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

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 the 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 level across eight horticultural types, 350 differentially methylated regions (DMR) were identified. Majority of the 41 pivotal DMR (PDMR) 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 of heritable variation in cytosine methylation in lettuce morphology. The results reveal that differences in methylation profiles of morphologically distinct horticultural types are detectable already in seeds. Identified DMR can be a focus of the future functional studies.