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Transcriptome Differences in Response Mechanisms to Low-Nitrogen Stress in Two Wheat Varieties. Int J Mol Sci 2021; 22:ijms222212278. [PMID: 34830160 PMCID: PMC8622133 DOI: 10.3390/ijms222212278] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/06/2021] [Accepted: 11/10/2021] [Indexed: 11/24/2022] Open
Abstract
Nitrogen plays a crucial role in wheat growth and development. Here, we analyzed the tolerance of wheat strains XM26 and LM23 to low-nitrogen stress using a chlorate sensitivity experiment. Subsequently, we performed transcriptome analyses of both varieties exposed to low-nitrogen (LN) and normal (CK) treatments. Compared with those under CK treatment, 3534 differentially expressed genes (DEGs) were detected in XM26 in roots and shoots under LN treatment (p < 0.05, and |log2FC| > 1). A total of 3584 DEGs were detected in LM23. A total of 3306 DEGs, including 863 DEGs in roots and 2443 DEGs in shoots, were specifically expressed in XM26 or showed huge differences between XM26 and LM23 (log2FC ratio > 3). These were selected for gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The calcium-mediated plant–pathogen interaction, MAPK signaling, and phosphatidylinositol signaling pathways were enriched in XM26 but not in LM23. We also verified the expression of important genes involved in these pathways in the two varieties using qRT-PCR. A total of 156 transcription factors were identified among the DEGs, and their expression patterns were different between the two varieties. Our findings suggest that calcium-related pathways play different roles in the two varieties, eliciting different tolerances to low-nitrogen stress.
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Alfatih A, Wu J, Zhang ZS, Xia JQ, Jan SU, Yu LH, Xiang CB. Rice NIN-LIKE PROTEIN 1 rapidly responds to nitrogen deficiency and improves yield and nitrogen use efficiency. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6032-6042. [PMID: 32585013 DOI: 10.1093/jxb/eraa292] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/17/2020] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is indispensable for crop growth and yield, but excessive agricultural application of nitrogenous fertilizers has generated severe environmental problems. A desirable and economical solution to cope with these issues is to improve crop nitrogen use efficiency (NUE). Plant NUE has been a focal point of intensive research worldwide, yet much still has to be learned about its genetic determinants and regulation. Here, we show that rice (Oryza sativa L.) NIN-LIKE PROTEIN 1 (OsNLP1) plays a fundamental role in N utilization. OsNLP1 protein localizes in the nucleus and its transcript level is rapidly induced by N starvation. Overexpression of OsNLP1 improves plant growth, grain yield, and NUE under different N conditions, while knockout of OsNLP1 impairs grain yield and NUE under N-limiting conditions. OsNLP1 regulates nitrate and ammonium utilization by cooperatively orchestrating multiple N uptake and assimilation genes. Chromatin immunoprecipitation and yeast one-hybrid assays showed that OsNLP1 can directly bind to the promoter of these genes to activate their expression. Therefore, our results demonstrate that OsNLP1 is a key regulator of N utilization and represents a potential target for improving NUE and yield in rice.
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Affiliation(s)
- Alamin Alfatih
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Jie Wu
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Zi-Sheng Zhang
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Jin-Qiu Xia
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Sami Ullah Jan
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Lin-Hui Yu
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
| | - Cheng-Bin Xiang
- School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China
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Hu B, Wang W, Ou S, Tang J, Li H, Che R, Zhang Z, Chai X, Wang H, Wang Y, Liang C, Liu L, Piao Z, Deng Q, Deng K, Xu C, Liang Y, Zhang L, Li L, Chu C. Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nat Genet 2015; 47:834-8. [PMID: 26053497 DOI: 10.1038/ng.3337] [Citation(s) in RCA: 362] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/15/2015] [Indexed: 02/07/2023]
Abstract
Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.
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Affiliation(s)
- Bin Hu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shujun Ou
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hua Li
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ronghui Che
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhihua Zhang
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuyang Chai
- College of Life Science, Capital Normal University, Beijing, China
| | - Hongru Wang
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yiqin Wang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chengzhen Liang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Linchuan Liu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Zhongze Piao
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qiyun Deng
- China National Hybrid Rice Research and Development Center, Changsha, China
| | - Kun Deng
- School of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Chi Xu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Liang
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lianhe Zhang
- School of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Legong Li
- College of Life Science, Capital Normal University, Beijing, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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