Reducing phosphorus accumulation in rice grains with an impaired transporter in the node

An Erratum to this article was published on 01 February 2017

Abstract

Phosphorus is an important nutrient for crop productivity. More than 60% of the total phosphorus in cereal crops is finally allocated into the grains and is therefore removed at harvest. This removal accounts for 85% of the phosphorus fertilizers applied to the field each year1,2. However, because humans and non-ruminants such as poultry, swine and fish cannot digest phytate, the major form of phosphorus in the grains, the excreted phosphorus causes eutrophication of waterways. A reduction in phosphorus accumulation in the grain would contribute to sustainable and environmentally friendly agriculture. Here we describe a rice transporter, SULTR-like phosphorus distribution transporter (SPDT), that controls the allocation of phosphorus to the grain. SPDT is expressed in the xylem region of both enlarged- and diffuse-vascular bundles of the nodes, and encodes a plasma-membrane-localized transporter for phosphorus. Knockout of this gene in rice (Oryza sativa) altered the distribution of phosphorus, with decreased phosphorus in the grains but increased levels in the leaves. Total phosphorus and phytate in the brown de-husked rice were 20–30% lower in the knockout lines, whereas yield, seed germination and seedling vigour were not affected. These results indicate that SPDT functions in the rice node as a switch to allocate phosphorus preferentially to the grains. This finding provides a potential strategy to reduce the removal of phosphorus from the field and lower the risk of eutrophication of waterways.

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Figure 1: Tissue specificity of SPDT expression and subcellular localization of SPDT.
Figure 2: Transport activity of SPDT protein.
Figure 3: Phenotypic analysis of spdt mutants at different growth stages.
Figure 4: Role of node-localized SPDT in P distribution in rice and effect of SPDT knockout on P resource.

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Acknowledgements

This work was supported by Grant-in-Aid for Specially Promoted Research (JSPS KAKENHI Grant Number 15H04469 to N.Y. and 16H06296 to J.F.M.).

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Authors

Contributions

N.Y. and Y.T. contributed equally to this work. N.Y. and J.F.M. designed research; N.Y. and Y.T. performed most experiments. Transport activity for Pi was determined by T.M. in vitro and by N.M.-U. in oocytes. K.T.Y. determined the phytic acid concentration; N.Y., Y.T. and J.F.M. analysed data; and N.Y. and J.F.M. wrote the paper.

Corresponding author

Correspondence to Jian Feng Ma.

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The authors declare no competing financial interests.

Additional information

Reviewer Information Nature thanks C. Vance and M. Wissuwa and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Figure 1 Gene structure, Tos-17 insertion mutants and phylogeny of SPDT.

a, Structure of the SPDT gene. The gene consists of 10 exons and 9 introns. The exons are indicated as white boxes. Positions of the Tos-17 insertion are indicated as triangles. Primers (F1 and R2) for reverse transcription PCR (RT–PCR) are shown as arrows. b, Expression of SPDT mRNA in wild-type rice and three Tos-17 insertion mutants (spdt-1spdt-3) examined by RT–PCR. c, Phylogenetic tree of sulfate transporter (Sultr) proteins in rice (Os) and Arabidopsis thaliana (At). Bootstrap values from 1,000 trials are indicated. The 0.1 scale shows substitution distance.

Extended Data Figure 2 Expression pattern of SPDT gene at different growth stages of rice.

a, b, Response of SPDT expression to different P (a) or S (b) supply at the vegetative growth stage. Seedlings (12 days old) were exposed to various external P or S concentrations for 1 week. The roots, shoot basal region (5 mm above the root-shoot junction), and shoots were sampled for RNA extraction. c, Expression pattern of SPDT at the reproductive growth stage. Samples of various organs were taken from rice grown in a paddy field at flowering and grain filling stages. The expression level was determined by quantitative RT–PCR. Expression relative to the shoot basal region in the control condition (a, b) or roots at the flowering stage (c) are shown. Histone H3 was used as the internal standard. Data are mean ± s.d. of biological replicates (n = 3). Source data

Extended Data Figure 3 Subcellular localization of SPDT.

ah, GFP:SPDT (ad) or GFP control (eh) together with DsRed were transiently introduced into onion epidermal cells by particle bombardment. Fluorescence signals from GFP (a, e), DsRed (b, f) and the merged images (c, g) are shown. Magnified image of boxed area in c and g are shown in d and h, respectively. Data are representative of three independent cells. Scale bars, 100 μm.

