Assessment of Genetic and Epigenetic Changes in Virus-Free Garlic (Allium sativum L.) Plants Obtained by Meristem Culture Followed by In Vitro Propagation
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Key message This is the first report assessing epigenetic variation in garlic. High genetic and epigenetic polymorphism during in vitro culture was detected.Sequencing of MSAP fragments revealed homology with ESTs. Garlic (Allium sativum) is a worldwide crop of economic importance susceptible to viral infections that can cause significant yield losses. Meristem tissue culture is the most employed method to sanitize elite cultivars.Often the virus-free garlic plants obtained are multiplied in vitro (micro propagation). However, it was reported that micro-propagation frequently produces somaclonal variation at the phenotypic level, which is an undesirable trait when breeders are seeking to maintain varietal stability. We employed amplification fragment length polymorphism and methylation sensitive amplified polymorphism (MSAP) methodologies to assess genetic and epigenetic modifications in two culture systems: virus-free plants obtained by meristem culture followed by in vitro multiplication and field culture. Our results suggest that garlic exhibits genetic and epigenetic polymorphism under field growing conditions. However, during in vitro culture system both kinds of polymorphisms intensify indicating that this system induces somaclonal variation. Furthermore, while genetic changes accumulated along the time of in vitro culture, epigenetic polymorphism reached the major variation at 6 months and then stabilize, being demethylation and CG methylation the principal conversions.Cloning and sequencing differentially methylated MSAP fragments allowed us to identify coding and unknown sequences of A. sativum, including sequences belonging to LTR Gypsy retrotransposons. Together, our results highlight that main changes occur in the initial 6 months of micro propagation. For the best of our knowledge, this is the first report on epigenetic assessment in garlic.
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Epigenetic variation, including demethylation and CG methylation, was most pronounced in the first six months of micropropagation, with these changes stabilizing thereafter.
“For instance, epigenetic variation, including demethylation and CG methylation, was most pronounced in the first six months of micropropagation, with these changes stabilizing thereafter.”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [34]
The Loci-specific genetic and epigenetic changes section reports that most changes, including demethylation and CG methylation, occurred in the first six months, with few changes in the next six. But the Global genetic and epigenetic analyses section says the abundance of both types of sites then decreased toward initial values, rather than simply stabilizing. (LLM, conf=0.85)
Experimental — accuracy not yet measuredMSAP analysis identified coding sequences and LTR Gypsy retrotransposons, indicating that epigenetic modifications contribute to somaclonal variation in Allium sativum.
“MSAP analysis identified coding sequences and LTR Gypsy retrotransposons, indicating that epigenetic modifications contribute to somaclonal variation in Allium sativum [34].”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [34]
The ‘Sequence analysis of MSAP fragments’ section reports differentially methylated fragments matching coding regions and three proteins of the Gypsy LTR retroelement superfamily. It suggests that epigenetic activation of retroelements might be one mechanism by which genetic variability accumulates during in vitro culture; it does not establish that epigenetic modifications contribute to somaclonal variation. (LLM, conf=0.83)
Experimental — accuracy not yet measuredIn Allium sativum, genetic and epigenetic polymorphism was observed under field growing conditions.
“Genetic and epigenetic polymorphism under field growing conditions”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [34]
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- Authors
- Gimenez, M. D., Yañez-Santos, A. M., Paz, R. C., Quiroga, M. P., Marfil, C. F., Conci, V. C., & García-Lampasona, S. C.
- Affiliations
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- National Agricultural Technology Institute (AR)
- Corresponding author
- García-Lampasona, Sandra Claudia
- ORCID
- Venue
- Plant Cell Reports
- Published
- 2015-10-14
- Volume
- 35
- Issue
- 1
- Pages
- 129-141
- ISSN
- 0721-7714 (ISSN-L)
- 1432-203X
- OpenAlex
- W1954948702
- Cited by
- 47
- References
- 80
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 5 · 2023: 4 · 2022: 2 · 2021: 6 · 2020: 9 · 2019: 3 · 2018: 8 · 2017: 2 · 2016: 2
- FWCI
- 1.74
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Plant Cell Reports (publishedVersion)
- PubMed (publishedVersion)
- Conicet (submittedVersion, cc-by-nc-sa)
- Funders
- INTA (INTA-PNHFA061251)
- SECTYP UNCuyo (06/A49)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant tissue culture and regeneration
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Keywords
- garlic, epigenetic variation, somaclonal variation, virus-free plants, meristem culture, micropropagation, DNA methylation, CG methylation, demethylation, genetic polymorphism
- MeSH terms
- Garlic, Phenotype, Reproduction, Specific Pathogen-Free Organisms, Genetic Variation, Cluster Analysis, Sequence Analysis, DNA, Meristem, Retroelements, DNA Methylation, Genomic Instability, Epigenesis, Genetic, Tissue Culture Techniques, Genetic Loci
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