Variation at CPE but not CEBPA appears to be associated with intramuscular fat deposition in the longissimus muscle of cattle

2009 ◽  
Vol 49 (7) ◽  
pp. 558 ◽  
Author(s):  
William Barendse ◽  
Rowan J. Bunch ◽  
Blair E. Harrison
Keyword(s):  
Substitution Effect ◽  
Intramuscular Fat ◽  
High Linkage Disequilibrium ◽  
Substitution Effects ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
Allele Substitution Effect ◽  
Single Nucleotide ◽  
Enhancer Binding Protein ◽  
Allele Substitution

An important step in the localisation of quantitative trait loci is the confirmation of trait-marker associations in independent studies. In this report, we test three single nucleotide polymorphisms (SNP) of two genes for associations to intramuscular fat (IMF) measurements in cattle. We genotyped SNP of carboxypeptidase E (CPE) and ccaat/enhancer binding protein, α (CEBPA) in a sample of a total of 813 cattle of taurine, composite and indicine breeds. All three polymorphisms showed significant differences between breeds, with the widest range found in CEBPA:g.271A > C where the A allele frequency ranged from P = 0.07 in Brahman to 0.88 in Shorthorn. The taurine breeds showed high linkage disequilibrium between the pair of CPE SNP, with all four breeds showing r2 = 1.0. The Brahman and Santa Gertrudis showed r2 ≤ 0.17. Both CPE:g.445C > T and CPE:g.601C > T SNP showed significant allele substitution effects to IMF in animals of taurine ancestry, with an allele substitution effect of α = 0.22, P = 0.020 for CPE:g.445C > T, explaining 0.4% of the phenotypic variance.

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

Animals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 858 ◽  
Author(s):  
Wang ◽  
Li ◽  
Zhou ◽  
Gao ◽  
Liu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Gene Polymorphisms ◽  
Genetic Correlations ◽  
Intramuscular Fat ◽  
Fat Content ◽  
Backfat Thickness ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Coefficients Of Variation ◽  
Intramuscular Fat Content

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.

scholarly journals Association of predicted deleterious single nucleotide polymorphisms with carcass traits in meat-type chickens

2018 ◽  
Author(s):  
Priscila Anchieta Trevisoli ◽  
Gabriel Costa Monteiro Moreira ◽  
Clarissa Boschiero ◽  
Aline Silva Mello Cesar ◽  
Juliana Petrini ◽  
...  
Keyword(s):  
Carcass Traits ◽  
Muscle Growth ◽  
Substitution Effects ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Coding Regions ◽  
Genome Wide ◽  
Allele Substitution ◽  
Steroid Hormone Signaling ◽  
Breast Weight

ABSTRACTIn previous studies, we used genome wide association (GWAS) to identify quantitative trait loci (QTL) associated with weight and yield of abdominal fat, drumstick, thigh and breast traits in chickens. However, this methodology assumes that the studied variants are in linkage disequilibrium with the causal mutation and consequently do not identify it. In an attempt to identify causal mutations in candidate genes for carcass traits in broilers, we selected 20 predicted deleterious SNPs within QTLs for association analysis. Additive, dominance and allele substitution effects were tested. From the 20 SNPs analyzed, we identified six SNPs with significant association (p-value <0.05) with carcass traits, and three are highlighted here. The SNP rs736010549 was associated with drumstick weight and yield with significant additive and dominance effects. The SNP rs739508259 was associated with thigh weight and yield, and with significant additive and allele substitution effects. The SNP rs313532967 was associated with breast weight and yield. The three SNPs that were associated with carcass traits (rs736010549, rs739508259 and rs313532967) are respectively located in the coding regions of the WDR77, VWA8 and BARL genes. These genes are involved in biological processes such as steroid hormone signaling pathway, estrogen binding, and regulation of cell proliferation. Our strategy allowed the identification of putative casual mutations associated with muscle growth.

scholarly journals An Exploratory Association Analysis of the Insulin Gene Region With Diabetes Mellitus in Two Dog Breeds

2019 ◽  
Vol 110 (7) ◽  
pp. 793-800 ◽  
Author(s):  
Rebecka Hess ◽  
Paula Henthorn ◽  
Marcella Devoto ◽  
Fan Wang ◽  
Rui Feng
Keyword(s):  
Diabetes Mellitus ◽  
The United States ◽  
High Linkage Disequilibrium ◽  
Gene Region ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Stage 1 ◽  
Stage Stage

