Improving the efficiency of genomic selection

Marco Scutari, Ian Mackay, David Balding

Research output: Contribution to journalArticle

14 Citations (Scopus)

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 with continuous phenotypic traits 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.

Original languageEnglish
Pages (from-to)517-27
Number of pages11
JournalStatistical Applications in Genetics and Molecular Biology
Volume12
Issue number4
DOIs
Publication statusPrint publication - Aug 2013
Externally publishedYes

Fingerprint

kinship
Linkage Disequilibrium
marker-assisted selection
Genomics
Best Linear Unbiased Prediction
Cost Savings
Feature extraction
Elastic Net
Animals
linkage disequilibrium
Least-Squares Analysis
Selection Model
prediction
Feature Selection
Genotype
Genome
genomics
animal genetics
plant genetics
animal breeding

Keywords

  • Algorithms
  • Animals
  • Breeding/methods
  • Genetic Markers
  • Genomics
  • Hordeum/genetics
  • Linkage Disequilibrium
  • Markov Chains
  • Models, Genetic
  • Oryza/genetics
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Regression Analysis

Cite this

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title = "Improving the efficiency of genomic selection",
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 with continuous phenotypic traits 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.",
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Improving the efficiency of genomic selection. / Scutari, Marco; Mackay, Ian; Balding, David.

In: Statistical Applications in Genetics and Molecular Biology, Vol. 12, No. 4, 08.2013, p. 517-27.

Research output: Contribution to journalArticle

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T1 - Improving the efficiency of genomic selection

AU - Scutari, Marco

AU - Mackay, Ian

AU - Balding, David

PY - 2013/8

Y1 - 2013/8

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AB - 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 with continuous phenotypic traits 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.

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KW - Breeding/methods

KW - Genetic Markers

KW - Genomics

KW - Hordeum/genetics

KW - Linkage Disequilibrium

KW - Markov Chains

KW - Models, Genetic

KW - Oryza/genetics

KW - Phenotype

KW - Polymorphism, Single Nucleotide

KW - Regression Analysis

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