Single‐marker and haplotype‐based genome‐wide association studies for the number of teats in two heavy pig breeds

Use of the Multivariate Discriminant Analysis for Genome-Wide Association Studies in Cattle

Animals ◽

10.3390/ani10081300 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1300 ◽

Cited By ~ 1

Author(s):

Elisabetta Manca ◽

Alberto Cesarani ◽

Giustino Gaspa ◽

Silvia Sorbolini ◽

Nicolò P.P. Macciotta ◽

...

Keyword(s):

Discriminant Analysis ◽

Association Studies ◽

Real Data ◽

Genome Wide Association ◽

Stepwise Discriminant Analysis ◽

Genome Wide Association Studies ◽

Multivariate Method ◽

Genome Wide ◽

Single Marker ◽

Multivariate Gwas

Genome-wide association studies (GWAS) are traditionally carried out by using the single marker regression model that, if a small number of individuals is involved, often lead to very few associations. The Bayesian methods, such as BayesR, have obtained encouraging results when they are applied to the GWAS. However, these approaches, require that an a priori posterior inclusion probability threshold be fixed, thus arbitrarily affecting the obtained associations. To partially overcome these problems, a multivariate statistical algorithm was proposed. The basic idea was that animals with different phenotypic values of a specific trait share different allelic combinations for genes involved in its determinism. Three multivariate techniques were used to highlight the differences between the individuals assembled in high and low phenotype groups: the canonical discriminant analysis, the discriminant analysis and the stepwise discriminant analysis. The multivariate method was tested both on simulated and on real data. The results from the simulation study highlighted that the multivariate GWAS detected a greater number of true associated single nucleotide polymorphisms (SNPs) and Quantitative trait loci (QTLs) than the single marker model and the Bayesian approach. For example, with 3000 animals, the traditional GWAS highlighted only 29 significantly associated markers and 13 QTLs, whereas the multivariate method found 127 associated SNPs and 65 QTLs. The gap between the two approaches slowly decreased as the number of animals increased. The Bayesian method gave worse results than the other two. On average, with the real data, the multivariate GWAS found 108 associated markers for each trait under study and among them, around 63% SNPs were also found in the single marker approach. Among the top 118 associated markers, 76 SNPs harbored putative candidate genes.

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Genome-wide association studies in elite varieties of German winter barley using single-marker and haplotype-based methods

Plant Breeding ◽

10.1111/pbr.12237 ◽

2015 ◽

Vol 134 (1) ◽

pp. 28-39 ◽

Cited By ~ 21

Author(s):

Inka Gawenda ◽

Patrick Thorwarth ◽

Torsten Günther ◽

Frank Ordon ◽

Karl J. Schmid

Keyword(s):

Association Studies ◽

Winter Barley ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Single Marker

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Multivariate genome-wide association studies on tenderness of Berkshire and Duroc pig breeds

Genes & Genomics ◽

10.1007/s13258-018-0672-6 ◽

2018 ◽

Vol 40 (7) ◽

pp. 701-705 ◽

Cited By ~ 1

Author(s):

Dongsung Jang ◽

Joon Yoon ◽

Mengistie Taye ◽

Wonseok Lee ◽

Taehyung Kwon ◽

...

Keyword(s):

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Pig Breeds ◽

Genome Wide

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Joint Genotype- and Ancestry-based Genome-wide Association Studies in Admixed Populations

10.1101/062554 ◽

2016 ◽

Cited By ~ 2

Author(s):

Piotr Szulc ◽

Malgorzata Bogdan ◽

Florian Frommlet ◽

Hua Tang

Keyword(s):

Linkage Disequilibrium ◽

Complex Traits ◽

Association Studies ◽

Real Data ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Single Marker Analysis ◽

