scholarly journals Genome-wide Association Studies Identify Quantitative Trait Loci Affecting Cattle Temperament

2020 ◽  
Author(s):  
Jiafei Shen ◽  
Qiuming Chen ◽  
Fengwei Zhang ◽  
Quratulain Hanif ◽  
Bizhi Huang ◽  
...  
Keyword(s):  
Open Field ◽  
Association Studies ◽  
Productive Efficiency ◽  
Genome Wide Association ◽  
Whole Genome Sequence ◽  
Receptor Interaction ◽  
Genome Wide Association Studies ◽  
Autosomal Snps ◽  
Novel Object ◽  
Genome Wide

Abstract BackgroundCattle temperament is one of the most interesting traits owing to its correlation to productive efficiency, labor safety and animal welfare, but its genetic basis is not clearly understood.ResultsHere, we performed genome-wide association studies for a series of temperament traits, assessed in an open field and novel object test, using autosomal SNPs derived from the whole-genome sequence. We identified 37 and 29 genome-wide significant loci in an open field and novel object test, respectively. Gene set analysis implicated the neuroactive ligand-receptor interaction pathway. Analysis in tissue specific expressions showed enrichment in the brain. While some candidate genes were involved in psychiatric and neurodegenerative diseases in humans. The first principal component explained the largest variance in the data of open field and novel object test, and the most significant loci were assigned to SORCS3 and SESTD1, respectively.ConclusionsOur findings will facilitate cattle breeding for sound temperament by pyramiding favorable alleles to further improve the cattle production in the future.

scholarly journals Imputation to whole-genome sequence using multiple pig populations and its use in genome-wide association studies

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Sanne van den Berg ◽  
Jérémie Vandenplas ◽  
Fred A. van Eeuwijk ◽  
Aniek C. Bouwman ◽  
Marcos S. Lopes ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Association Studies ◽  
Genome Wide Association ◽  
Whole Genome Sequence ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Wide

A genome-wide association study of colorectal cancer in Mexican mestizos suggest novel common tumor-risk variants

2020 ◽  
Author(s):  
AUGUSTO Rojas-Martinez ◽  
Valentina Colistro ◽  
Raquel Cruz ◽  
Clara Ruiz ◽  
Inés Quintela ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Latin American ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Statistical Significance ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Autosomal Snps ◽  
Genome Wide ◽  
A Genome

Abstract Background: Genome-wide association studies (GWAS) for colorectal cancer (CRC) have detected high-risk genetic variants associated with CRC in several ethnic groups, but Latin American communities are still underrepresented. The aim was to identify variants related to CRC in an admixed Latin American population. Methods: The study was performed in 831 cases and 881 controls from Mexico, who were genotyped for 1,006,703 autosomal SNPs. Logistic regression was carried out including covariants, such as sex, age and genetic ancestry. Lastly, we performed a sequence-kernel association test (SKAT) to consider the joint effect of several SNPs lying in genes.Results: Eight chromosomal regions reached genome-wide significance level ( p < 5×10 -8 ): 1p36.22, 1p31.1, 1q42.13, 6p22, 7p14.1, 12q24.32, 16q12.2 and 21q22.2 and 63 variants reached borderline statistical significance ( p < 1×10 − 6 ). SKAT analysis detected 13 loci associated with CRC, none of them previously associated with CRC. Conclusions: We found 8 SNPs and 13 loci associated with CRC. These signals may contribute to enrich the panoply of genes involved with CRC. Further analyses remain to be done to validate the associations in other Latin American populations. This study highlights the importance of conducting GWAS in poorly explored admixed populations.

scholarly journals Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 541
Author(s):  
Long Chen ◽  
Jennie E. Pryce ◽  
Ben J. Hayes ◽  
Hans D. Daetwyler
Keyword(s):  
Dairy Cattle ◽  
Genomic Prediction ◽  
Complex Traits ◽  
Prediction Accuracy ◽  
Association Studies ◽  
Genome Wide Association ◽  
Whole Genome Sequence ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Wide

Structural variations (SVs) are large DNA segments of deletions, duplications, copy number variations, inversions and translocations in a re-sequenced genome compared to a reference genome. They have been found to be associated with several complex traits in dairy cattle and could potentially help to improve genomic prediction accuracy of dairy traits. Imputation of SVs was performed in individuals genotyped with single-nucleotide polymorphism (SNP) panels without the expense of sequencing them. In this study, we generated 24,908 high-quality SVs in a total of 478 whole-genome sequenced Holstein and Jersey cattle. We imputed 4489 SVs with R2 > 0.5 into 35,568 Holstein and Jersey dairy cattle with 578,999 SNPs with two pipelines, FImpute and Eagle2.3-Minimac3. Genome-wide association studies for production, fertility and overall type with these 4489 SVs revealed four significant SVs, of which two were highly linked to significant SNP. We also estimated the variance components for SNP and SV models for these traits using genomic best linear unbiased prediction (GBLUP). Furthermore, we assessed the effect on genomic prediction accuracy of adding SVs to GBLUP models. The estimated percentage of genetic variance captured by SVs for production traits was up to 4.57% for milk yield in bulls and 3.53% for protein yield in cows. Finally, no consistent increase in genomic prediction accuracy was observed when including SVs in GBLUP.

