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.

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.

Detection of candidate genes for growth and carcass traits using genome-wide association strategy in Chinese Simmental beef cattle

2018 ◽  
Vol 58 (2) ◽  
pp. 224 ◽  
Author(s):  
Wengang Zhang ◽  
Lingyang Xu ◽  
Huijiang Gao ◽  
Yang Wu ◽  
Xue Gao ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Average Daily Gain ◽  
Carcass Traits ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Economic Traits ◽  
Cattle Industry ◽  
Genome Wide

In Chinese beef cattle industry, there are more than 60 million livestock, nearly half of which are Chinese Simmental beef cattle or Simmental crossbreds. Over the past decades, numerous quantitative trait loci for economic traits in cattle have been identified, while few studies for growth and carcass traits have been reported in Simmental beef cattle. In the present study, we conducted genome-wide association study based on BovineHD BeadChip and identified 41, 15, 3, 22 and 16 single-nucleotide polymorphisms significantly associated with average daily gain, liveweight before slaughter, carcass weight, dressing percentage and pure meat percentage respectively. In total, 18 candidate genes were found for growth and carcass traits, and four haplotype blocks for growth and carcass traits were discovered. These findings will facilitate detection of major genes and genetic variants involved in growth and carcass traits of beef cattle in further studies.

A family-based genome-wide association study reveals an association of spondyloarthritis with MAPK14

2016 ◽  
Vol 76 (1) ◽  
pp. 310-314 ◽  
Author(s):  
Félicie Costantino ◽  
Alice Talpin ◽  
Roula Said-Nahal ◽  
Ariane Leboime ◽  
Elena Zinovieva ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Gwas Study ◽  
Genome Wide ◽  
Multiplex Families ◽  
Family Based

ObjectiveMore than 40 loci have been associated with ankylosing spondylitis (AS), but less is known about genetic associations in spondyloarthritis (SpA) as a whole. We conducted a family-based genome-wide association study (GWAS) to identify new non-major histocompatibility complex (MHC) genetic factors associated with SpA.Methods906 subjects from 156 French multiplex families, including 438 with SpA, were genotyped using Affymetrix 250K microarrays. Association was tested with Unphased. The best-associated non-MHC single nucleotide polymorphisms (SNPs) were then genotyped in two independent familial cohorts (including 215 French and 294 North American patients with SpA, respectively) to replicate associations.Results43 non-MHC SNPs yielded an association signal with SpA in the discovery cohort (p<1×10−4). In the extension studies, association was replicated at a nominal p value of p<0.05 for 16 SNPs in the second cohort and for three SNPs in the third cohort. Combined analysis identified an association close to genome-wide significance between rs7761118, an intronic SNP of MAPK14, and SpA (p=3.5×10−7). Such association appeared to be independent of HLA-B27.ConclusionsWe report here for the first time a family-based GWAS study on SpA and identified an associated polymorphism near MAPK14. Further analyses are needed to better understand the functional basis of this genetic association.

scholarly journals Genome-wide association study identifies a novel susceptibility locus at 6p21.3 among familial CLL

Blood ◽  
2011 ◽  
Vol 117 (6) ◽  
pp. 1911-1916 ◽  
Author(s):  
Susan L. Slager ◽  
Kari G. Rabe ◽  
Sara J. Achenbach ◽  
Celine M. Vachon ◽  
Lynn R. Goldin ◽  
...  
Keyword(s):  
Family History ◽  
Genome Wide Association Study ◽  
Statistical Significance ◽  
Familial Risk ◽  
Lymphocytic Leukemia ◽  
Genome Wide Association ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
History Of

Abstract Prior genome-wide association (GWA) studies have identified 10 susceptibility loci for risk of chronic lymphocytic leukemia (CLL). To identify additional loci, we performed a GWA study in 407 CLL cases (of which 102 had a family history of CLL) and 296 controls. Moreover, given the strong familial risk of CLL, we further subset our GWA analysis to the CLL cases with a family history of CLL to identify loci specific to these familial CLL cases. Our top hits from these analyses were evaluated in an additional sample of 252 familial CLL cases and 965 controls. Using all available data, we identified and confirmed an independent association of 4 single-nucleotide polymorphisms (SNPs) that met genome-wide statistical significance within the IRF8 (interferon regulatory factor 8) gene (combined P values ≤ 3.37 × 10−8), located in the previously identified 16q24.1 locus. Subsetting to familial CLL cases, we identified and confirmed a new locus on chromosome 6p21.3 (combined P value = 6.92 × 10−9). This novel region harbors the HLA-DQA1 and HLA-DRB5 genes. Finally, we evaluated the 10 previously reported SNPs in the overall sample and replicated 8 of them. Our findings support the hypothesis that familial CLL cases have additional genetic variants not seen in sporadic CLL. Additional loci among familial CLL cases may be identified through larger studies.

