This study is led by Dr. Shouchuang Wang (Sanya Nanfan Research Institute of Hainan University), revealing the role of epigenetic variation in tomato domestication and metabolic diversity from the perspective of population DNA methylation.
The breeding history of tomato which is a world recognized model plant with high nutritional value can be divided into two main stages: domestication and improvement, while metabolites show a rich diversity in the population due to the 'hitchhiking effect'. Previous studies on metabolic diversity in plant populations have been based on single nucleotide polymorphisms (SNPs) as genetic markers, but DNA methylation, as an important epigenetic modification, in relation to domestication and metabolic diversity, is not yet known. By whole genome bisulfite sequencing of nearly 100 tomato core germplasm varieties from around the world, about 10 billion pairs-ended sequencing data were obtained (Figure 1A), and a total of 8,375 differentially methylated regions (DMR) were identified during domestication and improvement (Figure 1B), founding that DNA methylation variation was gradually reduced in multiple dimensions during tomato breeding. By integrating multi-omics data such as vairome, transcriptome and metabolome and association analyzing, a multi-omics association network of metabolite-single nucleotide polymorphism-differential methylation regions was constructed (Figure 1C). Based on this network, 13 candidate genes required for polyphenol production were identified and verified (Figure 1D). Several candidate genes could be identified by two variants simultaneously, but part of candidate genes, such as UGT71AV3, could only be identified by DMR.
This study revealed the role of population DNA methylation variation on tomato domestication and metabolic diversity, and showed that DMR can not only affect the biosynthesis of tomato metabolites together with SNP, but also can identified candidate genes that cannot be captured by SNPs, enriching insights into metabolic diversity.
