Relationships Between Single Nucleotide Polymorphisms of the H-FABP Gene and Slaughter and Meat Quality Traits in Chicken

Using PCR-SSCP with five primer pairs, we detected six single nucleotide polymorphisms of the H-FABP gene: 332G → A, 534G → A, 783C → T, 835C → T, 1198T → C, and 2329C → T. Chi-square results showed significant differences (P < 0.05) in genotype frequency among breeds in Fragment 1 and extremely significant differences (P < 0.01) in Fragments 2–4. We found a significant association between Fragment 2 genotype and muscle fiber number, Arg and Thr (P < 0.05); between Fragment 3 genotype and living weight, carcass weight, breast muscle weight, abdominal fat weight, and abdominal fat percentage (P < 0.05); between Fragment 4 genotype and Thr, Phe, and inosinic acid (P < 0.05). It was concluded that H-FABP was the major gene influencing slaughter performance and meat quality or was linked with the major gene in these strains and that the C783T mutation could be used as a candidate molecular genetic marker for breeding selection. The combination M1C2–B2B2–D1D1 is an ideal model for breeding in these strains because it can improve slaughter and meat quality traits.     

Three Novel SNPs in the Coding Region of the Bovine MC3R Gene and Their Associations with Growth Traits

The involvement of melanocortin-3 receptor (MC3R) is well recognized in the regulation of feeding efficiency, body weight, and energy homeostasis. The objective of this study was to investigate the associations between MC3R gene polymorphisms and growth traits. Three novel SNPs (c.24C→T, c.220T→A, c.734G→C) and five haplotypes were identified in 234 Xiangxi cattle. The associations between MC3R gene polymorphisms and growth traits indicated that the individuals with TT and AT genotypes maintained higher body weight than those with the AA genotype at the c.220T→A locus (P < 0.05). The animals with GG and CG genotypes had higher heart girth and body weight than those with the CC genotype at c.734G→C (P < 0.05). The animals with H3H3 and H2H3 haplotype combinations had higher body weight than those with other haplotype combinations (P < 0.05). The results suggest that these SNPs in the MC3R gene might be useful genetic markers for marker-assisted selection and cattle breeding.     

Association of FATP1 gene polymorphisms with chicken carcass traits in Chinese meat-type quality chicken populations

In this study, we aimed to detect the single nucleotide polymorphisms (SNPs) of the chicken FATP1 gene and discern the potential association between FATP1 SNPs and chicken carcass traits. A total of 620 meat-type quality chickens from six commercial pure lines (S01, S02, S03, S05, S06 and D99) and two cross lines (S05 × S01 and S06 × S01) were screened by using the single-strand conformational polymorphism analysis (SSCP) and DNA sequencing. Five SNPs [g.49360G > A, g.48195G > A, g.46847A > G, g.46818A > G, and g.46555A > G] were identified in chicken FATP1 gene. SNP g.46818 A > G was a rare variant and was not considered in the subsequent analysis. Sixteen haplotypes were reconstructed on the basis of the other four SNPs. The linear regression model analysis indicated that there were significant associations of certain diplotypes with part of carcass traits, such as live weight (LW), carcass weight (CW), and semi-eviscerated weight (SEW) (P < 0.05). In particular, diplotype H2H4 had a negative effect on LW, CW, SEW, and abdominal fat weight (AW); diplotype H6H10 had the highest reducing effect on subcutaneous fat thickness (SFT). Our results suggested that FATP1gene polymorphisms were associated with chicken carcass traits or was linked with the major gene. The SNPs in this gene may be utilized as potential markers for marker-assisted selection (MAS) during chicken breeding.     

Novel SNPs in the bovine ADIPOQ and PPARGC1A genes are associated with carcass traits in Hanwoo (Korean cattle)

