Tissue Culture-Induced Heritable Genomic Variation in Rice, and Their Phenotypic Implications
Open accessAbstract
BACKGROUND: Somaclonal variation generally occurs in plants regenerated from tissue culture. However, fundamental issues regarding molecular characteristics, mutation rates and mutation spectra of plant somatic variation as well as their phenotypic relevance have been addressed only recently. Moreover, these studies have reported highly discrepant results in different plant species and even in the same plant genotype. METHODOLOGY/PRINCIPAL FINDINGS: We investigated heritable genomic variation induced by tissue culture in rice by whole genome re-sequencing of an extensively selfed somaclonal line (TC-reg-2008) and its wild type (WT) donor (cv. Hitomebore). We computed the overall mutation rate, single nucleotide polymorphisms (SNPs), small scale insertions/deletions (Indels) and mobilization of transposable elements (TEs). We assessed chromosomal distribution of the various types of genomic variations, tested correlations between SNPs and Indels, and examined concomitancy between TE activity and its cytosine methylation states. We also performed gene ontology (GO) analysis of genes containing nonsynonymous mutations and large-effect mutations, and assayed effects of the genomic variations on phenotypes under both normal growing condition and several abiotic stresses. We found that heritable somaclonal genomic variation occurred extensively in rice. The genomic variations distributed non-randomly across each of the 12 rice chromosomes, and affected a large number of functional genes. The phenotypic penetrance of the genomic variations was condition-dependent. CONCLUSIONS/SIGNIFICANCE: Tissue culture is a potent means to generate heritable genetic variations in rice, which bear distinct difference at least in space (chromosomal distribution) from those occurred under natural settings. Our findings have provided new information regarding the mutation rate and spectrum as well as chromosomal distribution pattern of somaclonal variation in rice. Our data also suggest that rice possesses a strong capacity to canalize genetic variations under normal growing conditions to maintain phenotypic robustness, which however can be released by certain abiotic stresses to generate variable phenotypes.
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These interrelated factors dictate the frequency and type of somaclonal variation, emphasizing the need to optimize genotype selection, explant sourcing, culture media, environmental controls, and subculture protocols to minimize variability.
“These interrelated factors dictate the frequency and type of somaclonal variation, emphasizing the need to carefully optimize genotype selection, explant sourcing, culture media, environmental controls, and subculture protocols to minimize variability in micropropagated plant populations [79,80].”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [80]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredEpigenetic variation examined in rice using WGBS exhibits distinct differences, particularly in chromosomal distribution, compared to variations that occur under natural conditions.
“Similarly, epigenetic variation examined in rice using WGBS exhibits distinct differences, particularly in chromosomal distribution, compared to variations that occur under natural conditions [80].”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [80]
The Results section (page not provided) reports that tissue culture-induced DNA polymorphisms had little overlap with rice genomic regions known to be hyper-mutable under natural conditions, supporting a difference in chromosomal distribution. But this comparison concerns genetic variation (SNPs and Indels), not epigenetic variation measured by WGBS. The Methods section describes bisulfite sequencing of specific Tos17 loci, not whole-genome bisulfite sequencing. (LLM, conf=0.88)
Experimental — accuracy not yet measuredIn Oryza sativa callus culture, variation was observed.
“Variation observed”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [80]
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DNA Methylation Dynamics in Rice Regeneration and Transformation
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- Authors
- Zhang, D., Wang, Z., Wang, N., Gao, Y., Liu, Y., Wu, Y., Bai, Y., Zhang, Z., Lin, X., Dong, Y., Ou, X., Xu, C., & Liu, B.
- Affiliations
- Northeast Normal University (CN)
- Jilin Agricultural University (CN)
- Jilin Academy of Agricultural Sciences (CN)
- Corresponding author
- Xu, Chunming
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-05-07
- Volume
- 9
- Issue
- 5
- Pages
- e96879
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC4013045
- OpenAlex
- W2003326053
- Cited by
- 90
- References
- 51
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 11 · 2023: 11 · 2022: 14 · 2021: 11 · 2020: 8 · 2019: 10 · 2018: 9 · 2017: 2 · 2016: 6 · 2015: 2
- FWCI
- 3.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant tissue culture and regeneration
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- somaclonal variation, rice, mutation rate, mutation spectrum, single nucleotide polymorphisms, indels, transposable element mobilization, DNA methylation, abiotic stress response, phenotypic robustness, Hitomebore
- MeSH terms
- DNA Transposable Elements, Genotype, Oryza, Arabidopsis, Sequence Analysis, DNA, Genome, Plant, DNA Methylation, Genomics, Chromosomes, Plant, Tissue Culture Techniques, INDEL Mutation
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