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Salama EAA, Kambale R, Gnanapanditha Mohan SV, Premnath A, Fathy Yousef A, Moursy ARA, Abdelsalam NR, Abd El Moneim D, Muthurajan R, Manikanda Boopathi N. Empowering rice breeding with NextGen genomics tools for rapid enhancement nitrogen use efficiency. Gene 2024; 927:148715. [PMID: 38909967 DOI: 10.1016/j.gene.2024.148715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 06/25/2024]
Abstract
As rice has no physiological capacity of fixing nitrogen in the soil, its production had always been reliant on the external application of nitrogen (N) to ensure enhanced productivity. In the light of improving nitrogen use efficiency (NUE) in rice, several advanced agronomic strategies have been proposed. However, the soared increase of the prices of N fertilizers and subsequent environmental downfalls caused by the excessive use of N fertilizers, reinforces the prerequisite adaptation of other sustainable, affordable, and globally acceptable strategies. An appropriate alternative approach would be to develop rice cultivars with better NUE. Conventional breeding techniques, however, have had only sporadic success in improving NUE, and hence, this paper proposes a new schema that employs the wholesome benefits of the recent advancements in omics technologies. The suggested approach promotes multidisciplinary research, since such cooperation enables the synthesis of many viewpoints, approaches, and data that result in a comprehensive understanding of NUE in rice. Such collaboration also encourages innovation that leads to developing rice varieties that use nitrogen more effectively, facilitate smart technology transfer, and promotes the adoption of NUE practices by farmers and stakeholders to minimize ecological impact and contribute to a sustainable agricultural future.
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Affiliation(s)
- Ehab A A Salama
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; Agricultural Botany Department (Genetics), Faculty of Agriculture Saba Basha, Alexandria University, Alexandria 21531, Egypt.
| | - Rohit Kambale
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Shobhana V Gnanapanditha Mohan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Ameena Premnath
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Ahmed Fathy Yousef
- Department of Horticulture, College of Agriculture, University of Al-Azhar (Branch Assiut), Assiut 71524, Egypt.
| | - Ali R A Moursy
- Soil and Water Department, Faculty of Agriculture, Sohag University, Sohag 82524, Egypt.
| | - Nader R Abdelsalam
- Agricultural Botany Department (Genetics), Faculty of Agriculture Saba Basha, Alexandria University, Alexandria 21531, Egypt.
| | - Diaa Abd El Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt.
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Narayanan Manikanda Boopathi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
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Jin F, Huang W, Xie P, Wu B, Zhao Q, Fang Z. Amino acid permease OsAAP12 negatively regulates rice tillers and grain yield by transporting specific amino acids to affect nitrogen and cytokinin pathways. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112202. [PMID: 39069009 DOI: 10.1016/j.plantsci.2024.112202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
Amino acids are necessary nutrients for the growth of Oryza sativa (rice), which can be mediated by amino acid transporter; however, our understanding of these transporters is still limited. This study found that the expression levels of amino acid permease gene OsAAP12 differed between indica and japonica rice. Altered expression of OsAAP12 negatively regulated tillering and yield in transgenic rice lines. Subcellular localization revealed that OsAAP12 was primarily localized to the plasma membrane. Moreover, it was indicated that OsAAP12 transported polar neutral amino acids asparagine (Asn), threonine (Thr), and serine (Ser) through experiments involving yeast heterologous complementation, fluorescence amino acid uptake, and amino acid content determination. Additionally, exogenous application of amino acids Asn, Thr, and Ser suppressed axillary buds outgrowth in OsAAP12 overexpression lines compared with wild-type ZH11. Conversely, the opposite trend was observed in CRISPR mutant lines. RNA-seq analysis showed that the expression patterns of genes involved in the nitrogen and cytokinin pathways were generally altered in OsAAP12 modified lines. Hormone assays indicated that OsAAP12 mutant lines accumulated cytokinins in the basal part of rice, whereas overexpression lines had the opposite effect. In summary, CRISPR mutant of OsAAP12 boosted rice tillering and grain yield by coordinating the content of amino acids and cytokinins, which has potential application value in high-yield rice breeding.
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Affiliation(s)
- Feng Jin
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China
| | - Weiting Huang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China
| | - Pengfei Xie
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China
| | - Bowen Wu
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China
| | - Quanzhi Zhao
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China
| | - Zhongming Fang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China.
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3
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Li Y, Tian X, Liu T, Shi Y, Li Y, Wang H, Cui Y, Lu S, Gong X, Mao K, Li M, Ma F, Li C. MdSINA2-MdNAC104 Module Regulates Apple Alkaline Resistance by Affecting γ-Aminobutyric Acid Synthesis and Transport. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400930. [PMID: 39032167 DOI: 10.1002/advs.202400930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/10/2024] [Indexed: 07/22/2024]
Abstract
Soil alkalization is an adverse factor limiting plant growth and yield. As a signaling molecule and secondary metabolite, γ-aminobutyric acid (GABA) responds rapidly to alkaline stress and enhances the alkaline resistance of plants. However, the molecular mechanisms by which the GABA pathway adapts to alkaline stress remain unclear. In this study, a transcription factor, MdNAC104 is identified, from the transcriptome of the alkaline-stressed roots of apple, which effectively reduces GABA levels and negatively regulates alkaline resistance. Nevertheless, applying exogenous GABA compensates the negative regulatory mechanism of overexpressed MdNAC104 on alkaline resistance. Further research confirms that MdNAC104 repressed the GABA biosynthetic gene MdGAD1/3 and the GABA transporter gene MdALMT13 by binding to their promoters. Here, MdGAD1/3 actively regulates alkaline resistance by increasing GABA synthesis, while MdALMT13 promotes GABA accumulation and efflux in roots, resulting in an improved resistance to alkaline stress. This subsequent assays reveal that MdSINA2 interacts with MdNAC104 and positively regulates root GABA content and alkaline resistance by ubiquitinating and degrading MdNAC104 via the 26S proteasome pathway. Thus, the study reveals the regulation of alkaline resistance and GABA homeostasis via the MdSINA2-MdNAC104-MdGAD1/3/MdALMT13 module in apple. These findings provide novel insight into the molecular mechanisms of alkaline resistance in plants.
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Affiliation(s)
- Yuxing Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaocheng Tian
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tanfang Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanjiao Shi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yunhao Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hongtao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yinglian Cui
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuaiyu Lu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoqing Gong
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ke Mao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingjun Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cuiying Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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4
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Wu W, Dong X, Chen G, Lin Z, Chi W, Tang W, Yu J, Wang S, Jiang X, Liu X, Wu Y, Wang C, Cheng X, Zhang W, Xuan W, Terzaghi W, Ronald PC, Wang H, Wang C, Wan J. The elite haplotype OsGATA8-H coordinates nitrogen uptake and productive tiller formation in rice. Nat Genet 2024; 56:1516-1526. [PMID: 38872029 PMCID: PMC11250373 DOI: 10.1038/s41588-024-01795-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 05/09/2024] [Indexed: 06/15/2024]
Abstract
Excessive nitrogen promotes the formation of nonproductive tillers in rice, which decreases nitrogen use efficiency (NUE). Developing high-NUE rice cultivars through balancing nitrogen uptake and the formation of productive tillers remains a long-standing challenge, yet how these two processes are coordinated in rice remains elusive. Here we identify the transcription factor OsGATA8 as a key coordinator of nitrogen uptake and tiller formation in rice. OsGATA8 negatively regulates nitrogen uptake by repressing transcription of the ammonium transporter gene OsAMT3.2. Meanwhile, it promotes tiller formation by repressing the transcription of OsTCP19, a negative modulator of tillering. We identify OsGATA8-H as a high-NUE haplotype with enhanced nitrogen uptake and a higher proportion of productive tillers. The geographical distribution of OsGATA8-H and its frequency change in historical accessions suggest its adaption to the fertile soil. Overall, this study provides molecular and evolutionary insights into the regulation of NUE and facilitates the breeding of rice cultivars with higher NUE.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Zhixi Lin
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Wenchao Chi
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Weijie Tang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Jun Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Saisai Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Xingzhou Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Xiaolan Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Yujun Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Chunyuan Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Xinran Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Southern Japonica Rice R&D Corporation Ltd, Nanjing, China
| | - Wei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wei Xuan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | | | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Haiyang Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunming Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Southern Japonica Rice R&D Corporation Ltd, Nanjing, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, China.
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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5
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Jinlong H, Yu Z, Ruizhi W, Xiaoyu W, Zhiming F, Qiangqiang X, Nianbing Z, Yong Z, Haiyan W, Hongcheng Z, Jinyan Z. A genome-wide association study of panicle blast resistance to Magnaporthe oryzae in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:49. [PMID: 39007057 PMCID: PMC11236831 DOI: 10.1007/s11032-024-01486-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024]
Abstract
Rice blast, caused by Magnaporthe oryzae (M. oryzae), is one of the most serious diseases worldwide. Developing blast-resistant rice varieties is an effective strategy to control the spread of rice blast and reduce the reliance on chemical pesticides. In this study, 477 sequenced rice germplasms from 48 countries were inoculated and assessed at the booting stage. We found that 23 germplasms exhibited high panicle blast resistance against M. oryzae. Genome-wide association analysis (GWAS) identified 43 quantitative trait loci (QTLs) significantly associated (P < 1.0 × 10-4) with resistance to rice panicle blast. These QTL intervals encompass four genes (OsAKT1, OsRACK1A, Bsr-k1 and Pi25/Pid3) previously reported to contribute to rice blast resistance. We selected QTLs with -Log10 (P-value) greater than 6.0 or those detected in two-year replicates, amounting to 12 QTLs, for further candidate gene analysis. Three blast resistance candidate genes (Os06g0316800, Os06g0320000, Pi25/Pid3) were identified based on significant single nucleotide polymorphisms (SNP) distributions within annotated gene sequences across these 12 QTLs and the differential expression levels among blast-resistant varieties after 72 h of inoculation. Os06g0316800 encodes a glycine-rich protein, OsGrp6, an important component of plant cell walls involved in cellular stress responses and signaling. Os06g0320000 encodes a protein with unknown function (DUF953), part of the thioredoxin-like family, which is crucial for maintaining reactive oxygen species (ROS) homeostasis in vivo, named as OsTrxl1. Lastly, Pi25/Pid3 encodes a disease resistance protein, underscoring its potential importance in plant biology. By analyzing the haplotypes of these three genes, we identified favorable haplotypes for blast resistance, providing valuable genetic resources for future rice blast resistance breeding programs. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01486-5.
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Affiliation(s)
- Hu Jinlong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Zhang Yu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Wang Ruizhi
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Wang Xiaoyu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Feng Zhiming
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Xiong Qiangqiang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Zhou Nianbing
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Zhou Yong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Wei Haiyan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Zhang Hongcheng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Zhu Jinyan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
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6
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Ge Y, Chen G, Cheng X, Li C, Tian Y, Chi W, Li J, Dai Z, Wang C, Duan E, Liu Y, Sun Z, Li J, Wang B, Xu D, Sun X, Zhang H, Zhang W, Wang C, Wan J. The superior allele LEA12 OR in wild rice enhances salt tolerance and yield. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38923790 DOI: 10.1111/pbi.14419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/06/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024]
Abstract
Soil salinity has negative impacts on food security and sustainable agriculture. Ion homeostasis, osmotic adjustment and reactive oxygen species scavenging are the main approaches utilized by rice to resist salt stress. Breeding rice cultivars with high salt tolerance (ST) and yield is a significant challenge due to the lack of elite alleles conferring ST. Here, we report that the elite allele LEA12OR, which encodes a late embryogenesis abundant (LEA) protein from the wild rice Oryza rufipogon Griff., improves osmotic adjustment and increases yield under salt stress. Mechanistically, LEA12OR, as the early regulator of the LEA12OR-OsSAPK10-OsbZIP86-OsNCED3 functional module, maintains the kinase stability of OsSAPK10 under salt stress, thereby conferring ST by promoting abscisic acid biosynthesis and accumulation in rice. The superior allele LEA12OR provides a new avenue for improving ST and yield via the application of LEA12OR in current rice through molecular breeding and genome editing.
