A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species.
Abstract: With dense genotyping, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different methods using real data. We compared three methods that correct for relatedness either implicitly or explicitly: linkage and linkage disequilibrium haplotype-based analysis (LDLA), efficient mixed-model association (EMMA) analysis, and Bayesian whole-genome regression (BayesC). We analyzed one chromosome in each of five datasets (dairy cattle, beef cattle, sheep, horses, and pigs) using real genotypes based on dense single nucleotide polymorphisms and phenotypes. The P values corrected for multiple testing or Bayes factors greater than 150 were considered to be significant. To complete the real data study, we also simulated quantitative trait loci (QTL) for the same datasets based on the real genotypes. Several scenarios were chosen, with different QTL effects and linkage disequilibrium patterns. A pseudo-null statistical distribution was chosen to make the significance thresholds comparable across methods. Results: For the real data, the three methods generally agreed within 1 or 2 cM for the locations of QTL regions and disagreed when no signals were significant (e.g. in pigs). For certain datasets, LDLA had more significant signals than EMMA or BayesC, but they were concentrated around the same peaks. Therefore, the three methods detected approximately the same number of QTL regions. For the simulated data, LDLA was slightly less powerful and accurate than either EMMA or BayesC but this depended strongly on how thresholds were set in the simulations. Conclusions: All three methods performed similarly for real and simulated data. No method was clearly superior across all datasets or for any particular dataset. For computational efficiency and ease of interpretation, EMMA is recommended, but using more than one method is suggested.
Publication Date: 2015-02-12 PubMed ID: 25885597PubMed Central: PMC4324410DOI: 10.1186/s12711-015-0087-7Google Scholar: Lookup
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- Comparative Study
- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The research paper explores the effectiveness of three methods of detecting quantitative trait loci (QTL) in livestock populations using dense genotyping. It suggests that no method is distinctly superior and proposes using multiple methods to enhance computational efficiency and facilitate analysis.
Comparison of QTL Detection Methods
- The study compared three methods that correct for relatedness in livestock populations: Linkage and Linkage Disequilibrium Haplotype-based Analysis (LDLA), Efficient Mixed-Model Association (EMMA) analysis, and Bayesian Whole-Genome Regression (BayesC).
- The researchers evaluated the effectiveness of these methodologies by applying them to one chromosome in each of five datasets from different livestock (dairy cattle, beef cattle, sheep, horses, and pigs).
Data Analysis
- Both genotypes and phenotypes were based on dense single nucleotide polymorphisms (SNPs), which are common types of genetic variations among individuals.
- Those with P values corrected for multiple testing or Bayes factors greater than 150 were deemed significant.
Use of Simulated Data
- Beyond real data, the researchers simulated quantitative trait loci (QTL) for the same datasets, relying upon a pseudo-null statistical distribution to make comparisons across methods.
- Various scenarios were chosen, spanning different QTL effects and linkage disequilibrium patterns.
Research Findings
- For real data, the three methods generally agreed within 1 or 2 cM for the locations of QTL regions, however, they differed when no signals were significant, as with pigs.
- Notably, although LDLA sometimes had more signals, these signals predominantly clustered around the same peaks as the other two methods.
- In simulated data, LDLA was found to be slightly less accurate and powerful than EMMA or BayesC, substantially influenced by how thresholds were established in the simulations.
- Overall, all three methods performed similarly on both real and simulated data, with no significant advantage for any on any of the datasets.
Suggestions and Conclusions
- The researchers recommend using EMMA for computational efficiency and ease of interpretation, but advise employing multiple methods as a best practice.
Cite This Article
APA
Legarra A, Croiseau P, Sanchez MP, Teyssèdre S, Sallé G, Allais S, Fritz S, Moreno CR, Ricard A, Elsen JM.
(2015).
A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species.
Genet Sel Evol, 47(1), 6.
https://doi.org/10.1186/s12711-015-0087-7 Publication
Researcher Affiliations
- INRA, UMR 1388 GenPhySE, BP52627, 31326, Castanet Tolosan, France. andres.legarra@toulouse.inra.fr.
- INRA, UMR 1313 GABI, Domaine de Vilvert, 78352, Jouy-en-Josas, France. pascal.croiseau@jouy.inra.fr.
- INRA, UMR 1313 GABI, Domaine de Vilvert, 78352, Jouy-en-Josas, France. marie-pierre.sanchez@jouy.inra.fr.
- INRA, UMR 1388 GenPhySE, BP52627, 31326, Castanet Tolosan, France. steyssedre@ragt.fr.
- Current address: RAGT-R2n, Le bourg, 12510, Druelle, France. steyssedre@ragt.fr.
- INRA, UMR1282 Infectiologie et Santé Publique, F-37380, Nouzilly, France. guillaume.salle@tours.inra.fr.
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, 37000, Tours, France. guillaume.salle@tours.inra.fr.
- Agrocampus Ouest, UMR1348 Pegase, F-35000, Rennes, France. sophie.allais@agrocampus-ouest.fr.
- INRA, UMR1348 Pegase, F-35590, Saint-Gilles, France. sophie.allais@agrocampus-ouest.fr.
- Université Européenne de Bretagne, Rennes, France. sophie.allais@agrocampus-ouest.fr.
- UNCEIA, Genetics Team, 75595, Paris, France. sebastien.fritz@jouy.inra.fr.
- INRA, UMR 1388 GenPhySE, BP52627, 31326, Castanet Tolosan, France. carole.moreno@toulouse.inra.fr.
- INRA, UMR 1313 GABI, Domaine de Vilvert, 78352, Jouy-en-Josas, France. anne.ricard@toulouse.inra.fr.
- Recherche et Innovation, IFCE, 61310 Exmes, Paris, France. anne.ricard@toulouse.inra.fr.
- INRA, UMR 1388 GenPhySE, BP52627, 31326, Castanet Tolosan, France. jean-michel.elsen@toulouse.inra.fr.
MeSH Terms
- Animals
- Bayes Theorem
- Cattle / genetics
- Chromosome Mapping / methods
- Genetic Linkage
- Genetic Markers
- Genome
- Genotype
- Haplotypes / genetics
- Horses / genetics
- Linkage Disequilibrium
- Livestock / genetics
- Models, Genetic
- Phenotype
- Polymorphism, Single Nucleotide
- Quantitative Trait Loci / genetics
- Sheep / genetics
- Sus scrofa / genetics
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