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Islam S, Zhang J, Zhao Y, She M, Ma W. Genetic regulation of the traits contributing to wheat nitrogen use efficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110759. [PMID: 33487345 DOI: 10.1016/j.plantsci.2020.110759] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 05/25/2023]
Abstract
High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.
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Affiliation(s)
- Shahidul Islam
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Jingjuan Zhang
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Yun Zhao
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Maoyun She
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Wujun Ma
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia.
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Yan M, Zheng L, Li B, Shen R, Lan P. Comparative proteomics reveals new insights into the endosperm responses to drought, salinity and submergence in germinating wheat seeds. PLANT MOLECULAR BIOLOGY 2021; 105:287-302. [PMID: 33104943 DOI: 10.1007/s11103-020-01087-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/15/2020] [Indexed: 05/20/2023]
Abstract
Beyond the role of a nutrient reservoir during germination, the endosperm of wheat seeds also responds to different abiotic stresses via modification of the protein profiles. The endosperm is the main component of wheat seeds. During seed germination, it provides nutrients to support the embryo development, and its constituents vary under environmental stresses such as drought, salinity and submergence that are associated with disordered water supply. However, the molecular mechanism of these stress responses remains unclear. In this study, a comparative label-free proteomic analysis was performed on endosperm from the germinating wheat seeds subjected to PEG, NaCl and submergence treatments. In total, 2273 high confidence proteins were detected, and 234, 207 and 209 of them were identified as differentially expressed proteins (DEPs) under the three stresses, respectively. Functional classification revealed that the DEPs were mainly involved in protein, amino acid and organic acid metabolic process in all stress treatments. While some other metabolic processes were highlighted in one or two of the stresses specifically, such as oxidative phosphorylation in PEG and submergence, and β-alanine metabolism in PEG and NaCl treatments. The identification of a series of stress-related proteins and their biased expression in different stresses indicates the active stress-responding role of endosperm beyond a simple nutrient reservoir during germination, while the overall stress responses of the endosperm were found to be moderate and lag behind the embryo. Besides, some fundamental processes and DEPs shared by the three stresses could be selected priorly for future molecular breeding researches. Our results provide new insights into the mechanism of endosperm responses to abiotic stresses during seed germination.
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Affiliation(s)
- Mingke Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Bingjuan Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Cai J, Cai W, Huang X, Yang S, Wen J, Xia X, Yang F, Shi Y, Guan D, He S. Ca14-3-3 Interacts With CaWRKY58 to Positively Modulate Pepper Response to Low-Phosphorus Starvation. FRONTIERS IN PLANT SCIENCE 2021; 11:607878. [PMID: 33519860 PMCID: PMC7840522 DOI: 10.3389/fpls.2020.607878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Low-phosphorus stress (LPS) and pathogen attack are two important stresses frequently experienced by plants in their natural habitats, but how plant respond to them coordinately remains under-investigated. Here, we demonstrate that CaWRKY58, a known negative regulator of the pepper (Capsicum annuum) response to attack by Ralstonia solanacearum, is upregulated by LPS. Virus-induced gene silencing (VIGS) and overexpression of CaWRKY58 in Nicotiana benthamiana plants in combination with chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays (EMSA) demonstrated that CaWRKY58 positively regulates the response of pepper to LPS by directly targeting and regulating genes related to phosphorus-deficiency tolerance, including PHOSPHATE STARVATION RESPONSE1 (PHR1). Yeast two-hybrid assays revealed that CaWRKY58 interacts with a 14-3-3 protein (Ca14-3-3); this interaction was confirmed by pull-down, bimolecular fluorescence complementation (BiFC), and microscale thermophoresis (MST) assays. The interaction between Ca14-3-3 and CaWRKY58 enhanced the activation of PHR1 expression by CaWRKY58, but did not affect the expression of the immunity-related genes CaNPR1 and CaDEF1, which are negatively regulated by CaWRKY58 in pepper upon Ralstonia solanacearum inoculation. Collectively, our data indicate that CaWRKY58 negatively regulates immunity against Ralstonia solanacearum, but positively regulates tolerance to LPS and that Ca14-3-3 transcriptionally activates CaWRKY58 in response to LPS.
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Affiliation(s)
- Jinsen Cai
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weiwei Cai
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueying Huang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Yang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayu Wen
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoqin Xia
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feng Yang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Shi
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyi Guan
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuilin He
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
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Shi J, Tong Y. TaLAMP1 Plays Key Roles in Plant Architecture and Yield Response to Nitrogen Fertilizer in Wheat. FRONTIERS IN PLANT SCIENCE 2021; 11:598015. [PMID: 33505409 PMCID: PMC7832495 DOI: 10.3389/fpls.2020.598015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/01/2020] [Indexed: 05/24/2023]
Abstract
Understanding the molecular mechanisms in wheat response to nitrogen (N) fertilizer will help us to breed wheat varieties with improved yield and N use efficiency. Here, we cloned TaLAMP1-3A, -3B, and -3D, which were upregulated in roots and shoots of wheat by low N availability. In a hydroponic culture, lateral root length and N uptake were decreased in both overexpression and knockdown of TaLAMP1 at the seedling stage. In the field experiment with normal N supply, the grain yield of overexpression of TaLAMP1-3B is significantly reduced (14.5%), and the knockdown of TaLAMP1 was significantly reduced (15.5%). The grain number per spike of overexpression of TaLAMP1-3B was significantly increased (7.2%), but the spike number was significantly reduced (19.2%) compared with wild type (WT), although the grain number per spike of knockdown of TaLAMP1 was significantly decreased (15.3%), with no difference in the spike number compared with WT. Combined with the agronomic data from the field experiment of normal N and low N, both overexpression and knockdown of TaLAMP1 inhibited yield response to N fertilizer. Overexpressing TaLAMP1-3B greatly increased grain N concentration with no significant detrimental effect on grain yield under low N conditions; TaLAMP1-3 B is therefore valuable in engineering wheat for low input agriculture. These results suggested that TaLAMP1 is critical for wheat adaptation to N availability and in shaping plant architecture by regulating spike number per plant and grain number per spike. Optimizing TaLAMP1 expression may facilitate wheat breeding with improved yield, grain N concentration, and yield responses to N fertilizer.
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Affiliation(s)
- Ji Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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Kong L, Zhang Y, Du W, Xia H, Fan S, Zhang B. Signaling Responses to N Starvation: Focusing on Wheat and Filling the Putative Gaps With Findings Obtained in Other Plants. A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:656696. [PMID: 34135921 PMCID: PMC8200679 DOI: 10.3389/fpls.2021.656696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/08/2021] [Indexed: 05/16/2023]
Abstract
Wheat is one of the most important food crops worldwide. In recent decades, fertilizers, especially nitrogen (N), have been increasingly utilized to maximize wheat productivity. However, a large proportion of N is not used by plants and is in fact lost into the environment and causes serious environmental pollution. Therefore, achieving a low N optimum via efficient physiological and biochemical processes in wheat grown under low-N conditions is highly important for agricultural sustainability. Although N stress-related N capture in wheat has become a heavily researched subject, how this plant adapts and responds to N starvation has not been fully elucidated. This review summarizes the current knowledge on the signaling mechanisms activated in wheat plants in response to N starvation. Furthermore, we filled the putative gaps on this subject with findings obtained in other plants, primarily rice, maize, and Arabidopsis. Phytohormones have been determined to play essential roles in sensing environmental N starvation and transducing this signal into an adjustment of N transporters and phenotypic adaptation. The critical roles played by protein kinases and critical kinases and phosphatases, such as MAPK and PP2C, as well as the multifaceted functions of transcription factors, such as NF-Y, MYB, DOF, and WRKY, in regulating the expression levels of their target genes (proteins) for low-N tolerance are also discussed. Optimization of root system architecture (RSA) via root branching and thinning, improvement of N acquisition and assimilation, and fine-tuned autophagy are pivotal strategies by which plants respond to N starvation. In light of these findings, we attempted to construct regulatory networks for RSA modification and N uptake, transport, assimilation, and remobilization.
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Affiliation(s)
- Lingan Kong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Yunxiu Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Wanying Du
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Haiyong Xia
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shoujin Fan
- College of Life Science, Shandong Normal University, Jinan, China
| | - Bin Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- *Correspondence: Bin Zhang,
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Sandhu N, Sethi M, Kumar A, Dang D, Singh J, Chhuneja P. Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:657629. [PMID: 34149755 PMCID: PMC8213353 DOI: 10.3389/fpls.2021.657629] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/06/2021] [Indexed: 05/22/2023]
Abstract
Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.
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57
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Tiwari JK, Buckseth T, Singh RK, Kumar M, Kant S. Prospects of Improving Nitrogen Use Efficiency in Potato: Lessons From Transgenics to Genome Editing Strategies in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:597481. [PMID: 33424892 PMCID: PMC7785987 DOI: 10.3389/fpls.2020.597481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/10/2020] [Indexed: 05/27/2023]
Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Tanuja Buckseth
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, Centre for Agricultural Innovation, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
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58
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Maurya J, Bandyopadhyay T, Prasad M. Transcriptional regulators of nitrate metabolism: Key players in improving nitrogen use in crops. J Biotechnol 2020; 324:121-133. [PMID: 33031844 DOI: 10.1016/j.jbiotec.2020.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/19/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
Abstract
Green revolution has boosted crop yields by the development of varieties which rely on high fertilizer application. Since then, higher productivity has largely witnessed excessive nitrogen (N) fertilizer application resulting in many environmentally and agronomically unsustainable consequences. One possible solution to this problem is to develop varieties with efficient N use endowed with genetically superior N metabolizing machinery, thereby significantly reducing N loss in soil and facilitating gainful yield performance at lower N conditions. Nitrate (NO3-) is the major form of N acquired by plants in aerobic soils. Hence, its efficient acquisition, transport, assimilation into complex organic compounds, and overall homeostasis is crucial to ensure productivity under optimal and suboptimal N conditions. Transcription factors are prime regulators of these processes, and insights into their mechanism of action and the resultant effect on N metabolism are crucial to generating crops with efficient and durable nitrogen use efficiency. The present review, therefore, presents a comprehensive updated account of major N responsive transcription factor families, their cross-talk with other growth factors, and explores existing and potential areas of their biotechnological application to maximize crop yields.
