Transfer of endogenous small RNAs between branches of scions and rootstocks in grafted sweet cherry trees

Authors: ZHAO, DONGYAN - Michigan State University; Zhong, Gan-Yuan; SONG, GUO-QING - Michigan State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/3/2020
Publication Date: 7/28/2020
Citation: Zhao, D., Zhong, G., Song, G. 2020. Transfer of endogenous small RNAs between branches of scions and rootstocks in grafted sweet cherry trees. PLoS ONE. https://doi.org/10.1371/journal.pone.0236376.
DOI: https://doi.org/10.1371/journal.pone.0236376

Interpretive Summary: Grafting is a well-established agricultural practice in many crops. However, how the graft partners interact with each other to produce a vigorous grafted plant is largely unknown, particularly at the molecular level. Recently some exciting progress has been made in this area. One of the exciting discoveries is that some small RNAs could be transferred between graft partners, i.e. scions and rootstocks. Such exchanges of genetic information may contribute to some desirable changes we often observe at the plant level. In this study, we grafted a transgenic rootstock, which has a transgene producing small RNAs for virus resistance, to a non-transgenic scion in sweet cherry. Interestingly, we found the transfer of small RNAs from the transgene and many endogenous genes from the rootstock to the scion. We also observed many small RNAs transferred from the scion to the rootstock. These small RNAs likely play roles in biological processes of plant development and adaptation in the grafted cherry. This work provided an understanding of the long-distance transfer of sRNAs in sweet cherry rootstock-scion interactions.

Technical Abstract: Grafting is a well-established agricultural practice in cherry production for clonal propagation, altered plant vigor and architecture, increased tolerance to biotic and abiotic stresses, precocity, and higher yield. Mobile molecules, such as water, hormones, nutrients, DNAs, RNAs, and proteins play essential roles in rootstock-scion interactions. Small RNAs (sRNAs) are 19 to 30-nucleotides (nt) RNA molecules that are a group of mobile signals in plants. Rootstock-to-scion transfer of transgene-derived small interfering RNAs enabled virus resistance in nontransgenic sweet cherry scion. To determine whether there was long distance scion-to-rootstock transfer of endogenous sRNAs, we compared sRNAs profiles in bud tissues of an ungrafted ‘Gisela 6’ rootstock, two sweet cherry ‘Emperor Francis’ scions as well as their ‘Gisela 6’ rootstocks. Over two million sRNAs were detected in each sweet cherry scion, where 21-nt sRNA (56.1% and 55.8%) being the most abundant, followed by 24-nt sRNAs (13.1% and 12.5%). Furthermore, we identified over three thousand sRNAs that were potentially transferred from the sweet cherry scions to their corresponding rootstocks. In contrast to the sRNAs in scions, among the transferred sRNAs in rootstocks, the most abundant were 24-nt sRNAs (46.3% and 34.8%) followed by 21-nt sRNAs (14.6% and 19.3%). In other words, 21-nt sRNAs had the least transferred proportion out of the total sRNAs in sources (scions) while 24-nt had the largest proportion. The transferred sRNAs were from 574 cherry transcripts, of which 350 had a match from the Arabidopsis thaliana standard protein set. The finding that “DNA or RNA binding activity” was enriched in the transcripts producing transferred sRNAs indicated that they may affect the biological processes of the rootstocks at different regulatory levels. Overall, the profiles of the transported sRNAs and their annotations revealed in this study facilitate a better understanding of the role of the long-distance transported sRNAs in sweet cherry rootstock-scion interactions as well as in branch-to-branch interactions in a tree.