In vitro breeding: application of embryonic stem cells to animal production

DE Goszczynski, H Cheng… - Biology of …, 2019 - academic.oup.com
Embryonic stem cells (ESCs) are derived from the inner cell mass of preimplantation
blastocysts. For decades, attempts to efficiently derive ESCs in animal livestock species …

Efficient strategies for leave-one-out cross validation for genomic best linear unbiased prediction

H Cheng, DJ Garrick, RL Fernando - Journal of animal science and …, 2017 - Springer
Background A random multiple-regression model that simultaneously fit all allele
substitution effects for additive markers or haplotypes as uncorrelated random effects was …

Predicting the accuracy of genomic predictions

JCM Dekkers, H Su, J Cheng - Genetics Selection Evolution, 2021 - Springer
Background Mathematical models are needed for the design of breeding programs using
genomic prediction. While deterministic models for selection on pedigree-based estimates of …

Genomic prediction from multiple-trait Bayesian regression methods using mixture priors

H Cheng, K Kizilkaya, J Zeng, D Garrick, R Fernando - Genetics, 2018 - academic.oup.com
Bayesian multiple-regression methods incorporating different mixture priors for marker
effects are used widely in genomic prediction. Improvement in prediction accuracies from …

An upper bound for accuracy of prediction using GBLUP

E Karaman, H Cheng, MZ Firat, DJ Garrick… - PloS one, 2016 - journals.plos.org
This study aims at characterizing the asymptotic behavior of genomic prediction R 2 as the
size of the reference population increases for common or rare QTL alleles through …

Accuracy of genomic predictions using different imputation error rates in aquaculture breeding programs: A simulation study

P Dufflocq, M Pérez-Enciso, JP Lhorente, JM Yáñez - Aquaculture, 2019 - Elsevier
In breeding programs, genetic evaluations can be performed using phenotypic information
from the selection candidates per se or from relatives to obtain breeding values (EBV) by the …

Evaluating sequence-based genomic prediction with an efficient new simulator

M Pérez-Enciso, N Forneris, G de Los Campos… - Genetics, 2017 - academic.oup.com
The vast amount of sequence data generated to analyze complex traits is posing new
challenges in terms of the analysis and interpretation of the results. Although simulation is a …

A unifying concept of animal breeding programmes

H Simianer, L Büttgen, A Ganesan… - Journal of Animal …, 2021 - Wiley Online Library
Modern animal breeding programmes are constantly evolving with advances in breeding
theory, biotechnology and genetics. Surprisingly, there seems to be no generally accepted …

XSim version 2: simulation of modern breeding programs

CJ Chen, D Garrick, R Fernando, E Karaman… - G3, 2022 - academic.oup.com
Simulation can be an efficient approach to design, evaluate, and optimize breeding
programs. In the era of modern agriculture, breeding programs can benefit from a simulator …

Inferring trait-specific similarity among individuals from molecular markers and phenotypes with Bayesian regression

D Gianola, RL Fernando, CC Schön - Theoretical Population Biology, 2020 - Elsevier
Modeling covariance structure based on genetic similarity between pairs of relatives plays
an important role in evolutionary, quantitative and statistical genetics. Historically, genetic …