Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical …

J Spindel, H Begum, D Akdemir, P Virk, B Collard… - PLoS …, 2015 - journals.plos.org
trait were varied to determine their effect on prediction accuracy. For all three traits, genomic
prediction models outperformed predictionPrediction accuracies ranged from 0.31 and 0.34 …

Multi-trait, multi-environment genomic prediction of durum wheat with genomic best linear unbiased predictor and deep learning methods

OA Montesinos-López, A Montesinos-López… - Frontiers in Plant …, 2019 - frontiersin.org
… approach for genomic prediction, but also that the deep learning method is a practical
approach for predicting univariate and multivariate traits in the context of genomic selection. …

Predictive performance of genomic selection methods for carcass traits in Hanwoo beef cattle: impacts of the genetic architecture

H Mehrban, DH Lee, MH Moradi, C IlCho… - Genetics Selection …, 2017 - Springer
… The aim of our study was to evaluate methods for genomic prediction in Hanwoo cattle. …
architecture of traits, were used to compare the accuracy of genomic predictions for the traits BT, …

Parametric and nonparametric statistical methods for genomic selection of traits with additive and epistatic genetic architectures

R Howard, AL Carriquiry… - G3: Genes, Genomes …, 2014 - academic.oup.com
… Parametric and nonparametric methods have been developed for purposes of predicting
are unable to predict phenotypes of traits with known epistatic genetic architectures. Herein, we …

Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

SM Edwards, IF Sørensen, P Sarup, TFC Mackay… - Genetics, 2016 - academic.oup.com
… of genomic prediction models. We developed a genomic feature best linear unbiased
prediction (GFBLUP) model that implements this strategy and applied it to three quantitative traits (…

[HTML][HTML] Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

MF Scott, N Fradgley, AR Bentley, T Brabbs, F Corke… - Genome Biology, 2021 - Springer
… We trained genomic prediction models using three shrinkage methods: ridge regression (RR),
least absolute shrinkage and selection operator (LASSO), and elastic nets (EN), using 50 …

Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

IM MacLeod, PJ Bowman, CJ Vander Jagt… - BMC genomics, 2016 - Springer
… LD to improve the precision of QTL (quantitative trait loci) discovery and prediction. We
compare the accuracy of genomic prediction in validation individuals that are not closely related …

[HTML][HTML] Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster

U Ober, JF Ayroles, EA Stone, S Richards, D Zhu… - PLoS …, 2012 - journals.plos.org
… , but not using complete genome sequences. Here, we report genomic prediction for starvation
stress … We constructed a genomic relationship matrix from the SNP data and used it in a …

Genetic architecture of plant stress resistance: multi‐trait genome‐wide association mapping

MPM Thoen, NH Davila Olivas, KJ Kloth… - New …, 2017 - Wiley Online Library
… Finally, within each experiment, the traits were replaced by the first principal … all traits in this
experiment; in all other cases, the original traits were retained. An overview of final traits and …

Genomic prediction including SNP-specific variance predictors

EF Mouresan, M Selle… - G3: Genes, Genomes …, 2019 - academic.oup.com
… In order to investigate the performance of the alternative models for traits with different
genetic architectures we simulated a trait controlled by an increasing number of QTL with each …