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Affiliation(s)
- Jyoti Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Chen W, Hu T, Ye J, Wang B, Liu G, Wang Y, Yuan L, Li J, Li F, Ye Z, Zhang Y. A CCAAT-binding factor, SlNFYA10, negatively regulates ascorbate accumulation by modulating the D-mannose/L-galactose pathway in tomato. HORTICULTURE RESEARCH 2020; 7:200. [PMID: 33328457 PMCID: PMC7705693 DOI: 10.1038/s41438-020-00418-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/15/2020] [Accepted: 08/18/2020] [Indexed: 05/04/2023]
Abstract
Ascorbic acid (AsA), an important antioxidant and growth regulator, and it is essential for plant development and human health. Specifically, humans have to acquire AsA from dietary sources due to their inability to synthesize it. The AsA biosynthesis pathway in plants has been elucidated, but its regulatory mechanism remains largely unknown. In this report, we biochemically identified a CCAAT-box transcription factor (SlNFYA10) that can bind to the promoter of SlGME1, which encodes GDP-Man-3',5'-epimerase, a pivotal enzyme in the D-mannose/L-galactose pathway. Importantly, SlNFYA10 simultaneously binds to the promoter of SlGGP1, a downstream gene of SlGME1 in the D-mannose/L-galactose pathway. Binding assays in yeast and functional analyses in plants have confirmed that SlNFYA10 exerts a negative effect on the expression of both SlGME1 and SlGGP1. Transgenic tomato lines overexpressing SlNFYA10 show decreased levels of SlGME1 and SlGGP1 abundance and AsA concentration in their leaves and fruits, accompanied by enhanced sensitivity to oxidative stress. Overall, SlNFYA10 is the first CCAAT-binding factor identified to date to negatively regulate the AsA biosynthetic pathway at multiple sites and modulate plant responses to oxidative stress.
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Affiliation(s)
- Weifang Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Tixu Hu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jie Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Bing Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Genzhong Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ying Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Lei Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jiaming Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Fangman Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
- HZAU Chuwei Institute of Advanced Seeds, 430070, Wuhan, China
| | - Yuyang Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China.
- HZAU Chuwei Institute of Advanced Seeds, 430070, Wuhan, China.
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Zotova L, Shamambaeva N, Lethola K, Alharthi B, Vavilova V, Smolenskaya SE, Goncharov NP, Kurishbayev A, Jatayev S, Gupta NK, Gupta S, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y. TaDrAp1 and TaDrAp2, Partner Genes of a Transcription Repressor, Coordinate Plant Development and Drought Tolerance in Spelt and Bread Wheat. Int J Mol Sci 2020; 21:E8296. [PMID: 33167455 PMCID: PMC7663959 DOI: 10.3390/ijms21218296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 01/10/2023] Open
Abstract
Down-regulator associated protein, DrAp1, acts as a negative cofactor (NC2α) in a transcription repressor complex together with another subunit, down-regulator Dr1 (NC2β). In binding to promotors and regulating the initiation of transcription of various genes, DrAp1 plays a key role in plant transition to flowering and ultimately in seed production. TaDrAp1 and TaDrAp2 genes were identified, and their expression and genetic polymorphism were studied using bioinformatics, qPCR analyses, a 40K Single nucleotide polymorphism (SNP) microarray, and Amplifluor-like SNP genotyping in cultivars of bread wheat (Triticum aestivum L.) and breeding lines developed from a cross between spelt (T. spelta L.) and bread wheat. TaDrAp1 was highly expressed under non-stressed conditions, and at flowering, TaDrAp1 expression was negatively correlated with yield capacity. TaDrAp2 showed a consistently low level of mRNA production. Drought caused changes in the expression of both TaDrAp1 and TaDrAp2 genes in opposite directions, effectively increasing expression in lower yielding cultivars. The microarray 40K SNP assay and Amplifluor-like SNP marker, revealed clear scores and allele discriminations for TaDrAp1 and TaDrAp2 and TaRht-B1 genes. Alleles of two particular homeologs, TaDrAp1-B4 and TaDrAp2-B1, co-segregated with grain yield in nine selected breeding lines. This indicated an important regulatory role for both TaDrAp1 and TaDrAp2 genes in plant growth, ontogenesis, and drought tolerance in bread and spelt wheat.
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Affiliation(s)
- Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan 010000, Kazakhstan; (L.Z.); (N.S.); (A.K.)
| | - Nasgul Shamambaeva
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan 010000, Kazakhstan; (L.Z.); (N.S.); (A.K.)
| | - Katso Lethola
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Badr Alharthi
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Valeriya Vavilova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (V.V.); (S.E.S.); (N.P.G.)
| | - Svetlana E. Smolenskaya
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (V.V.); (S.E.S.); (N.P.G.)
| | - Nikolay P. Goncharov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (V.V.); (S.E.S.); (N.P.G.)
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan 010000, Kazakhstan; (L.Z.); (N.S.); (A.K.)
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan 010000, Kazakhstan; (L.Z.); (N.S.); (A.K.)
| | - Narendra K. Gupta
- Department of Plant Physiology, SKN Agriculture University, Jobner 303329, Rajasthan, India; (N.K.G.); (S.G.)
| | - Sunita Gupta
- Department of Plant Physiology, SKN Agriculture University, Jobner 303329, Rajasthan, India; (N.K.G.); (S.G.)
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Peter A. Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
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Szala K, Ogonowska H, Lugowska B, Zmijewska B, Wyszynska R, Dmochowska-Boguta M, Orczyk W, Nadolska-Orczyk A. Different sets of TaCKX genes affect yield-related traits in wheat plants grown in a controlled environment and in field conditions. BMC PLANT BIOLOGY 2020; 20:496. [PMID: 33121443 PMCID: PMC7597040 DOI: 10.1186/s12870-020-02713-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/20/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND TaCKX wheat gene family members (GFMs) encode the enzyme cytokinin oxidase/dehydrogenase (CKX), which irreversibly degrades cytokinins. The genes are important regulators of cytokinin content and take part in growth and development, with a major impact on yield-related traits. The goal of this research was to test whether these genes might be differentially expressed in the field compared to laboratory conditions and consequently differently affect plant development and yield. RESULTS We compared expression and crosstalk of the TaCKX GFMs and TaNAC2-5A gene in modern varieties grown in a growth chamber (GC) and in the field and looked for differences in their impact on yield-related traits. The TaNAC2-5A gene was included in the research since it was expected to play an important role in co-regulation of these genes. The range of relative expression levels of TaCKX GFMs and TaNAC2-5A gene among tested cultivars was from 5 for TaCKX8 to more than 100 for TaCKX9 in the GC and from 6 for TaCKX8 to 275 for TaCKX10 in the field. The range was similar for four of them in the GC, but was much higher for seven others and TaNAC2-5A in the field. The TaCKX GFMs and TaNAC2-5A form co-expression groups, which differ depending on growth conditions. Consequently, the genes also differently regulate yield-related traits in the GC and in the field. TaNAC2-5A took part in negative regulation of tiller number and CKX activity in seedling roots only in controlled GC conditions. Grain number and grain yield were negatively regulated by TaCKX10 in the GC but positively by TaCKX8 and others in the field. Some of the genes, which were expressed in seedling roots, negatively influenced tiller number and positively regulated seedling root weight, CKX activity in the spikes, thousand grain weight (TGW) as well as formation of semi-empty spikes. CONCLUSIONS We have documented that: 1) natural variation in expression levels of tested genes in both environments is very high, indicating the possibility of selection of beneficial genotypes for breeding purposes, 2) to create a model of an ideotype for breeding, we need to take into consideration the natural environment.
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Affiliation(s)
- Karolina Szala
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Hanna Ogonowska
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | | | - Barbara Zmijewska
- Plant Breeding Strzelce Ltd., Co. - IHAR Group, Konczewice 1, 87-140, Chelmza, Poland
| | - Renata Wyszynska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Marta Dmochowska-Boguta
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Waclaw Orczyk
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland.
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Wu L, Guo Y, Cai S, Kuang L, Shen Q, Wu D, Zhang G. The zinc finger transcription factor ATF1 regulates aluminum tolerance in barley. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6512-6523. [PMID: 32720977 DOI: 10.1093/jxb/eraa349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
Aluminum (Al) toxicity is a major abiotic stress that restricts crop production in acid soils. Plants have evolved internal and external mechanisms of tolerance, and among them it is well known that AtSTOP1 and OsART1 are key transcription factors involved in tolerance through regulation of multiple downstream genes. Here, we identified the closest homolog of these two proteins in barley, namely HvATF1, Al-tolerance Transcription Factor 1, and determined its potential function in Al stress. HvATF1 is expressed in the nucleus, and functions in transcriptional activation. The transcription of HvATF1 was found to be constitutive in different tissues, and was little affected by Al stress. Knockdown of HvATF1 by RNAi resulted in increased Al sensitivity. Transcriptomics analysis identified 64 differently expressed genes in the RNAi lines compared to the wild-type, and these were considered as candidate downstream genes regulated by HvATF1. This study provides insights into the different molecular mechanisms of Al tolerance in barley and other plants.
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Affiliation(s)
- Liyuan Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Yiyi Guo
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Shengguan Cai
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Liuhui Kuang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Qiufang Shen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Dezhi Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Guoping Zhang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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Baison J, Zhou L, Forsberg N, Mörling T, Grahn T, Olsson L, Karlsson B, Wu HX, Mellerowicz EJ, Lundqvist SO, García-Gil MR. Genetic control of tracheid properties in Norway spruce wood. Sci Rep 2020; 10:18089. [PMID: 33093525 PMCID: PMC7581746 DOI: 10.1038/s41598-020-72586-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 09/03/2020] [Indexed: 01/20/2023] Open
Abstract
Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 (PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.