Adiponectin (ADIPOQ) modulates several biological processes including energy homeostasis, glucose and lipid metabolism. The bovine ADIPOQ gene was located near the QTL affecting marbling, ribeye muscle area and fat thickness on BTA1. The gene encoding peroxisome proliferator-activated receptor-γ coactivator-1α (PPARGC1A) was located within the QTL region of the traits on BTA6. Moreover, its protein product has various biological functions such as cellular energy homeostasis, including adaptive thermogenesis, adipogenesis and gluconeogenesis. Therefore, the ADIPOQ and PPARGC1A genes are a positional and functional candidate gene for carcass traits in beef cattle. The objectives of this study were to identify polymorphisms in the bovine ADIPOQ and PPARGC1A genes, to evaluate their associations with carcass traits in Hanwoo (Korean cattle) population. We identified nine SNPs in the ADIPOQ gene. Two SNPs (DQ156119: g.1436T > C and DQ156119: g.1454A > G) in the promoter region were recognized as new SNPs identified in Hanwoo. Association analysis indicated that the g.1454A > G SNP genotype was significantly associated with effects on LMA (P = 0.004) and BF (P = 0.021). The ADIPOQ haplotype was also found to have significant effect on the LMA. In the PPARGC1A gene, we identified 11 SNPs in the two unexplored regions (intron 3 and 5). Among them, seven SNPs were located in intron 3 and four SNPs were located in intron 5. Of these 11 putative novel SNPs, two SNPs (AY839822: g.292C > T and AY839823: g.1064C > T) with minor allele frequency (MAF) > 0.20 were examined for associations with carcass traits. The association analysis revealed that both SNPs in PPARGC1A gene were significantly associated with LMA (P < 0.05). These findings suggest that the SNPs of bovine ADIPOQ and PPARGC1A genes may be a useful molecular marker for selection of carcass traits in Hanwoo.     

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.     

Polymorphisms in MC4R gene and correlations with economic traits in cattle

MC4R contributes to the control of food intake and energy expenditure, and single nucleotide polymorphisms (SNPs) in the MC4R gene have clearly been associated with backfat depth, feed intake and growth rate in pig. Our objectives were to scan the complete coding region by sequencing in samples from eight cattle breeds, to estimate the frequency of the SNPs in the MC4R gene and to determine if individual genotypes were associated with several economic traits. Five polymorphisms were detected at position 19 (C/A), 20 (A/T), 83(T/C), 128 (G/A), and 1069 (G/C), and the last one was significantly associated with backfat thickness value (P < 0.01, n = 245). The linkage disequilibrium analysis indicated that the SNP markers C19A, A20T, T83C and G128A were completely linked (r ² = 1).     

Interaction between obesity-related genes, FTO and MC4R, associated to an increase of breast cancer risk

Breast cancer (BC) is a complex disease and obesity is a well-known risk factor for its development, especially after menopause. Several studies have shown Single Nucleotide Polymorphisms (SNPs) linked to overweight and obesity, such as: rs1121980 (T/C) and rs9939609 (A/T) in Fat Mass and Obesity Associated gene (FTO) and rs17782313 (T/C) in Melanocortin 4 Receptor gene (MC4R). Thus, we aimed to investigate the association between these obesity-related SNPs and BC risk. One hundred BC patients and 148 healthy women from Santa Catarina, Brazil entered the study. SNPs were genotyped using Taqman assays. For statistical analyses SNPStats and SPSS softwares were used. Association analyses were performed by logistic regression and were adjusted for age and Body mass index (BMI). Multiple SNPs inheritance models (log-additive, dominant, recessive, codominant) were performed to determine odds ratios (ORs), assuming 95 % confidence interval (CI) and P value = 0.05 as the significance limit. When analyzed alone, FTO rs1121980 and rs9939609 did not show significant associations with BC development, however MC4R rs17782313 showed increased risk for BC even after adjustments (P-value = 0.032). Interestingly, the interaction of FTO and MC4R polymorphisms showed a powerful association with BC. We observed a 4.59-fold increased risk for woman who have the allele combination C/T/C (FTO rs1121980/FTO rs9939609/MC4R rs17782313) (P-value = 0.0011, adjusted for age and BMI). We found important and unpublished associations between these obesity-related genes and BC risk. These associations seem to be independent of their effect on BMI, indicating a direct role of the interaction between FTO and MC4R polymorphisms in BC development.     

SLCO2B1 genetic polymorphisms in a Korean population: pyrosequencing analyses and comprehensive comparison with other populations

SLCO2B1, also known as OATP2B1 (Organic Anion Transporter) or OATP-B or SLC21A9, is an organic anion uptake transporter that is encoded by the SLCO2B1 gene. In this study we assessed the frequencies of SLCO2B1 polymorphisms in a Korean population using newly developed pyrosequencing methods and compared their frequencies with those in other ethnic groups. We developed pyrosequencing methods to identify the following six SLCO2B1 non-synonymous polymorphisms: c.1175C > T (rs1621378), c.1457C > T (rs2306168), c.43C > T (rs56837383), c.935G > A (rs12422149), c.601G > A (rs35199625) and c.644A > T (rs72559740). The allele frequencies of these polymorphisms were analyzed in 227 Korean subjects. The allele frequencies of SLCO2B1 polymorphisms in the population tested were as follows: 0.0 for c.1175C > T, c.43C > T and c.644A > T; 0.2687 for c.1457C > T; 0.4273 for c.935G > A; and 0.0727 for c. 601G > A. Even though the allele frequencies of the c.1175C > T and c.1457C > T polymorphisms were comparable to those in Japanese subjects, the frequencies in this Korean population differed from those in other ethnic groups. The developed pyrosequencing methods are rapid and reliable for detecting non-synonymous SLCO2B1 polymorphisms. Large ethnic differences in the frequency of SLCO2B1 genetic polymorphisms were noted among ethnic groups. The SLCO2B1 polymorphisms at c.1175C > T, c.43C > T and c.644A > T were not found in the Korean population while c.1457C > T, c.935G > A and c.601G > A exhibited mostly higher frequencies in Koreans compared with Finnish, Caucasian and African-American populations.     

