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ABSTRACT Plant nitrogen (N)-use efficiency (NUE) is largely determined by the ability of root to take up external N sources, whose availability and distribution in turn trigger the

modification of root system architecture (RSA) for N foraging. Therefore, improving N-responsive reshaping of RSA for optimal N absorption is a major target for developing crops with high

NUE. In this study, we identified _RNR10_ (_REGULATOR OF N-RESPONSIVE RSA ON CHROMOSOME 10_) as the causal gene that underlies the significantly different root developmental plasticity in

response to changes in N level exhibited by the _indica_ (Xian) and _japonica_ (Geng) subspecies of rice. _RNR10_ encodes an F-box protein that interacts with a negative regulator of auxin

biosynthesis, DNR1 (DULL NITROGEN RESPONSE1). Interestingly, RNR10 monoubiquitinates DNR1 and inhibits its degradation, thus antagonizing auxin accumulation, which results in reduced root

responsivity to N and nitrate (NO3−) uptake. Therefore, modulating the RNR10-DNR1-auxin module provides a novel strategy for coordinating a desirable RSA and enhanced N acquisition for

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support SIMILAR CONTENT BEING VIEWED BY OTHERS PLASTID-LOCALIZED AMINO ACID METABOLISM COORDINATES RICE AMMONIUM TOLERANCE AND NITROGEN USE EFFICIENCY Article 21 August 2023 LOCAL AUXIN

BIOSYNTHESIS ACTS DOWNSTREAM OF BRASSINOSTEROIDS TO TRIGGER ROOT FORAGING FOR NITROGEN Article Open access 14 September 2021 TATCP6 IS REQUIRED FOR EFFICIENT AND BALANCED UTILIZATION OF

NITRATE AND PHOSPHORUS IN WHEAT Article Open access 16 February 2025 DATA AVAILABILITY Raw RNA-seq data are deposited at the National Center for Biotechnology Information’s Sequence Read

Archive (SRA) (accession number PRJNA986304). Proteomic identification and ubiquitination proteomics data are deposited at ProteomeXchange (accession number PXD043400). Source data are

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probabilistic framework for structural variant discovery. _Genome Biol._ 15, R84 (2014). Article  PubMed  PubMed Central  Google Scholar  Download references ACKNOWLEDGEMENTS We thank G. Xu

(Nanjing Agricultural University) for critical suggestions. This research was supported by the National Key Research and Development Program of China (No. 2021YFF1000400 to Shan Li), Jiangsu

Province Key Research and Development Program (No. BE2022335-2 to Shan Li), the National Natural Science Foundation of China (No. 32122065 to Shan Li), the Jiangsu Natural Science

Foundation (No. BK20200540 to Shan Li), Fundamental Research Funds for the Central Universities (No. KJYQ2022001 to Shan Li) and Jiangsu Collaborative Innovation Center for Modern Crop

Production. Work in N.P.H.’s laboratory was supported by the BBSRC-Newton ‘Rice’ Initiative (grant no. BB/N013611/1 to N.P.H.) and also by BBSRC Response Modes grant no. BB/S013741/1 to

N.P.H. AUTHOR INFORMATION Author notes * These authors contributed equally: Yunzhi Huang, Zhe Ji. AUTHORS AND AFFILIATIONS * State Key Laboratory of Crop Genetics & Germplasm Enhancement

and Utilization, Nanjing Agricultural University, Nanjing, China Yunzhi Huang, Yujun Tao, Shuxian Wei, Wu Jiao, Yongzhi Fang, Peng Jian, Chengbo Shen, Yaojun Qin, Siyu Zhang, Shunqi Li, 

Xuan Liu, Shuming Kang, Yanan Tian, Qingxin Song & Shan Li * Department of Biology, University of Oxford, Oxford, UK Zhe Ji & Nicholas P. Harberd * State Key Laboratory for

Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China Shaokui Wang * Jiangsu Collaborative Innovation Center for Modern Crop

Production, Nanjing Agricultural University, Nanjing, China Shan Li Authors * Yunzhi Huang View author publications You can also search for this author inPubMed Google Scholar * Zhe Ji View

author publications You can also search for this author inPubMed Google Scholar * Yujun Tao View author publications You can also search for this author inPubMed Google Scholar * Shuxian Wei

View author publications You can also search for this author inPubMed Google Scholar * Wu Jiao View author publications You can also search for this author inPubMed Google Scholar * Yongzhi

Fang View author publications You can also search for this author inPubMed Google Scholar * Peng Jian View author publications You can also search for this author inPubMed Google Scholar *

Chengbo Shen View author publications You can also search for this author inPubMed Google Scholar * Yaojun Qin View author publications You can also search for this author inPubMed Google

