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Dimensionality of genomic information and its impact on genome-wide associations and variant selection for genomic prediction: a simulation study
BackgroundIdentifying true positive variants in genome-wide associations (GWA) depends on several factors, including the number of genotyped...
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Genomic prediction in pigs using data from a commercial crossbred population: insights from the Duroc x (Landrace x Yorkshire) three-way crossbreeding system
BackgroundGenomic selection is widely applied for genetic improvement in livestock crossbreeding systems to select excellent nucleus purebred (PB)...
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A new strategy for using historical imbalanced yield data to conduct genome-wide association studies and develop genomic prediction models for wheat breeding
Using imbalanced historical yield data to predict performance and select new lines is an arduous breeding task. Genome-wide association studies...
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Genomic analysis and prediction of genomic values for distichiasis in Staffordshire bull terriers
BackgroundDistichiasis is a condition characterized by aberrant hairs along the eyelid margins. The symptoms are usually mild but can lead to...
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Enhancing winter wheat prediction with genomics, phenomics and environmental data
In the realm of multi-environment prediction, when the goal is to predict a complete environment using the others as a training set, the efficiency...
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Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine
BackgroundGenomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to...
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Identification of gene-level methylation for disease prediction
DNA methylation is an epigenetic alteration that plays a fundamental part in governing gene regulatory processes. The DNA methylation mechanism...
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Genome-wide association study and genomic prediction of resistance to stripe rust in current Central and Northern European winter wheat germplasm
Key messageWe found two loci on chromosomes 2BS and 6AL that significantly contribute to stripe rust resistance in current European winter wheat...
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Efficient large-scale single-step evaluations and indirect genomic prediction of genotyped selection candidates
BackgroundSingle-step genomic best linear unbiased prediction (ssGBLUP) models allow the combination of genomic, pedigree, and phenotypic data into a...
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Statistical Methods for Disease Risk Prediction with Genotype Data
Single-nucleotide polymorphism (SNP) is the basic unit to understand the heritability of complex traits. One attractive application of the...
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A computationally efficient method for approximating reliabilities in large-scale single-step genomic prediction
BackgroundIn this study, computationally efficient methods to approximate the reliabilities of genomic estimated breeding values (GEBV) in a...
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Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE
While tumor dynamic modeling has been widely applied to support the development of oncology drugs, there remains a need to increase predictivity,...
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Effects of marker density on genomic prediction for yield traits in sweet corn
By accounting for many traits, phenoty** sweet corn is a costly practice, making complementary strategies necessary. Thus, predictive methods...
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psBLUP: incorporating marker proximity for improving genomic prediction accuracy
Genomic selection entails the estimation of phenotypic traits of interest for plants without phenotype based on the association between...
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Sparse Phenoty** and Haplotype-Based Models for Genomic Prediction in Rice
The multi-environment genomic selection enables plant breeders to select varieties resilient to diverse environments or particularly adapted to...
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Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops
BackgroundWe consider two key problems in genomics involving multiple traits: multi-trait genome wide association studies (GWAS), where the goal is...
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Genomic prediction ability and genetic parameters for residual feed intake calculated using different approaches and their associations with growth, reproductive, and carcass traits in Nellore cattle
This study aimed to estimate prediction ability and genetic parameters for residual feed intake ( RFI ) calculated using a regression equation for each...
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Improvement of prediction ability by integrating multi-omic datasets in barley
BackgroundGenomic prediction (GP) based on single nucleotide polymorphisms (SNP) has become a broadly used tool to increase the gain of selection in...
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Importance of genetic architecture in marker selection decisions for genomic prediction
Key messageWe demonstrate potential for improved multi-environment genomic prediction accuracy using structural variant markers. However, the degree...
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Generalized Linear Models
In the generalized linear model (GLM) (which is not highly general) y = Xβ + ϵ, the response variables are normally distributed, with constant...