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Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity
- Source :
- SCIENCE CHINA Life Sciences; 20230101, Issue: Preprints p1-15, 15p
- Publication Year :
- 2023
-
Abstract
- DNA methylation is an important epigenetic marker, yet its diversity and consequences in tomato breeding at the population level are largely unknown. We performed whole-genome bisulfite sequencing (WGBS), RNA sequencing, and metabolic profiling on a population comprising wild tomatoes, landraces, and cultivars. A total of 8,375 differentially methylated regions (DMRs) were identified, with methylation levels progressively decreasing from domestication to improvement. We found that over 20% of DMRs overlapped with selective sweeps. Moreover, more than 80% of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms (SNPs), and DMRs had strong linkages with adjacent SNPs. We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs. We detected 971 and 711 large-effect loci via SNP and DMR markers, respectively. Combined with multi-omics, we identified 13 candidate genes and updated the polyphenol biosynthetic pathway. Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity. Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.
Details
- Language :
- English
- ISSN :
- 16747305 and 18691889
- Issue :
- Preprints
- Database :
- Supplemental Index
- Journal :
- SCIENCE CHINA Life Sciences
- Publication Type :
- Periodical
- Accession number :
- ejs62659877
- Full Text :
- https://doi.org/10.1007/s11427-022-2299-5