Abstract Samoyeds and Australian Terriers are the 2 dog breeds at highest risk (&gt;10-fold) for diabetes mellitus in the United States. It is unknown if the insulin (INS) gene is involved in the pathophysiology of diabetes in Samoyeds and Australian Terriers. It was hypothesized that the INS gene region provides a common genetic causality for diabetes in Samoyeds and Australian Terriers. We conducted a 2-stage genetic association study involving both breeds. In the discovery stage (Stage 1), Samoyeds with and without diabetes were compared in the frequencies of 447 tagging single-nucleotide polymorphisms (SNPs) within 2.5 megabases (Mb) up- and downstream of the INS gene on the Illumina CanineHD BeadChip. SNPs yielding a P-value &lt; 0.005 were selected for further follow-up. In the validation stage (Stage 2), Australian Terriers with and without diabetes were compared in the SNPs genotyped by the Affymetrix GeneChip Canine Genome 2.0 Array and within 1 Mb up- and downstream of the selected SNPs from Stage 1. Two SNPs that were in high linkage disequilibrium (LD, r2 = 0.7) were selected from Stage 1. In Stage 2, among the 76 SNPs examined, 5 were significantly associated with diabetes after Bonferroni’s correction for multiple comparisons. Three of these 5 SNPs were in complete LD (r2 = 1 for all associations) and the 2 remaining SNPs were in moderate LD (r2 = 0.4). In conclusion, an association between the INS gene region and diabetes was suggested in 2 dog breeds of different clades. This region could have importance in diabetes in other breeds or in canine diabetes at large.

scholarly journals Candidate SNPs for carcass and meat traits in Nelore animals and in their crosses with Bos taurus

2012 ◽  
Vol 47 (2) ◽  
pp. 294-301 ◽  
Author(s):  
Rogério Abdallah Curi ◽  
Monique Marcondes Krauskopf ◽  
Janaína Conte Hadlich ◽  
Marina Rufino Salinas Fortes ◽  
Dianne Margaret Vankan ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Multiple Testing ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Total Sample ◽  
Candidate Snps ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Fragmentation Index ◽  
Allele Substitution

The objective of this work was to evaluate the effects of single-nucleotide polymorphisms (SNPs) in the genes IGF1 (AF_017143.1:g.198C>T), MSTN (AF_320998.1:g.433C>A), MYOD1 (NC_007313:g.1274A>G) and MYF5 (NC_007303:g.1911A>G) on carcass and meat traits in Nelore (Bos indicus) and Nelore x B. taurus. A total of 300 animals were genotyped and phenotyped for rib eye area (REA), backfat thickness (BT), intramuscular fat (IF), shear force (SF) and myofibrillar fragmentation index (MFI). The effects of allele substitution for each SNP were estimated by regression of the evaluated phenotypes on the number of copies of a particular allele using the general linear model. The polymorphism at IGF1 was non-informative in Nelore animals. In crossbred animals, the IGF1 C allele was associated with greater REA. However, this relation was not significant after Bonferroni correction for multiple testing. The A allele of the MSTN polymorphism was absent in Nelore cattle and was only found in two crossbred animals. The polymorphisms of MYOD1 and MYF5 were little informative in Nelore animals with G allele frequency of 0.097 and A allele frequency of 0.031, respectively. These markers show no association with the analyzed traits in the total sample of evaluated animals.

Study of CXCL9-11 gene polymorphisms in liver fibrosis among patients with chronic hepatitis C

2021 ◽  
Author(s):  
Mariana Cavalheiro Magri ◽  
Maria Stella Montanha Alvarez ◽  
Anny Ayumi Iogi ◽  
Grayce Mendes Alves ◽  
Caroline Manchiero ◽  
...  
Keyword(s):  
Chronic Hepatitis ◽  
Hepatitis C ◽  
Liver Fibrosis ◽  
Chronic Hepatitis C ◽  
Genetic Model ◽  
High Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Advanced Fibrosis ◽  
Single Nucleotide ◽  
Pathogenic Factors

