Methylome and transcriptome analysis of alters leaf phenotype with autotetraploid in grape

Abstract

The doubling of the plant genome causes obvious morphological and physiological changes, and DNA 5-methylcytosine (5mCs) modification is a key epigenetic component that helps neopolyploids overcome challenges and acquire advantages. In the study of autotetraploid grape, we found that leaf thickness, photosynthetic and antioxidant capacity increased and anthocyanin coloring decreased in autotetraploid compared with diploids. To interpret the molecular and phenotypic changes after whole-genome doubling (WGD), we conducted whole-genome bisulfite sequencing (BS-seq) and transcriptomic analyses of autotetraploid and diploid accessions of grape (Vitis vinifera L.). From the global perspective, genome doubling did not bring significant changes to the methylation of the whole genome. In different grape genomic regions, high levels of methylation occurred in transposable elements (TEs), introns, and promoter regions. Autotetraploid ‘G4X’ grapes had significantly decreased levels of CG and CHH methylation in the TE body relative to diploid ‘G2X’ grapes. Differentially methylated regions (DMRs) between diploid and autotetraploid grapes were related to 1649 hypermethylated and 3418 hypomethylated differentially methylated genes (DMGs), which were enriched in lipid metabolism, phytohormone action in, cell wall organization, redox homeostasis, photosynthesis, and secondary metabolism. Gene expression changes also appeared in autopolyploidization processes, and a total of 68 genes overlapped between the DMGs and differentially expressed genes (DEGs), among which 41 key candidate genes were enriched in five processes related to phenotypic differences. We found that both DMGs and DEGs were enriched in secondary metabolite and anthocyanin biosynthesis, which is related to phenotypic changes in grape polyploid. Collectively, our results show epigenetic modifications in autopolyploid grapes for the first time and support the hypothesis that polyploidization-induced methylation is an important cause of phenotypic alterations.