Differentially methylated genomic regions of lettuce seeds relate to divergence across morphologically distinct horticultural types

Authors: Simko, Ivan

Submitted to: AoB Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/19/2023
Publication Date: 9/6/2023
Citation: Simko, I. 2023. Differentially methylated genomic regions of lettuce seeds relate to divergence across morphologically distinct horticultural types. AoB Plants. 15(5). Article plad060. https://doi.org/10.1093/aobpla/plad060.
DOI: https://doi.org/10.1093/aobpla/plad060

Interpretive Summary: Changes in DNA methylation can lead to differences in plant morphology. Analysis of DNA from seeds of 95 accessions from eight morphologically distinct horticultural types (Batavia = 11, butterhead = 10, iceberg = 11, Latin = 7, leaf = 16, oilseed = 3, romaine = 27, and stem = 10) revealed 350 regions of DNA that were differentially methylated. Majority of the 41 pivotal differentially methylated regions overlapped with genomic features predicted or confirmed to be involved in plant growth and development. The results reveal that differences in methylation profiles of morphologically distinct horticultural types are already detectable in seeds.

Technical Abstract: Heritable cytosine methylation plays a role in shaping plant phenotypes; however, no information is available about DNA methylation in cultivated lettuce (Lactuca sativa), one of the most important leafy vegetables. Whole-genome bisulfite sequencing (WGBS) performed on seeds of 95 accessions from eight morphologically distinct horticultural types (Batavia, butterhead, iceberg, Latin, leaf, oilseed, romaine and stem) revealed a high level of methylation in lettuce genome with an average methylation of 90.6 % in the CG context, 72.9 % in the CHG context and 7.5 % in the CHH context. Although WGBS did not show substantial differences in overall methylation levels across eight horticultural types, 350 differentially methylated regions (DMR) were identified. Majority of the 41 pivotal DMR overlapped with genomic features predicted or confirmed to be involved in plant growth and development. These results provide the first insight into lettuce DNA methylation and indicate a potential role for heritable variation in cytosine methylation in lettuce morphology. The results reveal that differences in methylation profiles of morphologically distinct horticultural types are already detectable in seeds. Identified DMR can be a focus of the future functional studies.