Genomic basis of geographical adaptation to soil nitrogen in rice

Yongqiang Liu, Hongru Wang, Zhimin Jiang, Wei Wang, Ruineng Xu, Qihui Wang, Zhihua Zhang, Aifu Li, Yan Liang, Shujun Ou, Xiujie Liu, Shouyun Cao, Hongning Tong, Yonghong Wang, Feng Zhou, Hong Liao, Bin Hu () and Chengcai Chu ()
Additional contact information
Yongqiang Liu: Chinese Academy of Sciences
Hongru Wang: Chinese Academy of Sciences
Zhimin Jiang: Chinese Academy of Sciences
Wei Wang: Chinese Academy of Sciences
Ruineng Xu: South China Agricultural University
Qihui Wang: Peking University
Zhihua Zhang: Chinese Academy of Sciences
Aifu Li: Chinese Academy of Sciences
Yan Liang: Chinese Academy of Sciences
Shujun Ou: Chinese Academy of Sciences
Xiujie Liu: Chinese Academy of Sciences
Shouyun Cao: Chinese Academy of Sciences
Hongning Tong: Chinese Academy of Agricultural Sciences
Yonghong Wang: Chinese Academy of Sciences
Feng Zhou: Peking University
Hong Liao: South China Agricultural University
Bin Hu: Chinese Academy of Sciences
Chengcai Chu: Chinese Academy of Sciences

Nature, 2021, vol. 590, issue 7847, 600-605

Abstract: Abstract The intensive application of inorganic nitrogen underlies marked increases in crop production, but imposes detrimental effects on ecosystems1,2: it is therefore crucial for future sustainable agriculture to improve the nitrogen-use efficiency of crop plants. Here we report the genetic basis of nitrogen-use efficiency associated with adaptation to local soils in rice (Oryza sativa L.). Using a panel of diverse rice germplasm collected from different ecogeographical regions, we performed a genome-wide association study on the tillering response to nitrogen—the trait that is most closely correlated with nitrogen-use efficiency in rice—and identified OsTCP19 as a modulator of this tillering response through its transcriptional response to nitrogen and its targeting to the tiller-promoting gene DWARF AND LOW-TILLERING (DLT)3,4. A 29-bp insertion and/or deletion in the OsTCP19 promoter confers a differential transcriptional response and variation in the tillering response to nitrogen among rice varieties. The allele of OsTCP19 associated with a high tillering response to nitrogen is prevalent in wild rice populations, but has largely been lost in modern cultivars: this loss correlates with increased local soil nitrogen content, which suggests that it might have contributed to geographical adaptation in rice. Introgression of the allele associated with a high tillering response into modern rice cultivars boosts grain yield and nitrogen-use efficiency under low or moderate levels of nitrogen, which demonstrates substantial potential for rice breeding and the amelioration of negative environment effects by reducing the application of nitrogen to crops.

Date: 2021
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DOI: 10.1038/s41586-020-03091-w

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