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Plant Phenome Journal
Article . 2025 . Peer-reviewed
License: CC BY NC ND
Data sources: Crossref
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
https://doi.org/10.1101/2025.0...
Article . 2025 . Peer-reviewed
License: CC BY
Data sources: Crossref
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Do not benchmark phenomic prediction against genomic prediction accuracy

Authors: Fangyi Wang; Mitchell J Feldmann; Daniel E Runcie;

Do not benchmark phenomic prediction against genomic prediction accuracy

Abstract

Abstract Phenomic selection is a new paradigm in plant breeding that uses high‐throughput phenotyping technologies and machine learning models to predict traits of new individuals and make selections. This can allow breeders to evaluate more plants in higher throughput more accurately, resulting in faster rates of gain and reduced labor costs. However, phenomic prediction models are frequently benchmarked against genomic prediction models using cross‐validation to demonstrate their usefulness to breeders. We argue that this is inappropriate for two reasons: (1) differences in the accuracy statistic measured by cross‐validation do not reliably indicate differences in the accuracy parameter of the breeder's equation, which we show analytically and through reanalysis of data from three representative phenomic prediction studies and (2) phenomic and genomic selection tools influence other parameters of the breeder's equation, so comparing accuracy, even if done properly, is insufficient to advocate for one approach over the other. We conclude that phenomic selection may be useful, but comparisons of accuracy between genomic prediction and phenomic prediction models are not.

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
9
Top 10%
Average
Top 10%
gold