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Affiliation(s)
- Yuwei Ge
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Xinran Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chao Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yunlu Tian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Wenchao Chi
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jin Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhaoyang Dai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chunyuan Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Erchao Duan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yan Liu
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, China
| | - Zhiguang Sun
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, China
| | - Jingfang Li
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, China
| | - Baoxiang Wang
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, China
| | - Dayong Xu
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, China
| | - Xianjun Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of AgriculturalSciences, Beijing, China
| | - Hui Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of AgriculturalSciences, Beijing, China
| | - Wenhua Zhang
- College of Life Sciences, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chunming Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
- Zhongshan Biological Breeding Laboratory, Southern Japonica Rice R&D Corporation Ltd, Nanjing, China
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of AgriculturalSciences, Beijing, China
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7
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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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8
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da Silva RC, Oliveira HC, Igamberdiev AU, Stasolla C, Gaspar M. Interplay between nitric oxide and inorganic nitrogen sources in root development and abiotic stress responses. JOURNAL OF PLANT PHYSIOLOGY 2024; 297:154241. [PMID: 38640547 DOI: 10.1016/j.jplph.2024.154241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/21/2024]
Abstract
Nitrogen (N) is an essential nutrient for plants, and the sources from which it is obtained can differently affect their entire development as well as stress responses. Distinct inorganic N sources (nitrate and ammonium) can lead to fluctuations in the nitric oxide (NO) levels and thus interfere with nitric oxide (NO)-mediated responses. These could lead to changes in reactive oxygen species (ROS) homeostasis, hormone synthesis and signaling, and post-translational modifications of key proteins. As the consensus suggests that NO is primarily synthesized in the reductive pathways involving nitrate and nitrite reduction, it is expected that plants grown in a nitrate-enriched environment will produce more NO than those exposed to ammonium. Although the interplay between NO and different N sources in plants has been investigated, there are still many unanswered questions that require further elucidation. By building on previous knowledge regarding NO and N nutrition, this review expands the field by examining in more detail how NO responses are influenced by different N sources, focusing mainly on root development and abiotic stress responses.
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Affiliation(s)
- Rafael Caetano da Silva
- Department of Biodiversity Conservation, Institute of Environmental Research, São Paulo, SP, 04301-902, Brazil
| | - Halley Caixeta Oliveira
- Department of Animal and Plant Biology, State University of Londrina, Londrina, PR, 86057-970, Brazil
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Marilia Gaspar
- Department of Biodiversity Conservation, Institute of Environmental Research, São Paulo, SP, 04301-902, Brazil.
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9
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Xia Z, Fan W, Liu D, Chen Y, Lv J, Xu M, Zhang M, Ren Z, Chen X, Wang X, Li L, Zhu P, Liu C, Song Z, Huang C, Wang X, Wang S, Zhao A. Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content. HORTICULTURE RESEARCH 2024; 11:uhae120. [PMID: 38919559 PMCID: PMC11197311 DOI: 10.1093/hr/uhae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/14/2024] [Indexed: 06/27/2024]
Abstract
Understanding the intricate regulatory mechanisms underlying the anthocyanin content (AC) in fruits and vegetables is crucial for advanced biotechnological customization. In this study, we generated high-quality haplotype-resolved genome assemblies for two mulberry cultivars: the high-AC 'Zhongsang5801' (ZS5801) and the low-AC 'Zhenzhubai' (ZZB). Additionally, we conducted a comprehensive analysis of genes associated with AC production. Through genome-wide association studies (GWAS) on 112 mulberry fruits, we identified MaVHAG3, which encodes a vacuolar-type H+-ATPase G3 subunit, as a key gene linked to purple pigmentation. To gain deeper insights into the genetic and molecular processes underlying high AC, we compared the genomes of ZS5801 and ZZB, along with fruit transcriptome data across five developmental stages, and quantified the accumulation of metabolic substances. Compared to ZZB, ZS5801 exhibited significantly more differentially expressed genes (DEGs) related to anthocyanin metabolism and higher levels of anthocyanins and flavonoids. Comparative analyses revealed expansions and contractions in the flavonol synthase (FLS) and dihydroflavonol 4-reductase (DFR) genes, resulting in altered carbon flow. Co-expression analysis demonstrated that ZS5801 displayed more significant alterations in genes involved in late-stage AC regulation compared to ZZB, particularly during the phase stage. In summary, our findings provide valuable insights into the regulation of mulberry fruit AC, offering genetic resources to enhance cultivars with higher AC traits.
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Affiliation(s)
- Zhongqiang Xia
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Wei Fan
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Duanyang Liu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Yuane Chen
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Jing Lv
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Mengxia Xu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Meirong Zhang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Zuzhao Ren
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Xuefei Chen
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Xiujuan Wang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Liang Li
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Panpan Zhu
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China
| | - Zhiguang Song
- Chongqing Sericulture Science and Technology Research Institute, Chongqing.400715, China
| | - Chuanshu Huang
- Chongqing Sericulture Science and Technology Research Institute, Chongqing.400715, China
| | - Xiling Wang
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Shuchang Wang
- Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 570100, China
| | - Aichun Zhao
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
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10
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Li Z, Chen H, Yuan DP, Jiang X, Li ZM, Wang ST, Zhou TG, Zhu HY, Bian Q, Zhu XF, Xuan YH. IDD10-NAC079 transcription factor complex regulates sheath blight resistance by inhibiting ethylene signaling in rice. J Adv Res 2024:S2090-1232(24)00222-4. [PMID: 38825317 DOI: 10.1016/j.jare.2024.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024] Open
Abstract
INTRODUCTION Rhizoctonia solani Kühn is a pathogen causing rice sheath blight (ShB). Ammonium transporter 1 (AMT1) promotes resistance of rice to ShB by activating ethylene signaling. However, how AMT1 activates ethylene signaling remains unclear. OBJECTIVE In this study, the indeterminate domain 10 (IDD10)-NAC079 interaction model was used to investigate whether ethylene signaling is modulated downstream of ammonium signaling and modulates ammonium-mediated ShB resistance. METHODS RT-qPCR assay was used to identify the relative expression levels of nitrogen and ethylene related genes. Yeast two-hybrid assays, Bimolecular fluorescence complementation (BiFC) and Co-immunoprecipitation (Co-IP) assay were conducted to verify the IDD10-NAC079-calcineurin B-like interacting protein kinase 31 (CIPK31) transcriptional complex. Yeast one-hybrid assay, Chromatin immunoprecipitation (ChIP) assay, and Electrophoretic mobility shift assay (EMSA) were used to verify whether ETR2 was activated by IDD10 and NAC079. Ethylene quantification assay was used to verify ethylene content in IDD10 transgenic plants. Genetic analysis is used to detect the response of IDD10, NAC079 and CIPK31 to ShB infestation. RESULTS IDD10-NAC079 forms a transcription complex that activates ETR2 to inhibit the ethylene signaling pathway to negatively regulating ShB resistance. CIPK31 interacts and phosphorylates NAC079 to enhance its transcriptional activation activity. In addition, AMT1-mediated ammonium absorption and subsequent N assimilation inhibit the expression of IDD10 and CIPK31 to activate the ethylene signaling pathway, which positively regulates ShB resistance. CONCLUSION The study identified the link between ammonium and ethylene signaling and improved the understanding of the rice resistance mechanism.
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Affiliation(s)
- Zhuo Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Huan Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - De Peng Yuan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Plant Protection, National Pesticide Engineering Research Center (Tianjin), Nankai University, Tianjin 300071, China
| | - Xu Jiang
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Zhi Min Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Si Ting Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Tian Ge Zhou
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Hong Yao Zhu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Qiang Bian
- National Pesticide Engineering Research Center (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao Feng Zhu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
| | - Yuan Hu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; State Key Laboratory of Elemento-Organic Chemistry and Department of Plant Protection, National Pesticide Engineering Research Center (Tianjin), Nankai University, Tianjin 300071, China.
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11
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Chen M, Feng S, Lv H, Wang Z, Zeng Y, Shao C, Lin W, Zhang Z. OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake. BMC PLANT BIOLOGY 2024; 24:285. [PMID: 38627617 PMCID: PMC11020999 DOI: 10.1186/s12870-024-04982-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/03/2024] [Indexed: 04/19/2024]
Abstract
Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth, development and contribute to elemental nutrient uptake. In conditions of nitrogen limitation, the over-expressed Calcineurin B-like interacting protein kinase 2 (OsCIPK2) gene with root-specific promoter (RC) has been shown to enhance growth and nitrogen uptake in rice. Analysis of root-associated bacteria through high-throughput sequencing revealed that OsCIPK2 has a significant impact on the diversity of the root microbial community under low nitrogen stress. The quantification of nifH gene expression demonstrated a significant enhancement in nitrogen-fixing capabilities in the roots of RC transgenetic rice. Synthetic microbial communities (SynCom) consisting of six nitrogen-fixing bacterial strains were observed to be enriched in the roots of RC, leading to a substantial improvement in rice growth and nitrogen uptake in nitrogen-deficient soils. Forty and twenty-three metabolites exhibiting differential abundance were identified in the roots and rhizosphere soils of RC transgenic rice compared to wild-type (WT) rice. These findings suggest that OSCIPK2 plays a role in restructuring the microbial community in the roots through the regulation of metabolite synthesis and secretion. Further experiments involving the exogenous addition of citric acid revealed that an optimal concentration of this compound facilitated the growth of nitrogen-fixing bacteria and substantially augmented their population in the soil, highlighting the importance of citric acid in promoting nitrogen fixation under conditions of low nitrogen availability. These findings suggest that OsCIPK2 plays a role in enhancing nitrogen uptake by rice plants from the soil by influencing the assembly of root microbial communities, thereby offering valuable insights for enhancing nitrogen utilization in rice cultivation.
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Affiliation(s)
- Mengying Chen
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Shizhong Feng
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - He Lv
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zewen Wang
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yuhang Zeng
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Caihong Shao
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Wenxiong Lin
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhixing Zhang
- College of JunCao Science and Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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12
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Tang W, Chen H, Zhang S, Tang J, Lin J, Fang X, Chen G, Zhang Y. A Novel Allele in the Promoter of Wx Decreases Gene Expression and Confers Lower Apparent Amylose Contents in Japonica Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:745. [PMID: 38475591 DOI: 10.3390/plants13050745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wxb is the major allele in japonica and produces moderate AC (15~18%). It was recently found that editing the promoter of Wx could produce a series of alleles that have different Wx activities. Although some studies have edited the promoter, few studies have focused on the natural variations in Wx. Here, we used the Rice3K database to investigate variations in the Wx promoter and found that the allele Wx1764178 (A/G) has a higher LD (linkage disequilibrium) with the two key SNPs (1765751, T/G; 1768006, A/C), which could produce different Wx alleles and influence AC, as reported previously. Further study showed that the Wx1764178 allele (A/G) is functional and influences the expression of Wx positively. Editing the A allele using CRISPR‒Cas9 produced 36 and 3 bp deletions and caused a decrease in the expression of Wx. The apparent amylose content (AAC) in the edited lines was decreased by 7.09% and 11.50% compared with that of the wild type, which was the japonica variety Nipponbare with Wxb and the A allele at 1764178, while a complementary line with the G allele showed a lower AAC than the A allele with no effect on other agronomic traits. The AAC of the edited lines showed a higher increase than that of the wild type (Nipponbare, Wxb) in low-nitrogen conditions relative to high-nitrogen conditions. We also developed a dCAPS marker to identify the allele and found that the G allele has widely been used (82.95%) in japonica-bred varieties from Jiangsu Province, China. Overall, we found a functional allele (Wx1764178, A/G) in the Wx promoter that could affect AAC in japonica cultivars and be developed as markers for quality improvement in rice breeding programs.
