Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency
Rice is an ideal crop for improvement of nitrogen use efficiency (NUE), especially with urea, its predominant fertilizer. There is a paucity of studies on rice genotypes contrasting for NUE. We compared low urea-responsive transcriptomes of contrasting rice genotypes, namely Nidhi (low NUE) and Panv...
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| Format: | Article |
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MDPI AG
2023-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/7/6080 |
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| author | Narendra Sharma Dinesh Kumar Jaiswal Supriya Kumari Goutam Kumar Dash Siddharth Panda Annamalai Anandan Nandula Raghuram |
| author_facet | Narendra Sharma Dinesh Kumar Jaiswal Supriya Kumari Goutam Kumar Dash Siddharth Panda Annamalai Anandan Nandula Raghuram |
| author_sort | Narendra Sharma |
| collection | DOAJ |
| description | Rice is an ideal crop for improvement of nitrogen use efficiency (NUE), especially with urea, its predominant fertilizer. There is a paucity of studies on rice genotypes contrasting for NUE. We compared low urea-responsive transcriptomes of contrasting rice genotypes, namely Nidhi (low NUE) and Panvel1 (high NUE). Transcriptomes of whole plants grown with media containing normal (15 mM) and low urea (1.5 mM) revealed 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors (TFs) and better photosynthesis, water use efficiency and post-translational modifications. Many of their genes co-localized to NUE-QTLs on chromosomes 1, 3 and 9. A field evaluation under different doses of urea revealed better agronomic performance including grain yield, transport/uptake efficiencies and NUE of Panvel1. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and TFs, among others, contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE. |
| first_indexed | 2024-03-11T05:35:40Z |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T05:35:40Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-3c33c24782b141cb9005135577e392532023-11-17T16:46:07ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-03-01247608010.3390/ijms24076080Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use EfficiencyNarendra Sharma0Dinesh Kumar Jaiswal1Supriya Kumari2Goutam Kumar Dash3Siddharth Panda4Annamalai Anandan5Nandula Raghuram6Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, IndiaCentre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, IndiaCentre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, IndiaCrop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCentre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, IndiaRice is an ideal crop for improvement of nitrogen use efficiency (NUE), especially with urea, its predominant fertilizer. There is a paucity of studies on rice genotypes contrasting for NUE. We compared low urea-responsive transcriptomes of contrasting rice genotypes, namely Nidhi (low NUE) and Panvel1 (high NUE). Transcriptomes of whole plants grown with media containing normal (15 mM) and low urea (1.5 mM) revealed 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors (TFs) and better photosynthesis, water use efficiency and post-translational modifications. Many of their genes co-localized to NUE-QTLs on chromosomes 1, 3 and 9. A field evaluation under different doses of urea revealed better agronomic performance including grain yield, transport/uptake efficiencies and NUE of Panvel1. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and TFs, among others, contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE.https://www.mdpi.com/1422-0067/24/7/6080nitrogen use efficiencyureanetworksQTLsricetranscriptome |
| spellingShingle | Narendra Sharma Dinesh Kumar Jaiswal Supriya Kumari Goutam Kumar Dash Siddharth Panda Annamalai Anandan Nandula Raghuram Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency International Journal of Molecular Sciences nitrogen use efficiency urea networks QTLs rice transcriptome |
| title | Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency |
| title_full | Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency |
| title_fullStr | Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency |
| title_full_unstemmed | Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency |
| title_short | Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency |
| title_sort | genome wide urea response in rice genotypes contrasting for nitrogen use efficiency |
| topic | nitrogen use efficiency urea networks QTLs rice transcriptome |
| url | https://www.mdpi.com/1422-0067/24/7/6080 |
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