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Cited by 23Epigenetics and DNA MethylationChromosomal and Genetic VariationsGenetic Mapping and Diversity in Plants and Animals

DNA methylation variations underlie lettuce domestication and divergence

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Cao, Shuai, Sawettalake, Nunchanoke, Li, Ping, Fan, Sheng, Shen, Lisha·2024·Genome Biology
DOI 10.1186/s13059-024-03310-xPMC PMC11184767
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Abstract

Background: Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated from a single wild ancestor Lactuca serriola and subsequently diverged into two major morphologically distinct vegetable types: leafy lettuce and stem lettuce. However, the role of epigenetic variation in lettuce domestication and divergence remains largely unknown. Results: To understand the genetic and epigenetic basis underlying lettuce domestication and divergence, we generate single-base resolution DNA methylomes from 52 Lactuca accessions, including major lettuce cultivars and wild relatives. We find a significant increase of DNA methylation during lettuce domestication and uncover abundant epigenetic variations associated with lettuce domestication and divergence. Interestingly, DNA methylation variations specifically associated with leafy and stem lettuce are related to regulation and metabolic processes, respectively, while those associated with both types are enriched in stress responses. Moreover, we reveal that domestication-induced DNA methylation changes could influence expression levels of nearby and distal genes possibly through affecting chromatin accessibility and chromatin loop. Conclusion: Our study provides population epigenomic insights into crop domestication and divergence and valuable resources for further domestication for diversity and epigenetic breeding to boost crop improvement.

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  • In Lactuca sativa callus culture, polymorphism was observed.

    “Polymorphism observed”

    From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [101]

    The Results section (‘DNA methylation variations in the Lactuca genus’; no page supplied) reports SNP and DNA-methylation variation in L. sativa. It does not establish that polymorphism was observed in callus culture: the Methods section (‘Plant materials and growth conditions’; no page supplied) describes leaves collected from soil-grown seedlings, not callus. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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Authors
Cao, S., Sawettalake, N., Li, P., Fan, S., & Shen, L.
Affiliations
Temasek Life Sciences Laboratory (SG)
Corresponding author
Shen, Lisha
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2024-06-17
Volume
25
Issue
1
Pages
158-158
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-024-03310-x
PMC
PMC11184767
OpenAlex
W4399739132
Cited by
23
References
90
Citations by year
2026: 6 · 2025: 14 · 2024: 3
FWCI
3.13
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Singapore Food Story R&D Programme (SFS_RND_SUFP_001_04)
  • National Research Foundation Singapore (NRF-CRP22-2019-0001)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords
DNA methylation, epigenetic variation, lettuce, Lactuca serriola, wild relatives, chromatin accessibility, chromatin looping, stress response genes
MeSH terms
Domestication, Genetic Variation, Gene Expression Regulation, Plant, Lactuca, Crops, Agricultural, Genome, Plant, DNA Methylation, Epigenesis, Genetic

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