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Affiliation(s)
- Weijie Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Haiyuan Chen
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Suobing Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Jun Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Jing Lin
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Xianwen Fang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunhui Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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13
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Chen N, Ma T, Xia S, Li C, Liu Y, Wang J, Qu G, Liu H, Zheng H, Yang L, Zou D, Wang J, Xin W. Mapping of Candidate Genes for Nitrogen Uptake and Utilization in Japonica Rice at Seedling Stage. Genes (Basel) 2024; 15:327. [PMID: 38540386 PMCID: PMC10970145 DOI: 10.3390/genes15030327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 06/14/2024] Open
Abstract
Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (Os01g0159250, Os02g0618200, Os02g0618400, Os02g0630300, and Os06g0619000) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice.
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Affiliation(s)
- Ning Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Tianze Ma
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Sijia Xia
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Chengxin Li
- Harbin Academy of Agricultural Sciences, Harbin 150030, China;
| | - Yinuo Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Jiaqi Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Guize Qu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Hualong Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Hongliang Zheng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Luomiao Yang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Detang Zou
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Jingguo Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Wei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
- Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
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14
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Li G, Guo X, Sun W, Hou L, Wang G, Tian R, Wang X, Qu C, Zhao C. Nitrogen application in pod zone improves yield and quality of two peanut cultivars by modulating nitrogen accumulation and metabolism. BMC PLANT BIOLOGY 2024; 24:48. [PMID: 38216909 PMCID: PMC10787501 DOI: 10.1186/s12870-024-04725-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024]
Abstract
Cultivated peanut (Arachis hypogaea L.) represents one of the most important oil and cash crops world-widely. Unlike many other legumes, peanuts absorb nitrogen through their underground pods. Despite this unique feature, the relationship between yield and nitrogen uptake within the pod zone remains poorly understood. In our pot experiment, we divided the underground peanut part into two zones-pod and root-and investigated the physiological and agronomic traits of two peanut cultivars, SH11 (large seeds, LS) and HY23 (small seeds, SS), at 10 (S1), 20 (S2), and 30 (S3) days after gynophores penetrated the soil, with nitrogen application in the pod zone. Results indicated that nitrogen application increased pod yield, kernel protein content, and nitrogen accumulation in plants. For both LS and SS peanut cultivars, optimal nitrogen content was 60 kg·hm- 2, leading to maximum yield. LS cultivar exhibited higher yield and nitrogen accumulation increases than SS cultivar. Nitrogen application up-regulated the expression of nitrogen metabolism-related genes in the pod, including nitrate reductase (NR), nitrite reductase (NIR), glutamine synthetase (GS), glutamate synthase (NADH-GOGAT), ATP binding cassette (ABC), and nitrate transporter (NRT2). Additionally, nitrogen application increased enzyme activity in the pod, including NR, GS, and GOGAT, consistent with gene expression levels. These nitrogen metabolism traits exhibited higher up-regulations in the large-seeded cultivar than in the small-seeded one and showed a significant correlation with yield in the large-seeded cultivar at S2 and S3. Our findings offer a scientific basis for the judicious application and efficient utilization of nitrogen fertilization in peanuts, laying the groundwork for further elucidating the molecular mechanisms of peanut nitrogen utilization.
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Affiliation(s)
- Guanghui Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xin Guo
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wei Sun
- Linyi Academy of Agricultural Sciences, Linyi, 276012, China
| | - Lei Hou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Guanghao Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Chunjuan Qu
- Shandong Peanut Research Institute, Qingdao, 266100, China.
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
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15
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Li Y, Zhao L, Guo C, Tang M, Lian W, Chen S, Pan Y, Xu X, Luo C, Yi Y, Cui Y, Chen L. OsNAC103, an NAC transcription factor negatively regulates plant height in rice. PLANTA 2024; 259:35. [PMID: 38193994 PMCID: PMC10776745 DOI: 10.1007/s00425-023-04309-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024]
Abstract
MAIN CONCLUSION OsNAC103 negatively regulates rice plant height by influencing the cell cycle and crosstalk of phytohormones. Plant height is an important characteristic of rice farming and is directly related to agricultural yield. Although there has been great progress in research on plant growth regulation, numerous genes remain to be elucidated. NAC transcription factors are widespread in plants and have a vital function in plant growth. Here, we observed that the overexpression of OsNAC103 resulted in a dwarf phenotype, whereas RNA interference (RNAi) plants and osnac103 mutants showed no significant difference. Further investigation revealed that the cell length did not change, indicating that the dwarfing of plants was caused by a decrease in cell number due to cell cycle arrest. The content of the bioactive cytokinin N6-Δ2-isopentenyladenine (iP) decreased as a result of the cytokinin synthesis gene being downregulated and the enhanced degradation of cytokinin oxidase. OsNAC103 overexpression also inhibited cell cycle progression and regulated the activity of the cell cyclin OsCYCP2;1 to arrest the cell cycle. We propose that OsNAC103 may further influence rice development and gibberellin-cytokinin crosstalk by regulating the Oryza sativa homeobox 71 (OSH71). Collectively, these results offer novel perspectives on the role of OsNAC103 in controlling plant architecture.
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Affiliation(s)
- Yan Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Liming Zhao
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Chiming Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, China
| | - Ming Tang
- Key Laboratory of National Forestry and Grassland Administration On Biodiversity Conservation in Karst Mountainous Areas of Southwestern, School of Life Science, Guizhou Normal University, Guiyang, 550025, China
| | - Wenli Lian
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Siyu Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Yuehan Pan
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiaorong Xu
- Key Laboratory of National Forestry and Grassland Administration On Biodiversity Conservation in Karst Mountainous Areas of Southwestern, School of Life Science, Guizhou Normal University, Guiyang, 550025, China
| | - Chengke Luo
- Agricultural College, Ningxia University, Yinchuan, 750021, China
| | - Yin Yi
- Key Laboratory of National Forestry and Grassland Administration On Biodiversity Conservation in Karst Mountainous Areas of Southwestern, School of Life Science, Guizhou Normal University, Guiyang, 550025, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
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Zhang Z, Peng C, Xu W, Li Y, Qi X, Zhao M. Genome-wide association study of agronomic traits related to nitrogen use efficiency in Henan wheat. BMC Genomics 2024; 25:7. [PMID: 38166525 PMCID: PMC10759698 DOI: 10.1186/s12864-023-09922-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Nitrogen use efficiency (NUE) is closely related to crop yield and nitrogen fertilizer application rate. Although NUE is susceptible to environments, quantitative trait nucleotides (QTNs) for NUE in wheat germplasm populations have been rarely reported in genome-wide associated study. RESULTS In this study, 244 wheat accessions were phenotyped by three NUE-related traits in three environments and genotyped by 203,224 SNPs. All the phenotypes for each trait were used to associate with all the genotypes of these SNP markers for identifying QTNs and QTN-by-environment interactions via 3VmrMLM. Among 279 QTNs and one QTN-by-environment interaction for low nitrogen tolerance, 33 were stably identified, especially, one large QTN (r2 > 10%), qPHR3A.2, was newly identified for plant height ratio in one environment and multi-environment joint analysis. Among 52 genes around qPHR3A.2, four genes (TraesCS3A01G101900, TraesCS3A01G102200, TraesCS3A01G104100, and TraesCS3A01G105400) were found to be differentially expressed in low-nitrogen-tolerant wheat genotypes, while TaCLH2 (TraesCS3A01G101900) was putatively involved in porphyrin metabolism in KEGG enrichment analyses. CONCLUSIONS This study identified valuable candidate gene for low-N-tolerant wheat breeding and provides new insights into the genetic basis of low N tolerance in wheat.
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Affiliation(s)
- Zaicheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Chaojun Peng
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China
| | - Weigang Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China.
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China.
| | - Yan Li
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China
| | - Xueli Qi
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China
| | - Mingzhong Zhao
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China
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17
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Chawla R, Poonia A, Samantara K, Mohapatra SR, Naik SB, Ashwath MN, Djalovic IG, Prasad PVV. Green revolution to genome revolution: driving better resilient crops against environmental instability. Front Genet 2023; 14:1204585. [PMID: 37719711 PMCID: PMC10500607 DOI: 10.3389/fgene.2023.1204585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/11/2023] [Indexed: 09/19/2023] Open
Abstract
Crop improvement programmes began with traditional breeding practices since the inception of agriculture. Farmers and plant breeders continue to use these strategies for crop improvement due to their broad application in modifying crop genetic compositions. Nonetheless, conventional breeding has significant downsides in regard to effort and time. Crop productivity seems to be hitting a plateau as a consequence of environmental issues and the scarcity of agricultural land. Therefore, continuous pursuit of advancement in crop improvement is essential. Recent technical innovations have resulted in a revolutionary shift in the pattern of breeding methods, leaning further towards molecular approaches. Among the promising approaches, marker-assisted selection, QTL mapping, omics-assisted breeding, genome-wide association studies and genome editing have lately gained prominence. Several governments have progressively relaxed their restrictions relating to genome editing. The present review highlights the evolutionary and revolutionary approaches that have been utilized for crop improvement in a bid to produce climate-resilient crops observing the consequence of climate change. Additionally, it will contribute to the comprehension of plant breeding succession so far. Investing in advanced sequencing technologies and bioinformatics will deepen our understanding of genetic variations and their functional implications, contributing to breakthroughs in crop improvement and biodiversity conservation.
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Affiliation(s)
- Rukoo Chawla
- Department of Genetics and Plant Breeding, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan, India
| | - Atman Poonia
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Bawal, Haryana, India
| | - Kajal Samantara
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Sourav Ranjan Mohapatra
- Department of Forest Biology and Tree Improvement, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - S. Balaji Naik
- Institute of Integrative Biology and Systems, University of Laval, Quebec City, QC, Canada
| | - M. N. Ashwath
- Department of Forest Biology and Tree Improvement, Kerala Agricultural University, Thrissur, Kerala, India
| | - Ivica G. Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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18
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Zhang K, Gao W, Zhou Y, Zhao H, Xia Y, Zhang M, Bo Y, Lyu X, Hu Z, Yang J, Zhang M. Allelic variations of ClACO gene improve nitrogen uptake via ethylene-mediated root architecture in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:199. [PMID: 37624448 DOI: 10.1007/s00122-023-04448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
KEY MESSAGE The ClACO gene encoding 1-aminocyclopropane-1-carboxylate oxidase enabled highly efficient 15N uptake in watermelon. Nitrogen is one of the most essential nutrient elements that play a pivotal role in regulating plant growth and development for crop productivity. Elucidating the genetic basis of high nitrogen uptake is the key to improve nitrogen use efficiency for sustainable agricultural productivity. Whereas previous researches on nitrogen absorption process are mainly focused on a few model plants or crops. To date, the causal genes that determine the efficient nitrogen uptake of watermelon have not been mapped and remains largely unknown. Here, we fine-mapped the 1-aminocyclopropane-1-carboxylate oxidase (ClACO) gene associated with nitrogen uptake efficiency in watermelon via bulked segregant analysis (BSA). The variations in the ClACO gene led to the changes of gene expression levels between two watermelon accessions with different nitrogen uptake efficiencies. Intriguingly, in terms of the transcript abundance of ClACO, it was concomitant with significant differences in ethylene evolutions in roots and root architectures between the two accessions and among the different genotypic offsprings of the recombinant BC2F1(ZJU132)-18. These findings suggest that ethylene as a negative regulator altered nitrogen uptake efficiency in watermelon by controlling root development. In conclusion, our current study will provide valuable target gene for precise breeding of 'green' watermelon varieties with high-nitrogen uptake efficiencies.