scholarly journals Identifying Liver Cancer-Related Enhancer SNPs by Integrating GWAS and Histone Modification ChIP-seq Data

2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Tianjiao Zhang ◽  
Yang Hu ◽  
Xiaoliang Wu ◽  
Rui Ma ◽  
Qinghua Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Cancer ◽  
Histone Modification ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Protein Coding ◽  
Noncoding Regions ◽  
Coding Regions ◽  
Genome Wide

Many disease-related single nucleotide polymorphisms (SNPs) have been inferred from genome-wide association studies (GWAS) in recent years. Numerous studies have shown that some SNPs located in protein-coding regions are associated with numerous diseases by affecting gene expression. However, in noncoding regions, the mechanism of how SNPs contribute to disease susceptibility remains unclear. Enhancer elements are functional segments of DNA located in noncoding regions that play an important role in regulating gene expression. The SNPs located in enhancer elements may affect gene expression and lead to disease. We presented a method for identifying liver cancer-related enhancer SNPs through integrating GWAS and histone modification ChIP-seq data. We identified 22 liver cancer-related enhancer SNPs, 9 of which were regulatory SNPs involved in distal transcriptional regulation. The results highlight that these enhancer SNPs may play important roles in liver cancer.

scholarly journals The metabolic profile associated with head and neck cancer genetic variation and dietary intake

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
I Hoxhaj ◽  
S Ahmad ◽  
J Liu ◽  
R Pastorino ◽  
S Boccia ◽  
...  
Keyword(s):  
Head And Neck Cancer ◽  
Dietary Intake ◽  
Head And Neck ◽  
Neck Cancer ◽  
Metabolic Profile ◽  
Minor Allele ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
The One

Abstract Introduction Various single nucleotide polymorphisms (SNPs) have been associated with Head and Neck Cancer (HNC) susceptibility and prognosis. The pathogenesis of HNC is related to alterations in metabolite concentrations. Dietary intake may also influence the metabolic profile. We aimed to evaluate the association between serologic metabolites on the one hand and on the other hand HNC related SNPs and dietary intake. Methods This study included participants from the Erasmus Rucphen Family Study (ERF). We identified the SNPs associated with HNC from the GWAS Catalog, reaching genome-wide significance at P &lt; 5 × 10−8. We performed regression analyses to evaluate the association of SNPs dosage with the metabolites and the association between metabolites and dietary intake. Results The study included 2758 participants, in whom 820 metabolites were analyzed. Four SNPs showed a significant association with circulating metabolites: rs174549 with phosphatidylcholine diacyl (β = 0.45; p-value= 7.17 × 10− 40), rs310518 with lipoprotein IDL sub-fraction, rs1229984 with triglycerides and rs1494961 with propionylcarnitine. The minor variant allele of the 4 SNPs showed increased level of the metabolites in blood. As to the association diet and metabolite concentration, significant associations were found for dairy products with sphingomyelin, fish intake with phosphatidylcholines, cholesterol esters with vegetables and myoinositol with fruits intake. When the results of both analyses were merged, 5 metabolites were found to be associated with dietary variables and rs174549. In the minor allele carriers, phosphatidylcholines increased with consumption of fish and phosphatidylethanolamine increased with consumption of diary products. Conclusions The genetic variants rs174549, which is a determinant of genetic HNC susceptibility, is associated with phosphatidylcholines and phosphatidylethanolamine in the circulation. Key messages In the minor allele carriers of rs174549, phosphatidylcholine diacyl level in circulation increased with consumption of fish. In the minor allele carriers of rs174549, phosphatidylethanolamine level in circulation increased with consumption of diary products.

