The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency

Zhenyu Gao,Chaolei Liu,Hongzhen Jiang,Anpeng Zhang,Guang Chen,Nicholas P Harberd,Longbiao Guo,Dali Zeng,Banpu Ruan,Danying Wang,Guojun Dong,Guohua Xu,Shenglong Yang,Jiang Hu,Li Zhu,Yufeng Wang,Lianguang Shang,Sheng Teng,Guangheng Zhang,Qian Qian

doi:10.1038/s41467-019-13110-8

Abstract

The indica and japonica rice (Oryza sativa) subspecies differ in nitrate (NO3−) assimilation capacity and nitrogen (N) use efficiency (NUE). Here, we show that a major component of this difference is conferred by allelic variation at OsNR2, a gene encoding a NADH/NADPH-dependent NO3− reductase (NR). Selection-driven allelic divergence has resulted in variant indica and japonica OsNR2 alleles encoding structurally distinct OsNR2 proteins, with indica OsNR2 exhibiting greater NR activity. Indica OsNR2 also promotes NO3− uptake via feed-forward interaction with OsNRT1.1B, a gene encoding a NO3− uptake transporter. These properties enable indica OsNR2 to confer increased effective tiller number, grain yield and NUE on japonica rice, effects enhanced by interaction with an additionally introgressed indica OsNRT1.1B allele. In consequence, indica OsNR2 provides an important breeding resource for the sustainable increases in japonica rice yields necessary for future global food security.

Highlights

The indica and japonica rice (Oryza sativa) subspecies differ in nitrate (NO3−) assimilation capacity and nitrogen (N) use efficiency (NUE)
We show that the indica OsNRT1.1B. Because qCR2 (OsNR2) allele confers superior grain yield and NUE, in part via feed-forward interaction with OsNRT1.1B, a gene coding for a NO3− uptake transporter[20]
We found that expression of 9311 OsNR2 coding sequence or reduction in OsNR2 mRNA abundance respectively caused increase or decrease in Nipponbare maximal and active nitrate reductase (NR) activity (Fig. 1e, Supplementary Fig. 2c), changes in enzymatic activity that mirror the effect of allelic variation at OsNR2 on relative ClO3− resistance

Summary

Introduction

The indica and japonica rice (Oryza sativa) subspecies differ in nitrate (NO3−) assimilation capacity and nitrogen (N) use efficiency (NUE). Indica OsNR2 promotes NO3− uptake via feedforward interaction with OsNRT1.1B, a gene encoding a NO3− uptake transporter. These properties enable indica OsNR2 to confer increased effective tiller number, grain yield and NUE on japonica rice, effects enhanced by interaction with an introgressed indica OsNRT1.1B allele. We identify major quantitative trait loci (QTLs) conferring the ClO3− resistance differences between the indica (variety 9311) and japonica (Nipponbare) rice subspecies. We show that the indica OsNR2 allele confers superior grain yield and NUE (versus the japonica allele), in part via feed-forward interaction with OsNRT1.1B, a gene coding for a NO3− uptake transporter[20]

Methods

Results

Conclusion