Genome-wide association study and transcriptome analysis reveal new QTL and candidate genes for nitrogen‐deficiency tolerance in rice
Qing Li,
Xueli Lu,
Changjian Wang,
Lan Shen,
Liping Dai,
Jinli He,
Long Yang,
Peiyuan Li,
Yifeng Hong,
Qiang Zhang,
Guojun Dong,
Jiang Hu,
Guangheng Zhang,
Deyong Ren,
Zhenyu Gao,
Longbiao Guo,
Qian Qian,
Li Zhu,
Dali Zeng
Affiliations
Qing Li
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Xueli Lu
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Changjian Wang
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Lan Shen
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Liping Dai
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Jinli He
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Long Yang
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Peiyuan Li
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Yifeng Hong
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Qiang Zhang
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Guojun Dong
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Jiang Hu
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Guangheng Zhang
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Deyong Ren
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Zhenyu Gao
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Longbiao Guo
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Qian Qian
Corresponding authors.; State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Li Zhu
Corresponding authors.; State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
Dali Zeng
Corresponding authors.; State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, Zhejiang, China
The development of rice cultivars with improved nitrogen use efficiency (NUE) is desirable for sustainable agriculture. Achieving this goal depends in part on understanding how rice responds to low soil nitrogen (N) and identifying causative genes underlying this trait. To identify quantitative trait loci (QTL) or genes associated with low N response, we conducted a genome-wide association study (GWAS) using a diverse panel of 230 rice accessions and performed a transcriptomic investigation of rice accessions with differential responses to low N stress at two N levels. We detected 411 GWAS-associated genes in 5 QTL and 2722 differentially expressed genes in response to low N, of which 24 were identified by both methods and ranked according to gene annotations, literature queries, gene expression, and genetic diversity analysis. The large-scale datasets obtained from this study reveal low N-responsive characteristics and provide insights towards understanding the regulatory mechanisms of N-deficiency tolerance in rice, and the candidate genes or QTL would be valuable resources for increasing rice NUE via molecular biotechnology.