scholarly journals Sex-specific genome-wide association study in glioma identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21

2017 ◽  
Author(s):  
Quinn T. Ostrom ◽  
Ben Kinnersley ◽  
Margaret R. Wrensch ◽  
Jeanette E. Eckel-Passow ◽  
Georgina Armstrong ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Sex Chromosome ◽  
Association Studies ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Autosomal Snps ◽  
Logistic Regression Models ◽  
Genome Wide ◽  
Using Data

AbstractIncidence of glioma is approximately 50% higher in males. Previous analyses have examined exposures related to sex hormones in women as potential protective factors for these tumors, with inconsistent results. Previous glioma genome-wide association studies (GWAS) have not stratified by sex. Potential sex-specific genetic effects were assessed in autosomal SNPs and sex chromosome variants for all glioma, GBM and non-GBM patients using data from four previous glioma GWAS. Datasets were analyzed using sex-stratified logistic regression models and combined using meta-analysis. There were 4,831 male cases, 5,216 male controls, 3,206 female cases and 5,470 female controls. A significant association was detected at rs11979158 (7p11.2) in males only. Association at rs55705857 (8q24.21) was stronger in females than in males. A large region on 3p21.31 was identified with significant association in females only. The identified differences in effect of risk variants do not fully explain the observed incidence difference in glioma by sex.

Genotype Imputation from Large Reference Panels

2018 ◽  
Vol 19 (1) ◽  
pp. 73-96 ◽  
Author(s):  
Sayantan Das ◽  
Gonçalo R. Abecasis ◽  
Brian L. Browning
Keyword(s):  
Statistical Power ◽  
Sequence Data ◽  
Single Nucleotide Polymorphism Array ◽  
Association Studies ◽  
Genotype Imputation ◽  
Genome Wide Association ◽  
Whole Genome Sequence ◽  
Computational Techniques ◽  
Genome Wide Association Studies ◽  
Genome Wide

Genotype imputation has become a standard tool in genome-wide association studies because it enables researchers to inexpensively approximate whole-genome sequence data from genome-wide single-nucleotide polymorphism array data. Genotype imputation increases statistical power, facilitates fine mapping of causal variants, and plays a key role in meta-analyses of genome-wide association studies. Only variants that were previously observed in a reference panel of sequenced individuals can be imputed. However, the rapid increase in the number of deeply sequenced individuals will soon make it possible to assemble enormous reference panels that greatly increase the number of imputable variants. In this review, we present an overview of genotype imputation and describe the computational techniques that make it possible to impute genotypes from reference panels with millions of individuals.

scholarly journals Novel Y Chromosome Retrocopies in Canids Revealed through a Genome-Wide Association Study for Sex

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 320 ◽  
Author(s):  
Kate L. Tsai ◽  
Jacquelyn M. Evans ◽  
Rooksana E. Noorai ◽  
Alison N. Starr-Moss ◽  
Leigh Anne Clark
Keyword(s):  
Y Chromosome ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Reference Sequence ◽  
Genome Wide Association Studies ◽  
Autosomal Snps ◽  
Genome Wide ◽  
A Genome

The lack of an annotated reference sequence for the canine Y chromosome has limited evolutionary studies, as well as our understanding of the role of Y-linked sequences in phenotypes with a sex bias. In genome-wide association studies (GWASs), we observed spurious associations with autosomal SNPs when sex was unbalanced in case-control cohorts and hypothesized that a subset of SNPs mapped to autosomes are in fact sex-linked. Using the Illumina 230K CanineHD array in a GWAS for sex, we identified SNPs that amplify in both sexes but possess significant allele frequency differences between males and females. We found 48 SNPs mapping to 14 regions of eight autosomes and the X chromosome that are Y-linked, appearing heterozygous in males and monomorphic in females. Within these 14 regions are eight genes: three autosomal and five X-linked. We investigated the autosomal genes (MITF, PPP2CB, and WNK1) and determined that the SNPs are diverged nucleotides in retrocopies that have transposed to the Y chromosome. MITFY and WNK1Y are expressed and appeared recently in the Canidae lineage, whereas PPP2CBY represents a much older insertion with no evidence of expression in the dog. This work reveals novel canid Y chromosome sequences and provides evidence for gene transposition to the Y from autosomes and the X.

Sign in / Sign up

Export Citation Format

Share Document