene, only the g. 101A>G polymorphism which located in intron 8 was polymorphic in two pig populations we investigated in the study. Association analyses revealed that the g. 101A>G polymorphism has a significant effect on lean meat percentage (P < 0.05), corrected backfat thickness (P < 0.05) and backfat at the rump (P < 0.05).     

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.     

Confirmed association between a single nucleotide polymorphism in the <Emphasis Type="Italic">FTO</Emphasis> gene and obesity-related traits in heavy pigs

We recently showed that a polymorphism in the fat mass and obesity associated (FTO) gene (AM931150: g.276T > G) is associated with fat deposition traits in pigs. To confirm this result, we genotyped this polymorphism in an Italian Duroc population made up by 313 performance tested pigs with known estimated breeding values (EBVs) for average daily gain, back fat thickness (BFT), feed:gain ratio, lean cuts (LC), and visible intermuscular fat (VIF, a measure of intermuscular fat in the hams). In addition, we genotyped 148 commercial heavy pigs for which several fat deposition traits and lean meat percentage were measured. The results of the association analyses confirmed the effect of the FTO mutation on obesity-related traits (VIF, BFT and LC) in the Italian Duroc pigs (P < 0.01) and in the commercial pigs (intramuscular fat content of different muscles, P < 0.05 or P < 0.10; lean meat content, P < 0.05; BFT, P < 0.05; intermuscular fat content in the hams, P < 0.05).     

Mutations of <Emphasis Type="Italic">MC4R</Emphasis> gene and its association with economic traits in Qinchuan cattle

MC4R belongs to a seven-transmembrane G-protein-coupled receptor which may regulate body composition and insulin action. Many mutations in the MC4R gene are associated with obesity, energy expenditure and serum triglyceride levels in human and animals. Six mutations in the MC4R gene were identified in our study (-293C>G, -193A>T, -192T>G, -129A>G, -84T>C and 1,069C>G). The -129A>G was significantly associated with live weight (LW) (P < 0.05), Cattle with the genotypes AG and GG had higher LW than genotype AA. The 1,069C>G was significantly associated with LW, carcass weight (CW), backfat thickness and marbling score (MS). Cattle with the genotype GG had higher LW, CW and MS than genotype CC; Cattle with the genotypes GG and CG had higher MS than CC. The results suggested that -129A>G and 1,069C>G SNP of the MC4R gene may be useful as a genetic marker for carcass and meat quality traits in Qinchuan cattle.