How to perform meaningful estimates of genetic effects

JM Alvarez-Castro, A Le Rouzic, Ö Carlborg - PLoS genetics, 2008 - journals.plos.org
Although the genotype-phenotype map plays a central role both in Quantitative and
Evolutionary Genetics, the formalization of a completely general and satisfactory model of …

Genomic prediction using individual-level data and summary statistics from multiple populations

J Vandenplas, MPL Calus, G Gorjanc - Genetics, 2018 - academic.oup.com
This study presents a method for genomic prediction that uses individual-level data and
summary statistics from multiple populations. Genome-wide markers are nowadays widely …

Modeling additive and non-additive effects in a hybrid population using genome-wide genotyping: prediction accuracy implications

JM Bouvet, G Makouanzi, D Cros, PH Vigneron - Heredity, 2016 - nature.com
Hybrids are broadly used in plant breeding and accurate estimation of variance components
is crucial for optimizing genetic gain. Genome-wide information may be used to explore …

Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits

L Crawford, P Zeng, S Mukherjee, X Zhou - PLoS genetics, 2017 - journals.plos.org
Epistasis, commonly defined as the interaction between multiple genes, is an important
genetic component underlying phenotypic variation. Many statistical methods have been …

Genotype imputation for the prediction of genomic breeding values in non-genotyped and low-density genotyped individuals

MA Cleveland, JM Hickey, BP Kinghorn - BMC proceedings, 2011 - Springer
Background There is wide interest in calculating genomic breeding values (GEBVs) in
livestock using dense, genome-wide SNP data. The general framework for genomic …

Using machine learning and partial dependence to evaluate robustness of best linear unbiased prediction (BLUP) for phenotypic values

P Bhandari, TG Lee - Journal of Applied Genetics, 2024 - Springer
Best linear unbiased prediction (BLUP) is widely used in plant research to address
experimental variation. For phenotypic values, BLUP accuracy is largely dependent on …

Understanding the potential bias of variance components estimators when using genomic models

BCD Cuyabano, AC Sørensen, P Sørensen - Genetics Selection Evolution, 2018 - Springer
Background Genomic models that link phenotypes to dense genotype information are
increasingly being used for infering variance parameters in genetics studies. The variance …

Genomic value prediction for quantitative traits under the epistatic model

Z Hu, Y Li, X Song, Y Han, X Cai, S Xu, W Li - BMC genetics, 2011 - Springer
Background Most quantitative traits are controlled by multiple quantitative trait loci (QTL).
The contribution of each locus may be negligible but the collective contribution of all loci is …

[PDF][PDF] Understanding genomic evaluations from various evaluation methods and GMACE

R Mrode, M Coffey, DP Berry - Interbull Bulletin, 2010 - journal.interbull.org
Genomic predictions (GEBVs) are often validated by predicting later deregressed
conventional evaluations or daughter yield deviations (dEBVs or DYDs) from earlier GEBVs …

An alternative covariance estimator to investigate genetic heterogeneity in populations

N Heslot, JL Jannink - Genetics Selection Evolution, 2015 - Springer
Background For genomic prediction and genome-wide association studies (GWAS) using
mixed models, covariance between individuals is estimated using molecular markers. Based …