Abstract
Cytokinins play important roles in the growth and development of plants. Physiological and photosynthetic characteristics are common indicators to measure the growth and development in plants. However, few reports have described the molecular mechanisms of physiological and photosynthetic changes in response to cytokinin, particularly in woody plants. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression in response to the external environment. In this study, we examined genome-wide DNA methylation variation and transcriptional variation in poplar (Populus tomentosa) after short-term treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA). We identified 460 significantly differentially methylated regions (DMRs) in response to 6-BA treatment. Transcriptome analysis showed that 339 protein-coding genes, 262 long non-coding RNAs (lncRNAs), and 15,793 24-nt small interfering RNAs (siRNAs) were differentially expressed under 6-BA treatment. Among these, 79% were differentially expressed between alleles in P. tomentosa, and 102,819 allele-specific expression (ASE) loci in 19,200 genes were detected showing differences in ASE levels after 6-BA treatment. Combined DNA methylation and gene expression analysis demonstrated that DNA methylation plays an important role in regulating allele-specific gene expression. To further investigate the relationship between these 6-BA-responsive genes and phenotypic variation, we performed SNP analysis of 460 6-BA-responsive DMRs via re-sequencing using a natural population of P. tomentosa, and we identified 206 SNPs that were significantly associated with growth and wood properties. Association analysis indicated that 53% of loci with allele-specific expression had primarily dominant effects on poplar traits. Our comprehensive analyses of P. tomentosa DNA methylation and the regulation of allele-specific gene expression suggest that DNA methylation is an important regulator of imbalanced expression between allelic loci.
Highlights
Cytokinins are an important class of phytohormones whose discovery was based on their ability to promote cell division in tobacco tissue [1]
After 6-BA treatment, both the total number of tags and number of unique tags of 24-nt small interfering RNAs (siRNAs) decreased, with the number of unique tags decreasing by 45.29%. These findings indicate that the diversity and abundance of 24-nt siRNAs in poplar sharply decreased under 6-BA treatment
We have shown that total protein content and POD activities increased and decreased, while sucrose phosphate synthase (SPS) and MDA activities decreased at the early stage and increased under 6-BA treatment in poplar
Summary
Cytokinins are an important class of phytohormones whose discovery was based on their ability to promote cell division in tobacco tissue [1]. Exploring the response patterns of P. tomentosa to 6-BA treatment and the interactions between various genetic regulatory elements and their effects on DNA methylation are of vital importance. Exogenous phytohormone treatment affects the diploid plant poplar at the transcriptional level by altering gene expression and by influencing the expression of alleles, as allelic differences play a critical role in gene regulation. To explore the molecular mechanism of these changes in response to short-term 6-BA treatment, we systematically identified 6-BA-responsive variation patterns in P. tomentosa leaf at the genome-wide scale, including transcriptional variation (transcriptional expression and allele-specific expression) and epigenetic variation (DNA methylation). Through annotating DMRs to the genome, we selected a variety of transcription elements located in DMRs that are potentially regulated by DNA methylation, including genes, lncRNAs, and siRNAs. We performed the first systematic survey of ASE in poplar under 6-BA treatment. The results of this study increase our understanding of the effects of 6-BA-responsive DNA methylation on allele-specific gene expression in Populus and lay the foundation for further research on the regulatory effects of 6-BA on plant growth
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