A Missense Mutation in the Rabbit Melanocortin 4 Receptor (MC4R) Gene is Associated with Finisching Weight in a Meat Rabbit Line

In this study we resequenced 1729 bp of the rabbit melanocortin 4 receptor (MC4 R) gene in 31 rabbits from different breeds/lines and identified ten polymorphisms: one was an indel and 9 were single nucleotide polymorphisms (SNPs). The indel and 5 SNPs were in the 5′-flanking region, 3 were synonymous SNPs and one was a missense mutation (c.101G>A; p.G34D), located in a conserved position of the extracellular tail of the MC4 R protein. The missense mutation was analyzed in a panel of 74 rabbits of different breeds and in 516 performance tested rabbits of a commercial paternal line under selection for growth efficiency. Association analysis indicated that rabbits with the less frequent genotype in this population (DD) had a lighter weight at 70 postnatal days than animals with genotype GD (P < 0.10) and animals with genotype GG (P < 0.05). This is the third study on candidate genes, after those on GH1 and IGF2 that reported a marker associated with finishing weight. Therefore, it seems that a candidate gene approach in rabbit based on previous information accumulated in other livestock species could be useful to identify genes explaining a fraction of variability of performance traits with potential application on rabbit breeding and selection.     

Genetic Association Study of Adiposity and Melanocortin-4 Receptor (MC4R) Common Variants: Replication and Functional Characterization of Non-Coding Regions

Common genetic variants 3′ of MC4R within two large linkage disequilibrium (LD) blocks spanning 288 kb have been associated with common and rare forms of obesity. This large association region has not been refined and the relevant DNA segments within the association region have not been identified. In this study, we investigated whether common variants in the MC4R gene region were associated with adiposity-related traits in a biracial population-based study. Single nucleotide polymorphisms (SNPs) in the MC4R region were genotyped with a custom array and a genome-wide array and associations between SNPs and five adiposity-related traits were determined using race-stratified linear regression. Previously reported associations between lower BMI and the minor alleles of rs2229616/Val103Ile and rs52820871/Ile251Leu were replicated in white female participants. Among white participants, rs11152221 in a proximal 3′ LD block (closer to MC4R) was significantly associated with multiple adiposity traits, but SNPs in a distal 3′ LD block (farther from MC4R) were not. In a case-control study of severe obesity, rs11152221 was significantly associated. The association results directed our follow-up studies to the proximal LD block downstream of MC4R. By considering nucleotide conservation, the significance of association, and proximity to the MC4R gene, we identified a candidate MC4R regulatory region. This candidate region was sequenced in 20 individuals from a study of severe obesity in an attempt to identify additional variants, and the candidate region was tested for enhancer activity using in vivo enhancer assays in zebrafish and mice. Novel variants were not identified by sequencing and the candidate region did not drive reporter gene expression in zebrafish or mice. The identification of a putative insulator in this region could help to explain the challenges faced in this study and others to link SNPs associated with adiposity to altered MC4R expression.     

Melanocortin-4 receptor (MC4R) polymorphisms are associated with growth and meat quality traits in sheep

The involvement of melanocortin 4 receptor gene (MC4R) in food intake and body weight regulation is well characterized. MC4R mutations are the most frequent monogenic cause of human obesity. Significant associations have been revealed between MC4R mutations and productive traits in pigs, cattle and poultry. Herein, fluorescence-based conformation sensitive gel electrophoresis was used to identify two single nucleotide polymorphisms (SNPs) in the coding region (93G>A and 292G>A) and two SNPs in the 3′-UTR area (1016G>A and 1240T>C) of MC4R gene in 132 German Merino sheep. We found that the 1016G>A mutation in the 3′-UTR was significantly associated with body weight at 120 and 180 days, average daily gain, back fat thickness and loin-eye area. Allele A located at the 292th position of MC4R gene representing Arg98 was associated with significantly higher loin-eye area in sheep. For the synonymous 93G>A mutation, A allele carrier animals had higher back fat thickness. Our results provide evidence that the MC4R gene may be a candidate gene for growth and meat quality traits with MC4R SNPs being potentially valuable as genetic markers for economic traits in German Merino sheep.     

