Genome-Wide Association Studies with a Genomic Relationship Matrix: A Case Study with Wheat and Arabidopsis [PDF]
G3: Genes, Genomes, Genetics, 2016 Standard genome-wide association studies (GWAS) scan for relationships between each of p molecular markers and a continuously distributed target trait.
Daniel Gianola +3 more
doaj +7 more sources
An efficient genomic prediction method without the direct inverse of the genomic relationship matrix [PDF]
Frontiers in Plant Science, 2022 GBLUP, the most widely used genomic prediction (GP) method, consumes large and increasing amounts of computational resources as the training population size increases due to the inverse of the genomic relationship matrix (GRM).
Hailan Liu, Chao Xia, Hai Lan
doaj +6 more sources
Impact of different genomic relationship matrix construction methods on the accuracy of genomic prediction in different species [PDF]
Frontiers in GeneticsObjectiveGenomic best linear unbiased prediction (GBLUP) is a key method in genomic prediction, relying on the construction of a genomic relationship matrix (G-matrix).
Shiyi Wang +6 more
doaj +6 more sources
AnimalThe traditional genomic relationship matrix (GRM) has shown to be a biased estimation of true kinship, which can affect subsequent genetic analyses. In this study, we employed an unbiased kinship (UKin) estimation method within the genomic best linear ...
M.Y. Li +8 more
doaj +6 more sources
ICGRM: integrative construction of genomic relationship matrix combining multiple genomic regions for big dataset [PDF]
BMC Bioinformatics, 2019 Background Genomic prediction is an advanced method for estimating genetic values, which has been widely accepted for genetic evaluation in animal and disease-risk prediction in human. It estimates genetic values with genome-wide distributed SNPs instead
Dan Jiang +4 more
doaj +5 more sources
Improvement of Genomic Predictions in Small Breeds by Construction of Genomic Relationship Matrix Through Variable Selection [PDF]
Frontiers in Genetics, 2022 Genomic selection has been increasingly implemented in the animal breeding industry, and it is becoming a routine method in many livestock breeding contexts.
Enrico Mancin +5 more
doaj +4 more sources
Inexpensive Computation of the Inverse of the Genomic Relationship Matrix in Populations with Small Effective Population Size [PDF]
Genetics, 2016 Abstract Many computations with SNP data including genomic evaluation, parameter estimation, and genome-wide association studies use an inverse of the genomic relationship matrix. The cost of a regular inversion is cubic and is prohibitively expensive for large matrices.
I Misztal, Misztal Ignacy
exaly +5 more sources
GViT-GP: injecting the genomic relationship matrix as an inductive bias into a vision transformer via cross-attention for genomic prediction [PDF]
Frontiers in GeneticsIntroductionGenomic Prediction (GP) faces significant challenges in balancing model complexity with computational efficiency, particularly for high-dimensional genomic data under limited sample sizes.MethodsWe propose GViT-GP, a Vision Transformer ...
Jingxuan Li +7 more
doaj +3 more sources
Impact of blending the genomic relationship matrix with different levels of pedigree relationships or the identity matrix on genetic evaluations. [PDF]
JDS Commun, 2022 Evaluations using single-step genomic BLUP require blending the genomic relationship matrix (G) with a positive definite matrix to ensure nonsingularity for solving the mixed model equations. Many organizations blend G with a proportion of the numerator relationship matrix for genotyped animals (A 22) to improve stability and possibly add a residual ...
Hollifield MK +3 more
europepmc +4 more sources
335 Genomic predictions with a multi-breed genomic relationship matrix [PDF]
J Anim Sci, 2019 Abstract Multi-breed evaluations have the advantage of increasing the size of the reference population for genomic evaluations and are quite simple; however, combining breeds usually have a negative impact on prediction accuracy. The aim of this study was to evaluate the use of a multi-breed genomic relationship matrix (G), where SNP for
Steyn Y, Lourenco D, Misztal I.
europepmc +3 more sources