Improving the efficiency of genomic selection
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Publication:2344249
DOI10.1515/SAGMB-2013-0002zbMATH Open1311.92126arXiv1301.2093OpenAlexW2963974687WikidataQ43595731 ScholiaQ43595731MaRDI QIDQ2344249FDOQ2344249
Authors: Marco Scutari, Ian Mackay, David Joseph Balding 
Publication date: 13 May 2015
Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)
Abstract: We investigate two approaches to increase the efficiency of phenotypic prediction from genome-wide markers, which is a key step for genomic selection (GS) in plant and animal breeding. The first approach is feature selection based on Markov blankets, which provide a theoretically-sound framework for identifying non-informative markers. Fitting GS models using only the informative markers results in simpler models, which may allow cost savings from reduced genotyping. We show that this is accompanied by no loss, and possibly a small gain, in predictive power for four GS models: partial least squares (PLS), ridge regression, LASSO and elastic net. The second approach is the choice of kinship coefficients for genomic best linear unbiased prediction (GBLUP). We compare kinships based on different combinations of centring and scaling of marker genotypes, and a newly proposed kinship measure that adjusts for linkage disequilibrium (LD). We illustrate the use of both approaches and examine their performances using three real-world data sets from plant and animal genetics. We find that elastic net with feature selection and GBLUP using LD-adjusted kinships performed similarly well, and were the best-performing methods in our study.
Full work available at URL: https://arxiv.org/abs/1301.2093
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Cited In (9)
- Accuracy and sensitivity of different Bayesian methods for genomic prediction using simulation and real data
- Kernel methods and haplotypes used in selection of sparse DNA markers for protein yield in dairy cattle
- A general framework for marker-assisted selection
- Data Rotation Improves Genomotyping Efficiency
- Modeling correlated marker effects in genome-wide prediction via Gaussian concentration graph models
- An approximate Bayesian significance test for genomic evaluations
- The study of genomic selection methods with environmental effects
- Genomic selection method considering gene-to-gene interactions
- On the accuracy in high-dimensional linear models and its application to genomic selection
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