Expression Profiles of <Emphasis Type="Italic">IGF</Emphasis>-<Emphasis Type="Italic">1R</Emphasis> Gene and Polymorphisms of its Regulatory Regions in Different Pig Breeds

Insulin like growth factor 1 receptor (IGF-1R) is a candidate gene for growth and carcass traits in regulating animal growth, metabolism and endocrine. It is widely expressed in liver, muscle, bone tissues where the IGF-1R functions as a factor that promotes cell growth. In this study, the protein expression level of IGF-1R gene in liver and muscle tissues of three periods (birth, weaning and adult) of three pig breeds (BamaXiang pigs (BM), Tibetan pigs (TM) and Junmu No.1 pigs (JM)) were tested by western blot. SNPs within the regulatory region of pig IGF-1R gene were detected using direct sequencing and then the genotypes were identified through AS-PCR approach. Results showed expression profiles of IGF-1R gene between liver and muscle tissues were different and significant differences were also found among pig breeds. In the same time, four SNPs were detected in the regulatory region of IGF-1R gene, among which the genotype frequency of three (g.?1468G > C, g.?1192 C > T and g.330,424 C > T) were significantly different among the pig breeds. BM tended to heterozygous (GC/CT) of the anterior two loci, while TM and JM preferred the other two homozygotes respectively. For the g.330,424 C > T, all pig breeds were tended to be the heterozygous. In conclusion, the SNPs with different genotype distribution among the three pig breeds may explain the gene expression difference between the different pig breeds.     

Examination of FGFRL1 as a candidate gene for diaphragmatic defects at chromosome 4p16.3 shows that Fgfrl1 null mice have reduced expression of Tpm3, sarcomere genes and Lrtm1 in the diaphragm

Fgfrl1 (also known as Fgfr5; OMIM 605830) homozygous null mice have thin, amuscular diaphragms and die at birth because of diaphragm hypoplasia. FGFRL1 is located at 4p16.3, and this chromosome region can be deleted in patients with congenital diaphragmatic hernia (CDH). We examined FGFRL1 as a candidate gene for the diaphragmatic defects associated with 4p16.3 deletions and re-sequenced this gene in 54 patients with CDH. We confirmed six known coding single nucleotide polymorphisms (SNPs): c.209G > A (p.Pro20Pro), c.977G > A (p.Pro276Pro), c.1040T > C (p.Asp297Asp), c.1234C > A (p.Pro362Gln), c.1420G > T (p.Arg424Leu), and c.1540C > T (p.Pro464Leu), but we did not identify any gene mutations. We genotyped additional CDH patients for four of these six SNPs, including the three non-synonymous SNPs, to make a total of 200 chromosomes, and found that the allele frequency for the four SNPs, did not differ significantly between patients and normal controls (p ≥ 0.05). We then used Affymetrix Genechip^® Mouse Gene 1.0 ST arrays and found eight genes with significantly reduced expression levels in the diaphragms of Fgfrl1 homozygous null mice when compared with wildtype mice—Tpm3, Fgfrl1 (p = 0.004), Myl2, Lrtm1, Myh4, Myl3, Myh7 and Hephl1. Lrtm1 is closely related to Slit3, a protein associated with herniation of the central tendon of the diaphragm in mice. The Slit proteins are known to regulate axon branching and cell migration, and inhibition of Slit3 reduces cell motility and decreases the expression of Rac and Cdc42, two genes that are essential for myoblast fusion. Further studies to determine if Lrtm1 has a similar function to Slit3 and if reduced Fgfrl1 expression can cause diaphragm hypoplasia through a mechanism involving decreased myoblast motility and/or myoblast fusion, seem indicated.     

Identification and analysis of <Emphasis Type="Italic">MC4R</Emphasis> polymorphisms and their association with economic traits of Korean cattle (Hanwoo)

Signaling by the melanocortin-4 receptor (MC4R) is important for mediation the effect of leptin on food intake and energy homeostasis, and is associated with obesity, energy homeostasis and control of feeding behavior. Presently, the bovine MC4R gene was characterized to detect genetic variation at this locus and to relate it to economic traits in Korean cattle (Hanwoo). Five single nucleotide polymorphisms (SNPs) were identified in the coding region (G709A, C927T, C1069G, C1343A, and C1786T). G709A changed amino acid 166 of the MC4R protein from valine to methionine and C1069G changed amino acid 286 of the MC4R protein from leucine to valine. A SNP at C927T significantly influenced the Marbling score, SNP markers C1069G and C1343A significantly affected the Backfat thickness, and the SNP marker C1786T significantly influenced backfat and Marbling score. The MC4R gene may thus be a candidate gene for carcass traits with MC4R SNPs being potentially valuable as genetic markers for economic traits in Hanwoo.     