Extended Data Figure 4 Growth of wild-type rice and spdt mutants at the vegetative growth stage under low P and S conditions.

ac, Wild-type rice and spdt mutants were grown in a nutrient solution containing 90 μM P and 460 μM S (a, control), 1 μM P and 460 μM S (b, low P), or 90 μM P and 10 μM S (c, low S) for 42 days. Plants were separated into roots, shoot basal region and individual leaves (2 to 9 from older to younger). Inset in b shows magnified image of leaf blade of leaf 7. For comparison, part pictures in a and b (WT and spdt-1) are the same as those in Fig. 3a, b. Pictures are representative of three biological replicates. df, Dry weight of each part sampled in ac, respectively. Data are mean ± s.d. of biological replicates (n = 3). **P < 0.01, mutants compared with wild type (Tukey’s multiple comparison test). Source data

Extended Data Figure 5 Accumulation, distribution and redistribution of P at the vegetative growth stage.

a, b, P content (a) and P concentration (b) in different organs. Wild-type rice and spdt mutants were grown hydroponically under a P-sufficient condition (90 μM) for 32 days. c, P re-distribution. Wild-type rice and three mutants were exposed to the nutrient solution free of P for 1 week. Samples of each organ were taken before and after P starvation treatment. The difference in P content (∆P) of each organ was calculated. d, Short-term (6 h) distribution analysis of P. Plants were treated with 1 μM radiolabelled 32P for 6 h. Distribution rate of newly absorbed P in different organ is shown. Data are mean ± s.d. of 3 (ac) or 5 (d) biological replicates. *P < 0.05, **P < 0.01, mutants compared with wild type (Tukey’s test). Source data

Extended Data Figure 6 Distribution of Mg, S, K and Ca in different organs at the vegetative growth stage.

ad, Wild-type rice and spdt mutants were grown hydroponically until the 8-leaf stage in half-strength Kimura B solution containing 90 μM Pi. Plants were separated into roots, shoot basal region and individual leaves (2 to 8 from older to younger) for the determination of Mg (a), S (b), K (c) and Ca (d) concentrations. Data are mean ± s.d. of biological replicates (n = 3). **P < 0.01, mutants compared with wild type (Tukey’s multiple comparison test). Source data

Extended Data Figure 7 Comparison of growth and yield between wild-type rice and spdt mutants.

ad, Wild-type rice and spdt mutants were grown in a paddy field until ripened. At harvest, plant height (a), stem length (b), tiller number (c) and panicle number (d) were recorded. Data are mean ± s.d. of 24 biological replicates (3 plots with 8 replicates each). *P < 0.05, **P < 0.01, mutants compared with wild type (Tukey’s multiple comparison test). e, f, Panicle (e) and brown rice (f) of wild-type rice and spdt mutants. Images are representative of 24 lines. Scale bars, 10 mm. Source data

Extended Data Figure 8 Concentration and distribution of P at the reproductive growth stage.

Wild-type rice and spdt mutants were grown in a paddy field until ripened. a, P concentration in different organs of above-ground part. b, P content in different organs per tiller. c, Dry weight in different organs per tiller. d, Dry weight distribution ratio in different organs of above-ground part. e, Total P content of above-ground part per plant. f, Inorganic phosphate (Pi) concentration in brown rice. g, Stem-fed short-term distribution analysis. At the grain-filling stage, the plants were cut at the internode III. Solution containing 1 μM radiolabelled P was fed from the cut-end of the stem for 24 h. Distribution ratio of newly absorbed P in different organs above node I was calculated. Data are mean ± s.d. of 9 (3 plots with 3 replicates each; ae), 3 (f) or 10 (g) biological replicates. *P < 0.05, **P < 0.01, compared with wild-type (Tukey’s test). Source data

Extended Data Figure 9 Effect of SPDT knockout on seed germination and early growth.

a, Day-dependent germination rate. Thirty seeds each of wild-type rice and spdt mutants were used for the germination test, which was conducted in water at 30 °C in the dark. The water was changed every day. Data are mean ± s.d. of biological replicates (n = 3). b, c, Time-dependent growth of the shoot (b) and root (c) after germination. Twenty germinated seeds were grown in a 0.5 mM CaCl2 solution up to 5 days at 25 °C. Shoot and root lengths were measured with a ruler daily. Data are mean ± s.d. of biological replicates (n = 20). d, Phenotype of wild-type rice and spdt mutants grown in soil for 3 weeks. Source data

Extended Data Figure 10 Element concentration of brown rice.

Wild-type rice and three spdt mutants were grown in a paddy field until ripened. Concentrations of elements in the brown rice were determined with a CHN analyser (C and N), MP-AES (S) or by ICP-MS (other elements) after digestion. Data are mean ± s.d. of 3 (C and N) or 9 (3 plots with 3 replicates each; other elements) biological replicates. *P < 0.05, **P < 0.01, compared with wild type (Tukey’s test). Source data

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The file contains the uncropped scans for Figure 2a and Extended Data Figure 1b. (PDF 1492 kb)

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Yamaji, N., Takemoto, Y., Miyaji, T. et al. Reducing phosphorus accumulation in rice grains with an impaired transporter in the node. Nature 541, 92–95 (2017). https://doi.org/10.1038/nature20610

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