Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance
<p>Abstract</p> <p>The objective of this simulation study was to compare the effect of the number of QTL and distribution of QTL variance on the accuracy of breeding values estimated with genomewide markers (MEBV). Three distinct methods were used to calculate MEBV: a Bayesian Meth...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2010-03-01
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| Series: | Genetics Selection Evolution |
| Online Access: | http://www.gsejournal.org/content/42/1/9 |
| _version_ | 1818062744862064640 |
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| author | van Arendonk Johan AM Calus Mario PL Bastiaansen John WM Coster Albart Bovenhuis Henk |
| author_facet | van Arendonk Johan AM Calus Mario PL Bastiaansen John WM Coster Albart Bovenhuis Henk |
| author_sort | van Arendonk Johan AM |
| collection | DOAJ |
| description | <p>Abstract</p> <p>The objective of this simulation study was to compare the effect of the number of QTL and distribution of QTL variance on the accuracy of breeding values estimated with genomewide markers (MEBV). Three distinct methods were used to calculate MEBV: a Bayesian Method (BM), Least Angle Regression (LARS) and Partial Least Square Regression (PLSR). The accuracy of MEBV calculated with BM and LARS decreased when the number of simulated QTL increased. The accuracy decreased more when QTL had different variance values than when all QTL had an equal variance. The accuracy of MEBV calculated with PLSR was affected neither by the number of QTL nor by the distribution of QTL variance. Additional simulations and analyses showed that these conclusions were not affected by the number of individuals in the training population, by the number of markers and by the heritability of the trait. Results of this study show that the effect of the number of QTL and distribution of QTL variance on the accuracy of MEBV depends on the method that is used to calculate MEBV.</p> |
| first_indexed | 2024-12-10T14:09:05Z |
| format | Article |
| id | doaj.art-d3949177ef0541d895e7f35dd564feba |
| institution | Directory Open Access Journal |
| issn | 0999-193X 1297-9686 |
| language | deu |
| last_indexed | 2024-12-10T14:09:05Z |
| publishDate | 2010-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-d3949177ef0541d895e7f35dd564feba2022-12-22T01:45:33ZdeuBMCGenetics Selection Evolution0999-193X1297-96862010-03-01421910.1186/1297-9686-42-9Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variancevan Arendonk Johan AMCalus Mario PLBastiaansen John WMCoster AlbartBovenhuis Henk<p>Abstract</p> <p>The objective of this simulation study was to compare the effect of the number of QTL and distribution of QTL variance on the accuracy of breeding values estimated with genomewide markers (MEBV). Three distinct methods were used to calculate MEBV: a Bayesian Method (BM), Least Angle Regression (LARS) and Partial Least Square Regression (PLSR). The accuracy of MEBV calculated with BM and LARS decreased when the number of simulated QTL increased. The accuracy decreased more when QTL had different variance values than when all QTL had an equal variance. The accuracy of MEBV calculated with PLSR was affected neither by the number of QTL nor by the distribution of QTL variance. Additional simulations and analyses showed that these conclusions were not affected by the number of individuals in the training population, by the number of markers and by the heritability of the trait. Results of this study show that the effect of the number of QTL and distribution of QTL variance on the accuracy of MEBV depends on the method that is used to calculate MEBV.</p>http://www.gsejournal.org/content/42/1/9 |
| spellingShingle | van Arendonk Johan AM Calus Mario PL Bastiaansen John WM Coster Albart Bovenhuis Henk Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance Genetics Selection Evolution |
| title | Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance |
| title_full | Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance |
| title_fullStr | Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance |
| title_full_unstemmed | Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance |
| title_short | Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance |
| title_sort | sensitivity of methods for estimating breeding values using genetic markers to the number of qtl and distribution of qtl variance |
| url | http://www.gsejournal.org/content/42/1/9 |
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