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Affiliation(s)
- Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wei Gao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haoshun Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuelin Xia
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengyi Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China.
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19
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Jia L, Hu D, Wang J, Liang Y, Li F, Wang Y, Han Y. Genome-Wide Identification and Functional Analysis of Nitrate Transporter Genes ( NPF, NRT2 and NRT3) in Maize. Int J Mol Sci 2023; 24:12941. [PMID: 37629121 PMCID: PMC10454388 DOI: 10.3390/ijms241612941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Nitrate is the primary form of nitrogen uptake in plants, mainly transported by nitrate transporters (NRTs), including NPF (NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY), NRT2 and NRT3. In this study, we identified a total of 78 NPF, seven NRT2, and two NRT3 genes in maize. Phylogenetic analysis divided the NPF family into eight subgroups (NPF1-NPF8), consistent with the results in Arabidopsis thaliana and rice. The NRT2 family appears to have evolved more conservatively than the NPF family, as NRT2 genes contain fewer introns. The promoters of all NRTs are rich in cis-acting elements responding to biotic and abiotic stresses. The expression of NRTs varies in different tissues and developmental stages, with some NRTs only expressed in specific tissues or developmental stages. RNA-seq analysis using Xu178 revealed differential expression of NRTs in response to nitrogen starvation and nitrate resupply. Moreover, the expression patterns of six key NRTs genes (NPF6.6, NPF6.8, NRT2.1, NRT2.5 and NRT3.1A/B) varied in response to alterations in nitrogen levels across distinct maize inbred lines with different nitrogen uptake rates. This work enhances our understanding of the structure and expression of NRTs genes, and their roles in nitrate response, paving the way for improving maize nitrogen efficiency through molecular breeding.
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Affiliation(s)
- Lihua Jia
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou 450046, China; (L.J.); (D.H.); (J.W.); (Y.L.); (F.L.)
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Desheng Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou 450046, China; (L.J.); (D.H.); (J.W.); (Y.L.); (F.L.)
| | - Junbo Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou 450046, China; (L.J.); (D.H.); (J.W.); (Y.L.); (F.L.)
| | - Yuanyuan Liang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou 450046, China; (L.J.); (D.H.); (J.W.); (Y.L.); (F.L.)
| | - Fang Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou 450046, China; (L.J.); (D.H.); (J.W.); (Y.L.); (F.L.)
| | - Yi Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou 450046, China; (L.J.); (D.H.); (J.W.); (Y.L.); (F.L.)
| | - Yanlai Han
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou 450046, China; (L.J.); (D.H.); (J.W.); (Y.L.); (F.L.)
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20
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Xu Y, Bai L, Liu M, Liu Y, Peng S, Hu P, Wang D, Liu Q, Yan S, Gao L, Wang X, Ning Y, Zuo S, Zheng W, Liu S, Xiang W, Wang G, Kang H. Identification of two novel rice S genes through combination of association and transcription analyses with gene-editing technology. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1628-1641. [PMID: 37154202 PMCID: PMC10363757 DOI: 10.1111/pbi.14064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 04/04/2023] [Accepted: 04/16/2023] [Indexed: 05/10/2023]
Abstract
Traditional rice blast resistance breeding largely depends on utilizing typical resistance (R) genes. However, the lack of durable R genes has prompted rice breeders to find new resistance resources. Susceptibility (S) genes are potential new targets for resistance genetic engineering using genome-editing technologies, but identifying them is still challenging. Here, through the integration of genome-wide association study (GWAS) and transcriptional analysis, we identified two genes, RNG1 and RNG3, whose polymorphisms in 3'-untranslated regions (3'-UTR) affected their expression variations. These polymorphisms could serve as molecular markers to identify rice blast-resistant accessions. Editing the 3'-UTRs using CRISPR/Cas9 technology affected the expression levels of two genes, which were positively associated with rice blast susceptibility. Knocking out either RNG1 or RNG3 in rice enhanced the rice blast and bacterial blight resistance, without impacting critical agronomic traits. RNG1 and RNG3 have two major genotypes in diverse rice germplasms. The frequency of the resistance genotype of these two genes significantly increased from landrace rice to modern cultivars. The obvious selective sweep flanking RNG3 suggested it has been artificially selected in modern rice breeding. These results provide new targets for S gene identification and open avenues for developing novel rice blast-resistant materials.
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Affiliation(s)
- Yuchen Xu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of AgronomyHunan Agricultural UniversityChangshaHunanChina
| | - Lu Bai
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Minghao Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Yanchen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shasha Peng
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of AgronomyHunan Agricultural UniversityChangshaHunanChina
| | - Pei Hu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Dan Wang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of AgronomyHunan Agricultural UniversityChangshaHunanChina
| | - Qi Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetic BreedingTianjin Crop Research Institute, Tianjin Academy of Agriculture SciencesTianjinChina
| | - Lijun Gao
- Guangxi Crop Genetic Improvement and Biotechnology LaboratoryGuangxi Academy of Agricultural SciencesNanningChina
| | - Xuli Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhouChina
| | - Wenjing Zheng
- Rice Research Institute of Liaoning Province, Liaoning Academy of Agricultural SciencesShenyangChina
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Guo‐Liang Wang
- Department of Plant PathologyOhio State UniversityColumbusOhioUSA
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
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21
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Phan NTH, Draye X, Pham CV, Bertin P. Identification of quantitative trait loci controlling nitrogen use efficiency-related traits in rice at the seedling stage under salt condition by genome-wide association study. FRONTIERS IN PLANT SCIENCE 2023; 14:1197271. [PMID: 37575915 PMCID: PMC10415682 DOI: 10.3389/fpls.2023.1197271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
Rice cultivation is facing both salt intrusion and overuse of nitrogen fertilizers. Hence, breeding new varieties aiming to improve nitrogen use efficiency (NUE), especially under salt conditions, is indispensable. We selected 2,391 rice accessions from the 3K Rice Genomes Project to evaluate the dry weight under two N concentrations [2.86 mM - standard N (SN), and 0.36 mM - low N (LN)] crossed with two NaCl concentrations [0 (0Na) and 60 mM (60Na)] at the seedling stage. Genome-wide association studies for shoot, root, and plant dry weight (DW) were carried out. A total of 55 QTLs - 32, 16, and 7 in the whole, indica, and japonica panel - associated with one of the tested traits were identified. Among these, 27 QTLs co-localized with previously identified QTLs for DW-related traits while the other 28 were newly detected; 24, 8, 11, and 4 QTLs were detected in SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively, and the remaining 8 QTLs were for the relative plant DW between treatments. Three of the 11 QTLs in SN-60Na were close to the regions containing three QTLs detected in SN-0Na. Eleven candidate genes for eight important QTLs were identified. Only one of them was detected in both SN-0Na and SN-60Na, while 5, 0, 3, and 2 candidate genes were identified only once under SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively. The identified QTLs and genes provide useful materials and genetic information for future functional characterization and genetic improvement of NUE in rice, especially under salt conditions.
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Affiliation(s)
- Nhung Thi Hong Phan
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
- Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Xavier Draye
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Cuong Van Pham
- Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Pierre Bertin
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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22
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Liao Z, Xia X, Zhang Z, Nong B, Guo H, Feng R, Chen C, Xiong F, Qiu Y, Li D, Yang X. Genome-wide association study using specific-locus amplified fragment sequencing identifies new genes influencing nitrogen use efficiency in rice landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1126254. [PMID: 37521918 PMCID: PMC10375723 DOI: 10.3389/fpls.2023.1126254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/28/2023] [Indexed: 08/01/2023]
Abstract
Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10-7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10-6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.
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Affiliation(s)
- Zuyu Liao
- College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hui Guo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rui Feng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Can Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Faqian Xiong
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yongfu Qiu
- College of Agriculture, Guangxi University, Nanning, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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Yu J, Zhu C, Xuan W, An H, Tian Y, Wang B, Chi W, Chen G, Ge Y, Li J, Dai Z, Liu Y, Sun Z, Xu D, Wang C, Wan J. Genome-wide association studies identify OsWRKY53 as a key regulator of salt tolerance in rice. Nat Commun 2023; 14:3550. [PMID: 37321989 PMCID: PMC10272163 DOI: 10.1038/s41467-023-39167-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Salinity stress progressively reduces plant growth and productivity, while plant has developed complex signaling pathways to confront salt stress. However, only a few genetic variants have been identified to mediate salt tolerance in the major crop rice, and the molecular mechanism remains poorly understood. Here, we identify ten candidate genes associated with salt-tolerance (ST) traits by performing a genome-wide association analysis in rice landraces. We characterize two ST-related genes, encoding transcriptional factor OsWRKY53 and Mitogen-activated protein Kinase Kinase OsMKK10.2, that mediate root Na+ flux and Na+ homeostasis. We further find that OsWRKY53 acts as a negative modulator regulating expression of OsMKK10.2 in promoting ion homeostasis. Furthermore, OsWRKY53 trans-represses OsHKT1;5 (high-affinity K+ transporter 1;5), encoding a sodium transport protein in roots. We show that the OsWRKY53-OsMKK10.2 and OsWRKY53-OsHKT1;5 module coordinate defenses against ionic stress. The results shed light on the regulatory mechanisms underlying plant salt tolerance.
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Affiliation(s)
- Jun Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Chengsong Zhu
- Department of Immunology, The University of Texas Southwestern Medical Centre, Dallas, TX, 75390, USA
| | - Wei Xuan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongzhou An
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Baoxiang Wang
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, 222006, China
| | - Wenchao Chi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Yuwei Ge
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Jin Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Zhaoyang Dai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Yan Liu
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, 222006, China
| | - Zhiguang Sun
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, 222006, China
| | - Dayong Xu
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, 222006, China
| | - Chunming Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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24
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Qin X, Li X, Xiao J, Wu Q, Li Y, Li C, Jiang D, Tang T, Nan W, Liang Y, Zhang H. Transcriptomic and Physiological Analyses of Two Rice Restorer Lines under Different Nitrogen Supplies Provide Novel Insights into Hybrid Rice Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:2276. [PMID: 37375901 DOI: 10.3390/plants12122276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
Improving plant nitrogen-use efficiency (NUE) has great significance for various crops, particularly in hybrid breeding. Reducing nitrogen inputs is key to achieving sustainable rice production and mitigating environmental problems. In this study, we analyzed the transcriptomic and physiological changes in two indica restorer lines (Nanhui511 [NH511] and Minghui23 [MH23]) under high nitrogen (HN) and low nitrogen (LN) conditions. Compared to MH23, NH511 was more sensitive to different nitrogen supplies and exhibited higher nitrogen uptake and NUE under HN conditions by increasing lateral root and tiller numbers in the seedling and maturation stages, respectively. NH511 also exhibited a lower survival rate than MH23 when planted in a chlorate-containing hydroponic solution, indicating its HN uptake ability under different nitrogen-supply conditions. Transcriptomic analysis showed that NH511 has 2456 differentially expressed genes, whereas MH23 had only 266. Furthermore, these genes related to nitrogen utilization showed differential expression in NH511 under HN conditions, while the opposite was observed in MH23. Our findings revealed that NH511 could be regarded as elite rice and used for breeding high-NUE restorer lines by regulating and integrating nitrogen-utilization genes, which provides novel insights for the cultivation of high-NUE hybrid rice.
