Natural variation of OsWRKY23 drives difference in nitrate use efficiency between indica and japonica rice

Siyu Zhang, Zhe Ji, Wu Jiao, Chengbo Shen, Yaojun Qin, Yunzhi Huang, Menghan Huang, Shuming Kang, Xuan Liu, Shunqi Li, Zulong Mo, Ying Yu, Bingyu Jiang, Yanan Tian, Longfei Wang, Qingxin Song, Shaokui Wang and Shan Li ()
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Siyu Zhang: Nanjing Agricultural University
Zhe Ji: University of Oxford
Wu Jiao: Nanjing Agricultural University
Chengbo Shen: Nanjing Agricultural University
Yaojun Qin: Nanjing Agricultural University
Yunzhi Huang: Nanjing Agricultural University
Menghan Huang: Nanjing Agricultural University
Shuming Kang: Nanjing Agricultural University
Xuan Liu: Nanjing Agricultural University
Shunqi Li: Nanjing Agricultural University
Zulong Mo: Nanjing Agricultural University
Ying Yu: Nanjing Agricultural University
Bingyu Jiang: Nanjing Agricultural University
Yanan Tian: Nanjing Agricultural University
Longfei Wang: Nanjing Agricultural University
Qingxin Song: Nanjing Agricultural University
Shaokui Wang: South China Agricultural University
Shan Li: Nanjing Agricultural University

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Between the two major rice subspecies, indica varieties generally exhibit higher nitrate (NO3‒) uptake and nitrogen (N)-use efficiency (NUE) than japonica varieties. Introducing efficient NO3‒ utilization alleles from indica into japonica could improve NUE, and at the same time uncover unknown regulators of NO3‒ metabolism. Here, we identify OsWRKY23 as a key regulator of NO3‒ uptake and NUE differences between indica and japonica rice. The OsWRKY23indica allele exhibits reduced transcriptional activation of a negative regulator of auxin accumulation, DULL NITROGEN RESPONSE1 (DNR1). The resultant increase in auxin level improves NO3‒ uptake and assimilation, which ultimately enhances grain yield. Geographical and evolutionary analyses reveal overlapping distribution of OsWRKY23indica and DNR1indica, particularly in low-fertility soils, suggesting their involvement in the adaptation to low N conditions to improve NUE and grain yield. Incorporating the OsWRKY23-DNR1 module from indica rice represents a promising strategy to enhance japonica NUE, which is crucial for sustainable agriculture.

Date: 2025
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DOI: 10.1038/s41467-025-56752-7

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