Genome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice

Weijie Tang, Jian Ye, Xiangmei Yao, Pingzhi Zhao, Wei Xuan, Yunlu Tian, Yuanyan Zhang, Shuang Xu, Hongzhou An, Gaoming Chen, Jun Yu, Wei Wu, Yuwei Ge, Xiaolan Liu, Jin Li, Hanzhi Zhang, Yaqin Zhao, Bing Yang, Xingzhou Jiang, Chao Peng, Cong Zhou, William Terzaghi, Chunming Wang () and Jianmin Wan ()
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Weijie Tang: Nanjing Agricultural University
Jian Ye: Chinese Academy of Sciences
Xiangmei Yao: Chinese Academy of Sciences
Pingzhi Zhao: Chinese Academy of Sciences
Wei Xuan: Nanjing Agricultural University
Yunlu Tian: Nanjing Agricultural University
Yuanyan Zhang: Nanjing Agricultural University
Shuang Xu: Chinese Academy of Sciences
Hongzhou An: Nanjing Agricultural University
Gaoming Chen: Nanjing Agricultural University
Jun Yu: Nanjing Agricultural University
Wei Wu: Nanjing Agricultural University
Yuwei Ge: Nanjing Agricultural University
Xiaolan Liu: Nanjing Agricultural University
Jin Li: Nanjing Agricultural University
Hanzhi Zhang: Nanjing Agricultural University
Yaqin Zhao: Nanjing Agricultural University
Bing Yang: Nanjing Agricultural University
Xingzhou Jiang: Nanjing Agricultural University
Chao Peng: Nanjing Agricultural University
Cong Zhou: Nanjing Agricultural University
William Terzaghi: Wilkes University
Chunming Wang: Nanjing Agricultural University
Jianmin Wan: Nanjing Agricultural University

Nature Communications, 2019, vol. 10, issue 1, 1-11

Abstract: Abstract Over-application of nitrogen fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high nitrogen use efficiency (NUE) reduce fertilizer for sustainable agriculture. Here, we perform genome-wide association analysis of a diverse rice population displaying extreme nitrogen-related phenotypes over three successive years in the field, and identify an elite haplotype of nitrate transporter OsNPF6.1HapB that enhances nitrate uptake and confers high NUE by increasing yield under low nitrogen supply. OsNPF6.1HapB differs in both the protein and promoter element with natural variations, which are differentially trans-activated by OsNAC42, a NUE-related transcription factor. The rare natural allele OsNPF6.1HapB, derived from variation in wild rice and selected for enhancing both NUE and yield, has been lost in 90.3% of rice varieties due to the increased application of fertilizer. Our discovery highlights this NAC42-NPF6.1 signaling cascade as a strategy for high NUE and yield breeding in rice.

Date: 2019
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DOI: 10.1038/s41467-019-13187-1

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