Scholar * Siyu Zhang View author publications You can also search for this author inPubMed Google Scholar * Shunqi Li View author publications You can also search for this author inPubMed 

Google Scholar * Xuan Liu View author publications You can also search for this author inPubMed Google Scholar * Shuming Kang View author publications You can also search for this author

inPubMed Google Scholar * Yanan Tian View author publications You can also search for this author inPubMed Google Scholar * Qingxin Song View author publications You can also search for this

author inPubMed Google Scholar * Nicholas P. Harberd View author publications You can also search for this author inPubMed Google Scholar * Shaokui Wang View author publications You can

also search for this author inPubMed Google Scholar * Shan Li View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS Shan Li, Y.H. and Z.J.

conceived and designed this study. Y.H. performed most of the experiments; Y.H., Y. Tao, S. Wei, S.K. and C.S. conducted map-based cloning. Y.H., S.Z., Y.F., Y.Q., P.J. Shunqi Li, X.L., and

Y. Tian constructed transgenic rice plants and performed field experiments and biochemical experiments. Y.H. and Z.J. conducted phylogenetic analysis. W.J. performed bioinformatic analysis.

S. Wang provided SSSL lines. Z.J. and Shan Li wrote the manuscript. Z.J., Q.S., N.P.H., S. Wang and Shan Li revised the manuscript. All authors discussed the results and contributed to the

manuscript. CORRESPONDING AUTHOR Correspondence to Shan Li. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. PEER REVIEW PEER REVIEW INFORMATION _Nature

Plants_ thanks Nicolaus von Wirén and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature

remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EXTENDED DATA EXTENDED DATA FIG. 1 N-DEPENDENT DEVELOPMENTAL PLASTICITY RESPONSES OF

_INDICA_ AND _JAPONICA_ RICE PLANTS. A, 21-day-old rice plants grown at LN (0.375 mM NH4NO3) versus HN (1.25 mM NH4NO3) supply. Scale bar, 10 cm. B, C, The absolute value of total length (B)

and total area (C) of visible roots of 10-day old _indica_ and _japonica_ varieties. Source data EXTENDED DATA FIG. 2 _RNR10_ WAS IDENTIFIED BY FINE-SCALE MAPPING, AND ITS SEQUENCE DIVERGES

BETWEEN _INDICA_ AND _JAPONICA_. A, Successive maps of the candidate gene, _RNR10_, using indicated recombination break points and linked DNA markers to an ~ 3.3 kb segment flanked by the

markers P241 and P242 on chromosome 10. The gene structure of _RNR10_ is shown underneath, where the thick black bars represent the protein-coding sequence, and the start and stop codons are

labelled as ATG and TGA, respectively. The 3496-bp SV and 604-bp deletion in the _RNR10__IRAT261_ promoter relative to the _RNR10_ start ATG (nucleotide 1), are shown. B, Agarose gel

electrophoresis of PCR amplified products from _RNR10_ promoter, open reading frame and protein coding region, respectively. C, D, Agarose gel electrophoresis of PCR amplified products using

primer pairs flanking the 3496-bp segment in the promoter region (C) and the 604-bp segment in the open reading frame (D) from our collection of 12 _indica_ and 12 _japonica_ varieties. E,

Agarose gel electrophoresis shows that there is no detectable difference in the size of the protein coding region. F, The differences in _RNR10_ transcript level between _indica_ and

_japonica_ varieties. Different letters denote significant differences (_P_ < 0.05) from a Duncan’s multiple range test. Exact _P_ values are listed in Supplemental Information Table 11.

Data are mean ± s.e.m. (_n_ = 3 biologically independent samples). Source data EXTENDED DATA FIG. 3 THE ROOT AND SHOOT PHENOTYPES OF THE NIL PLANTS. A, The ratio [(LN-HN)/HN] of total length

of visible roots. B, The absolute value of total length of visible roots. C, The ratio [(LN-HN)/HN] of total area of visible roots. D, The absolute value of total area of visible roots.

E-I, Mature plant height (E), the number of tillers per plant (F), the number of secondary branches per panicle (G), the number of grains per panicle (H), and grain yield per plant (I) of

the NIL plants. J, The ratio [(LN-HN)/HN] of root to shoot biomass ratio. K, L, The changes in the ratios [(LN-HN)/HN] of root biomass (K) and shoot biomass (L) over time. M, N, The absolute

values of root biomass (L) and shoot biomass (M). A, C, E-I, _P_ values were generated from two-sided Student’s _t_ tests. B, D, J-L, Different letters denote significant differences (_P_ 

< 0.05) from a Duncan’s multiple range test. Exact _P_ values are listed in Supplemental Information Table 11. A-D, J-N, Data are mean ± s.e.m. (_n_ = 3 biologically independent samples).

