Ridge regression and other kernels for genomic selection with R package rrBLUP

JB Endelman - The plant genome, 2011 - Wiley Online Library
Many important traits in plant breeding are polygenic and therefore recalcitrant to traditional
marker‐assisted selection. Genomic selection addresses this complexity by including all …

Evaluation of RR‐BLUP genomic selection models that incorporate peak genome‐wide association study signals in maize and sorghum

B Rice, AE Lipka - The Plant Genome, 2019 - Wiley Online Library
Certain agronomic crop traits are complex and thus governed by many small‐effect loci.
Statistical models typically used in a genome‐wide association study (GWAS) and genomic …

Genomic‐enabled prediction based on molecular markers and pedigree using the Bayesian linear regression package in R

P Pérez, G de Los Campos, J Crossa… - The plant …, 2010 - Wiley Online Library
The availability of dense molecular markers has made possible the use of genomic selection
in plant and animal breeding. However, models for genomic selection pose several …

Genomic selection using multiple populations

T Schulz‐Streeck, JO Ogutu, Z Karaman… - Crop …, 2012 - Wiley Online Library
Using different populations in genomic selection raises the possibility of marker effects
varying across populations. However, common models for genomic selection only account …

Genomic selection using regularized linear regression models: ridge regression, lasso, elastic net and their extensions

JO Ogutu, T Schulz-Streeck, HP Piepho - BMC proceedings, 2012 - Springer
Background Genomic selection (GS) is emerging as an efficient and cost-effective method
for estimating breeding values using molecular markers distributed over the entire genome …

BWGS: AR package for genomic selection and its application to a wheat breeding programme

G Charmet, LG Tran, J Auzanneau, R Rincent… - PloS one, 2020 - journals.plos.org
We developed an integrated R library called BWGS to enable easy computation of Genomic
Estimates of Breeding values (GEBV) for genomic selection. BWGS, for BreedWheat …

Comparison between linear and non-parametric regression models for genome-enabled prediction in wheat

P Pérez-Rodríguez, D Gianola… - G3: Genes …, 2012 - academic.oup.com
In genome-enabled prediction, parametric, semi-parametric, and non-parametric regression
models have been used. This study assessed the predictive ability of linear and non-linear …

Ridge regression and extensions for genomewide selection in maize

HP Piepho - Crop Science, 2009 - Wiley Online Library
This paper reviews properties of ridge regression for genomewide (genomic) selection and
establishes close relationships with other methods to model genetic correlation among …

Implementation of Genomic Prediction in Lolium perenne (L.) Breeding Populations

NF Grinberg, A Lovatt, M Hegarty, A Lovatt… - Frontiers in plant …, 2016 - frontiersin.org
Perennial ryegrass (Lolium perenne L.) is one of the most widely grown forage grasses in
temperate agriculture. In order to maintain and increase its usage as forage in livestock …

A novel generalized ridge regression method for quantitative genetics

X Shen, M Alam, F Fikse, L Rönnegård - Genetics, 2013 - academic.oup.com
As the molecular marker density grows, there is a strong need in both genome-wide
association studies and genomic selection to fit models with a large number of parameters …