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• W2893828004 abstract "Grafting is commonly used in agriculture. For example, in grapes, scions with desirable fruit qualities are grafted to a disease-resistant root stock, and some tree fruit cultivars are clonally propagated, for example, to promote growth and hasten flowering time (reviewed by Melnyk, 2017; Tsutsui and Notaguchi, 2017). Phenotypic changes in the scion can occur, and sometimes be transmitted, either sexually or asexually (e.g. Cao et al., 2016). In the highlighted paper (Yu et al., 2018), Liping Chen's group provide a possible molecular mechanism underlying such phenotypic changes. They addressed this question by generating and analyzing adventitious shoots regenerated from stem segments of a periclinal chimera from two phenotypically different parents, Brassica juncea (tuber mustard), an important vegetable crop in China, and Brassica oleracea (red cabbage), as illustrated in Figure 1. Liping Chen has been a professor in the Horticulture Department at Zhejiang University in Hangzhou since 2006; she received her Ph.D. with Yutaka Hirata at Tokyo University of Agriculture and Technology, where she first started to use chimeras in the Brassicaceae to analyze grafting-induced variations. Liping spent a 3 month visit in Susheng Gan's lab at Cornell in 2012, and since 2012 Susheng has visited Hangzhou every year, to facilitate their continued collaboration. The first author, Ningning Yu, as well as Lu Yuan, are Ph.D. students in Liping's lab, and Xiao Zhi and Yiqian Chen are M.S. students. Liwen Cao was a joint Zheijiang and Cornell Ph.D. student supervised by both Liping and Susheng, and is now a postdoc in Liping's lab, where she is studying grafting-induced epigenetic variations in the sexual progeny of Brassica juncea and B. oleracea. The Chen lab had shown that adventitious shoots from stem segments are derived from layer 2 and/or layer 3 (Zhu et al., 2007), so they expected that the constitution of the adventitious shoots derived from TCC would have a CCC constitution, and they confirmed this using PCR with B. oleracea- or B. juncea-specific primers. The adventitious shoots derived from the TCC chimera had a similar appearance to CCC plantlets, namely smooth purple leaves and no epidermal hairs. However, they had less wax content than the corresponding red cabbage parent. Yu et al. (2018) therefore hypothesized that some sort of communication from the T outermost layer of the periclinal chimera had influenced these phenotypes in the derived adventitious shoots. Before testing what sort of communication this was and how persistent it might be, they also regenerated adventitious shoots from self-grafted TTT and CCC (regenerated and self-grafted, denoted with r-s), as controls (as passage through tissue culture can sometimes yield phenotypic changes), and then propagated the axillary shoots derived from r-s-TTT, r-s-CCC and r-CCC asexually through ‘generations’, denoted with a number (e.g. r-CCC4). They then compared the global DNA methylation changes and small RNA fluctuations in the adventitious shoots derived from the periclinal chimera and the corresponding parents. They found that both CG and CHH methylation levels were higher in r-CCC4 than in r-s-CCC4. Among the differentially methylated genes, thirteen genes encoded proteins in the wax biosynthetic pathway; and they further examined four of these via bisulfite sequencing. Indeed, for three of the genes, the expression levels were inversely correlated with their methylation level; there was more CG-hypermethylation at these genes in r-CCC4 than in r-s-CCC4. Furthermore, the expression levels of MET1, encoding a methyltransferase responsible for maintaining symmetrical context methylated CG residues, was higher in r-CCC4 than in r-s-CCC4, while the total CHG methylation was slightly lower in r-CCC4, consistent with the higher transcript abundance of MET1 and lower expression level of CMT3, which encodes a chromomethylase responsible for maintaining CHG methylation. The types and expression levels of siRNAs in the asexual progeny and the corresponding parents were then explored to characterize their potential role in the hetero-grafting process. From their small RNA sequencing, a majority of siRNAs showed higher expression levels in r-CCC than in r-s-CCC. Specifically, 1135 siRNA tags were expressed in r-CCC and subsequent generations but not in r-s-CCC. Notably, 159 of these siRNA tags were candidates for mobile signals between T cells and C cells, as they were also expressed in r-s-TTT. 65% of the 1135 specific siRNAs were associated with repeat elements, and the methylation levels of the overlapping regions were mainly hypermethylated in r-CCC4. As methylation of transposable elements is usually controlled by siRNAs through the RdDM pathway (reviewed by Houri-Zeevi and Rechavi, 2017), Yu et al. (2018) proposed that grafting-mobile or triggered siRNAs might direct establishment of DNA methylation, primarily at repeat elements. Notably, these repeat element-associated siRNAs showed constitutive expression in the asexual progeny for at least four generations, and therefore might have an important role in maintaining genome stability. They are further investigating the status of grafting-induced epigenetic modifications in sperm cells, to understand why some phenotypic changes are heritable sexually but some are not. In addition to the wax biosynthesis differences between r-s-CCC4 and r-CCC4, they noticed that r-CCC4 plants flower a bit earlier than the parental red cabbage line. As another of the differentially methylated genes identified in r-CCC4 encodes a component of the circadian clock, they plan to test if the flowering response is another target for siRNAs and differential methylation in shoots derived from TCC stem segments. Lastly, they are expanding their work beyond the Brassicaceae, using fir tree chimeras to test if phenotypic differences in this system can also be explained by siRNAs and differential methylation." @default.
• W2893828004 created "2018-10-05" @default.
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• W2893828004 date "2018-09-21" @default.
• W2893828004 modified "2023-09-27" @default.
• W2893828004 title "Altered phenotypes via graft-transmitted siRNAs" @default.
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• W2893828004 doi "https://doi.org/10.1111/tpj.14082" @default.
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