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Affiliation(s)
- J Baison
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Linghua Zhou
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Nils Forsberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Tommy Mörling
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Thomas Grahn
- RISE Bioeconomy, Box 5604, 114 86, Stockholm, Sweden
| | - Lars Olsson
- RISE Bioeconomy, Box 5604, 114 86, Stockholm, Sweden
| | - Bo Karlsson
- Skogforsk, Ekebo 2250, 268 90, Svalov, Sweden
| | - Harry X Wu
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Ewa J Mellerowicz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Sven-Olof Lundqvist
- RISE Bioeconomy, Box 5604, 114 86, Stockholm, Sweden
- IIC, Rosenlundsgatan 48B, 11863, Stockholm, Sweden
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden.
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Zheng X, Liu C, Qiao L, Zhao J, Han R, Wang X, Ge C, Zhang W, Zhang S, Qiao L, Zheng J, Hao C. The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5808-5822. [PMID: 32725154 DOI: 10.1093/jxb/eraa355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Improved inorganic phosphate (Pi) use efficiency in crops will be important for sustainable agriculture. Exploring molecular mechanisms that regulate Pi uptake could provide useful information for breeding wheat with improved Pi use efficiency. Here, a TaPHR3-A1 (Gene ID: TraesCS7A02G415800) ortholog of rice OsPHR3 that functions in transcriptional regulation of Pi signaling was cloned from wheat chromosome 7A. Ectopic expression of TaPHR3-A1 in Arabidopsis and rice produced enhanced vegetative growth and more seeds. Overexpression in transgenic rice led to increased biomass, grain number, and primary panicle branching by 61.23, 42.12, and 36.34% compared with the wild type. Transgenic wheat lines with down-regulation of TaPHR3-A1 exhibited retarded growth and root hair development at the seedling stage, and showed yield-related effects at the adult stage when grown in both low- and sufficient Pi conditions, indicating that TaPHR3-A1 positively regulated tolerance to low Pi. Introgression lines further confirmed the effect of TaPHR3-A1 in improving grain number. The Chinese wheat mini core collection and a recombinant inbred line analysis demonstrated that the favorable allele TaPHR3-A1-A associated with higher grain number was positively selected in breeding. A TaPHR3-A1-derived cleaved amplified polymorphic sequence marker effectively identified haplotype TaPHR3-A1-A. Our results suggested that TaPHR3-A1 was a functional regulatory factor for Pi uptake and provided useful information for marker-assisted selection for high yield in wheat.
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Affiliation(s)
- Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Chuan Ge
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Wenyun Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Shuwei Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Linyi Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Chenyang Hao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Grabowska A, Smoczynska A, Bielewicz D, Pacak A, Jarmolowski A, Szweykowska-Kulinska Z. Barley microRNAs as metabolic sensors for soil nitrogen availability. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110608. [PMID: 32900446 DOI: 10.1016/j.plantsci.2020.110608] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Barley (Hordeum vulgare) is one of the most important crops in the world, ranking 4th in the worldwide production. Crop breeders are facing increasing environmental obstacles in the field, such as drought, salinity but also toxic over fertilization which not only impacts quality of the grain but also an yield. One of the most prevalent mechanisms of gene expression regulation in plants is microRNA-mediated silencing of target genes. We identified 13 barley microRNAs and 2 microRNAs* that are nitrogen excess responsive. Four microRNAs respond only in root, eight microRNAs only in shoot and one displays broad response in roots and shoots. We demonstrate that 2 microRNAs* are induced in barley shoot by nitrogen excess. For all microRNAs we identified putative target genes and confirmed microRNA-guided cleavage sites for ten out of thirteen mRNAs. None of the identified microRNAs or their target genes is known as nitrogen excess responsive. Analysis of expression pattern of thirteen target mRNAs and their cognate microRNAs showed expected correlations of their levels. The plant microRNAs analyzed are also known to respond to nitrogen deprivation and exhibit the opposite expression pattern when nitrogen excess/deficiency conditions are compared. Thus, they can be regarded as metabolic sensors of the regulation of nitrogen homeostasis in plants.
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Affiliation(s)
- Aleksandra Grabowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Aleksandra Smoczynska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
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Vidal EA, Alvarez JM, Araus V, Riveras E, Brooks MD, Krouk G, Ruffel S, Lejay L, Crawford NM, Coruzzi GM, Gutiérrez RA. Nitrate in 2020: Thirty Years from Transport to Signaling Networks. THE PLANT CELL 2020; 32:2094-2119. [PMID: 32169959 PMCID: PMC7346567 DOI: 10.1105/tpc.19.00748] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/05/2020] [Accepted: 03/10/2020] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) is an essential macronutrient for plants and a major limiting factor for plant growth and crop production. Nitrate is the main source of N available to plants in agricultural soils and in many natural environments. Sustaining agricultural productivity is of paramount importance in the current scenario of increasing world population, diversification of crop uses, and climate change. Plant productivity for major crops around the world, however, is still supported by excess application of N-rich fertilizers with detrimental economic and environmental impacts. Thus, understanding how plants regulate nitrate uptake and metabolism is key for developing new crops with enhanced N use efficiency and to cope with future world food demands. The study of plant responses to nitrate has gained considerable interest over the last 30 years. This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology. We discuss how we have reached our current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants. We hope this summary will serve not only as a timeline and information repository but also as a baseline to define outstanding questions for future research.
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Affiliation(s)
- Elena A Vidal
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
| | - José M Alvarez
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Viviana Araus
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Eleodoro Riveras
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile, 8331150
- FONDAP Center for Genome Regulation, Santiago, Chile, 8370415
| | - Matthew D Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Gabriel Krouk
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Sandrine Ruffel
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Laurence Lejay
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, 92093
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile, 8331150
- FONDAP Center for Genome Regulation, Santiago, Chile, 8370415
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67
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Liu N, Cheng F. Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome. BMC PLANT BIOLOGY 2020; 20:245. [PMID: 32487017 PMCID: PMC7265254 DOI: 10.1186/s12870-020-02449-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). RESULTS The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%). CONCLUSIONS Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.
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Affiliation(s)
- Na Liu
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Fangyun Cheng
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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Wang K, Gong Q, Ye X. Recent developments and applications of genetic transformation and genome editing technologies in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1603-1622. [PMID: 31654081 DOI: 10.1007/s00122-019-03464-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/19/2019] [Indexed: 05/24/2023]
Abstract
Wheat (Triticum aestivum) is a staple crop across the world and plays a remarkable role in food supplying security. Over the past few decades, basic and applied research on wheat has lagged behind other cereal crops due to the complex and polyploid genome and difficulties in genetic transformation. A breakthrough called as PureWheat was made in the genetic transformation of wheat in 2014 in Asia, leading to a noticeable progress of wheat genome editing. Due to this great achievement, it is predicated that wheat biotechnology revolution is arriving. Genome editing technologies using zinc finger nucleases, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats-associated endonucleases (CRISR/Cas) are becoming powerful tools for crop modification which can help biologists and biotechnologists better understand the processes of mutagenesis and genomic alteration. Among the three genome editing systems, CRISR/Cas has high specificity and activity, and therefore it is widely used in genetic engineering. Generally, the genome editing technologies depend on an efficient genetic transformation system. In this paper, we summarize recent progresses and applications on genetic transformation and genome editing in wheat. We also examine the future aspects of genetic transformation and genome editing. We believe that the technologies for wheat efficient genetic engineering and functional studies will become routine with the emergence of high-quality genomic sequences.
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Affiliation(s)
- Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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69
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Yan M, Xue C, Xiong Y, Meng X, Li B, Shen R, Lan P. Proteomic dissection of the similar and different responses of wheat to drought, salinity and submergence during seed germination. J Proteomics 2020; 220:103756. [PMID: 32201361 DOI: 10.1016/j.jprot.2020.103756] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 12/11/2022]
Abstract
Wheat (Triticum aestivum L.) is one of the major crops worldwide and its production is inevitably subjected to various biotic/abiotic stresses during the life cycle. Drought, salinity and flooding are among the most severe abiotic stresses restricting wheat yields and could occur at very early stages such as seed germination. How wheat seed germination responds to these different stresses remains incomplete. To fill the information gap, a label-free proteomic analysis was applied to decipher the proteomic profiling of the germinating wheat seeds subjected to PEG, NaCl and submergence treatments. In total, 4295 proteins were detected, of which 465, 397 and 732 showed significant alterations in abundance under those stresses when compared with control. A common denominator found in the response observed to all three stresses are changes related to small molecule metabolic processes, and particularly in pathways associated with phenylpropanoid biosynthesis and fatty acid degradation. It was also noticeable that pathways like cysteine and methionine metabolism in the PEG or submergence treatment and starch and sucrose metabolism in the submergence treatment are specifically pronounced. Functional analysis of putative proteins participating in these pathways revealed distinct responsive patterns across different stresses. SIGNIFICANCE: Wheat (Triticum aestivum L.) is one of the most important staple crops in the world, but its growth and productivity are frequently restrained by stresses such as drought, salinity and flooding. To date, many resources have been documented to investigate how wheat responds and adapts to these individual stresses during plant development and yield formation, but little attention was paid to the understandings of the internal link between different conditions, especially during the germination process, a critical stage that determines the optimal growth of wheat. In this study, we carried out the proteome profiling of the germinating seeds of a common wheat cultivar, Chinese Spring, subjected to PEG, NaCl and submergence stresses. We found that the phenylpropanoid biosynthesis and fatty acid degradation pathways were enriched as the ubiquitous stress responses, while some pathways were stress-specific, for instance, starch and sucrose metabolism against submergence. The changes in some of the altered processes were further validated by physiological and molecular approaches. Our results suggest that the overall pathway profiles concerned with the three stresses were similar, but the specific procedures and components in each process varied greatly. The altered proteins and processes can be taken as effective candidates in future breeding and agronomic modification researches.