Abstract Several factors are associated with the progression of chronic hepatitis C: comorbidities, lifestyle, and pathogenic factors, including immune response, apoptosis and heredity. Single nucleotide polymorphisms (SNPs) in the PNPLA3 and TM6SF2 genes are more widely studied genetic risk factors, while CXCL9–11 chemokines produced by hepatocytes in the process of infection are less well studied. Our aim was to evaluate the influence of CXCL9 rs10336, CXCL10 rs3921 and CXCL11 rs4619915 in liver fibrosis when analysed together with PNPLA3 rs738409 and TM6SF2 rs58542926. The study included 219 patients with chronic hepatitis C. SNP genotyping was performed by real-time PCR. Univariate and multivariate analyses were used to detect the association between SNPs and advanced fibrosis in a recessive genetic model. All SNPs had a minimum allele frequency &gt; 5%, and CXCL9 rs10336, CXCL10 rs3921 and CXCL11 rs4619915 were in high linkage disequilibrium (D’ ≥0.84). In the multivariate analysis, we observed that male gender (p = 0.000), older age (p = 0.025), moderate to intense inflammatory activity (p = 0.002), moderate to accentuated hepatic steatosis (p = 0.026) and the CT genotype of the TM6SF2 rs58542926 SNP (p = 0.014) presented significant associations with advanced fibrosis. Overall, the CXCL9 rs10336, CXCL10 rs3921, CXCL11 rs4619915 and PNPLA3 rs738409 SNPs did not influence liver fibrosis among patients with chronic hepatitis C.

Lack of an association between single nucleotide polymorphisms in the bovine leptin gene and intramuscular fat in Bos taurus cattle

Meat Science ◽  
2009 ◽  
Vol 81 (4) ◽  
pp. 731-737 ◽  
Author(s):  
L. Pannier ◽  
T. Sweeney ◽  
R.M. Hamill ◽  
F. Ipek ◽  
P.C. Stapleton ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Bos Taurus ◽  
Intramuscular Fat ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Genes Related to Fat Metabolism in Pigs and Intramuscular Fat Content of Pork: A Focus on Nutrigenetics and Nutrigenomics

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 150
Author(s):  
Isaac Hyeladi Malgwi ◽  
Veronika Halas ◽  
Petra Grünvald ◽  
Stefano Schiavon ◽  
Ildikó Jócsák
Keyword(s):  
Molecular Mechanisms ◽  
Fat Metabolism ◽  
Gene Interaction ◽  
Acid Synthesis ◽  
Intramuscular Fat ◽  
Genomic Research ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Nutritional Science ◽  
Intramuscular Fat Content

Fat metabolism and intramuscular fat (IMF) are qualitative traits in pigs whose development are influenced by several genes and metabolic pathways. Nutrigenetics and nutrigenomics offer prospects in estimating nutrients required by a pig. Application of these emerging fields in nutritional science provides an opportunity for matching nutrients based on the genetic make-up of the pig for trait improvements. Today, integration of high throughput “omics” technologies into nutritional genomic research has revealed many quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs) for the mutation(s) of key genes directly or indirectly involved in fat metabolism and IMF deposition in pigs. Nutrient–gene interaction and the underlying molecular mechanisms involved in fatty acid synthesis and marbling in pigs is difficult to unravel. While existing knowledge on QTLs and SNPs of genes related to fat metabolism and IMF development is yet to be harmonized, the scientific explanations behind the nature of the existing correlation between the nutrients, the genes and the environment remain unclear, being inconclusive or lacking precision. This paper aimed to: (1) discuss nutrigenetics, nutrigenomics and epigenetic mechanisms controlling fat metabolism and IMF accretion in pigs; (2) highlight the potentials of these concepts in pig nutritional programming and research.

scholarly journals Effect of single nucleotide polymorphisms on intramuscular fat content in Hungarian Simmental cattle

2018 ◽  
Vol 31 (9) ◽  
pp. 1415-1419 ◽  
Author(s):  
István Anton ◽  
Balázs Húth ◽  
Imre Füller ◽  
László Rózsa ◽  
Gabriella Holló ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Intramuscular Fat ◽  
Fat Content ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Simmental Cattle ◽  
Intramuscular Fat Content
Sign in / Sign up

Export Citation Format

Share Document