Identification of novel single nucleotide polymorphisms (SNPs) of the lipoprotein lipase (LPL) gene associated with fatty acid composition in Korean cattle

The lipoprotein lipase (LPL) gene can be considered a functional candidate gene that regulates fatty acid composition. In this study, genetic associations between fatty acid composition and exonic single nucleotide polymorphisms (SNPs) in the LPL gene were examined using 612 Korean cattle. We investigated the relationship between unsaturated fatty acids and five novel SNPs (c.322G>A, c.329A>T, c.527T>G, c.988C>T and c.1591G>A), and confirmed that three polymorphic SNPs (c.322G>A, c.329A>T and c.1591G>A) were associated with fatty acid composition. Korean cattle with an AA genotype of c.322G>A, c.329A>T, and GA genotype of c.1591G>A had higher levels of monounsaturated fatty acids and carcass traits (P < 0.05). Our findings confirmed that three novel SNPs we identified in the LPL gene can affect fatty acid composition and carcass traits. Therefore, selection for AA and GA genotypes should be recommended to genetically improve beef quality and flavor.     

Melanocortin-4 Receptor Mutations and Polymorphisms Do Not Affect Weight Loss after Bariatric Surgery

Bariatric surgery is the most effective long term weight-loss therapy for severe and morbidly obese patients. Melanocortin-4 Receptor (MC4R) mutations, the most frequent known cause of monogenic obesity, affect the regulation of energy homeostasis. The impact of such mutations on weight loss after bariatric surgery is still debated.The objective is to determine the impact of MC4R status on weight loss in obese subjects over one year after bariatric surgery.A total of 648 patients, who were referred to bariatric surgery in a single clinical nutrition department, were genotyped for their MC4R status. The following four groups were categorized: functional MC4R mutations, MC4R single nucleotide polymorphisms (SNPs): Val103Ile (V103L) and Ile251Leu (I251L), MC4R variant rs17782313 (downstream of MC4R) and MC4R SNP A-178C on the promoter. Each patient was matched with two randomly paired controls without mutation. Matching factors were age, sex, baseline weight and type of surgery procedure (Roux-en-Y gastric bypass and adjustable gastric banding). We compared weight loss between cases and controls at 3, 6 and 12 months after surgery.Among 648 patients, we identified 9 carriers of functional MC4R mutations, 10 carriers of MC4R V103L and I251L SNPs, 7 carriers of the rs17792313 variant and 22 carriers of the A-178C SNP. Weight loss at 3, 6 and 12 months did not differ between cases and controls, whatever the MC4R mutations.This is the first case-control study to show that MC4R mutations and polymorphisms do not affect weight loss and body composition over one year after bariatric surgery.     

Cloning of TPO gene and associations of polymorphisms with chicken growth and carcass traits

Thyroid peroxidase (TPO), which located on the apical membrane surface of thyrocytes, is the key enzyme involved in thyroid hormone synthesis, mainly catalyses the iodination of tyrosine residues and the coupling of iodotyrosines on thyroglobulin to form thyroxine and triiodothyronine. The objectives of this study were to identify genetic polymorphisms of the chicken TPO gene and to analyze potential association between single nucleotide polymorphisms (SNPs) and growth and carcass traits in chicken. Partial sequences of TPO gene were cloned firstly. The nucleotide sequence was found to have 72 % identity with that of humans. The chicken TPO amino acid sequence was 71 %. Through polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing methods, three novel mutations of the chicken TPO gene were detected in the F₂ resource population from Gushi chickens and Anka broilers. The association analysis indicated that all of the three SNPs showed association with chicken growth at different periods. The g.29996C>T polymorphisms was significantly associated with body weight, breast bone length, pectoral angle at 12 weeks, claw weight and leg muscle weight (P < 0.05). In addition, individuals with the TT genotype had higher value for almost all the traits than CC and CT genotype. Meanwhile for CLW, the additive effects were significant (P < 0.05). Hence, we suggest that genotype TT can be regarded as a potential molecular marker for later growth and carcass traits in chicken.