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Affiliation(s)
- Xiaojian Qin
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Xiaowei Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Juan Xiao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Qian Wu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Yuntong Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Cuiping Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Dan Jiang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Tingting Tang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Wenbin Nan
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Yongshu Liang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Hanma Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
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25
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Siddiqui MN, Pandey K, Bhadhury SK, Sadeqi B, Schneider M, Sanchez-Garcia M, Stich B, Schaaf G, Léon J, Ballvora A. Convergently selected NPF2.12 coordinates root growth and nitrogen use efficiency in wheat and barley. THE NEW PHYTOLOGIST 2023; 238:2175-2193. [PMID: 36808608 DOI: 10.1111/nph.18820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/13/2023] [Indexed: 05/04/2023]
Abstract
Understanding the genetic and molecular function of nitrate sensing and acquisition across crop species will accelerate breeding of cultivars with improved nitrogen use efficiency (NUE). Here, we performed a genome-wide scan using wheat and barley accessions characterized under low and high N inputs that uncovered the NPF2.12 gene, encoding a homolog of the Arabidopsis nitrate transceptor NRT1.6 and other low-affinity nitrate transporters that belong to the MAJOR FACILITATOR SUPERFAMILY. Next, it is shown that variations in the NPF2.12 promoter correlated with altered NPF2.12 transcript levels where decreased gene expression was measured under low nitrate availability. Multiple field trials revealed a significantly enhanced N content in leaves and grains and NUE in the presence of the elite allele TaNPF2.12TT grown under low N conditions. Furthermore, the nitrate reductase encoding gene NIA1 was up-regulated in npf2.12 mutant upon low nitrate concentrations, thereby resulting in elevated levels of nitric oxide (NO) production. This increase in NO correlated with the higher root growth, nitrate uptake, and N translocation observed in the mutant when compared to wild-type. The presented data indicate that the elite haplotype alleles of NPF2.12 are convergently selected in wheat and barley that by inactivation indirectly contribute to root growth and NUE by activating NO signaling under low nitrate conditions.
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Affiliation(s)
- Md Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Kailash Pandey
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
| | - Suzan Kumer Bhadhury
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
| | - Bahman Sadeqi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
| | - Michael Schneider
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Miguel Sanchez-Garcia
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, 10101, Morocco
| | - Benjamin Stich
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Gabriel Schaaf
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, D-53115, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Klein-Altendorf 2, Rheinbach, 53359, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
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26
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Sharma N, Jaiswal DK, Kumari S, Dash GK, Panda S, Anandan A, Raghuram N. Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency. Int J Mol Sci 2023; 24:ijms24076080. [PMID: 37047052 PMCID: PMC10093866 DOI: 10.3390/ijms24076080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 04/14/2023] Open
Abstract
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.
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Affiliation(s)
- Narendra Sharma
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Dinesh Kumar Jaiswal
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Supriya Kumari
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Goutam Kumar Dash
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Siddharth Panda
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, India
- Institute of Agricultural Sciences, SOA (DU), Bhubaneswar 751003, India
| | - Annamalai Anandan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, India
- Regional Station, Indian Council of Agricultural Research (ICAR)-Indian Institute of Seed Science, Bengaluru 560065, India
| | - Nandula Raghuram
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
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27
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Li B, Wei A, Tong X, Han Y, Liu N, Chen Z, Yang H, Wu H, Lv M, Wang NN, Du S. A Genome-Wide Association Study to Identify Novel Candidate Genes Related to Low-Nitrogen Tolerance in Cucumber (Cucumis sativus L.). Genes (Basel) 2023; 14:genes14030662. [PMID: 36980933 PMCID: PMC10048605 DOI: 10.3390/genes14030662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Cucumber is one of the most important vegetables, and nitrogen is essential for the growth and fruit production of cucumbers. It is crucial to develop cultivars with nitrogen limitation tolerance or high nitrogen efficiency for green and efficient development in cucumber industry. To reveal the genetic basis of cucumber response to nitrogen starvation, a genome-wide association study (GWAS) was conducted on a collection of a genetically diverse population of cucumber (Cucumis sativus L.) comprising 88 inbred and DH accessions including the North China type, the Eurasian type, the Japanese and South China type mixed subtype, and the South China type subtype. Phenotypic evaluation of six traits under control (14 mM) and treatment (3.5 mM) N conditions depicted the presence of broad natural variation in the studied population. The GWAS results showed that there were significant differences in the population for nitrogen limitation treatment. Nine significant loci were identified corresponding to six LD blocks, three of which overlapped. Sixteen genes were selected by GO annotation associated with nitrogen. Five low-nitrogen stress tolerance genes were finally identified by gene haplotype analysis: CsaV3_3G003630 (CsNRPD1), CsaV3_3G002970 (CsNRT1.1), CsaV3_4G030260 (CsSnRK2.5), CsaV3_4G026940, and CsaV3_3G011820 (CsNPF5.2). Taken together, the experimental data and identification of candidate genes presented in this study offer valuable insights and serve as a useful reference for the genetic enhancement of nitrogen limitation tolerance in cucumbers.
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Affiliation(s)
- Bowen Li
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Aimin Wei
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin 300192, China
| | - Xueqiang Tong
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Yike Han
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin 300192, China
| | - Nan Liu
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
| | - Zhengwu Chen
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin 300192, China
| | - Hongyu Yang
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Huaxiang Wu
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Mingjie Lv
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300061, China
| | - Ning Ning Wang
- College of Life Science, Nankai University, Tianjin 300071, China
- College of Agricultural Science, Nankai University, Tianjin 300071, China
| | - Shengli Du
- College of Life Science, Nankai University, Tianjin 300071, China
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin 300192, China
- Correspondence:
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28
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Aluko OO, Kant S, Adedire OM, Li C, Yuan G, Liu H, Wang Q. Unlocking the potentials of nitrate transporters at improving plant nitrogen use efficiency. FRONTIERS IN PLANT SCIENCE 2023; 14:1074839. [PMID: 36895876 PMCID: PMC9989036 DOI: 10.3389/fpls.2023.1074839] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/16/2023] [Indexed: 05/27/2023]
Abstract
Nitrate ( NO 3 - ) transporters have been identified as the primary targets involved in plant nitrogen (N) uptake, transport, assimilation, and remobilization, all of which are key determinants of nitrogen use efficiency (NUE). However, less attention has been directed toward the influence of plant nutrients and environmental cues on the expression and activities of NO 3 - transporters. To better understand how these transporters function in improving plant NUE, this review critically examined the roles of NO 3 - transporters in N uptake, transport, and distribution processes. It also described their influence on crop productivity and NUE, especially when co-expressed with other transcription factors, and discussed these transporters' functional roles in helping plants cope with adverse environmental conditions. We equally established the possible impacts of NO 3 - transporters on the uptake and utilization efficiency of other plant nutrients while suggesting possible strategic approaches to improving NUE in plants. Understanding the specificity of these determinants is crucial to achieving better N utilization efficiency in crops within a given environment.
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Affiliation(s)
- Oluwaseun Olayemi Aluko
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Chuanzong Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guang Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haobao Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qian Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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29
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Liu Y, Hu B, Chu C. Toward improving nitrogen use efficiency in rice: Utilization, coordination, and availability. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102327. [PMID: 36525788 DOI: 10.1016/j.pbi.2022.102327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Nitrogen (N) fertilizer drives crop productivity and underlies intensive agriculture, but overuse of fertilizers also causes detrimental effects to ecosystem. To cope with this challenge while meeting the ever-growing demand for food, it is critical and urgent to improve nitrogen use efficiency (NUE) of crops. To date, numerous efforts have been made in developing strategies for NUE improvement with different disciplines. Given the intricate and interconnected route of N for delivering its effect, it is necessary to comprehensively understand various procedures and their interplays in determining NUE. In this review, we expand the scope of NUE improvement, not only the N utilization by plants, but also the N coordination with other resources as well as the N availability in the soil, which represent the major dimensions in manipulating NUE. Moreover, both agronomic practices and genetic improvement in facilitating NUE are also included and discussed. Lastly, we provide our perspective in improving the NUE in the future, particularly highlighting the integration of various agronomic and genetic approaches for NUE improvement underlying the sustainable agriculture.
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Affiliation(s)
- Yongqiang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bin Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.
| | - Chengcai Chu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.
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30
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Crop germplasm: Current challenges, physiological-molecular perspective, and advance strategies towards development of climate-resilient crops. Heliyon 2023; 9:e12973. [PMID: 36711267 PMCID: PMC9880400 DOI: 10.1016/j.heliyon.2023.e12973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 01/01/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Germplasm is a long-term resource management mission and investment for civilization. An estimated ∼7.4 million accessions are held in 1750 plant germplasm centres around the world; yet, only 2% of these assets have been utilized as plant genetic resources (PGRs). According to recent studies, the current food yield trajectory will be insufficient to feed the world's population in 2050. Additionally, possible negative effects in terms of crop failure because of climate change are already being experienced across the world. Therefore, it is necessary to reconciliation of research advancement and innovation of practices for further exploration of the potential of crop germplasm especially for the complex traits associated with yield such as water- and nitrogen use efficiency. In this review, we tried to address current challenges, research gaps, physiological and molecular aspects of two broad spectrum complex traits such as water- and nitrogen-use efficiency, and advanced integrated strategies that could provide a platform for combined stress management for climate-smart crop development. Additionally, recent development in technologies that are directly related to germplasm characterization was highlighted for further molecular utilization towards the development of elite varieties.
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31
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Hu B, Wang W, Chen J, Liu Y, Chu C. Genetic improvement toward nitrogen-use efficiency in rice: Lessons and perspectives. MOLECULAR PLANT 2023; 16:64-74. [PMID: 36380584 DOI: 10.1016/j.molp.2022.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
The indispensable role of nitrogen fertilizer in ensuring world food security together with the severe threats it poses to the ecosystem makes the usage of nitrogen fertilizer a major challenge for sustainable agriculture. Genetic improvement of crops with high nitrogen-use efficiency (NUE) is one of the most feasible solutions for tackling this challenge. In the last two decades, extensive efforts toward dissecting the variation of NUE-related traits and the underlying genetic basis in different germplasms have been made, and a series of achievements have been obtained in crops, especially in rice. Here, we summarize the approaches used for genetic dissection of NUE and the functions of the causal genes in modulating NUE as well as their applications in NUE improvement in rice. Strategies for exploring the variants controlling NUE and breeding future crops with "less-input-more-output" for sustainable agriculture are also proposed.
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Affiliation(s)
- Bin Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, 510642, Guangzhou, China.
| | - Wei Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, 510642, Guangzhou, China
| | - Jiajun Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yongqiang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, 510642, Guangzhou, China.