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Affiliation(s)
- Mingke Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caiwen Xue
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Xiong
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangxiang Meng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingjuan Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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He X, Liu G, Li B, Xie Y, Wei Y, Shang S, Tian L, Shi H. Functional analysis of the heterotrimeric NF-Y transcription factor complex in cassava disease resistance. ANNALS OF BOTANY 2020; 124:1185-1198. [PMID: 31282544 PMCID: PMC6943695 DOI: 10.1093/aob/mcz115] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/01/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The nuclear factor Y (NF-Y) transcription factor complex is important in plant growth, development and stress response. Information regarding this transcription factor complex is limited in cassava (Manihot esculenta). In this study, 15 MeNF-YAs, 21 MeNF-YBs and 15 MeNF-YCs were comprehensively characterized during plant defence. METHODS Gene expression in MeNF-Ys was examined during interaction with the bacterial pathogen Xanthomonas axonopodis pv. manihotis (Xam). The yeast two-hybrid system was employed to investigate protein-protein interactions in the heterotrimeric NF-Y transcription factor complex. The in vivo roles of MeNF-Ys were revealed by virus-induced gene silencing (VIGS) in cassava. KEY RESULTS The regulation of MeNF-Ys in response to Xam indicated their possible roles in response to cassava bacterial blight. Protein-protein interaction assays identified the heterotrimeric NF-Y transcription factor complex (MeNF-YA1/3, MeNF-YB11/16 and MeNF-YC11/12). Moreover, the members of the heterotrimeric NF-Y transcription factor complex were located in the cell nucleus and conferred transcriptional activation activity to the CCAAT motif. Notably, the heterotrimeric NF-Y transcription factor complex positively regulated plant disease resistance to Xam, confirmed by a disease phenotype in overexpressing plants in Nicotiana benthamiana and VIGS in cassava. Consistently, the heterotrimeric NF-Y transcription factor complex positively regulated the expression of pathogenesis-related genes (MePRs). CONCLUSIONS The NF-Y transcription factor complex (MeNF-YA1/3, MeNF-YB11/16 and MeNF-YC11/12) characterized here was shown to play a role in transcriptional activation of MePR promoters, contributing to the plant defence response in cassava.
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Affiliation(s)
- Xinyi He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Bing Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yanwei Xie
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Sang Shang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Libo Tian
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
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71
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Fan H, Quan S, Qi S, Xu N, Wang Y. Novel Aspects of Nitrate Regulation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:574246. [PMID: 33362808 PMCID: PMC7758431 DOI: 10.3389/fpls.2020.574246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Nitrogen (N) is one of the most essential macronutrients for plant growth and development. Nitrate (NO3 -), the major form of N that plants uptake from the soil, acts as an important signaling molecule in addition to its nutritional function. Over the past decade, significant progress has been made in identifying new components involved in NO3 - regulation and starting to unravel the NO3 - regulatory network. Great reviews have been made recently by scientists on the key regulators in NO3 - signaling, NO3 - effects on plant development, and its crosstalk with phosphorus (P), potassium (K), hormones, and calcium signaling. However, several novel aspects of NO3 - regulation have not been previously reviewed in detail. Here, we mainly focused on the recent advances of post-transcriptional regulation and non-coding RNA (ncRNAs) in NO3 - signaling, and NO3 - regulation on leaf senescence and the circadian clock. It will help us to extend the general picture of NO3 - regulation and provide a basis for further exploration of NO3 - regulatory network.
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Affiliation(s)
- Hongmei Fan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Na Xu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yong Wang,
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72
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Safdar LB, Andleeb T, Latif S, Umer MJ, Tang M, Li X, Liu S, Quraishi UM. Genome-Wide Association Study and QTL Meta-Analysis Identified Novel Genomic Loci Controlling Potassium Use Efficiency and Agronomic Traits in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:70. [PMID: 32133017 PMCID: PMC7041172 DOI: 10.3389/fpls.2020.00070] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/17/2020] [Indexed: 05/21/2023]
Abstract
Potassium use efficiency, a complex trait, directly impacts the yield potential of crop plants. Low potassium efficiency leads to a high use of fertilizers, which is not only farmer unfriendly but also deteriorates the environment. Genome-wide association studies (GWAS) are widely used to dissect complex traits. However, most studies use single-locus one-dimensional GWAS models which do not provide true information about complex traits that are controlled by multiple loci. Here, both single-locus GWAS (MLM) and multi-locus GWAS (pLARmEB, FASTmrMLM, mrMLM, FASTmrEMMA) models were used with genotyping from 90 K Infinium SNP array and phenotype derived from four normal and potassium-stress environments, which identified 534 significant marker-trait associations (MTA) for agronomic and potassium related traits: pLARmEB = 279, FASTmrMLM = 213, mrMLM = 35, MLM = 6, FASTmrEMMA = 1. Further screening of these MTA led to the detection of eleven stable loci: q1A, q1D, q2B-1, q2B-2, q2D, q4D, q5B-1, q5B-2, q5B-3, q6D, and q7A. Moreover, Meta-QTL (MQTL) analysis of four independent QTL studies for potassium deficiency in bread wheat located 16 MQTL on 13 chromosomes. One locus identified in this study (q5B-1) colocalized with an MQTL (MQTL_11 ), while the other ten loci were novel associations. Gene ontology of these loci identified 20 putative candidate genes encoding functional proteins involved in key pathways related to stress tolerance, sugar metabolism, and nutrient transport. These findings provide potential targets for breeding potassium stress resistant wheat cultivars and advocate the advantages of multi-locus GWAS models for studying complex traits.
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Affiliation(s)
- Luqman Bin Safdar
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Tayyaba Andleeb
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sadia Latif
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Minqiang Tang
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiang Li
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
- *Correspondence: Shengyi Liu, ; Umar Masood Quraishi,
| | - Umar Masood Quraishi
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- *Correspondence: Shengyi Liu, ; Umar Masood Quraishi,
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73
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Yang J, Wang M, Li W, He X, Teng W, Ma W, Zhao X, Hu M, Li H, Zhang Y, Tong Y. Reducing expression of a nitrate-responsive bZIP transcription factor increases grain yield and N use in wheat. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1823-1833. [PMID: 30811829 PMCID: PMC6686140 DOI: 10.1111/pbi.13103] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/16/2019] [Accepted: 02/21/2019] [Indexed: 05/19/2023]
Abstract
Nitrogen (N) plays critical role in plant growth; manipulating N assimilation could be a target to increase grain yield and N use. Here, we show that ABRE-binding factor (ABF)-like leucine zipper transcription factor TabZIP60 mediates N use and growth in wheat. The expression of TabZIP60 is repressed when the N-deprived wheat plants is exposed to nitrate. Knock down of TabZIP60 through RNA interference (RNAi) increases NADH-dependent glutamate synthase (NADH-GOGAT) activity, lateral root branching, N uptake and spike number, and improves grain yield more than 25% under field conditions, while overexpression of TabZIP60-6D had the opposite effects. Further investigation shows TabZIP60 binds to ABRE-containing fragment in the promoter of TaNADH-GOGAT-3B and negatively regulates its expression. Genetic analysis reveals that TaNADH-GOGAT-3B overexpression overcomes the spike number and yield reduction caused by overexpressing TabZIP60-6D. As such, TabZIP60-mediated wheat growth and N use is associated with its negative regulation on TaNADH-GOGAT expression. These findings indicate that TabZIP60 and TaNADH-GOGAT interaction plays important roles in mediating N use and wheat growth, and provides valuable information for engineering N use efficiency and yield in wheat.
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Affiliation(s)
- Junbo Yang
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Meiyue Wang
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Wenjing Li
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xue He
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wan Teng
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenying Ma
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xueqiang Zhao
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mengyun Hu
- The Institute for Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Hui Li
- The Institute for Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yijing Zhang
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yiping Tong
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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74
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Zuluaga DL, Sonnante G. The Use of Nitrogen and Its Regulation in Cereals: Structural Genes, Transcription Factors, and the Role of miRNAs. PLANTS 2019; 8:plants8080294. [PMID: 31434274 PMCID: PMC6724420 DOI: 10.3390/plants8080294] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/31/2023]
Abstract
Cereals and, especially, rice, maize, and wheat, are essential commodities, on which human nutrition is based. Expanding population and food demand have required higher production which has been achieved by increasing fertilization, and especially nitrogen supply to cereal crops. In fact, nitrogen is a crucial nutrient for the plant, but excessive use poses serious environmental and health issues. Therefore, increasing nitrogen use efficiency in cereals is of pivotal importance for sustainable agriculture. The main steps in the use of nitrogen are uptake and transport, reduction and assimilation, and translocation and remobilization. Many studies have been carried out on the genes involved in these phases, and on transcription factors regulating these genes. Lately, increasing attention has been paid to miRNAs responding to abiotic stress, including nutrient deficiency. Many miRNAs have been found to regulate transcription factors acting on the expression of specific genes for nitrogen uptake or remobilization. Recent studies on gene regulatory networks have also demonstrated that miRNAs can interact with several nodes in the network, functioning as key regulators in nitrogen metabolism.
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Affiliation(s)
- Diana L Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy.
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy.
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75
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Khan S, Anwar S, Yu S, Sun M, Yang Z, Gao ZQ. Development of Drought-Tolerant Transgenic Wheat: Achievements and Limitations. Int J Mol Sci 2019; 20:E3350. [PMID: 31288392 PMCID: PMC6651533 DOI: 10.3390/ijms20133350] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 01/25/2023] Open
Abstract
Crop yield improvement is necessary to keep pace with increasing demand for food. Due to climatic variability, the incidence of drought stress at crop growth stages is becoming a major hindering factor to yield improvement. New techniques are required to increase drought tolerance along with improved yield. Genetic modification for increasing drought tolerance is highly desirable, and genetic engineering for drought tolerance requires the expression of certain stress-related genes. Genes have been identified which confer drought tolerance and improve plant growth and survival in transgenic wheat. However, less research has been conducted for the development of transgenic wheat as compared to rice, maize, and other staple food. Furthermore, enhanced tolerance to drought without any yield penalty is a major task of genetic engineering. In this review, we have focused on the progress in the development of transgenic wheat cultivars for improving drought tolerance and discussed the physiological mechanisms and testing of their tolerance in response to inserted genes under control or field conditions.
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Affiliation(s)
- Shahbaz Khan
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Sumera Anwar
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaobo Yu
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Min Sun
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Zhenping Yang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Zhi-Qiang Gao
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China.