E, Data are mean ± s.e.m. (_n_ = 16 biologically independent samples). F-I, Data are mean ± s.e.m. (_n_ = 12 biologically independent samples). Source data EXTENDED DATA FIG. 4 THE HIGHER

EXPRESSION OF _RNR10_ DRIVEN BY THE _RNR10__IRAT261_ PROMOTER IN THE HJX74 BACKGROUND RESULTED IN REDUCED ROOT GROWTH AND NO3− UPTAKE. A, Morphology of mature HJX74 and

HJX74/_pRNR10__IRAT261__::RNR10-GFP_ plants. Scale bar, 10 cm. B, Root _RNR10_ transcript abundance. Transcript abundance was measured relative to HJX74 (set to 1). C, Root RNR10-GFP protein

abundance. HSP82 severs as loading control. The pictures of western blots represent one of the three experiments performed independently with similar results. D, Root systems of HJX74 and

HJX74/_pRNR10__IRAT261__::RNR10-GFP_ plants. Scale bar, 10 cm. E, The ratio [(LN-HN)/HN] of total length of visible roots. F, The absolute value of total length of visible roots. G, The

ratio [(LN-HN)/HN] of total area of visible roots. H, The absolute value of total area of visible roots. I, The ratio [(LN-HN)/HN] of root to shoot biomass ratio. J, The absolute value of

the ratio of root to shoot biomass. K-N, Mature plant height (K), the number of tillers per plant (L), the number of grains per panicle (M), and grain yield per plant (N). B, E, G, I, K-N,

_P_ values were generated from two-sided Student’s _t_ tests. F, H, J, Different letters denote significant differences (_P_ < 0.05) from a Duncan’s multiple range test. Exact _P_ values

are listed in Supplemental Information Table 11. B, E-J, Data are mean ± s.e.m. (_n_ = 3 biologically independent samples). K, Data are mean ± s.e.m. (_n_ = 16 biologically independent

samples). L-N, Data are mean ± s.e.m. (_n_ = 12 biologically independent samples). Source data EXTENDED DATA FIG. 5 _RNR10_ TRANSCRIPT ABUNDANCE, RNR10 PROTEIN ACCUMULATION AND RSA OF ZH11,

ZH11/_PACT::RNR10-FLAG_ AND ZH11/_RNR10_ PLANTS. A, _RNR10_ mRNA abundance in ZH11/_pAct::RNR10-Flag-_1, ZH11/_pAct::RNR10-Flag-_2 and ZH11/_rnr10_ plants, relative to ZH11 (set to 1). B,

Comparison of RNR10 protein abundance detected by an anti-DDDDK-tag antibody in ZH11 versus ZH11/_pAct::DNR1-Flag_. HSP82 severs as loading control. C, Gene structure of the _RNR10_ gene

showing the location of the CRISPR/Cas9-generated 1-bp deletion in the ZH11/_rnr10_ mutant. D, Comparison of RNR10 protein abundance detected by an anti-RNR10 antibody in ZH11 versus

ZH11/_rnr10_. E-G, The absolute values of total length of visible roots (E), total area of visible roots (F) and root to shoot biomass ratio(G). A, E-G, Different letters denote significant

differences (_P_ < 0.05) from a Duncan’s multiple range test. Exact _P_ values are listed in Supplemental Information Table 11. Data are mean ± s.e.m. (_n_ = 3 biologically independent

samples). The experiments in B and D were repeated independently at least three times with similar results. Source data EXTENDED DATA FIG. 6 PHYLOGENETIC RELATIONSHIP AMONG THE RICE F-BOX

PROTEINS AND THEIR HOMOLOGOUS GENES, AND AMINO ACID SEQUENCE ALIGNMENT OF THE FBA SUBFAMILY. A, Phylogenetic tree of _RNR10_ and its homologous genes, constructed in MEGA11 using the

Neighbour-Joining method. _RNR10_ is indicated by the star. B, Alignment of the protein sequences of members in the FBA subfamily. Black represents identical amino acids. The numbers

indicate the positions of the amino acids. EXTENDED DATA FIG. 7 RNR10 INTERACTS WITH DNR1 AND OSKS. A-D, Four unique peptide sequences were identified by immunoprecipitation followed by mass

spectrometry assays. E-G, Three amino acids were identified by mass spectrometric analysis. H, I, SFLC assays. cLUC-tagged RNR10 was co-transformed into tobacco leaves along with

nLUC-tagged OSK1 (H) or OSK20 (I). J, K, Co-IP experiments. Flag-tagged RNR10 was co-transformed into rice protoplasts with HA-tagged OSK1 (J) or OSK20 (K). The experiments in J and K were

repeated independently at least three times with similar results. Source data EXTENDED DATA FIG. 8 ROOT PHENOTYPES AND THE RATIO OF ROOT TO SHOOT BIOMASS OF NIL-_RNR10__HJX74_-_DNR1__HJX74_,

