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Two Y-chromosome-encoded genes determine sex in kiwifruit

Nature Plants volume 5, pages 801–809 (2019)Cite this article

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Abstract

Dioecy, the presence of male and female individuals, has evolved independently in multiple flowering plant lineages1,2,3. Although theoretical models for the evolution of dioecy, such as the ‘two-mutations’ model, are well established4,5, little is known about the specific genes determining sex and their evolutionary history3. Kiwifruit, a major tree crop consumed worldwide, is a dioecious species. In kiwifruit we previously identified a Y-encoded sex-determinant candidate gene acting as the suppressor of feminization (SuF), named Shy Girl (SyGI)6. Here, we identify a second Y-encoded sex-determinant that we named Friendly Boy (FrBy), which exhibits strong expression in tapetal cells. Gene-editing and complementation analyses in Arabidopsis thaliana and Nicotiana tabacum indicated that FrBy acts for the maintenance of male (M) functions, independently of SyGI, and that these functions are conserved across angiosperm species. We further characterized the genomic architecture of the small (<1 megabase pairs (Mb)) male-specific region of the Y chromosome (MSY), which harbours only two genes expressed extensively in developing gynoecia and androecia, respectively: SyGI and FrBy. Re-sequencing of the genome of a natural hermaphrodite kiwifruit revealed that this individual is genetically male but carries deletion(s) of parts of the Y chromosome, including SyGI. Additionally, expression of FrBy in female kiwifruit resulted in hermaphrodite plants. These results clearly indicate that Y-encoded SyGI and FrBy act independently as the SuF and M factors in kiwifruit, respectively, and provide insight into not only the evolutionary path leading to a two-factor sex-determination system, but also a new breeding approach for dioecious species.

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Fig. 1: Identification of the fasciclin-like FrBy as the candidate of the M factor.
Fig. 2: Functional validation of FrBy in two model plants.
Fig. 3: Sequence architecture of the kiwifruit Y chromosome, including the two sex determinants.
Fig. 4: Loss of SyGI, or gain of FrBy, resulted in a natural and synthetic hermaphrodite kiwifruit, respectively.
Fig. 5: Evolutionary model for the establishment of dioecy in Actinidia.

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Data availability

The data that support the findings of this study are available from the corresponding author upon request. All sequence data generated in the context of this manuscript have been deposited in the appropriate DNA Database of Japan: Illumina reads for gDNA-seq and mRNA-seq in the Short Read Archives (SRA) database (SRA Submission ID: DRA008474, Run IDs: DRR180225–180236), and the genomic contig sets constructed with 10X Genomics reads were submitted to Genbank (IDs LC482704–482713).

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Acknowledgements

We thank L. Comai (UC Davis Department Plant Biology and Genome Center) for technical advice and bioinformatics support; Y. Kazama and K. Ishii (Riken Institute) for technical support in using the DelMapper programme; and N. Nieuwenhuizen and J. (L.) Zhang (Plant and Food Research) for vector construction. The KE population was originally provided by Kagawa Prefectural Agricultural Experiment Station. Some of this work was performed at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation (grant No. S10 OD018174). This work was supported by PRESTO (grant Nos. JPMJPR15Q1 (to T.A.) and JPMJPR15Q6 (to S.S.S.)) from the Japan Science and Technology Agency (JST), by a Grant-in-Aid for Scientific Research on Innovative Areas (No. 19H04862 to T.A.) from JSPS and by the National Science Foundation (NSF) IOS award (grant No. 1457230 to I.M.H.).

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  1. Takashi Akagi

    Present address: Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan

Authors and Affiliations

  1. Graduate School of Agriculture, Kyoto University, Kyoto, Japan

    Takashi Akagi, Minori Sonoda & Ryutaro Tao

  2. JST, PRESTO, Kawaguchi-shi, Saitama, Japan

    Takashi Akagi & Shigeo S. Sugano

  3. The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand

    Sarah M. Pilkington, Erika Varkonyi-Gasic, Mark A. McNeilage, Mikaela J. Douglas, Tianchi Wang, Ria Rebstock, Charlotte Voogd, Paul Datson & Andrew C. Allan

  4. Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA

    Isabelle M. Henry & Alana Firl

  5. R-GIRO, Ritsumeikan University, Shiga, Japan

    Shigeo S. Sugano

  6. School of Biological Sciences, University of Auckland, Auckland, New Zealand

    Andrew C. Allan

  7. Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan

    Kenji Beppu & Ikuo Kataoka

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Contributions

T.A., I.K. and R.T. conceived the study. T.A. designed the experiments. T.A., S.M.P., E.V.-G., S.S.S., M.S., A.F., M.J.D., T.W., R.R. and C.V. conducted the experiments. T.A., S.M.P., E.V.-G., S.S.S., M.S., I.M.H. and A.F. analysed the data. S.M.P., M.A.M., P.D., A.C.A., K.B. and I.K. initiated/bred and maintained the plant materials. T.A., S.M.P., E.V. and I.M.H. drafted the manuscript. All authors approved the manuscript.

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Correspondence to Takashi Akagi.

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Peer review information: Nature Plants thanks Roberta Bergero, Susanne Renner and Qi Zhou for their contribution to the peer review of this work.

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Akagi, T., Pilkington, S.M., Varkonyi-Gasic, E. et al. Two Y-chromosome-encoded genes determine sex in kiwifruit. Nat. Plants 5, 801–809 (2019). https://doi.org/10.1038/s41477-019-0489-6

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