scholarly journals A Genome-Wide Association Study for Melatonin Secretion

2021 ◽  
Author(s):  
Pi-Hua Liu ◽  
Gwo-Tsann Chuang ◽  
Chia-Ni Hsiung ◽  
Wei-Shun Yang ◽  
Hsiao-Chia Ku ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
P Value ◽  
Melatonin Level ◽  
Nucleotide Polymorphisms ◽  
Melatonin Secretion ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

Abstract SummaryPurpose: Melatonin exerts a wide range of effects among various tissues and organs. However, there is currently no study to investigate the genetic determinants of melatonin secretion. Here, we conducted a genome-wide association study (GWAS) for melatonin secretion using morning urine 6-hydroxymelatonin sulfate-to-creatinine ratio (UMCR). Methods: We initially enrolled 5,000 participants from Taiwan Biobank in this study. After excluding individuals that did not have their urine collected in the morning and those who failed to pass quality control, association of single nucleotide polymorphisms with log-transformed UMCR adjusted for age, sex and principal components of ancestry were analyzed. A second model additionally adjusted for estimated glomerular filtration rate (eGFR). Results: A total of 2,504 participants underwent the genome-wide analysis. Six candidate loci associated with log UMCR (P value ranging from 7.54 x 10-7 to 4.65 x 10-6) encompassing GALNT15, ZFHX3, NKAIN2, MME and NBPF22P were identified. Similar results were yielded with further adjustment for eGFR. Interestingly, the identified genes are associated with central nervous system function and clinical condition such as Alzheimer's disease or sleep disorders.Conclusions: We conducted the first GWAS for melatonin secretion and identified six candidate genetic loci associated with melatonin level. Replication and functional studies are needed in the future.

Abstract 17111: Genetic Influences on Human Plasma Metabolites That Determine Mortality in Heart Failure Patients

Circulation ◽  
2018 ◽  
Vol 138 (Suppl_1) ◽  
Author(s):  
David E Lanfear ◽  
Hongsheng Gui ◽  
Jia Li ◽  
Ruicong She ◽  
Edward Peterson ◽  
...  
Keyword(s):  
Heart Failure ◽  
Strong Association ◽  
Plasma Metabolites ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Association Analyses ◽  
Reduced Ejection Fraction ◽  
Genome Wide ◽  
Plasma Metabolite

Background: Heart failure with reduced ejection fraction (HFrEF) continues to be a global health burden. We recently reported a strong association of plasma metabolite profile (thirteen different metabolites) with survival among patients with HFrEF but the mechanism of this association is unclear. We studied the genetic associations of plasma metabolite to try to illuminate the disease mechanisms at work. Methods: A prospective genetic registry including 1032 HFrEF with genome-wide genotyping and imputation of single nucleotide polymorphisms (SNP; ~7 millions) and targeted metabolomics profiling. Genome-wide (GW) association analyses were performed to investigate the genetic impact of each SNP on the 13 metabolites of interest. Analyses were performed using linear models stratified by race (European Americans [N=516] and African Americans [N=516] and including the top five principal components (PC) for each population to avoid spurious associations due to population stratification. A fixed-effect meta-analysis was then used to combine results from the two populations. Threshold for GW significance was p<5E-8. As a second step, Cox proportional hazard regression models of overall survival were tested for each SNP that met GW significance. Results: We found at least one SNP reaching GW significance for 6 metabolites metabolites (a-KG, C5.Isovaleryl, Fumarate, Leucine, Succinate and X3.HBA). The most significant SNP (rs77836784, an intronic variant within PACRG) was associated with X3.HBA in African American HF patients (Beta estimate=22.82, P-value=7.14E-14). A cross-checking of SNP associations on both metabolites and HF survival identified 13 independent SNPs that may partially explain the contribution of the metabolites on HF mortality (Table 1) and seem to have biologic plausibility including for example a G-protein coupled receptor (GPR68) and protein kinase C (PRKC1). Conclusion: Genetic variants are associated with predictive plasma metabolites and survival. This may be useful to understand the underlying pathways connecting metabolites to HF progression. A complete investigation of genomic and metabolomics determinants including causal mediation and pathway analyses are on-going.

scholarly journals PSX-16 Genome-wide association studies for growth and carcass traits in Russian sheep

