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Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies



Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.

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Figure 1: NRT1.1B variation contributes to differences in nitrate use.
Figure 2: Functional characterization and tissue-localization assay of NRT1.1B.
Figure 3: Variation in NRT1.1B could affect nitrate uptake, nitrate root-to-shoot transport and the expression of nitrate-responsive genes.
Figure 4: Phylogenetic analysis of NRT1.1B.
Figure 5: NRT1.1B-indica introgression improves NUE.
Figure 6: NRT1.1B-indica transgenic plants showed higher NUE than 1B-japonica transgenic plants.


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We thank H. Xue (Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China) for providing the nrt1.1b mutant and M. Schläppi (Marquette University, Milwaukee, Wisconsin, USA) and X. Wang (China Agricultural University, Beijing, China) for language editing. This work was supported by grants from the Ministry of Science and Technology of China (2014AA10A602-5, 2015CB755702) and the Chinese Academy of Sciences (XDA08010400).

Author information




B.H. performed most of the experiments. J.T. and W.W. constructed the NIL. W.W., Z.Z., Z.P., Q.D. and Y.L. performed the field test. S.O. and H.W. performed the population genetic analysis. H.L. assayed 15N accumulation in rice cultivars. R.C. carried out the in situ hybridization. X.C. and L. Li performed the Xenopus oocyte injection. Y.W., C.L., L. Liu, K.D. and C.X. performed the chlorate-sensitivity assay. C.C., B.H. and L.Z. designed the experiments. B.H., C.C. and S.O. wrote the manuscript.

Corresponding author

Correspondence to Chengcai Chu.

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The authors declare no competing financial interests.

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Supplementary Figures 1–14, Supplementary Tables 1–3 and Supplementary Note (PDF 2815 kb)

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Hu, B., Wang, W., Ou, S. et al. Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nat Genet 47, 834–838 (2015).

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