Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP)
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The epigenetic diversity of six genotype groups (commercial cultivars, S. officinarum, S. spontaneum, S. robustum, S. barberi, and Erianthus sp.) was assessed through methylation-sensitive amplification polymorphism (MSAP). A total of 1341 MSAP loci were analyzed, of which 1117 (83.29%) were susceptible to cytosine methylation and responsible for a higher proportion of overall diversity among genotypes. The MSAP selective primer combinations captured different proportions of internal and external cytosine methylation loci across genotype groups, while the average external cytosine frequency was higher for all genotype groups. The genotypes were divided into two subpopulations with a high differentiation index (φ st = 0.086) based on epigenetic loci. The genotypes were clustered in three subgroups for both methylated and unmethylated loci, considering dissimilarity values. Four methylated fragments (MFs) were randomly selected and subsequently sequenced and compared with sugarcane public databases using BLASTN. MF alignments suggest that cytosine methylation occurs in sugarcane near CpG islands and tandem repeats within transcribed regions and putative cis-regulatory sequences, which assigned functions are associated with stress adaptation. These results provide the first insights about the distribution of this epigenetic mark in sugarcane genome, and suggest a biological relevance of methylated loci.
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In six sugarcane genotype groups, MSAP analysis of 1341 loci showed 83.29% cytosine methylation, contributing significantly to overall genetic diversity.
“A total of 1341 MSAP loci were analyzed, with 83.29% showing cytosine methylation, contributing significantly to overall genetic diversity.”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [146]
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Experimental — accuracy not yet measuredSugarcane genotypes were divided into two subpopulations with high differentiation, and methylated fragments were found near CpG islands and regulatory sequences, suggesting their role in stress adaptation.
“The genotypes were divided into two subpopulations with high differentiation, and methylated fragments were found near CpG islands and regulatory sequences, suggesting their role in stress adaptation [146].”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [146]
The Abstract reports two subpopulations and links methylated fragments near CpG islands and putative cis-regulatory sequences to functions associated with stress adaptation. It calls the differentiation index high, but the Structure analysis and Discussion describe the measured 8.6% differentiation as moderate, so the claim overstates the degree of differentiation. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIn Saccharum spp., variation was observed.
“Variation observed”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [146]
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- Authors
- Martins, A. A., da Silva, M. F., & Pinto, L. R.
- Affiliations
- Universidade Estadual Paulista (Unesp) (BR)
- Corresponding author
- Pinto, Luciana Rossini
- Venue
- 3 Biotech
- Published
- 2020-05-24
- Volume
- 10
- Issue
- 6
- Pages
- 265-265
- ISSN
- 2190-572X (ISSN-L)
- 2190-5738
- PMC
- PMC7246279
- OpenAlex
- W3027810313
- Cited by
- 6
- References
- 58
- Citations by year
- 2026: 2 · 2025: 1 · 2022: 3
- FWCI
- 0.48
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- 3 Biotech (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- Funders
- FAPESP (FAPESP2013/22500-5)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Sugarcane Cultivation and Processing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- sugarcane, Saccharum, epigenetic variation, DNA methylation, cytosine methylation, methylation-sensitive amplification polymorphism, Saccharum spontaneum, Saccharum robustum, Saccharum barberi, Erianthus, CpG islands, tandem repeats, cis-regulatory sequences, stress adaptation, genotype differentiation
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