High Genetic and Epigenetic Stability in Coffea arabica Plants Derived from Embryogenic Suspensions and Secondary Embryogenesis as Revealed by AFLP, MSAP and the Phenotypic Variation Rate
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Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings) were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200,000 plant). Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0-0.003% and 0.07-0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied) and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1-3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee somatic embryogenesis. The main change in most of the rare phenotypic variants was aneuploidy, indicating that mitotic aberrations play a major role in somaclonal variation in coffee.
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AFLP and MSAP analyses of 145 three-year-old somatic embryogenesis-derived Coffea arabica plants showed extremely low polymorphism between mother plants and embryos, with ranges of 0-0.003% and 0.07-0.18%, respectively.
“Similarly, AFLP and MSAP analyses of 145 three-year-old somatic embryogenesis-derived plants showed extremely low polymorphism between mother plants and embryos of Coffea arabica, with ranges of 0-0.003% and 0.07-0.18%,respectively.”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [94]
Materials and Methods says molecular analysis used three-year-old plants, and the Discussion reports 145 plants analyzed. The MSAP Results give the claimed 0.07–0.18% range. However, AFLP Results Table 3 reports 0–0.03% total polymorphism, not 0–0.003%. (LLM, conf=0.93)
Experimental — accuracy not yet measuredIn Coffea arabica, somatic embryogenesis/nodal segments regeneration was genetically stable.
“Genetically stable”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [94]
The Conclusions report very low variation and extremely low polymorphism in Coffea arabica plants produced by embryogenic suspensions and secondary somatic embryogenesis under controlled culture conditions. The paper does not report genetic stability for regeneration from nodal segments, so that part of the claim is unsupported. (LLM, conf=0.88)
Experimental — accuracy not yet measuredNo significant differences were found between proliferation systems for the two hybrids, and no correlation was observed between variant phenotypes and specific MSAP patterns.
“No significant differences were found between proliferation systems for the two hybrids, and no correlation was observed between variant phenotypes and specific MSAP patterns [94].”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [94]
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Self-citation
- Authors
- Bobadilla Landey, R., Cenci, A., Georget, F., Bertrand, B., Camayo, G., Dechamp, E., Herrera, J. C., Santoni, S., Lashermes, P., Simpson, J., & Etienne, H.
- Affiliations
- Institut de Recherche pour le Développement (BJ)
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR)
- Centro Nacional de Investigaciones de Café (CO)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (MX)
- Corresponding author
- Etienne, Hervé
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-02-13
- Volume
- 8
- Issue
- 2
- Pages
- e56372
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3572038
- OpenAlex
- W2049765785
- Cited by
- 95
- References
- 81
- Citations by year
- 2026: 1 · 2025: 6 · 2024: 7 · 2023: 15 · 2022: 5 · 2021: 10 · 2020: 11 · 2019: 8 · 2018: 5 · 2017: 8 · 2016: 10 · 2015: 5 · 2014: 3 · 2013: 1
- FWCI
- 2.84
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Agritrop (Cirad) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant tissue culture and regeneration
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetics and Plant Breeding
- Keywords
- Coffea arabica, somaclonal variation, somatic embryogenesis, embryogenic suspension culture, secondary embryogenesis, epigenetic stability, aneuploidy, chromosome loss, 2,4-D concentration, coffee hybrids, phenotypic variability
- MeSH terms
- Hybridization, Genetic, Mitosis, Phenotype, Ploidies, Polymorphism, Genetic, Seeds, Genetic Variation, DNA Methylation, Chromosomes, Plant, Coffea, Epigenesis, Genetic, Tissue Culture Techniques, Amplified Fragment Length Polymorphism Analysis, Karyotype
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