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Unidirectional movement of small RNAs from shoots to roots in interspecific heterografts

Nature Plants volume 7, pages 50–59 (2021)Cite this article

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Abstract

Long-distance RNA movement is important for plant growth and environmental responses; however, the extent to which RNAs move between distant tissues, their relative magnitude and functional importance remain to be elucidated on a genomic scale. Using a soybean (Glycine max)–common bean (Phaseolus vulgaris) grafting system, we identified 100 shoot–root mobile microRNAs and 32 shoot–root mobile phased secondary small interfering RNAs (phasiRNAs), which were predominantly produced in shoots and transported to roots, and, in most cases, accumulated to a level similar to that observed in shoots. Many of these microRNAs or phasiRNAs enabled cleavage of their messenger RNA targets or phasiRNA precursors in roots. In contrast, most mobile-capable mRNAs were transcribed in both shoots and roots, with only small proportions transported to recipient tissues. These findings suggest that the regulatory mechanisms for small RNA movement are different from those for mRNA movement, and that the former is more strictly regulated and, probably, more functionally important than the latter.

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Fig. 1: Mobility and relative abundance of soybean and common bean sRNAs.
Fig. 2: Relative abundance and systemic gene regulation of mobile miRNAs.
Fig. 3: Relative abundance and systemic gene regulation of mobile phasiRNAs.
Fig. 4: Differences in directionality and relative abundance between mobile sRNAs and mRNAs.

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Data availability

The raw read sequences are deposited in the National Center for Biotechnology Information Sequence Read Achieve (http://www.ncbi.nlm.nih.gov/sra/) under the accession number PRJNA648759. The miRNAbase53 database (Release 22.1, 2018) was used for identifying known soybean and common bean miRNAs and their precursors.

Code availability

Custom Perl codes used for data analysis in this paper can be found at https://github.com/wang3283/sRNA-normalize-and-GO-anlaysis-input.

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Acknowledgements

This work was partially supported by the Agriculture and Food Research Initiative of the USDA National Institute of Food and Agriculture (grant no. 2018-67013-27425 to J.M.), the National Natural Science Foundation of China (grant no. 31971898 to S.L.), the National Key R&D Project of China (grant no. 2016YFD0100304 to C.C. and S.L.) and the Purdue AgSEED programme to J.M.

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  1. These authors contributed equally: Shuai Li, Xutong Wang.

Authors and Affiliations

  1. Department of Agronomy, Purdue University, West Lafayette, IN, USA

    Shuai Li, Xutong Wang, Liyang Chen, Chancelor B. Clark & Jianxin Ma

  2. College of Life Sciences, Qingdao Agricultural University, Qingdao, China

    Shuai Li, Wenying Xu, Tong Liu & Chunmei Cai

  3. Center for Plant Biology, Purdue University, West Lafayette, IN, USA

    Jianxin Ma

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Contributions

J.M., S.L. and X.W. designed the research. X.W. analysed the data. S.L., X.W., W.X., T.L., C.C., L.C. and C.B.C. performed the research. J.M. wrote the manuscript with input from X.W. and S.L.

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Correspondence to Jianxin Ma.

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Peer review information Nature Plants thanks Margaret Frank, Charles Melnyk and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Relative abundances of both the mobile and immobile sRNAs in grafted shoot and root tissues.

a. Comparison of soybean-specific hcsiRNA abundances between the Pv/Gm and Gm/Gm roots. b, Comparison of common bean-specific hcsiRNA abundances between the Gm/Pv and Pv/Pv roots. c. Comparison of soybean-specific miRNA abundances between the Pv/Gm and Gm/Gm roots. d, Comparison of common bean-specific miRNA abundances between the Gm/Pv and Pv/Pv roots. e. Comparison of soybean-specific phasiRNA abundances between the Pv/Gm and Gm/Gm roots. f, Comparison of common bean-specific phasiRNA abundances between the Gm/Pv and Pv/Pv roots. Gm and Pv indicate soybean and common bean, respectively, and the specific tissue in two grafted samples is underlined below using the shoot/root notation.

