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,a...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.展开更多
基金supported by the Hainan Province Science and Technology Special Fund(ZDYF2022XDNY144)the National Natural Science Foundation of China(32100212)+3 种基金the National Key Research and Development Program of China(2021YFA0909600,2022YFF1001900)the Young Elite Scientists Sponsorship Program by CAST(2019QNRC001)the Hainan Provincial Academician Innovation Platform Project(HD-YSZX-202003,HD-YSZX-202004)the Hainan University Startup Fund(KYQD(ZR)1916,KYQD(ZR)21025)。
文摘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.