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76
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Song X, Li Y, Cao X, Qi Y. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:489-525. [PMID: 30848930 DOI: 10.1146/annurev-arplant-050718-100334] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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77
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Wang J, Song K, Sun L, Qin Q, Sun Y, Pan J, Xue Y. Morphological and Transcriptome Analysis of Wheat Seedlings Response to Low Nitrogen Stress. PLANTS 2019; 8:plants8040098. [PMID: 30991719 PMCID: PMC6524375 DOI: 10.3390/plants8040098] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/25/2022]
Abstract
Nitrogen (N) is one of the essential macronutrients that plays an important role in plant growth and development. Unfortunately, low utilization rate of nitrogen has become one of the main abiotic factors affecting crop growth. Nevertheless, little research has been done on the molecular mechanism of wheat seedlings resisting or adapting to low nitrogen environment. In this paper, the response of wheat seedlings against low nitrogen stress at phenotypic changes and gene expression level were studied. The results showed that plant height, leaf area, shoot and root dry weight, total root length, and number under low nitrogen stress decreased by 26.0, 28.1, 24.3, 38.0, 41.4, and 21.2 percent, respectively compared with plants under normal conditions. 2265 differentially expressed genes (DEGs) were detected in roots and 2083 DEGs were detected in leaves under low nitrogen stress (N-) compared with the control (CK). 1688 genes were up-regulated and 577 genes were down-regulated in roots, whilst 505 genes were up-regulated and 1578 were down-regulated in leaves. Among the most addressed Gene Ontology (GO) categories, oxidation reduction process, oxidoreductase activity, and cell component were mostly represented. In addition, genes involved in the signal transduction, carbon and nitrogen metabolism, antioxidant activity, and environmental adaptation were highlighted. Our study provides new information for further understanding the response of wheat to low nitrogen stress.
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Affiliation(s)
- Jun Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Ke Song
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Scientific Observation and Experimental Station for Agricultural Environment and Land Conservation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Environmental Protection Monitoring Station of Agriculture, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERLA), Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Lijuan Sun
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Scientific Observation and Experimental Station for Agricultural Environment and Land Conservation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Environmental Protection Monitoring Station of Agriculture, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERLA), Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Qin Qin
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Scientific Observation and Experimental Station for Agricultural Environment and Land Conservation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Environmental Protection Monitoring Station of Agriculture, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERLA), Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Yafei Sun
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Scientific Observation and Experimental Station for Agricultural Environment and Land Conservation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Environmental Protection Monitoring Station of Agriculture, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERLA), Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Jianjun Pan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yong Xue
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Scientific Observation and Experimental Station for Agricultural Environment and Land Conservation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Environmental Protection Monitoring Station of Agriculture, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERLA), Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
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Genetic Modification for Wheat Improvement: From Transgenesis to Genome Editing. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6216304. [PMID: 30956982 PMCID: PMC6431451 DOI: 10.1155/2019/6216304] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/08/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022]
Abstract
To feed the growing human population, global wheat yields should increase to approximately 5 tonnes per ha from the current 3.3 tonnes by 2050. To reach this goal, existing breeding practices must be complemented with new techniques built upon recent gains from wheat genome sequencing, and the accumulated knowledge of genetic determinants underlying the agricultural traits responsible for crop yield and quality. In this review we primarily focus on the tools and techniques available for accessing gene functions which lead to clear phenotypes in wheat. We provide a view of the development of wheat transformation techniques from a historical perspective, and summarize how techniques have been adapted to obtain gain-of-function phenotypes by gene overexpression, loss-of-function phenotypes by expressing antisense RNAs (RNA interference or RNAi), and most recently the manipulation of gene structure and expression using site-specific nucleases, such as CRISPR/Cas9, for genome editing. The review summarizes recent successes in the application of wheat genetic manipulation to increase yield, improve nutritional and health-promoting qualities in wheat, and enhance the crop's resistance to various biotic and abiotic stresses.
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Zotova L, Kurishbayev A, Jatayev S, Goncharov NP, Shamambayeva N, Kashapov A, Nuralov A, Otemissova A, Sereda S, Shvidchenko V, Lopato S, Schramm C, Jenkins C, Soole K, Langridge P, Shavrukov Y. The General Transcription Repressor TaDr1 Is Co-expressed With TaVrn1 and TaFT1 in Bread Wheat Under Drought. Front Genet 2019; 10:63. [PMID: 30800144 PMCID: PMC6375888 DOI: 10.3389/fgene.2019.00063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
The general transcription repressor, TaDr1 gene, was identified during screening of a wheat SNP database using the Amplifluor-like SNP marker KATU-W62. Together with two genes described earlier, TaDr1A and TaDr1B, they represent a set of three homeologous genes in the wheat genome. Under drought, the total expression profiles of all three genes varied between different bread wheat cultivars. Plants of four high-yielding cultivars exposed to drought showed a 2.0-2.4-fold increase in TaDr1 expression compared to controls. Less strong, but significant 1.3-1.8-fold up-regulation of the TaDr1 transcript levels was observed in four low-yielding cultivars. TaVrn1 and TaFT1, which controls the transition to flowering, revealed similar profiles of expression as TaDr1. Expression levels of all three genes were in good correlation with grain yields of evaluated cultivars growing in the field under water-limited conditions. The results could indicate the involvement of all three genes in the same regulatory pathway, where the general transcription repressor TaDr1 may control expression of TaVrn1 and TaFT1 and, consequently, flowering time. The strength of these genes expression can lead to phenological changes that affect plant productivity and hence explain differences in the adaptation of the examined wheat cultivars to the dry environment of Northern and Central Kazakhstan. The Amplifluor-like SNP marker KATU-W62 used in this work can be applied to the identification of wheat cultivars differing in alleles at the TaDr1 locus and in screening hybrids.
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Affiliation(s)
- Lyudmila Zotova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Nikolay P. Goncharov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nazgul Shamambayeva
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Azamat Kashapov
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Arystan Nuralov
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Ainur Otemissova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergey Sereda
- A.F.Khristenko Karaganda Agricultural Experimental Station, Karaganda, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergiy Lopato
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Carly Schramm
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Colin Jenkins
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Kathleen Soole
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- Wheat Initiative, Julius Kühn-Institut, Berlin, Germany
| | - Yuri Shavrukov
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
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Xu Y, Ren Y, Li J, Li L, Chen S, Wang Z, Xin Z, Chen F, Lin T, Cui D, Tong Y. Comparative Proteomic Analysis Provides New Insights Into Low Nitrogen-Promoted Primary Root Growth in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:151. [PMID: 30842781 PMCID: PMC6391680 DOI: 10.3389/fpls.2019.00151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 01/29/2019] [Indexed: 05/08/2023]
Abstract
Nitrogen deficient environments can promote wheat primary root growth (PRG) that allows for nitrogen uptake in deep soil. However, the mechanisms of low nitrogen-promoted root growth remain largely unknown. Here, an integrated comparative proteome study using iTRAQ analysis on the roots of two wheat varieties and their descendants with contrasting response to low nitrogen (LN) stress was performed under control (CK) and LN conditions. In total, 84 differentially abundant proteins (DAPs) specifically involved in the process of LN-promoted PRG were identified and 11 pathways were significantly enriched. The Glutathione metabolism, endocytosis, lipid metabolism, and phenylpropanoid biosynthesis pathways may play crucial roles in the regulation of LN-promoted PRG. We also identified 59 DAPs involved in the common response to LN stress in different genetic backgrounds. The common responsive DAPs to LN stress were mainly involved in nitrogen uptake, transportation and remobilization, and LN stress tolerance. Taken together, our results provide new insights into the metabolic and molecular changes taking place in contrasting varieties under LN conditions, which provide useful information for the genetic improvement of root traits and nitrogen use efficiency in wheat.
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Affiliation(s)
- Yanhua Xu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Department of Life Sciences, Shangqiu Normal University, Shangqiu, China
| | - Yongzhe Ren
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Yongzhe Ren
| | - Jingjing Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Le Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Shulin Chen
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhiqiang Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zeyu Xin
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Feng Chen
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Tongbao Lin
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Tongbao Lin
| | - Dangqun Cui
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Dangqun Cui
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, China
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Myers ZA, Holt BF. NUCLEAR FACTOR-Y: still complex after all these years? CURRENT OPINION IN PLANT BIOLOGY 2018; 45:96-102. [PMID: 29902675 DOI: 10.1016/j.pbi.2018.05.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/11/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
The NUCLEAR FACTOR-Y (NF-Y) families of transcription factors are important regulators of plant development and physiology. Though NF-Y regulatory roles have recently been suggested for numerous aspects of plant biology, their roles in flowering time, early seedling development, stress responses, hormone signaling, and nodulation are the best characterized. The past few years have also seen significant advances in our understanding of the mechanistic function of the NF-Y, and as such, increasingly complex and interesting questions are now more approachable. This review will primarily focus on these developmental, physiological, and mechanistic roles of the NF-Y in recent research.
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Affiliation(s)
- Zachary A Myers
- University of Oklahoma, Department of Microbiology and Plant Biology, 770 Van Vleet Oval, Norman, OK 73019, United States.
| | - Ben F Holt
- University of Oklahoma, Department of Microbiology and Plant Biology, 770 Van Vleet Oval, Norman, OK 73019, United States.