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 449-450
Author(s):  
Tatiana Evgenievna Deniskova ◽  
Sergey N Petrov ◽  
Alexander A Sermyagin ◽  
Margaret S Fornara ◽  
Arsen V Dotsev ◽  
...  
Keyword(s):  
Association Studies ◽  
Carcass Traits ◽  
Practical Interest ◽  
Chromosome 7 ◽  
P Value ◽  
Genome Wide Association Studies ◽  
Chromosome 2 ◽  
Sheep Population ◽  
Fast Growing ◽  
Genome Wide

Abstract Breeding fast-growing sheep with good carcass traits is beneficial for lamb producers. However, genomic selection for relevant traits is still lagging in Russian sheep industry. In this regard, detection of the QTLs and candidate genes specific for local sheep is of great scientific and practical interest in Russia. In our research, we aimed to perform GWAS for growth and carcass traits in the QTL-mapping sheep population obtained from crossing slow- and fast-growing breeds. Backcrosses from (Katahdin× Romanov) × Romanov mapping population were genotyped with Ovine Infinium HD SNP BeadChip (Illumina, USA). Quality control in PLINK v.1.9 resulted in 459,868 SNPs which were used for GWAS. Threshold p-value for Bonferroni genome-wide significance was estimated as p = 1.09х10–7. The Manhattan plots were visualized in R package qqman. The measurements included body weight (BW), chest depth (CD), chest width (CW), and width at the iliac tubercle (WT) were recorded at the age of 6, 42 and 180 days. Significant SNPs including oar3_OAR7_44462236 (p = 8.40E-07), oar3_OAR7_44496608 (p = 8.40E-07) and oar3_OAR7_44975375 (p = 8.60E-07) were associated with WT at age of 180 days (13.31±0.23 cm). In addition, genomic regions located on chromosome 7 (44462236 – 44975375) and chromosome 2 (148067154 – 148077728) contained SNPs associated with CD at age of 180 days (21.42±0.39 cm) as well as with WT at age of 180 days. One SNPs (oar3_OAR4_4568047) on chromosome 4 and four SNPs on chromosome 7 (oar3_OAR7_44462236, oar3_OAR7_44496608, oar3_OAR7_44975375, and oar3_OAR7_45012432) were associated with BW at age of 180 days (22.61± 0.89 cm). The genes identified by GWAS were annotated. There were candidates responsible for bone metabolism, prenatal growth, skeletal muscle growth, related to meat quality and involved in carbohydrate and lipid metabolism. The reported study was funded by RFBR, project No. 17-29-08015.

scholarly journals Polymorphism, linkage mapping, and association analysis with carcass traits of four porcine candidate genes selected from gene-expression profiles of Czech Large White and Wild Boar muscles

2014 ◽  
Vol 59 (No. 3) ◽  
pp. 116-127
Author(s):  
P. Chalupová ◽  
V. Dvořáková ◽  
A. Knoll ◽  
A. Stratil ◽  
H. Bartenschlager ◽  
...  
Keyword(s):  
Wild Boar ◽  
Association Analysis ◽  
Skeletal Muscles ◽  
Muscle Development ◽  
Expression Profiles ◽  
Carcass Traits ◽  
Muscle Growth ◽  
Gene Expression Profiles ◽  
P Value ◽  
Large White

Genes that are expressed in skeletal muscles may play a role in prenatal muscle development and postnatal muscle growth and can be considered candidates for economically important traits. Four porcine genes that were differentially expressed in skeletal muscles of Czech Large White and Wild Boar (SORT1, EMP3, IL18, and BTG2) were selected to search for polymorphism, linkage assignment, and association analysis with carcass traits. Through comparative sequencing of portions of the genes numerous polymorphisms were revealed (SORT1 &ndash; 21, EMP3 &ndash; 6, IL18 &ndash; 41, BTG2 &ndash; 9). Linkage analysis in a Meishan &times; Pietrain F<sub>2</sub> pedigree showed the positions of the genes relative to other genes and markers on the respective chromosomes &ndash; SORT1 on SSC4, EMP3 on SSC6, IL18 and BTG2 on SSC9. Preliminary association analysis in pig commercial crosses with selected SNPs showed associations with several carcass traits at nominal P value of &lt; 0.05, which may indicate their involvement in muscle growth and fat deposition. The tested polymorphisms may not be causal for the associations, but they may be in linkage disequilibrium with causative mutations. &nbsp;

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