The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
Genetic evaluation including intermediate omics features
Open accessAbstract
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.
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“Compared to the single-step mixed effects model by Christensen et al. (2021), NN-MM demonstrated superior prediction accuracy, especially for individuals with missing omics data, as shown in Supplementary Table 4.”
From A review of multimodal deep learning methods for genomic-enabled prediction in plant breeding (2024) · cites this paper as Christensen et al. (2021)
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Cited by
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“Compared to the single-step mixed effects model by Christensen et al .”
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Background
Metadata
- Authors
- Christensen, O. F., Börner, V., Varona, L., & Legarra, A.
- Affiliations
- Aarhus University (DK)
- Universidad de Zaragoza (ES)
- GenPhySE (Génétique, Physiologie et Systèmes d’Elevage), INRA, 31326 Castanet-Tolosan, France
- Corresponding author
- Christensen, Ole F
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-08-07
- Volume
- 219
- Issue
- 2
- Pages
- 14 p;
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- PMC
- PMC8633135
- OpenAlex
- W3198274722
- Cited by
- 81
- References
- 29
- Citations by year
- 2026: 6 · 2025: 15 · 2024: 23 · 2023: 15 · 2022: 20 · 2021: 2
- FWCI
- 10.45
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Genetics (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- Green Development and Demonstration Programme
- Ministry of Food, Agriculture and Fisheries of Denmark (34009-19-1586)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetics and Plant Breeding
- Keywords
- genetic evaluation, metabolomics, transcriptomics, breeding value estimation, BLUP, mixed model equations, restricted maximum likelihood, animal breeding, plant breeding
- MeSH terms
- Plant Breeding, Animals, Breeding, Models, Genetic, Plants, Genomics, Genetic Fitness
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