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82
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Zotova L, Kurishbayev A, Jatayev S, Khassanova G, Zhubatkanov A, Serikbay D, Sereda S, Sereda T, Shvidchenko V, Lopato S, Jenkins C, Soole K, Langridge P, Shavrukov Y. Genes Encoding Transcription Factors TaDREB5 and TaNFYC-A7 Are Differentially Expressed in Leaves of Bread Wheat in Response to Drought, Dehydration and ABA. FRONTIERS IN PLANT SCIENCE 2018; 9:1441. [PMID: 30319682 PMCID: PMC6171087 DOI: 10.3389/fpls.2018.01441] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/10/2018] [Indexed: 05/18/2023]
Abstract
Two groups of six spring bread wheat varieties with either high or low grain yield under the dry conditions of Central and Northern Kazakhstan were selected for analysis. Experiments were set up with the selected wheat varieties in controlled environments as follows: (1) slowly progressing drought imposed on plants in soil, (2) rapid dehydration of whole plants grown in hydroponics, (3) dehydration of detached leaves, and (4) ABA treatment of whole plants grown in hydroponics. Representatives of two different families of transcription factors (TFs), TaDREB5 and TaNFYC-A7, were found to be linked to yield-under-drought using polymorphic Amplifluor-like SNP marker assays. qRT-PCR revealed differing patterns of expression of these genes in the leaves of plants subjected to the above treatments. Under drought, TaDREB5 was significantly up-regulated in leaves of all high-yielding varieties tested and down-regulated in all low-yielding varieties, and the level of expression was independent of treatment type. In contrast, TaNFYC-A7 expression levels showed different responses in the high- and low-yield groups of wheat varieties. TaNFYC-A7 expression under dehydration (treatments 2 and 3) was higher than under drought (treatment 1) in all high-yielding varieties tested, while in all low-yielding varieties the opposite pattern was observed: the expression levels of this gene under drought were higher than under dehydration. Rapid dehydration of detached leaves and intact wheat plants grown in hydroponics produced similar changes in gene expression. ABA treatment of whole plants caused rapid stomatal closure and a rise in the transcript level of both genes during the first 30 min, which decreased 6 h after treatment. At this time-point, expression of TaNFYC-A7 was again significantly up-regulated compared to untreated controls, while TaDREB5 returned to its initial level of expression. These findings reveal significant differences in the transcriptional regulation of two drought-responsive and ABA-dependent TFs under slowly developing drought and rapid dehydration of wheat plants. The results obtained suggest that correlation between grain yield in dry conditions and TaNFYC-A7 expression levels in the examined wheat varieties is dependent on the length of drought development and/or strength of drought; while in the case of TaDREB5, no such dependence is observed.
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Affiliation(s)
- Lyudmila Zotova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Askar Zhubatkanov
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergey Sereda
- Karaganda Research Institute of Plant Industry and Breeding, Karaganda, Kazakhstan
| | - Tatiana Sereda
- Karaganda Research Institute of Plant Industry and Breeding, Karaganda, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Colin Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Kathleen Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
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83
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Perchlik M, Tegeder M. Leaf Amino Acid Supply Affects Photosynthetic and Plant Nitrogen Use Efficiency under Nitrogen Stress. PLANT PHYSIOLOGY 2018; 178:174-188. [PMID: 30082496 PMCID: PMC6130036 DOI: 10.1104/pp.18.00597] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/23/2018] [Indexed: 05/18/2023]
Abstract
The coordinated distribution of nitrogen to source leaves and sinks is essential for supporting leaf metabolism while also supplying sufficient nitrogen to seeds for development. This study aimed to understand how regulated amino acid allocation to leaves affects photosynthesis and overall plant nitrogen use efficiency in Arabidopsis (Arabidopsis thaliana) and how soil nitrogen availability influences these processes. Arabidopsis plants with a knockout of AAP2, encoding an amino acid permease involved in xylem-to-phloem transfer of root-derived amino acids, were grown in low-, moderate-, and high-nitrogen environments. We analyzed nitrogen allocation to shoot tissues, photosynthesis, and photosynthetic and plant nitrogen use efficiency in these knockout plants. Our results demonstrate that, independent of nitrogen conditions, aap2 plants allocate more nitrogen to leaves than wild-type plants. Increased leaf nitrogen supply positively affected chlorophyll and Rubisco levels, photosynthetic nitrogen use efficiency, and carbon assimilation and transport to sinks. The aap2 plants outperformed wild-type plants with respect to growth, seed yield and carbon storage pools, and nitrogen use efficiency in both high and deficient nitrogen environments. Overall, this study demonstrates that increasing nitrogen allocation to leaves represents an effective strategy for improving carbon fixation and photosynthetic nitrogen use efficiency. The results indicate that an optimized coordination of nitrogen and carbon partitioning processes is critical for high oilseed production in Arabidopsis, including in plants exposed to limiting nitrogen conditions.
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Affiliation(s)
- Molly Perchlik
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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84
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Wang Y, Lysøe E, Armarego-Marriott T, Erban A, Paruch L, van Eerde A, Bock R, Liu-Clarke J. Transcriptome and metabolome analyses provide insights into root and root-released organic anion responses to phosphorus deficiency in oat. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3759-3771. [PMID: 29757407 DOI: 10.1093/jxb/ery176] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/09/2018] [Indexed: 05/23/2023]
Abstract
Roots and root-released organic anions play important roles in uptake of phosphorus (P), an essential macronutrient for food production. Oat, ranking sixth in the world's cereal production, contains valuable nutritional compounds and can withstand poor soil conditions. Our aim was to investigate root transcriptional and metabolic responses of oat grown under P-deficient and P-sufficient conditions. We conducted a hydroponic experiment and measured root morphology and organic anion exudation, and analysed changes in the transcriptome and metabolome. Oat roots showed enhanced citrate and malate exudation after 4 weeks of P deficiency. After 10 d of P deficiency, we identified 9371 differentially expressed transcripts with a 2-fold or greater change (P<0.05): 48 sequences predicted to be involved in organic anion biosynthesis and efflux were consistently up-regulated; 24 up-regulated transcripts in oat were also found to be up-regulated upon P starvation in rice and wheat under similar conditions. Phosphorylated metabolites (i.e. glucose-6-phosphate, myo-inositol phosphate) were reduced dramatically, while citrate and malate, some sugars and amino acids increased slightly in P-deficient oat roots. Our data are consistent with a strategy of increased organic anion efflux and a shift in primary metabolism in response to P deficiency in oat.
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Affiliation(s)
- Yanliang Wang
- Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Erik Lysøe
- Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | | | - Alexander Erban
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Lisa Paruch
- Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - André van Eerde
- Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Ralph Bock
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
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85
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MicroRNAs in durum wheat seedlings under chronic and short-term nitrogen stress. Funct Integr Genomics 2018; 18:645-657. [PMID: 29948458 DOI: 10.1007/s10142-018-0619-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
Nitrogen is an essential macronutrient for plant growth and reproduction. In durum wheat, an appropriate nitrogen soil availability is essential for an optimal seed development. miRNAs contribute to the environmental change adaptation of plants through the regulation of important genes involved in stress processes. In this work, nitrogen stress response was evaluated in durum wheat seedlings of Ciccio and Svevo cultivars. Eight small RNA libraries from leaves and roots of chronically stressed plants were sequenced to detect conserved and novel miRNAs. A total of 294 miRNAs were identified, 7 of which were described here for the first time. The expression level of selected miRNAs and target genes was analyzed by qPCR in seedlings subjected to chronic (Ciccio and Svevo, leaves and roots) or short-term (Svevo roots) stress conditions. Some miRNAs showed an immediate stress response, and their level of expression was either maintained or returned to a basal level during a long-term stress. Other miRNAs showed a gradual up- or downregulation during the short-term stress. The newly identified miRNA ttu-novel-106 showed an immediate strongly downregulation after nitrogen stress, which was negatively correlated with the expression of MYB-A, its putative target gene. PHO2 gene was significantly upregulated after 24-48-h stress, corresponding to a downregulation of miR399b. Ttu-miR399b putative binding sites in the 5' UTR region of the Svevo PHO2 gene were identified in the A and B genomes. Both MYB-A and PHO2 genes were validated for their cleavage site using 5' RACE assay.
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86
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Lei L, Li G, Zhang H, Powers C, Fang T, Chen Y, Wang S, Zhu X, Carver BF, Yan L. Nitrogen use efficiency is regulated by interacting proteins relevant to development in wheat. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1214-1226. [PMID: 29193541 PMCID: PMC5978868 DOI: 10.1111/pbi.12864] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/01/2017] [Accepted: 11/04/2017] [Indexed: 05/08/2023]
Abstract
Wheat (Triticum aestivum) has low nitrogen use efficiency (NUE). The genetic mechanisms controlling NUE are unknown. Positional cloning of a major quantitative trait locus for N-related agronomic traits showed that the vernalization gene TaVRN-A1 was tightly linked with TaNUE1, the gene shown to influence NUE in wheat. Because of an Ala180 /Val180 substitution, TaVRN-A1a and TaVRN-A1b proteins interact differentially with TaANR1, a protein encoded by a wheat orthologue of Arabidopsis nitrate regulated 1 (ANR1). The transcripts of both TaVRN-A1 and TaANR1 were down-regulated by nitrogen. TaANR1 was functionally characterized in TaANR1::RNAi transgenic wheat, and in a natural mutant with a 23-bp deletion including 10-bp at the 5' end of intron 5 and 13-bp of exon 6 in gDNA sequence in its gDNA sequence, which produced transcript that lacked the full 84-bp exon 6. Both TaANR1 and TaHOX1 bound to the Ala180 /Val180 position of TaVRN-A1. Genetically incorporating favourable alleles from TaVRN-A1, TaANR1 and TaHOX1 increased grain yield from 9.84% to 11.58% in the field. Molecular markers for allelic variation of the genes that regulate nitrogen can be used in breeding programmes aimed at improving NUE and yield in novel wheat cultivars.