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Govindasamy P, Muthusamy SK, Bagavathiannan M, Mowrer J, Jagannadham PTK, Maity A, Halli HM, G. K. S, Vadivel R, T. K. D, Raj R, Pooniya V, Babu S, Rathore SS, L. M, Tiwari G. Nitrogen use efficiency-a key to enhance crop productivity under a changing climate. FRONTIERS IN PLANT SCIENCE 2023; 14:1121073. [PMID: 37143873 PMCID: PMC10151540 DOI: 10.3389/fpls.2023.1121073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/20/2023] [Indexed: 05/06/2023]
Abstract
Nitrogen (N) is an essential element required for the growth and development of all plants. On a global scale, N is agriculture's most widely used fertilizer nutrient. Studies have shown that crops use only 50% of the applied N effectively, while the rest is lost through various pathways to the surrounding environment. Furthermore, lost N negatively impacts the farmer's return on investment and pollutes the water, soil, and air. Therefore, enhancing nitrogen use efficiency (NUE) is critical in crop improvement programs and agronomic management systems. The major processes responsible for low N use are the volatilization, surface runoff, leaching, and denitrification of N. Improving NUE through agronomic management practices and high-throughput technologies would reduce the need for intensive N application and minimize the negative impact of N on the environment. The harmonization of agronomic, genetic, and biotechnological tools will improve the efficiency of N assimilation in crops and align agricultural systems with global needs to protect environmental functions and resources. Therefore, this review summarizes the literature on nitrogen loss, factors affecting NUE, and agronomic and genetic approaches for improving NUE in various crops and proposes a pathway to bring together agronomic and environmental needs.
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Affiliation(s)
- Prabhu Govindasamy
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Senthilkumar K. Muthusamy
- Division of Crop Improvement, Indian Council of Agricultural Research (ICAR)-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - Muthukumar Bagavathiannan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Jake Mowrer
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | | | - Aniruddha Maity
- Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Hanamant M. Halli
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Sujayananad G. K.
- Crop Protection, Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulse Research, Kanpur, India
| | - Rajagopal Vadivel
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Das T. K.
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rishi Raj
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Vijay Pooniya
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Subhash Babu
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sanjay Singh Rathore
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Muralikrishnan L.
- Division of Agricultural Extension, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gopal Tiwari
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Kasemsap P, Bloom AJ. Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 12:85. [PMID: 36616214 PMCID: PMC9823454 DOI: 10.3390/plants12010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.
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Du S, Cai Y, Qiu S, Hao Y, Tian K, Zou Z, Luo L. Metabolic Profiling of Oryza sativa L. Triggered by Chilling Stress Using Ultraperformance Liquid Chromatography Coupled with Quadrupole/Time-of-Flight Mass Spectrometry (UPLC-QTOF-MS) with Transcriptome Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15703-15714. [PMID: 36473722 DOI: 10.1021/acs.jafc.2c05949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Low temperature, a major abiotic stress, often causes molecular changes in crops, which leads to metabolic disturbances and probably affects crop yield. In this study, chilling stress induced distinct metabolic profiles associated with transcriptome regulation, exhibiting great metabolic differences between Qiutianxiaoting (japonica) and 93-11 (indica). In total, 41 and 58 differential metabolites were screened and identified in Qiutianxiaoting and 93-11, respectively. Five key metabolites were screened in response to chilling stress, which were involved or related to different metabolic pathways. Moreover, starch and sucrose metabolism, aminoacyl-tRNA biosynthesis, and phenylpropanoid biosynthesis were significantly enriched in Qiutianxiaoting to maintain cellular homeostasis. Aminoacyl-tRNA biosynthesis and antioxidation metabolism were significantly enriched in 93-11, but disorders of the metabolome and transcriptome occurred at recovery stage. The results could provide some useful information for in-depth understanding of cold-resistant mechanisms, as well as reference for the selection and breeding of rice varieties.
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Affiliation(s)
- Shangguang Du
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
- School of Life Sciences, Nanchang Normal University, Nanchang 330031, China
| | - Yali Cai
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Shengrong Qiu
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Yingbin Hao
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Kaili Tian
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Zhengrong Zou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Liping Luo
- College of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Life Sciences, Nanchang University, Nanchang 330031, China
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Cheng J, Tan H, Shan M, Duan M, Ye L, Yang Y, He L, Shen H, Yang Z, Wang X. Genome-wide identification and characterization of the NPF genes provide new insight into low nitrogen tolerance in Setaria. FRONTIERS IN PLANT SCIENCE 2022; 13:1043832. [PMID: 36589108 PMCID: PMC9795848 DOI: 10.3389/fpls.2022.1043832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Introduction Nitrogen (N) is essential for plant growth and yield production and can be taken up from soil in the form of nitrate or peptides. The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) genes play important roles in the uptake and transportation of these two forms of N. Methods Bioinformatic analysis was used to identify and characterize the NPF genes in Setaria. RNA-seq was employed to analyze time-series low nitrate stress response of the SiNPF genes. Yeast and Arabidopsis mutant complementation were used to test the nitrate transport ability of SiNRT1.1B1 and SiNRT1.1B2. Results We identified 92 and 88 putative NPF genes from foxtail millet (Setaria italica L.) and its wild ancestor green foxtail (Setaria viridis L.), respectively. These NPF genes were divided into eight groups according to their sequence characteristics and phylogenetic relationship, with similar intron-exon structure and motifs in the same subfamily. Twenty-six tandem duplication and 13 segmental duplication events promoted the expansion of SiNPF gene family. Interestingly, we found that the tandem duplication of the SiNRT1.1B gene might contribute to low nitrogen tolerance of foxtail millet. The gene expression atlas showed that the SiNPFs were divided into two major clusters, which were mainly expressed in root and the above ground tissues, respectively. Time series transcriptomic analysis further revealed the response of these SiNPF genes to short- and long- time low nitrate stress. To provide natural variation of gene information, we carried out a haplotype analysis of these SiNPFs and identified 2,924 SNPs and 400 InDels based on the re-sequence data of 398 foxtail millet accessions. We also predicted the three-dimensional structure of the 92 SiNPFs and found that the conserved proline 492 residues were not in the substrate binding pocket. The interactions of SiNPF proteins withNO 3 - were analyzed using molecular docking and the pockets were then identified. We found that the SiNPFs-NO 3 - binding energy ranged from -3.8 to -2.7 kcal/mol. Discussion Taken together, our study provides a comprehensive understanding of the NPF gene family in Setaria and will contribute to function dissection of these genes for crop breeding aimed at improving high nitrogen use efficiency.
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Affiliation(s)
- Jinjin Cheng
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Helin Tan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Meng Shan
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Mengmeng Duan
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Ling Ye
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Yulu Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Lu He
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Huimin Shen
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Zhirong Yang
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taigu, China
| | - Xingchun Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taigu, China
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Shi H, Chen M, Gao L, Wang Y, Bai Y, Yan H, Xu C, Zhou Y, Xu Z, Chen J, Tang W, Wang S, Shi Y, Wu Y, Sun D, Jia J, Ma Y. Genome-wide association study of agronomic traits related to nitrogen use efficiency in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4289-4302. [PMID: 36136127 DOI: 10.1007/s00122-022-04218-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
GWAS identified 347 QTLs associated with eight traits related to nitrogen use efficiency in a 389-count wheat panel. Four novel candidate transcription factor genes were verified using qRT-PCR. Nitrogen is an essential nutrient for plants that determines crop yield. Improving nitrogen use efficiency (NUE) should considerably increase wheat yield and reduce the use of nitrogen fertilisers. However, knowledge on the genetic basis of NUE during wheat maturity is limited. In this study, a diversity panel incorporating 389 wheat accessions was phenotyped for eight NUE-related agronomic traits across five different environments. A total of 347 quantitative trait loci (QTLs) for low nitrogen tolerance indices (ratio of agronomic characters under low and high nitrogen conditions) were identified through a genome-wide association study utilising 397,384 single nucleotide polymorphisms (SNPs) within the MLM (Q + K) model, including 11 stable QTLs. Furthermore, 69 candidate genes were predicted for low nitrogen tolerance indices of best linear unbiased predictions values of the eight studied agronomic traits, and four novel candidate transcription factors (TraesCS5A02G237500 for qFsnR5A.2, TraesCS5B02G384500 and TraesCS5B02G384600 for qSLR5B.1, and TraesCS3B02G068800 for qTKWR3B.1) showed differing expression patterns in contrasting low-nitrogen-tolerant wheat genotypes. Moreover, the number of favourable marker alleles calculated using NUE that were significantly related to SNP in accessions decreased over the decades, indicating a decline in the NUE of the 389 wheat varieties. These findings denote promising NUE markers that could be useful in breeding high-NUE wheat varieties, and the candidate genes could further detail the NUE-related regulation network in wheat.
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Affiliation(s)
- Huawei Shi
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Lifeng Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Research Center of Wheat Engineering Technology of Hebei, Shijiazhuang, 050041, Hebei, China
| | - Yanming Bai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Huishu Yan
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Chengjie Xu
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yongbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Zhaoshi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Wensi Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Shuguang Wang
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yugang Shi
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yuxiang Wu
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Daizhen Sun
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
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Zhang M, Lai L, Liu X, Liu J, Liu R, Wang Y, Liu J, Chen J. Overexpression of Nitrate Transporter 1/Peptide Gene OsNPF7.6 Increases Rice Yield and Nitrogen Use Efficiency. LIFE (BASEL, SWITZERLAND) 2022; 12:life12121981. [PMID: 36556346 PMCID: PMC9786031 DOI: 10.3390/life12121981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022]
Abstract
Overuse of nitrogen fertilizer in fields has raised production costs, and caused environmental problems. Improving nitrogen use efficiency (NUE) of rice is essential for sustainable agriculture. Here we report the cloning, characterization and roles for rice of OsNPF7.6, a member of the nitrate transporter 1/peptide transporter family (NPF). The OsNPF7.6 protein is located in the plasma membrane, expressed in each tissue at all stages and is significantly regulated by nitrate in rice. Our study shows that the overexpression of OsNPF7.6 can increase the nitrate uptake rate of rice. Additionally, field experiments showed that OsNPF7.6 overexpression increased the total tiller number per plant and the grain weight per panicle, thereby improving grain yield and agronomic NUE in rice. Thus, OsNPF7.6 can be applied to be a novel target gene for breeding rice varieties with high NUE, and provide a reference for breeding higher yielding rice.
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Affiliation(s)
- Min Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Liuru Lai
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Shenzhen 518107, China
| | - Xintong Liu
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Shenzhen 518107, China
| | - Jiajia Liu
- Shandong Jinchunyu Seed Technology Co., Ltd., Jining 272200, China
| | - Ruifang Liu
- The High School Affiliated to Renmin University of China, Shenzhen 518119, China
| | - Yamei Wang
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Shenzhen 518107, China
| | - Jindong Liu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Correspondence: (J.L.); (J.C.)
| | - Jingguang Chen
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Shenzhen 518107, China
- Correspondence: (J.L.); (J.C.)
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The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet. Int J Mol Sci 2022; 23:ijms232314735. [PMID: 36499063 PMCID: PMC9741022 DOI: 10.3390/ijms232314735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Panicle traits are important factors affecting yield, and their improvement has long been a critical goal in foxtail millet breeding. In order to understand the genetic basis of panicle formation, a large-scale genome-wide association study (GWAS) was performed in this study for six panicle-related traits based on 706,646 high-polymorphism SNP loci in 407 accessions. As a result, 87 quantitative trait loci (QTL) regions with a physical distance of less than 100 kb were detected to be associated with these traits in three environments. Among them, 27 core regions were stably detected in at least two environments. Based on rice-foxtail millet homologous comparison, expression, and haplotype analysis, 27 high-confidence candidate genes in the QTL regions, such as Si3g11200 (OsDER1), Si1g27910 (OsMADS6), Si7g27560 (GS5), etc., affected panicle-related traits by involving multiple plant growth regulator pathways, a photoperiod response, as well as panicle and grain development. Most of these genes showed multiple effects on different panicle-related traits, such as Si3g11200 affecting all six traits. In summary, this study clarified a strategy based on the integration of GWAS, a homologous comparison, and haplotype analysis to discover the genomic regions and candidate genes for important traits in foxtail millet. The detected QTL regions and candidate genes could be further used for gene clone and marker-assisted selection in foxtail millet breeding.
