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The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency


As an essential macroelement for all living cells, phosphorus is indispensable in agricultural production systems. Natural phosphorus reserves are limited1, and it is therefore important to develop phosphorus-efficient crops. A major quantitative trait locus for phosphorus-deficiency tolerance, Pup1, was identified in the traditional aus-type rice variety Kasalath about a decade ago2,3. However, its functional mechanism remained elusive4,5 until the locus was sequenced, showing the presence of a Pup1-specific protein kinase gene6, which we have named phosphorus-starvation tolerance 1 (PSTOL1). This gene is absent from the rice reference genome and other phosphorus-starvation-intolerant modern varieties7,8. Here we show that overexpression of PSTOL1 in such varieties significantly enhances grain yield in phosphorus-deficient soil. Further analyses show that PSTOL1 acts as an enhancer of early root growth, thereby enabling plants to acquire more phosphorus and other nutrients. The absence of PSTOL1 and other genes—for example, the submergence-tolerance gene SUB1A—from modern rice varieties underlines the importance of conserving and exploring traditional germplasm. Introgression of this quantitative trait locus into locally adapted rice varieties in Asia and Africa is expected to considerably enhance productivity under low phosphorus conditions.

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Figure 1: Origin of the donor variety Kasalath and Pup1 candidate genes.
Figure 2: PSTOL1 overexpression enhances tolerance of P deficiency.
Figure 3: PSTOL1 is an enhancer of root growth.
Figure 4: PSTOL1 putative downstream genes co-localize with root and drought QTLs.

Accession codes

Data deposits

GenBank protein accession numbers for OsPupK04-1, OsPupK05-1, OsPupK20-2, OsPupK29-1 and PSTOL1/OsPupK46-2 are BAH79993, BAH79994, BAK26565, BAH80018 and BAK26566, respectively.


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We would like to thank A. Cruz, E. Ramos and L. Olivo for technical and secretarial support, the staff at the transformation laboratory, F. Rossi for help with the Pstol1 kinase assay, M. Akutsu for help with the analysis of transgenic plants, and S. Haefele and his team for their support. We thank J. Prasetiyono, M. Bustamam and S. Moeljopawiro for their long-term collaboration. This project has been primarily funded by the Generation Challenge Program (GCP) since 2005.

Author information

Authors and Affiliations



R.G. cloned and transformed the PSTOL1 gene into IR64 and Nipponbare. R.G., J.P.T. and M.W. performed the phenotyping of transgenic plants. J.H.C. conducted the root meta-QTL analysis and J.H.C. and C.D. developed the IR64-Pup1 and IR74-Pup1 NILs. P.P. carried out the Pstol1 kinase assay. S.C. conducted the expression analysis of putative PSTOL1 downstream genes. E.M.T.M. provided advice about the experiments and I.S.-L. provided technical support and infrastructure for rice transformation. R.G., M.W. and S.H. designed the experiments and wrote the manuscript.

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Correspondence to Sigrid Heuer.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-9. (PDF 1264 kb)

Supplementary Data 1

This file contains Supplementary Table 1, which shows a summary of P starvation responsive genes. (XLS 224 kb)

Supplementary Data 2

This file contains Supplementary Table 2 showing a list of genes with constitutively altered expression in 35S::OsPSTOL1 roots. (XLS 40 kb)

Supplementary Data 3

This file contains Supplementary Table 3, which shows a list of primers used in this study. (XLS 26 kb)

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Gamuyao, R., Chin, J., Pariasca-Tanaka, J. et al. The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488, 535–539 (2012).

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