Marker Analysis ◽

Genome Wide ◽

Single Marker

AbstractIn Genome-Wide Association Studies (GWAS) genetic loci that influence complex traits are localized by inspecting associations between genotypes of genetic markers and the values of the trait of interest. On the other hand Admixture Mapping, which is performed in case of populations consisting of a recent mix of two ancestral groups, relies on the ancestry information at each locus (locus-specific ancestry).Recently it has been proposed to jointly model genotype and locus-specific ancestry within the framework of single marker tests. Here we extend this approach for population-based GWAS in the direction of multi marker models. A modified version of the Bayesian Information Criterion is developed for building a multi-locus model, which accounts for the differential correlation structure due to linkage disequilibrium and admixture linkage disequilibrium. Simulation studies and a real data example illustrate the advantages of this new approach compared to single-marker analysis and modern model selection strategies based on separately analyzing genotype and ancestry data, as well as to single-marker analysis combining genotypic and ancestry information. Depending on the signal strength our procedure automatically chooses whether genotypic or locus-specific ancestry markers are added to the model. This results in a good compromise between the power to detect causal mutations and the precision of their localization. The proposed method has been implemented in R and is available at http://www.math.uni.wroc.pl/~mbogdan/admixtures/.

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EigenGWAS: finding loci under selection through genome-wide association studies of eigenvectors in structured populations

10.1101/023457 ◽

2015 ◽

Cited By ~ 1

Author(s):

Guo-Bo Chen ◽

Sang Hong Lee ◽

Zhi-Xiang Zhu ◽

Beben Benyamin ◽

Matthew R Robinson

Keyword(s):

Association Studies ◽

Structured Populations ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Statistical Framework ◽

Snp Data ◽

Genome Wide ◽

Single Marker ◽

Marker Regression ◽

Value Decomposition

We apply the statistical framework for genome-wide association studies (GWAS) to eigenvector decomposition (EigenGWAS), which is commonly used in population genetics to characterise the structure of genetic data. We show that loci under selection can be detected in a structured population by using eigenvectors as phenotypes in a single-marker GWAS. We find LCT to be under selection between HapMap CEU-TSI cohorts, a finding that was replicated across European countries in the POPRES samples. HERC2 was also found to be differentiated between both the CEU-TSI cohort and among POPRES samples, reflecting the likely anthropological differences in skin and hair colour between northern and southern European populations. We show that when determining the effect of a SNP on an eigenvector, three methods of single-marker regression of eigenvectors, best linear unbiased prediction of eigenvectors, and singular value decomposition of SNP data are equivalent to each other. We also demonstrate that estimated SNP effects on eigenvectors from a reference panel can be used to predict eigenvectors (the projected eigenvectors) in a target sample with high accuracy, particularly for the primary eigenvectors. Under this GWAS framework, ancestry informative markers and loci under selection can be identified, and population structure can be captured and easily interpreted. We have developed freely available software to facilitate the application of the methods (https://github.com/gc5k/GEAR/wiki/EigenGWAS).

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Analysis of Hematological Traits in Polled Yak by Genome-Wide Association Studies Using Individual SNPs and Haplotypes

Genes ◽

10.3390/genes10060463 ◽

2019 ◽

Vol 10 (6) ◽

pp. 463 ◽

Cited By ~ 4

Author(s):

Xiaoming Ma ◽

Congjun Jia ◽

Donghai Fu ◽

Min Chu ◽

Xuezhi Ding ◽

...

Keyword(s):

Association Studies ◽

Significant Snps ◽

Domestic Animal ◽

Genome Wide Association ◽

Economic Losses ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Individual Snps ◽

Causal Genes ◽

Single Marker

Yak (Bos grunniens) is an important domestic animal living in high-altitude plateaus. Due to inadequate disease prevention, each year, the yak industry suffers significant economic losses. The identification of causal genes that affect blood- and immunity-related cells could provide preliminary reference guidelines for the prevention of diseases in the population of yaks. The genome-wide association studies (GWASs) utilizing a single-marker or haplotype method were employed to analyze 15 hematological traits in the genome of 315 unrelated yaks. Single-marker GWASs identified a total of 43 significant SNPs, including 35 suggestive and eight genome-wide significant SNPs, associated with nine traits. Haplotype analysis detected nine significant haplotype blocks, including two genome-wide and seven suggestive blocks, associated with seven traits. The study provides data on the genetic variability of hematological traits in the yak. Five essential genes (GPLD1, EDNRA, APOB, HIST1H1E, and HIST1H2BI) were identified, which affect the HCT, HGB, RBC, PDW, PLT, and RDWSD traits and can serve as candidate genes for regulating hematological traits. The results provide a valuable reference to be used in the analysis of blood properties and immune diseases in the yak.

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