Extended Data Fig. 2 Relative abundance of mobile hcsiRNAs in grafted shoot and root tissues.

a. Comparison of soybean hcsiRNA abundances between the Gm/Pv shoots and the Gm/Pv roots. b, Comparison of common bean hcsiRNA abundances between the Pv/Gm shoots and the Pv/Gm roots. c, Comparison of soybean hcsiRNA abundances between the Gm/Gm and the Gm/Pv shoots. d, Comparison of common bean hcsiRNA abundances between the Pv/Pv and Pv/Gm shoots. Gm and Pv indicate soybean and common bean, respectively, and the specific tissue in two grafted samples is underlined below using the shoot/root notation.

Extended Data Fig. 3 Relative abundances of a representative subset of mobile miRNAs in grafted shoot and root tissues validated by stem-loop qRT-PCR.

Gm and Pv indicate soybean and common bean, respectively, and two specific tissue in grafted samples is underlined below using the shoot/root notation. Values are shown as means ± standard errors (s.e.) from three biological replicates. All statistically differences between means with p < 0.01 are indicated as different letters on barplots (one-way ONOVA, Tukey HSD).

Extended Data Fig. 4 Relative abundance of mobile miRNAs and MiRNA transcripts in grafted tissues.

a. Comparison of soybean miRNA abundances between the Gm/Pv shoots and the Gm/Pv roots. b, Comparison of common bean miRNA abundances between the Pv/Gm shoots and the Pv/Gm roots. c, Comparison of soybean miRNA abundances between the Gm/Gm sand the Gm/Pv shoots. d, Comparison of common bean miRNA abundances between the Pv/Pv and the Pv/Gm shoots. e, Comparison of soybean MiRNA abundances between the Gm/Pv shoots and the Pv/Gm roots. f, Comparison of common bean MiRNA abundances between the Pv/Gm shoots and the Gm/Pv roots. Gm and Pv indicate soybean and common bean, respectively, and the specific tissue in two grafted samples is underlined below using the shoot/root notation.

Extended Data Fig. 5 Relative abundance and of mobile phasiRNAs and PHAS transcripts in grafted tissues.

a, Comparison of soybean phasiRNA abundances between the Gm/Pv shoots and the Gm/Pv roots. b, Comparison of common bean phasiRNA abundances between the Pv/Gm shoots and the Pv/Gm roots. c, Comparison of soybean phasiRNA abundances between the Gm/Gm and the Gm/Pv shoots. d, Comparison of common bean phasiRNA abundances between the Pv/Pv and the Pv/Gm shoots. e, Comparison of soybean PHAS abundances between the Gm/Pv shoots and the Pv/Gm roots. f, Comparison of common bean PHAS abundances between the Pv/Gm shoots and the Gm/Pv roots. Gm and Pv indicate soybean and common bean, respectively, and the specific tissue in two grafted samples is underlined below using the shoot/root notation.

Extended Data Fig. 6 Relative abundance of a representative subset of mobile mRNAs validated by qRT-PCR.

Gm and Pv indicate soybean and common bean, respectively, and the specific tissue in two grafted samples is underlined below using the shoot/root notation. Values are shown as means ± standard errors (s.e.) from three biological replicates. All statistically differences between means with p < 0.01 are indicated as different letters on barplots (one-way ONOVA, Tukey HSD).

Extended Data Fig. 7 Gene ontology (GO) terms enrichment of mobile mRNAs in soybean and common bean.

“S->R” indicates the shoot-to-root movement of mRNAs, whereas “R->S” indicates the root-to-shoot movement of mRNAs. GO slims, the cut-down versions of the GO ontologies containing a subset of the terms in the whole GO in plants were used for the enrichment analysis.

Supplementary information

Supplementary Information

Supplementary Tables 1 and 3.

Reporting Summary

Supplementary Tables

Supplementary Tables 2 and 4–13.

Supplementary Data 1

Soybean and common bean mobile sRNAs detected by grafting.

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Li, S., Wang, X., Xu, W. et al. Unidirectional movement of small RNAs from shoots to roots in interspecific heterografts. Nat. Plants 7, 50–59 (2021). https://doi.org/10.1038/s41477-020-00829-2

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