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Affiliation(s)
- Lei Lei
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Genqiao Li
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
- Present address:
Wheat, Peanut and Other Field Crops Research UnitUSDA‐ARSStillwaterOKUSA
| | - Hailin Zhang
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Carol Powers
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Tilin Fang
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Yihua Chen
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Shuwen Wang
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
- Present address:
The Land InstituteSalinaKSUSA
| | - Xinkai Zhu
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
- Present address:
Key Laboratory of Crop Genetics and Physiology of Jiangsu ProvinceYangzhou UniversityYangzhouJiangsuChina
| | - Brett F. Carver
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Liuling Yan
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
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87
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Wang YY, Cheng YH, Chen KE, Tsay YF. Nitrate Transport, Signaling, and Use Efficiency. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:85-122. [PMID: 29570365 DOI: 10.1146/annurev-arplant-042817-040056] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nitrogen accounts for approximately 60% of the fertilizer consumed each year; thus, it represents one of the major input costs for most nonlegume crops. Nitrate is one of the two major forms of nitrogen that plants acquire from the soil. Mechanistic insights into nitrate transport and signaling have enabled new strategies for enhancing nitrogen utilization efficiency, for lowering input costs for farming, and, more importantly, for alleviating environmental impacts (e.g., eutrophication and production of the greenhouse gas N2O). Over the past decade, significant progress has been made in understanding how nitrate is acquired from the surroundings, how it is efficiently distributed into different plant tissues in response to environmental changes, how nitrate signaling is perceived and transmitted, and how shoot and root nitrogen status is communicated. Several key components of these processes have proven to be novel tools for enhancing nitrate- and nitrogen-use efficiency. In this review, we focus on the roles of NRT1 and NRT2 in nitrate uptake and nitrate allocation among different tissues; we describe the functions of the transceptor NRT1.1, transcription factors, and small signaling peptides in nitrate signaling and tissue communication; and we compile the new strategies for improving nitrogen-use efficiency.
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Affiliation(s)
- Ya-Yun Wang
- Department of Life Science and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Hsuan Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan;
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Kuo-En Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan;
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Yi-Fang Tsay
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan;
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88
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89
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Olatunji D, Geelen D, Verstraeten I. Control of Endogenous Auxin Levels in Plant Root Development. Int J Mol Sci 2017; 18:E2587. [PMID: 29194427 PMCID: PMC5751190 DOI: 10.3390/ijms18122587] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/26/2017] [Accepted: 11/28/2017] [Indexed: 12/24/2022] Open
Abstract
In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.
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Affiliation(s)
- Damilola Olatunji
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
| | - Danny Geelen
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
| | - Inge Verstraeten
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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90
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Chen XY, Yang Y, Ran LP, Dong ZD, Zhang EJ, Yu XR, Xiong F. Novel Insights into miRNA Regulation of Storage Protein Biosynthesis during Wheat Caryopsis Development under Drought Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:1707. [PMID: 29046684 PMCID: PMC5632728 DOI: 10.3389/fpls.2017.01707] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/19/2017] [Indexed: 05/02/2023]
Abstract
Drought stress is a significant abiotic stress factor that affects wheat yield and quality. MicroRNA (miRNA) plays an important role in regulating caryopsis development in response to drought stress. However, little is known about the expression characteristics of miRNAs and how they regulate protein accumulation in wheat caryopsis under drought stress. To address this, two small RNA libraries of wheat caryopsis under control and drought stress conditions were constructed and sequenced. A total of 125 miRNAs were identified in the two samples, of which 110 were known and 15 were novel. A total of 1,981 miRNA target genes were predicted and functional annotations were obtained from various databases for 1,641 of them. Four miRNAs were identified as differential expression under drought stress, and the expression patterns of three of them were consistent with results obtained by reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription quantitative polymerase chain reaction (RT-qPCR). Moreover, three miRNA-target pairs showed negative regulation tendency, as revealed by RT-qPCR. Functional enrichment and pathway analysis revealed that four pathways might be involved in storage protein biosynthesis. Furthermore, drought stress significantly increased the accumulation of protein bodies and protein content in wheat endosperm. In summary, our findings suggest that drought stress may enhance storage protein by regulating the expression of miRNAs and their target genes.
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Affiliation(s)
| | | | | | | | | | | | - Fei Xiong
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
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91
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Chen L, Liao H. Engineering crop nutrient efficiency for sustainable agriculture. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:710-735. [PMID: 28600834 DOI: 10.1111/jipb.12559] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/21/2023]
Abstract
Increasing crop yields can provide food, animal feed, bioenergy feedstocks and biomaterials to meet increasing global demand; however, the methods used to increase yield can negatively affect sustainability. For example, application of excess fertilizer can generate and maintain high yields but also increases input costs and contributes to environmental damage through eutrophication, soil acidification and air pollution. Improving crop nutrient efficiency can improve agricultural sustainability by increasing yield while decreasing input costs and harmful environmental effects. Here, we review the mechanisms of nutrient efficiency (primarily for nitrogen, phosphorus, potassium and iron) and breeding strategies for improving this trait, along with the role of regulation of gene expression in enhancing crop nutrient efficiency to increase yields. We focus on the importance of root system architecture to improve nutrient acquisition efficiency, as well as the contributions of mineral translocation, remobilization and metabolic efficiency to nutrient utilization efficiency.
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Affiliation(s)
- Liyu Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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92
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Perchlik M, Tegeder M. Improving Plant Nitrogen Use Efficiency through Alteration of Amino Acid Transport Processes. PLANT PHYSIOLOGY 2017; 175:235-247. [PMID: 28733388 PMCID: PMC5580756 DOI: 10.1104/pp.17.00608] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/18/2017] [Indexed: 05/08/2023]
Abstract
Improving the efficiency of nitrogen (N) uptake and utilization in plants could potentially increase crop yields while reducing N fertilization and, subsequently, environmental pollution. Within most plants, N is transported primarily as amino acids. In this study, pea (Pisum sativum) plants overexpressing AMINO ACID PERMEASE1 (AAP1) were used to determine if and how genetic manipulation of amino acid transport from source to sink affects plant N use efficiency. The modified plants were grown under low, moderate, or high N fertilization regimes. The results showed that, independent of the N nutrition, the engineered plants allocate more N via the vasculature to the shoot and seeds and produce more biomass and higher seed yields than wild-type plants. Dependent on the amount of N supplied, the AAP1-overexpressing plants displayed improved N uptake or utilization efficiency, or a combination of the two. They also showed significantly increased N use efficiency in N-deficient as well as in N-rich soils and, impressively, required half the amount of N to produce as many fruits and seeds as control plants. Together, these data support that engineering N allocation from source to sink presents an effective strategy to produce crop plants with improved productivity as well as N use efficiency in a range of N environments.
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Affiliation(s)
- Molly Perchlik
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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93
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Zuluaga DL, De Paola D, Janni M, Curci PL, Sonnante G. Durum wheat miRNAs in response to nitrogen starvation at the grain filling stage. PLoS One 2017; 12:e0183253. [PMID: 28813501 PMCID: PMC5558935 DOI: 10.1371/journal.pone.0183253] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/01/2017] [Indexed: 11/24/2022] Open
Abstract
Durum wheat highly depends on nitrogen for seed development and yield, and the obtainment of varieties with a better nitrogen use efficiency is crucial to reduce production costs and environmental pollution. In this study, sequencing of two small RNA libraries obtained from tissues of Ciccio and Svevo cultivars grown under nitrogen starvation conditions produced 84 novel, and 161 conserved miRNAs. Of these, 7 novel and 13 known miRNAs were newly identified in this work. Quantitative PCR analysis of selected miRNAs highlighted that the expression levels of some of them depends on the tissue and on the cultivar, Svevo being the most responsive to nitrogen starvation. A number of target genes were predicted to be involved in nitrogen metabolism. An inverse correlation for the qPCR expression data of miRNA/target pairs miR399b/PHO2, miR393c/AFB2, ttu-novel-61/CCAAT-TF was observed in specific tissues or cultivar. Especially, ttu-novel-61 was down-regulated and its target CCAAT-TF up-regulated in almost all tissues both in Svevo and in Ciccio. Moreover, CCAAT-TF was confirmed to be cleaved by ttu-novel-61 at the expected site. The discovery of miRNAs involved in the response to nitrogen stress represents an important step towards functional analyses, with the final aim to design strategies for improving nitrogen use efficiency in durum wheat.
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Affiliation(s)
- Diana L. Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
| | - Domenico De Paola
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
| | - Michela Janni
- Institute for Electronics and Magnetism, National Research Council (CNR), Parma, Italy
| | - Pasquale Luca Curci
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
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94
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Nadolska-Orczyk A, Rajchel IK, Orczyk W, Gasparis S. Major genes determining yield-related traits in wheat and barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1081-1098. [PMID: 28314933 PMCID: PMC5440550 DOI: 10.1007/s00122-017-2880-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 02/17/2017] [Indexed: 05/20/2023]
Abstract
Current development of advanced biotechnology tools allows us to characterize the role of key genes in plant productivity. The implementation of this knowledge in breeding strategies might accelerate the progress in obtaining high-yielding cultivars. The achievements of the Green Revolution were based on a specific plant ideotype, determined by a single gene involved in gibberellin signaling or metabolism. Compared with the 1950s, an enormous increase in our knowledge about the biological basis of plant productivity has opened new avenues for novel breeding strategies. The large and complex genomes of diploid barley and hexaploid wheat represent a great challenge, but they also offer a large reservoir of genes that can be targeted for breeding. We summarize examples of productivity-related genes/mutants in wheat and barley, identified or characterized by means of modern biology. The genes are classified functionally into several groups, including the following: (1) transcription factors, regulating spike development, which mainly affect grain number; (2) genes involved in metabolism or signaling of growth regulators-cytokinins, gibberellins, and brassinosteroids-which control plant architecture and in consequence stem hardiness and grain yield; (3) genes determining cell division and proliferation mainly impacting grain size; (4) floral regulators influencing inflorescence architecture and in consequence seed number; and (5) genes involved in carbohydrate metabolism having an impact on plant architecture and grain yield. The implementation of selected genes in breeding programs is discussed, considering specific genotypes, agronomic and climate conditions, and taking into account that many of the genes are members of multigene families.