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Saeed S, Usman B, Shim SH, Khan SU, Nizamuddin S, Saeed S, Shoaib Y, Jeon JS, Jung KH. CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111435. [PMID: 36031021 DOI: 10.1016/j.plantsci.2022.111435] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
To improve future agricultural production, major technological advances are required to increase crop production and yield. Targeting the coding region of genes via the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein (CRISPR/Cas) system has been well established and has enabled the rapid generation of transgene-free plants, which can lead to crop improvement. The emergence of the CRISPR/Cas system has also enabled scientists to achieve cis-regulatory element (CRE) editing and, consequently, engineering endogenous critical CREs to modulate the expression of target genes. Recent genome-wide association studies have identified the domestication of natural CRE variants to regulate complex agronomic quantitative traits and have allowed for their engineering via the CRISPR/Cas system. Although engineering plant CREs can be advantageous to drive gene expression, there are still many limitations to its practical application. Here, we review the current progress in CRE editing and propose future strategies to effectively target CREs for transcriptional regulation for crop improvement.
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Affiliation(s)
- Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Babar Usman
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Su-Hyeon Shim
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Shahid Ullah Khan
- Department of Biochemistry, Women Medical and Dental College, Khyber Medical University KPK, Pakistan
| | - Sabzoi Nizamuddin
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Sundus Saeed
- School of Engineering, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Yasira Shoaib
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
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Sun G, Lu H, Zhao Y, Zhou J, Jackson R, Wang Y, Xu L, Wang A, Colmer J, Ober E, Zhao Q, Han B, Zhou J. AirMeasurer: open-source software to quantify static and dynamic traits derived from multiseason aerial phenotyping to empower genetic mapping studies in rice. THE NEW PHYTOLOGIST 2022; 236:1584-1604. [PMID: 35901246 PMCID: PMC9796158 DOI: 10.1111/nph.18314] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/31/2022] [Indexed: 05/11/2023]
Abstract
Low-altitude aerial imaging, an approach that can collect large-scale plant imagery, has grown in popularity recently. Amongst many phenotyping approaches, unmanned aerial vehicles (UAVs) possess unique advantages as a consequence of their mobility, flexibility and affordability. Nevertheless, how to extract biologically relevant information effectively has remained challenging. Here, we present AirMeasurer, an open-source and expandable platform that combines automated image analysis, machine learning and original algorithms to perform trait analysis using 2D/3D aerial imagery acquired by low-cost UAVs in rice (Oryza sativa) trials. We applied the platform to study hundreds of rice landraces and recombinant inbred lines at two sites, from 2019 to 2021. A range of static and dynamic traits were quantified, including crop height, canopy coverage, vegetative indices and their growth rates. After verifying the reliability of AirMeasurer-derived traits, we identified genetic variants associated with selected growth-related traits using genome-wide association study and quantitative trait loci mapping. We found that the AirMeasurer-derived traits had led to reliable loci, some matched with published work, and others helped us to explore new candidate genes. Hence, we believe that our work demonstrates valuable advances in aerial phenotyping and automated 2D/3D trait analysis, providing high-quality phenotypic information to empower genetic mapping for crop improvement.
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Affiliation(s)
- Gang Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co‐sponsored by Province and MinistryNanjing Agricultural UniversityNanjing210095China
| | - Hengyun Lu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200233China
| | - Yan Zhao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200233China
| | - Jie Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co‐sponsored by Province and MinistryNanjing Agricultural UniversityNanjing210095China
| | - Robert Jackson
- Cambridge Crop ResearchNational Institute of Agricultural Botany (NIAB)CambridgeCB3 0LEUK
| | - Yongchun Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200233China
| | - Ling‐xiang Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co‐sponsored by Province and MinistryNanjing Agricultural UniversityNanjing210095China
| | - Ahong Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200233China
| | - Joshua Colmer
- Earlham InstituteNorwich Research ParkNorwichNR4 7UHUK
| | - Eric Ober
- Cambridge Crop ResearchNational Institute of Agricultural Botany (NIAB)CambridgeCB3 0LEUK
| | - Qiang Zhao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200233China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200233China
| | - Ji Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co‐sponsored by Province and MinistryNanjing Agricultural UniversityNanjing210095China
- Cambridge Crop ResearchNational Institute of Agricultural Botany (NIAB)CambridgeCB3 0LEUK
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Li J, Xin W, Wang W, Zhao S, Xu L, Jiang X, Duan Y, Zheng H, Yang L, Liu H, Jia Y, Zou D, Wang J. Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings. RICE (NEW YORK, N.Y.) 2022; 15:51. [PMID: 36243857 PMCID: PMC9569405 DOI: 10.1186/s12284-022-00597-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency.
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Affiliation(s)
- Jia Li
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Wei Xin
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Weiping Wang
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Shijiao Zhao
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Lu Xu
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Xingdong Jiang
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Yuxuan Duan
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Hongliang Zheng
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Luomiao Yang
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Hualong Liu
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Yan Jia
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Detang Zou
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China.
| | - Jingguo Wang
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China.
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42
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Sun Q, Li Y, Gong D, Hu A, Zhong W, Zhao H, Ning Q, Tan Z, Liang K, Mu L, Jackson D, Zhang Z, Yang F, Qiu F. A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination. Nat Commun 2022; 13:5708. [PMID: 36175574 PMCID: PMC9522829 DOI: 10.1038/s41467-022-33513-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Maize early endosperm development is initiated in coordination with elimination of maternal nucellar tissues. However, the underlying mechanisms are largely unknown. Here, we characterize a major quantitative trait locus for maize kernel size and weight that encodes an EXPANSIN gene, ZmEXPB15. The encoded β-expansin protein is expressed specifically in nucellus, and positively controls kernel size and weight by promoting nucellus elimination. We further show that two nucellus-enriched transcription factors (TFs), ZmNAC11 and ZmNAC29, activate ZmEXPB15 expression. Accordingly, these two TFs also promote kernel size and weight through nucellus elimination regulation, and genetic analyses support their interaction with ZmEXPB15. Importantly, hybrids derived from a ZmEXPB15 overexpression line have increased kernel weight, demonstrates its potential value in breeding. Together, we reveal a pathway modulating the cellular processes of maternal nucellus elimination and early endosperm development, and an approach to improve kernel weight. Current studies of maize kernel development mostly focus on endosperm and embryo development, and little is known about the control of the nucellus tissue. Here, the authors report a NAC-EXPB15 pathway that regulate maize kernel size by modulating nucellus elimination and early endosperm development.
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Affiliation(s)
- Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Yunfu Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Aoqing Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Qiang Ning
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Kun Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Luyao Mu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China. .,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China. .,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
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Chattha MS, Ali Q, Haroon M, Afzal MJ, Javed T, Hussain S, Mahmood T, Solanki MK, Umar A, Abbas W, Nasar S, Schwartz-Lazaro LM, Zhou L. Enhancement of nitrogen use efficiency through agronomic and molecular based approaches in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:994306. [PMID: 36237509 PMCID: PMC9552886 DOI: 10.3389/fpls.2022.994306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/22/2022] [Indexed: 05/22/2023]
Abstract
Cotton is a major fiber crop grown worldwide. Nitrogen (N) is an essential nutrient for cotton production and supports efficient crop production. It is a crucial nutrient that is required more than any other. Nitrogen management is a daunting task for plants; thus, various strategies, individually and collectively, have been adopted to improve its efficacy. The negative environmental impacts of excessive N application on cotton production have become harmful to consumers and growers. The 4R's of nutrient stewardship (right product, right rate, right time, and right place) is a newly developed agronomic practice that provides a solid foundation for achieving nitrogen use efficiency (NUE) in cotton production. Cropping systems are equally crucial for increasing production, profitability, environmental growth protection, and sustainability. This concept incorporates the right fertilizer source at the right rate, time, and place. In addition to agronomic practices, molecular approaches are equally important for improving cotton NUE. This could be achieved by increasing the efficacy of metabolic pathways at the cellular, organ, and structural levels and NUE-regulating enzymes and genes. This is a potential method to improve the role of N transporters in plants, resulting in better utilization and remobilization of N in cotton plants. Therefore, we suggest effective methods for accelerating NUE in cotton. This review aims to provide a detailed overview of agronomic and molecular approaches for improving NUE in cotton production, which benefits both the environment and growers.
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Affiliation(s)
- Muhammad Sohaib Chattha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Qurban Ali
- Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sadam Hussain
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Tahir Mahmood
- Department of Plant Breeding & Genetics, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Manoj K. Solanki
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Aisha Umar
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Waseem Abbas
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shanza Nasar
- Department of Botany, University of Gujrat Hafiz Hayat Campus, Gujrat, Pakistan
| | - Lauren M. Schwartz-Lazaro
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Tang W, Lin J, Wang Y, An H, Chen H, Pan G, Zhang S, Guo B, Yu K, Li H, Fang X, Zhang Y. Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2022; 15:48. [PMID: 36152074 PMCID: PMC9509510 DOI: 10.1186/s12284-022-00594-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Breeding of conventional and hybrid rice (Oryza sativa L.) have solved hunger problems and increased farmers' income in the world. Molecular markers have been widely used in marker-assisted breeding and identification of larger numbers of different bred varieties in the past decades. The recently developed SNP markers are applied for more stable and detectable compared with other markers. But the cost of genotyping lots SNPs is high. So, it is essential to select less representative SNPs and inexpensive detecting methods to lower the cost and accelerate variety identification and breeding process. KASP (Kompetitive Allele-Specific PCR) is a flexible method to detect the SNPs, and large number of KASP markers have been widely used in variety identification and breeding. However, the ability of less KASP markers on massive variety identification and breeding remains unknown. RESULTS Here, 48 KASP markers were selected from 378 markers to classify and analyze 518 varieties including conventional and hybrid rice. Through analyzing the population structure, the 48 markers could almost represent the 378 markers. In terms of variety identification, the 48 KASP markers had a 100% discrimination rate in 53 conventional indica varieties and 193 hybrid varieties, while they could distinguish 89.1% conventional japonica rice from different breeding institutes. Two more markers added would increase the ratio from 68.38 to 77.94%. Additionally, the 48 markers could be used for classification of subpopulations in the bred variety. Also, 8 markers had almost completely different genotypes between japonica and indica, and 3 markers were found to be very important for japonica hybrid rice. In hybrid varieties, the heterozygosity of chromosomes 3, 6 and 11 was relatively higher than others. CONCLUSIONS Our results showed that 48 KASP markers could be used to identify rice varieties, and the panel we tested could provide a database for breeders to identify new breeding lines. Also, the specific markers we found were useful for marker-assisted breeding in rice, including conventional and hybrid.
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Affiliation(s)
- Weijie Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Jing Lin
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Yanping Wang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Hongzhou An
- The Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, People's Republic of China
| | - Haiyuan Chen
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Gen Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Suobing Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Baowei Guo
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, People's Republic of China
| | - Kun Yu
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Huayong Li
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China.
| | - Xianwen Fang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China.
| | - Yunhui Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, People's Republic of China.
