Epistasis and covariance: how gene interaction translates into genomic relationship

JWR Martini, V Wimmer, M Erbe, H Simianer - Theoretical and Applied …, 2016 - Springer
Key message Models based on additive marker effects and on epistatic interactions can be
translated into genomic relationship models. This equivalence allows to perform predictions …

Genome-Wide Association Studies with a Genomic Relationship Matrix: A Case Study with Wheat and Arabidopsis

D Gianola, MI Fariello, H Naya… - G3: Genes, Genomes …, 2016 - academic.oup.com
Standard genome-wide association studies (GWAS) scan for relationships between each of
p molecular markers and a continuously distributed target trait. Typically, a marker-based …

[HTML][HTML] On the approximation of interaction effect models by Hadamard powers of the additive genomic relationship

JWR Martini, FH Toledo, J Crossa - Theoretical population biology, 2020 - Elsevier
Whole genome epistasis models with interactions between different loci can be
approximated by genomic relationship models based on Hadamard powers of the additive …

[HTML][HTML] Locally epistatic models for genome-wide prediction and association by importance sampling

D Akdemir, JL Jannink, J Isidro-Sánchez - Genetics Selection Evolution, 2017 - Springer
Background In statistical genetics, an important task involves building predictive models of
the genotype–phenotype relationship to attribute a proportion of the total phenotypic …

Bayesian Networks Illustrate Genomic and Residual Trait Connections in Maize (Zea mays L.)

K Töpner, GJM Rosa, D Gianola… - G3: Genes, Genomes …, 2017 - academic.oup.com
Relationships among traits were investigated on the genomic and residual levels using
novel methodology. This included inference on these relationships via Bayesian networks …

[HTML][HTML] Genotype–covariate correlation and interaction disentangled by a whole-genome multivariate reaction norm model

G Ni, J Van Der Werf, X Zhou, E Hyppönen… - Nature …, 2019 - nature.com
The genomics era has brought useful tools to dissect the genetic architecture of complex
traits. Here we propose a multivariate reaction norm model (MRNM) to tackle genotype …

Phantom epistasis in genomic selection: on the predictive ability of epistatic models

MF Schrauf, JWR Martini, H Simianer… - G3: Genes …, 2020 - academic.oup.com
Genomic selection uses whole-genome marker models to predict phenotypes or genetic
values for complex traits. Some of these models fit interaction terms between markers, and …

Optimising the identification of causal variants across varying genetic architectures in crops

C Miao, J Yang, JC Schnable - Plant biotechnology journal, 2019 - Wiley Online Library
Association studies use statistical links between genetic markers and the phenotype
variation across many individuals to identify genes controlling variation in the target …

Haplotype-based genome-wide prediction models exploit local epistatic interactions among markers

Y Jiang, RH Schmidt, JC Reif - G3: Genes, Genomes, Genetics, 2018 - academic.oup.com
Genome-wide prediction approaches represent versatile tools for the analysis and
prediction of complex traits. Mostly they rely on marker-based information, but scenarios …

Efficient algorithms for calculating epistatic genomic relationship matrices

Y Jiang, JC Reif - Genetics, 2020 - academic.oup.com
The genomic relationship matrix plays a key role in the analysis of genetic diversity, genomic
prediction, and genome-wide association studies. The epistatic genomic relationship matrix …