The vast majority of somatic mutations in plants are layer-specific
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Abstract
Background: Plant meristems are structured organs consisting of distinct layers of stem cells, which differentiate into new plant tissue. Mutations in meristematic layers can propagate into large sectors of the plant. However, the characteristics of meristematic mutations remain unclear, limiting our understanding of the genetic basis of somaclonal phenotypic variation. Results: Here, we analyse the frequency and distribution of somatic mutations in an apricot tree. We separately sequence the epidermis (developing from meristem layer 1) and the flesh (developing from meristem layer 2) of several fruits sampled across the entire tree. We find that most somatic mutations (> 90%) are specific to individual layers. Interestingly, layer 1 shows a higher mutation load than layer 2, implying different mutational dynamics between the layers. The distribution of somatic mutations follows the branching of the tree. This suggests that somatic mutations are propagated to developing branches through axillary meristems. In turn, this leads us to the unexpected observation that the genomes of layer 1 of distant branches are more similar to each other than to the genomes of layer 2 of the same branches. Finally, using single-cell RNA sequencing, we demonstrate that layer-specific mutations were only transcribed in the cells of the respective layers and can form the genetic basis of somaclonal phenotypic variation. Conclusions: Here, we analyse the frequency and distribution of somatic mutations with meristematic origin. Our observations on the layer specificity of somatic mutations outline how they are distributed, how they propagate, and how they can impact clonally propagated crops.
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- Authors
- Goel, M., Campoy, J. A., Krause, K., Baus, L. C., Sahu, A., Sun, H., Walkemeier, B., Marek, M., Beaudry, R., Ruiz, D., Huettel, B., & Schneeberger, K.
- Affiliations
- Max Planck Institute for Plant Breeding Research (DE)
- Consejo Superior de Investigaciones Científicas (ES)
- University Hospital Bonn (DE)
- Michigan State University (US)
- Cluster of Excellence on Plant Sciences (DE)
- Corresponding author
- Schneeberger, Korbinian
- ORCID
- Venue
- Genome Biology
- Published
- 2024-07-24
- Volume
- 25
- Issue
- 1
- Pages
- 194-194
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC11267851
- OpenAlex
- W4400955400
- Cited by
- 31
- References
- 87
- Citations by year
- 2026: 9 · 2025: 15 · 2024: 7
- FWCI
- 7.57
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Alexander von Humboldt-Stiftung
- Marie Skłodowska-Curie Individual Fellowship (789673)
- Deutsche Forschungsgemeinschaft (EXC 2048/1–390686111)
- HORIZON EUROPE European Research Council (802629)
- Max Planck Institute for Plant Breeding Research
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Keywords
- somatic mutations, plant meristems, somaclonal variation, apricot, axillary meristem, clonal crops, single-cell RNA sequencing, fruit epidermis, mutational dynamics
- MeSH terms
- Fruit, Mutation, Phenotype, Meristem, Genome, Plant
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