Pitfalls of predicting complex traits from SNPs

NR Wray, J Yang, BJ Hayes, AL Price… - Nature Reviews …, 2013 - nature.com
The success of genome-wide association studies (GWASs) has led to increasing interest in
making predictions of complex trait phenotypes, including disease, from genotype data …

[HTML][HTML] Invited review: Genomic selection in dairy cattle: Progress and challenges

BJ Hayes, PJ Bowman, AJ Chamberlain… - Journal of dairy …, 2009 - Elsevier
A new technology called genomic selection is revolutionizing dairy cattle breeding. Genomic
selection refers to selection decisions based on genomic breeding values (GEBV). The …

[PDF][PDF] ASReml-R reference manual version 4

DG Butler, BR Cullis, AR Gilmour… - … , HP1 1ES, UK, 2017 - asreml.kb.vsni.co.uk
ASReml-R is a statistical package that fits linear mixed models using Residual Maximum
Likelihood (REML) in the R environment. This package uses the same computational kernel …

Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

F Li, C Li, Y Chen, J Liu, C Zhang, B Irving… - Microbiome, 2019 - Springer
Background The symbiotic rumen microbiota is essential for the digestion of plant fibers and
contributes to the variation of production and health traits in ruminants. However, to date, the …

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

AC Bouwman, HD Daetwyler, AJ Chamberlain… - Nature …, 2018 - nature.com
Stature is affected by many polymorphisms of small effect in humans. In contrast, variation in
dogs, even within breeds, has been suggested to be largely due to variants in a small …

Superior field performance of waxy corn engineered using CRISPR–Cas9

H Gao, MJ Gadlage, HR Lafitte, B Lenderts… - Nature …, 2020 - nature.com
We created waxy corn hybrids by CRISPR–Cas9 editing of a waxy allele in 12 elite inbred
maize lines, a process that was more than a year faster than conventional trait introgression …

Canopy temperature and vegetation indices from high-throughput phenotyping improve accuracy of pedigree and genomic selection for grain yield in wheat

J Rutkoski, J Poland, S Mondal… - G3: Genes …, 2016 - academic.oup.com
Genomic selection can be applied prior to phenotyping, enabling shorter breeding cycles
and greater rates of genetic gain relative to phenotypic selection. Traits measured using …

GCTA: a tool for genome-wide complex trait analysis

J Yang, SH Lee, ME Goddard, PM Visscher - The American Journal of …, 2011 - cell.com
For most human complex diseases and traits, SNPs identified by genome-wide association
studies (GWAS) explain only a small fraction of the heritability. Here we report a user-friendly …

MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package

JD Hadfield - Journal of statistical software, 2010 - jstatsoft.org
Generalized linear mixed models provide a flexible framework for modeling a range of data,
although with non-Gaussian response variables the likelihood cannot be obtained in closed …

Methodological issues and advances in biological meta-analysis

S Nakagawa, ESA Santos - Evolutionary Ecology, 2012 - Springer
Meta-analysis has changed the way researchers conduct literature reviews not only in
medical and social sciences but also in biological sciences. Meta-analysis in biological …