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Affiliation(s)
- Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland.
| | - Izabela K Rajchel
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Wacław Orczyk
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Sebastian Gasparis
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
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95
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Gnesutta N, Kumimoto RW, Swain S, Chiara M, Siriwardana C, Horner DS, Holt BF, Mantovani R. CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer. THE PLANT CELL 2017; 29:1516-1532. [PMID: 28526714 PMCID: PMC5502446 DOI: 10.1105/tpc.16.00864] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/07/2017] [Accepted: 05/18/2017] [Indexed: 05/19/2023]
Abstract
Nuclear Factor Y (NF-Y) is a heterotrimeric transcription factor that binds CCAAT elements. The NF-Y trimer is composed of a Histone Fold Domain (HFD) dimer (NF-YB/NF-YC) and NF-YA, which confers DNA sequence specificity. NF-YA shares a conserved domain with the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) proteins. We show that CONSTANS (CO/B-BOX PROTEIN1 BBX1), a master flowering regulator, forms a trimer with Arabidopsis thaliana NF-YB2/NF-YC3 to efficiently bind the CORE element of the FLOWERING LOCUS T promoter. We term this complex NF-CO. Using saturation mutagenesis, electrophoretic mobility shift assays, and RNA-sequencing profiling of co, nf-yb, and nf-yc mutants, we identify CCACA elements as the core NF-CO binding site. CO physically interacts with the same HFD surface required for NF-YA association, as determined by mutations in NF-YB2 and NF-YC9, and tested in vitro and in vivo. The co-7 mutation in the CCT domain, corresponding to an NF-YA arginine directly involved in CCAAT recognition, abolishes NF-CO binding to DNA. In summary, a unifying molecular mechanism of CO function relates it to the NF-YA paradigm, as part of a trimeric complex imparting sequence specificity to HFD/DNA interactions. It is likely that members of the large CCT family participate in similar complexes with At-NF-YB and At-NF-YC, broadening HFD combinatorial possibilities in terms of trimerization, DNA binding specificities, and transcriptional regulation.
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Affiliation(s)
- Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Roderick W Kumimoto
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Swadhin Swain
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Chamindika Siriwardana
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - David S Horner
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Ben F Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
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96
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Wang D, Lv S, Jiang P, Li Y. Roles, Regulation, and Agricultural Application of Plant Phosphate Transporters. FRONTIERS IN PLANT SCIENCE 2017; 8:817. [PMID: 28572810 PMCID: PMC5435767 DOI: 10.3389/fpls.2017.00817] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/01/2017] [Indexed: 05/20/2023]
Abstract
Phosphorus (P) is an essential mineral nutrient for plant growth and development. Low availability of inorganic phosphate (orthophosphate; Pi) in soil seriously restricts the crop production, while excessive fertilization has caused environmental pollution. Pi acquisition and homeostasis depend on transport processes controlled Pi transporters, which are grouped into five families so far: PHT1, PHT2, PHT3, PHT4, and PHT5. This review summarizes the current understanding on plant PHT families, including phylogenetic analysis, function, and regulation. The potential application of Pi transporters and the related regulatory factors for developing genetically modified crops with high phosphorus use efficiency (PUE) are also discussed in this review. At last, we provide some potential strategies for developing high PUE crops under salt or drought stress conditions, which can be valuable for improving crop yields challenged by global scarcity of water resources and increasing soil salinization.
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Affiliation(s)
- Duoliya Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
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97
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Transcriptomic response of durum wheat to nitrogen starvation. Sci Rep 2017; 7:1176. [PMID: 28446759 PMCID: PMC5430780 DOI: 10.1038/s41598-017-01377-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/27/2017] [Indexed: 11/29/2022] Open
Abstract
Nitrogen (N) is a key macronutrient representing a limiting factor for plant growth and development and affects productivity in wheat. In this study, durum wheat response to N chronic starvation during grain filling was investigated through a transcriptomic approach in roots, leaves/stems, flag leaf and spikes of cv. Svevo. Nitrogen stress negatively influenced plant height, tillering, flag leaf area, spike and seed traits, and total N content. RNA-seq data revealed 4,626 differentially expressed genes (DEGs). Most transcriptomic changes were observed in roots, with 3,270 DEGs, while 963 were found in leaves/stems, 470 in flag leaf, and 355 in spike tissues. A total of 799 gene ontology (GO) terms were identified, 180 and 619 among the upregulated and downregulated genes, respectively. Among the most addressed GO categories, N compound metabolism, carbon metabolism, and photosynthesis were mostly represented. Interesting DEGs, such as N transporters, genes involved in N assimilation, along with transcription factors, protein kinases and other genes related to stress were highlighted. These results provide valuable information about the transcriptomic response to chronic N stress in durum wheat, which could be useful for future improvement of N use efficiency.
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98
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Ferdous J, Sanchez-Ferrero JC, Langridge P, Milne L, Chowdhury J, Brien C, Tricker PJ. Differential expression of microRNAs and potential targets under drought stress in barley. PLANT, CELL & ENVIRONMENT 2017; 40:11-24. [PMID: 27155357 DOI: 10.1111/pce.12764] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 04/22/2016] [Accepted: 04/24/2016] [Indexed: 05/04/2023]
Abstract
Drought is a crucial environmental constraint limiting crop production in many parts of the world. microRNA (miRNA) based gene regulation has been shown to act in several pathways, including crop response to drought stress. Sequence based profiling and computational analysis have revealed hundreds of miRNAs and their potential targets in different plant species under various stress conditions, but few have been biologically verified. In this study, 11 candidate miRNAs were tested for their expression profiles in barley. Differences in accumulation of only four miRNAs (Ath-miR169b, Osa-miR1432, Hv-miRx5 and Hv-miR166b/c) were observed between drought-treated and well-watered barley in four genotypes. miRNA targets were predicted using degradome analysis of two, different genotypes, and genotype-specific target cleavage was observed. Inverse correlation of mature miRNA accumulation with miRNA target transcripts was also genotype dependent under drought treatment. Drought-responsive miRNAs accumulated predominantly in mesophyll tissues. Our results demonstrate genotype-specific miRNA regulation under drought stress and evidence for their role in mediating expression of target genes for abiotic stress response in barley.
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Affiliation(s)
- Jannatul Ferdous
- Australian Centre for Plant Functional Genomics, PMB1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Juan Carlos Sanchez-Ferrero
- Australian Centre for Plant Functional Genomics, PMB1, Glen Osmond, SA, 5064, Australia
- Phenomics and Bioinformatics Research Centre, School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Linda Milne
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Jamil Chowdhury
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
- ARC Centre of Excellence in Plant Cell Walls, PMB1, Glen Osmond, SA, 5064, Australia
| | - Chris Brien
- Phenomics and Bioinformatics Research Centre, School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Penny J Tricker
- Australian Centre for Plant Functional Genomics, PMB1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
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99
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Li Y, Zhao SL, Li JL, Hu XH, Wang H, Cao XL, Xu YJ, Zhao ZX, Xiao ZY, Yang N, Fan J, Huang F, Wang WM. Osa-miR169 Negatively Regulates Rice Immunity against the Blast Fungus Magnaporthe oryzae. FRONTIERS IN PLANT SCIENCE 2017; 8:2. [PMID: 28144248 PMCID: PMC5239796 DOI: 10.3389/fpls.2017.00002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/03/2017] [Indexed: 05/18/2023]
Abstract
miR169 is a conserved microRNA (miRNA) family involved in plant development and stress-induced responses. However, how miR169 functions in rice immunity remains unclear. Here, we show that miR169 acts as a negative regulator in rice immunity against the blast fungus Magnaporthe oryzae by repressing the expression of nuclear factor Y-A (NF-YA) genes. The accumulation of miR169 was significantly increased in a susceptible accession but slightly fluctuated in a resistant accession upon M. oryzae infection. Consistently, the transgenic lines overexpressing miR169a became hyper-susceptible to different M. oryzae strains associated with reduced expression of defense-related genes and lack of hydrogen peroxide accumulation at the infection site. Consequently, the expression of its target genes, the NF-YA family members, was down-regulated by the overexpression of miR169a at either transcriptional or translational level. On the contrary, overexpression of a target mimicry that acts as a sponge to trap miR169a led to enhanced resistance to M. oryzae. In addition, three of miR169's target genes were also differentially up-regulated in the resistant accession upon M. oryzae infection. Taken together, our data indicate that miR169 negatively regulates rice immunity against M. oryzae by differentially repressing its target genes and provide the potential to engineer rice blast resistance via a miRNA.
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Affiliation(s)
- Yan Li
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Sichuan Agricultural University at WenjiangChengdu, China
| | - Sheng-Li Zhao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Jin-Lu Li
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Xiao-Hong Hu
- College of Agronomy, Sichuan Agricultural University at WenjiangChengdu, China
| | - He Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Xiao-Long Cao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Yong-Ju Xu
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Zhi-Xue Zhao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Zhi-Yuan Xiao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Nan Yang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Jing Fan
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Sichuan Agricultural University at WenjiangChengdu, China
| | - Fu Huang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
- College of Agronomy, Sichuan Agricultural University at WenjiangChengdu, China
| | - Wen-Ming Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Sichuan Agricultural University at WenjiangChengdu, China
- *Correspondence: Wen-Ming Wang,
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100
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Yu P, Gutjahr C, Li C, Hochholdinger F. Genetic Control of Lateral Root Formation in Cereals. TRENDS IN PLANT SCIENCE 2016; 21:951-961. [PMID: 27524642 DOI: 10.1016/j.tplants.2016.07.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/19/2016] [Accepted: 07/28/2016] [Indexed: 05/03/2023]
Abstract
Cereals form complex root systems composed of different root types. Lateral root formation is a major determinant of root architecture and is instrumental for the efficient uptake of water and nutrients. Positioning and patterning of lateral roots and cell types involved in their formation are unique in monocot cereals. Recent discoveries advanced the molecular understanding of the intrinsic genetic control of initiation and elongation of lateral roots in cereals by distinct, in part root-type-specific genetic programs. Moreover, molecular networks modulating the plasticity of lateral root formation in response to water and nutrient availability and arbuscular mycorrhizal fungal colonization have been identified. These novel discoveries provide a better mechanistic understanding of postembryonic lateral root development in cereals.
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Affiliation(s)
- Peng Yu
- China Agricultural University, College of Resources and Environmental Science, Department of Plant Nutrition, 100193 Beijing, China; University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, 53113 Bonn, Germany
| | | | - Chunjian Li
- China Agricultural University, College of Resources and Environmental Science, Department of Plant Nutrition, 100193 Beijing, China.
| | - Frank Hochholdinger
- University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, 53113 Bonn, Germany.
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