Bienvenu, C and Garin, V and Salas, N and Théra, K and Tekete, M L and Sarathjith, M S and Diallo, C and Berger, A and Calatayud, C and Bellis, F D and Bellis, F D and Rami, J-F and Vaksmann, M and Segura, V and Pot, D and Verdal, H de (2025) Factors influencing phenomic prediction: A case study on a large sorghum back cross nested association mapping population. The Plant Phenome Journal, 8 (1). pp. 1-22. ISSN 2578-2703
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Abstract
Plant breeding is crucial to develop varieties able to cope with climate change and support food and feed value chains. Genomic prediction (GP) has been a major step in increasing their efficiency and recently, phenomic prediction (PP) has gained attention as a promising complementary approach to GP, potentially further increasing this efficiency. Factors impacting PP are not fully clarified. Thus, we studied the impacts of spectra preprocessing, prediction methods, population structure, training set size, near infrared reflectance spectroscopy (NIRS) acquisition environment, and wavelength selection on a large multi-parental sorghum population including 2498 BC1F3:5 families from 29 crosses with a strong population structure. Using 51,545 single nucleotide polymorphisms and 1154 NIRS features, we show that PP can reach predictive abilities (PAs) similar to GP, that it is less affected by population structure, and can reach its maximal PA with smaller training sets than GP, but its performances are trait dependent. We also show that NIRS can be acquired in a reference environment to perform prediction in other environments and that it is possible to randomly select wavelengths to perform predictions. Finally, we show that spectra preprocessing and statistical methods have an inconsistent impact on PA. Our study confirms that PP is a relevant trait prediction method that deserves attention to optimize breeding schemes. The main challenges for the future will be to better understand the information contained in the spectra and disentangle their genetic and proxy components to optimize the use of PP in breeding programs.
| Item Type: | Article |
|---|---|
| Divisions: | Research Program : West & Central Africa |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | phenomic prediction, Genomic prediction (GP), phenomic prediction (PP), sorghum |
| Subjects: | Mandate crops > Sorghum Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 03 Mar 2026 04:12 |
| Last Modified: | 03 Mar 2026 04:12 |
| URI: | http://oar.icrisat.org/id/eprint/13508 |
| Official URL: | https://acsess.onlinelibrary.wiley.com/doi/full/10... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | We acknowledge the MGX-Genotyping platform (UMR AGAP—CIRAD, Montpellier, France) for its support regarding the genotyping of the BCNAM population. We would like to thank the anonymous reviewers of the previous versions of this article for their highly relevant comments and suggestions regarding the genetic value estimations used to train the prediction models and Section 4 that greatly contributed to the current version. This work was supported by grant from the Generation Challenge Programme (Project Numbers G7010.05.01 and G7010.05.02). The work of Clément Bienvenu was supported by a doctoral allowance from the French Ministry of Higher Education and Research. |
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