Genetic evaluation including intermediate omics features.
Genetics
; 219(2)2021 10 02.
Article
in En
| MEDLINE
| ID: mdl-34849886
ABSTRACT
In animal and plant breeding and genetics, there has been an increasing interest in intermediate omics traits, such as metabolomics and transcriptomics, which mediate the effect of genetics on the phenotype of interest. For inclusion of such intermediate traits into a genetic evaluation system, there is a need for a statistical model that integrates phenotypes, genotypes, pedigree, and omics traits, and a need for associated computational methods that provide estimated breeding values. In this paper, a joint model for phenotypes and omics data is presented, and a formula for the breeding values on individuals is derived. For complete omics data, three equivalent methods for best linear unbiased prediction of breeding values are presented. In all three cases, this requires solving two mixed model equation systems. Estimation of parameters using restricted maximum likelihood is also presented. For incomplete omics data, extensions of two of these methods are presented, where in both cases, the extension consists of extending an omics-related similarity matrix to incorporate individuals without omics data. The methods are illustrated using a simulated data set.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Breeding
/
Genomics
/
Models, Genetic
Type of study:
Prognostic_studies
Limits:
Animals
Language:
En
Journal:
Genetics
Year:
2021
Document type:
Article
Affiliation country:
Dinamarca