NIL-_RNR10__IRAT261_, NIL-_DNR1__IRAP9_, AND NIL-_RNR10__IRAT261_-_DNR1__IRAP9_. A, Root systems of NIL-_RNR10__HJX74_-_DNR1__HJX74_, NIL-_RNR10__IRAT261_, NIL-_DNR1__IRAP9_, and

NIL-_RNR10__IRAT261_-_DNR1__IRAP9_ plants. Scale bar, 10 cm. B, The ratio [(LN-HN)/HN] of total length of visible roots. C, The absolute value of total length of visible roots. D, The ratio

[(LN-HN)/HN] of total area of visible roots. E, The absolute value of total area of visible roots. F, 15NO3− uptake rates. G, The ratio [(LN-HN)/HN] of root to shoot biomass ratio. H, The

absolute value of ratio of root to shoot biomass. B-H, Different letters denote significant differences (_P_ < 0.05) from a Duncan’s multiple range test. Exact _P_ values are listed in

Supplemental Information Table 11. Data are mean ± s.e.m. (_n_ = 3 biologically independent samples). Source data EXTENDED DATA FIG. 9 GENE STRUCTURE, ROOT SIZE AND ABOVE-GROUND PHENOTYPES

OF NIL-_DNR1__HJX74_, NIL-_DNR1__IRAP9_, AND NIL-_DNR1__IRAP9__/RNR10_. A, Gene structure of the _RNR10_ gene showing the location of the CRISPR/Cas9-generated 5-bp deletion in the

NIL-_DNR1__IRAP9__/rnr10_ mutant. B, C, The absolute value of total length of visible roots (B) and total area of visible roots (C). D-F, The number of tillers per plant (D), the number of

secondary branches per panicle (E) and the number of grains per panicle (F) of NIL-_DNR1__HJX74_, NIL-_DNR1__IRAP9_ and NIL-_DNR1__IRAP9__/rnr10_. B-F, Different letters denote significant

differences (_P_ < 0.05) from a Duncan’s multiple range test. Exact _P_ values are listed in Supplemental Information Table 11. B, C, Data are mean ± s.e.m. (_n_ = 3 biologically

independent samples). D-F, Data are mean ± s.e.m. (_n_ = 12 biologically independent samples). Source data EXTENDED DATA FIG. 10 EFFECTS ON DNR1 AND RNR10 ABUNDANCE BY EXTERNAL N, AND

_RNR10_ EXPRESSION PATTERN. A, B, Shoot mRNA and protein abundances of DNR1 (A) and RNR10 (B) in HJX74 grown in nutrient solutions with different N supply (0.15 N, 0.1875 mM NH4NO3; 0.3 N,

0.375 mM NH4NO3; 0.6 N, 0.75 mM NH4NO3; 1 N, 1.25 mM NH4NO3). Transcript abundance was measured relative to 0.15 N (set to 1). HSP82 severs as loading control. The experiments in A and B

were repeated independently at least three times with similar results. C, Expression profile of _RNR10_ in root, stem, leaf, node, and panicle tissues. _RNR10_ transcript abundance in root

was set to 1. A-C, Different letters denote significant differences (_P_ < 0.05) from a Duncan’s multiple range test. Exact _P_ values are listed in Supplemental Information Table 11.

Data are mean ± s.e.m. (_n_ = 3 biologically independent samples). Source data SUPPLEMENTARY INFORMATION REPORTING SUMMARY SUPPLEMENTARY TABLE Supplementary Tables 1–11. SOURCE DATA SOURCE

DATA FIG. 1 Statistical source data. SOURCE DATA FIG. 2 Statistical source data. SOURCE DATA FIG. 3 Statistical source data. SOURCE DATA FIG. 4 Statistical source data. SOURCE DATA FIG. 5

Statistical source data. SOURCE DATA FIG. 6 Statistical source data. SOURCE DATA FIG. 7 Statistical source data. SOURCE DATA FIGS. 1, 3, 4, 5 AND 6 Unprocessed blots and gels. SOURCE DATA

EXTENDED DATA FIGS. 1, 3, 4, 5, 8, 9 AND 10 Statistical source data. SOURCE DATA EXTENDED DATA FIGS. 2, 4, 5, 7 AND 10 Unprocessed blots and gels. RIGHTS AND PERMISSIONS Springer Nature or

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Huang, Y., Ji, Z., Tao, Y. _et al._ Improving rice nitrogen-use efficiency by modulating a novel monouniquitination machinery for optimal root plasticity response to nitrogen. _Nat. Plants_

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