Abstract
Potato vigour, the growth potential of seed potatoes, is a key agronomic trait that varies significantly across production fields due to factors such as genetic background and environmental conditions. Seed tuber microbiomes are thought to influence plant health and crop performance, yet the precise relationships between microbiome composition and potato vigour remain unclear. Here we conducted microbiome sequencing on seed tuber eyes and heel ends from 6 potato varieties grown in 240 fields. By using time-resolved drone imaging of three trial fields in the next season to track crop development, we were able to link microbiome composition with potato vigour. We used microbiome data at varying taxonomic resolutions to build random forest predictive models and found that amplicon sequence variants provided the highest predictive accuracy for potato vigour. The model revealed variety-specific relationships between the seed tuber microbiome and next season’s crop vigour in independent trial fields. With a coefficient of determination value of 0.69 for the best-performing variety, the model accurately predicted vigour in seed tubers from fields not previously included in the analysis. Moreover, the model identified key microbial indicators of vigour from which a Streptomyces, an Acinetobacter and a Cellvibrio amplicon sequence variant stood out as the most important contributors to the model’s accuracy. This study shows that seed potato vigour can be reliably predicted based on the microbiota associated with seed tuber eyes, potentially guiding future microbiome-informed breeding strategies.
| Original language | English |
|---|---|
| Pages (from-to) | 28-40 |
| Number of pages | 13 |
| Journal | Nature Microbiology |
| Volume | 10 |
| Issue number | 1 |
| Early online date | 27 Dec 2024 |
| DOIs | |
| Publication status | Published - Jan 2025 |
Bibliographical note
Publisher Copyright:© The Author(s), under exclusive licence to Springer Nature Limited 2024.
Funding
We acknowledge the valuable contributions of the Royal HZPC Group B.V. and Averis Seeds B.V. for providing the seed tuber material and supporting the field trials. Their collaboration was essential to the successful execution of this research. Special thanks are extended to F. Hofstra and M. ten Klooster from HZPC Holding B.V. for their contribution to the sample collection and J. Hopman from Averis Seeds B.V. for his valuable advice. We also thank C. Jongekrijg, E. Manders and E. de Kloe for excellent technical assistance in the laboratory. In addition, we acknowledge the funding support received from Europees Landbouwfonds voor Plattelandsontwikkeling (ELFPO) on the 'Flight-to-vitality' project. This work was also partly supported by the Dutch Research Council (NWO) through the Gravitation program MiCRop (grant number 024.004.014) and through project 'Sequence-based POTato Microbiome tools for microbiome-optimized potatoes' (project number 19769).
| Funders | Funder number |
|---|---|
| Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research) | |
| Royal HZPC Group B.V. | |
| Averis Seeds B.V. | |
| HZPC Holding B.V. | |
| Europees Landbouwfonds voor Plattelandsontwikkeling (ELFPO) on the 'Flight-to-vitality' project | 024.004.014, 19769 |
| Dutch Research Council (NWO) through the Gravitation program MiCRop |
Keywords
- Solanum tuberosum/microbiology
- Microbiota/genetics
- Seeds/microbiology
- Plant Tubers/microbiology
- Bacteria/genetics
- Acinetobacter/genetics