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Liu X, Jiang H, Yang J, Han J, Jin M, Zhang H, Chen L, Chen S, Teng S. Comprehensive QTL analyses of nitrogen use efficiency in indica rice. FRONTIERS IN PLANT SCIENCE 2022; 13:992225. [PMID: 36212385 PMCID: PMC9539535 DOI: 10.3389/fpls.2022.992225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen-use efficiency (NUE) in rice is a complex quantitative trait involved in multiple biological processes and agronomic traits; however, the genetic basis and regulatory network of NUE remain largely unknown. We constructed a high-resolution microarray-based genetic map for 261 recombinant inbred lines derived from two indica parents. Using 2,345 bin markers, comprehensive analyses of quantitative trait loci (QTLs) of seven key agronomic traits under two different N levels were performed. A total of 11 non-redundant QTLs for effective panicle number (EPN), 7 for grain number per panicle, 13 for thousand-grain weight, 2 for seed-setting percentage, 15 for plant height, 12 for panicle length, and 6 for grain yield per plant were identified. The QTL regions were as small as 512 kb on average, and more than half spanned an interval smaller than 100 kb. Using this advantage, we identified possible candidate genes of two major EPN-related QTLs. One QTL detected under both N levels possibly encodes a DELLA protein SLR1, which is known to regulate NUE, although the natural variations of this protein have not been reported. The other QTL detected only under a high N level could encode the transcription factor OsbZIP59. We also predicted the possible candidate genes for another three of the NUE-related QTLs. Our results provide a reference for improving NUE-related QTL cloning and promote our understanding of NUE regulation in indica rice.
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Affiliation(s)
- Xiuyan Liu
- College of Material and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, China
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hong Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jing Yang
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jiajia Han
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Mengxian Jin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Sheng Teng
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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Chen Q, Lian M, Guo J, Zhang B, Yang S, Huang K, Peng F, Xiao Y. Comparative Transcriptome Analysis of Two Peach Rootstocks Uncovers the Effect of Gene Differential Expression on Nitrogen Use Efficiency. Int J Mol Sci 2022; 23:ijms231911144. [PMID: 36232452 PMCID: PMC9570093 DOI: 10.3390/ijms231911144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 11/24/2022] Open
Abstract
Nitrogen is an important nutrient element that limits plant growth and yield formation, but excessive nitrogen has negative effects on plants and the environment. It is important to reveal the molecular mechanism of high NUE (nitrogen use efficiency) for breeding peach rootstock and variety with high NUE. In this study, two peach rootstocks, Shannong–1 (S) and Maotao (M), with different NUE were used as materials and treated with 0.1 mM KNO3 for transcriptome sequencing together with the control group. From the results of comparison between groups, we found that the two rootstocks had different responses to KNO3, and 2151 (KCL_S vs. KCL_M), 327 (KNO3_S vs. KCL_S), 2200 (KNO3_S vs. KNO3_M) and 146 (KNO3_M vs. KCL_M) differentially expressed genes (DEGs) were identified, respectively, which included multiple transcription factor families. These DEGs were enriched in many biological processes and signal transduction pathways, including nitrogen metabolism and plant hormone signal transduction. The function of PpNRT2.1, which showed up-regulated expression under KNO3 treatment, was verified by heterologous expression in Arabidopsis. The plant height, SPAD (soil and plant analyzer development) of leaf and primary root length of the transgenic plants were increased compared with those of WT, indicating the roles of PpNRT2.1 in nitrogen metabolism. The study uncovered for the first time the different molecular regulatory pathways involved in nitrogen metabolism between two peach rootstocks and provided gene reserve for studying the molecular mechanism of nitrogen metabolism and theoretical basis for screening peach rootstock or variety with high NUE.
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GWAS and Transcriptome Analysis Reveal Key Genes Affecting Root Growth under Low Nitrogen Supply in Maize. Genes (Basel) 2022; 13:genes13091632. [PMID: 36140800 PMCID: PMC9498817 DOI: 10.3390/genes13091632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022] Open
Abstract
Nitrogen (N) is one of the most important factors affecting crop production. Root morphology exhibits a high degree of plasticity to nitrogen deficiency. However, the mechanisms underlying the root foraging response under low-N conditions remain poorly understood. In this study, we analyzed 213 maize inbred lines using hydroponic systems and regarding their natural variations in 22 root traits and 6 shoot traits under normal (2 mM nitrate) and low-N (0 mM nitrate) conditions. Substantial phenotypic variations were detected for all traits. N deficiency increased the root length and decreased the root diameter and shoot related traits. A total of 297 significant marker-trait associations were identified by a genome-wide association study involving different N levels and the N response value. A total of 51 candidate genes with amino acid variations in coding regions or differentially expressed under low nitrogen conditions were identified. Furthermore, a candidate gene ZmNAC36 was resequenced in all tested lines. A total of 38 single nucleotide polymorphisms and 12 insertions and deletions were significantly associated with lateral root length of primary root, primary root length between 0 and 0.5 mm in diameter, primary root surface area, and total length of primary root under a low-N condition. These findings help us to improve our understanding of the genetic mechanism of root plasticity to N deficiency, and the identified loci and candidate genes will be useful for the genetic improvement of maize tolerance cultivars to N deficiency.
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Shi X, Cui F, Han X, He Y, Zhao L, Zhang N, Zhang H, Zhu H, Liu Z, Ma B, Zheng S, Zhang W, Liu J, Fan X, Si Y, Tian S, Niu J, Wu H, Liu X, Chen Z, Meng D, Wang X, Song L, Sun L, Han J, Zhao H, Ji J, Wang Z, He X, Li R, Chi X, Liang C, Niu B, Xiao J, Li J, Ling HQ. Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 9204. MOLECULAR PLANT 2022; 15:1440-1456. [PMID: 35864747 DOI: 10.1016/j.molp.2022.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/09/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Studying the regulatory mechanisms that drive nitrogen-use efficiency (NUE) in crops is important for sustainable agriculture and environmental protection. In this study, we generated a high-quality genome assembly for the high-NUE wheat cultivar Kenong 9204 and systematically analyzed genes related to nitrogen uptake and metabolism. By comparative analyses, we found that the high-affinity nitrate transporter gene family had expanded in Triticeae. Further studies showed that subsequent functional differentiation endowed the expanded family members with saline inducibility, providing a genetic basis for improving the adaptability of wheat to nitrogen deficiency in various habitats. To explore the genetic and molecular mechanisms of high NUE, we compared genomic and transcriptomic data from the high-NUE cultivar Kenong 9204 (KN9204) and the low-NUE cultivar Jing 411 and quantified their nitrogen accumulation under high- and low-nitrogen conditions. Compared with Jing 411, KN9204 absorbed significantly more nitrogen at the reproductive stage after shooting and accumulated it in the shoots and seeds. Transcriptome data analysis revealed that nitrogen deficiency clearly suppressed the expression of genes related to cell division in the young spike of Jing 411, whereas this suppression of gene expression was much lower in KN9204. In addition, KN9204 maintained relatively high expression of NPF genes for a longer time than Jing 411 during seed maturity. Physiological and transcriptome data revealed that KN9204 was more tolerant of nitrogen deficiency than Jing 411, especially at the reproductive stage. The high NUE of KN9204 is an integrated effect controlled at different levels. Taken together, our data provide new insights into the molecular mechanisms of NUE and important gene resources for improving wheat cultivars with a higher NUE trait.
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Affiliation(s)
- Xiaoli Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai 264025, China
| | - Xinyin Han
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yilin He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Hao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haidong Zhu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhexin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Jiajia Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaoli Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianqing Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuemei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Deyuan Meng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaoyan Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Liqiang Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Lijing Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Jie Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Hui Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Jun Ji
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Zhiguo Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaoyu He
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruilin Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xuebin Chi
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Junming Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China.
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Yazhou Bay Seed Laboratory of Hainan Province, Sanya 572019, China.
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49
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Li K, Zhang S, Tang S, Zhang J, Dong H, Yang S, Qu H, Xuan W, Gu M, Xu G. The rice transcription factor Nhd1 regulates root growth and nitrogen uptake by activating nitrogen transporters. PLANT PHYSIOLOGY 2022; 189:1608-1624. [PMID: 35512346 PMCID: PMC9237666 DOI: 10.1093/plphys/kiac178] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Plants adjust root architecture and nitrogen (N) transporter activity to meet the variable N demand, but their integrated regulatory mechanism remains unclear. We have previously reported that a floral factor in rice (Oryza sativa), N-mediated heading date-1 (Nhd1), regulates flowering time. Here, we show that Nhd1 can directly activate the transcription of the high-affinity ammonium (NH4+) transporter 1;3 (OsAMT1;3) and the dual affinity nitrate (NO3-) transporter 2.4 (OsNRT2.4). Knockout of Nhd1 inhibited root growth in the presence of NO3- or a low concentration of NH4+. Compared to the wild-type (WT), nhd1 and osamt1;3 mutants showed a similar decrease in root growth and N uptake under low NH4+ supply, while nhd1 and osnrt2.4 mutants showed comparable root inhibition and altered NO3- translocation in shoots. The defects of nhd1 mutants in NH4+ uptake and root growth response to various N supplies were restored by overexpression of OsAMT1;3 or OsNRT2.4. However, when grown in a paddy field with low N availability, nhd1 mutants accumulated more N and achieved a higher N uptake efficiency (NUpE) due to the delayed flowering time and prolonged growth period. Our findings reveal a molecular mechanism underlying the growth duration-dependent NUpE.
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Affiliation(s)
- Kangning Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Shuo Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongzhang Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shihan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongye Qu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mian Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- Authors for correspondence: (S.Z.); (G.X.)
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50
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Zhang Y, Wang Y, Sun X, Yuan J, Zhao Z, Gao J, Wen X, Tang F, Kang M, Abliz B, Zhang Z, Zhang H, Wang F, Li Z. Genome-Wide Identification of MDH Family Genes and Their Association with Salt Tolerance in Rice. PLANTS 2022; 11:plants11111498. [PMID: 35684271 PMCID: PMC9182821 DOI: 10.3390/plants11111498] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022]
Abstract
Malate dehydrogenase (MDH) is widely present in nature and regulates plant growth and development, as well as playing essential roles, especially in abiotic stress responses. Nevertheless, there is no comprehensive knowledge to date on MDH family members in rice. In this study, a total of 12 MDH members in rice were identified through genome-wide analysis and divided into three groups on the basis of their phylogenetic relationship and protein-conserved motifs. Evolutionary analysis showed that MDH proteins from rice, maize and wheat shared a close phylogenetic relationship, and the MDH family was conserved in the long-term process of domestication. We identified two segmental duplication events involving four genes, which could be the major force driving the expansion of the OsMDH family. The expression profile, cis-regulatory elements and qRT-PCR results of these genes revealed that a few OsMDH showed high tissue specificity, almost all of which had stress response elements in the promoter region, and ten MDH members were significantly induced by salt stress. Through gene-based association analysis, we found a significant correlation between salt tolerance at the seedling stage and the genetic variation of OsMDH8.1 and OsMDH12.1. Additionally, we found that the polymorphism in the promoter region of OsMDH8.1 might be related to the salt tolerance of rice. This study aimed to provide valuable information on the functional study of the rice MDH gene family related to salt stress response and revealed that OsMDH8.1 might be an important gene for the cultivar improvement of salt tolerance in rice.
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Affiliation(s)
- Yanhong Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
| | - Yulong Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xingming Sun
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Yuan
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
| | - Zhiqiang Zhao
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
| | - Jie Gao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaorong Wen
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
| | - Fusen Tang
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
| | - Mintai Kang
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
| | - Buhaliqem Abliz
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Fengbin Wang
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Correspondence: (F.W.); (Z.L.)
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Correspondence: (F.W.); (Z.L.)
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