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Kaur S, Tiwari V, Kumari A, Chaudhary E, Sharma A, Ali U, Garg M. Protective and defensive role of anthocyanins under plant abiotic and biotic stresses: An emerging application in sustainable agriculture. J Biotechnol 2023; 361:12-29. [PMID: 36414125 DOI: 10.1016/j.jbiotec.2022.11.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Global warming is the major cause of abiotic and biotic stresses that reduce plant growth and productivity. Various stresses such as drought, low temperature, pathogen attack, high temperature and salinity all negatively influence plant growth and development. Due to sessile beings, they cannot escape from these adverse conditions. However, plants develop a variety of systems that can help them to tolerate, resist, and escape challenges imposed by the environment. Among them, anthocyanins are a good example of stress mitigators. They aid plant growth and development by increasing anthocyanin accumulation, which leads to increased resistance to various biotic and abiotic stresses. In the primary metabolism of plants, anthocyanin improves the photosynthesis rate, membrane permeability, up-regulates many enzyme transcripts related to anthocyanin biosynthesis, and optimizes nutrient uptake. Generally, the most important genes of the anthocyanin biosynthesis pathways were up-regulated under various abiotic and biotic stresses. The present review will highlight anthocyanin mediated stress tolerance in plants under various abiotic and biotic stresses. We have also compiled literature related to genetically engineer stress-tolerant crops generated using over-expression of genes belonging to anthocyanin biosynthetic pathway or its regulation. To sum up, the present review provides an up-to-date description of various signal transduction mechanisms that modulate or enhance anthocyanin accumulation under stress conditions.
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Affiliation(s)
- Satveer Kaur
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India; Department of Biotechnology, Panjab University, Chandigarh, India.
| | - Vandita Tiwari
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
| | - Anita Kumari
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India; University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - Era Chaudhary
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
| | - Anjali Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
| | - Usman Ali
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
| | - Monika Garg
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India.
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Nascimento FDS, Rocha ADJ, Soares JMDS, Mascarenhas MS, Ferreira MDS, Morais Lino LS, Ramos APDS, Diniz LEC, Mendes TADO, Ferreira CF, dos Santos-Serejo JA, Amorim EP. Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020305. [PMID: 36679018 PMCID: PMC9860801 DOI: 10.3390/plants12020305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 05/22/2023]
Abstract
Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR/Cas-is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.
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Affiliation(s)
| | - Anelita de Jesus Rocha
- Department of Biological Sciences, Feira de Santana State University, Feira de Santana 44036-900, BA, Brazil
| | | | | | - Mileide dos Santos Ferreira
- Department of Biological Sciences, Feira de Santana State University, Feira de Santana 44036-900, BA, Brazil
| | | | | | | | | | | | | | - Edson Perito Amorim
- Embrapa Mandioca e Fruticultura, Cruz das Almas 44380-000, BA, Brazil
- Correspondence: ; Tel.: +55-75-3312-8058; Fax: +55-75-3312-8097
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Meng Y, Du Q, Du H, Wang Q, Wang L, Du L, Liu P. Analysis of chemotypes and their markers in leaves of core collections of Eucommia ulmoides using metabolomics. FRONTIERS IN PLANT SCIENCE 2023; 13:1029907. [PMID: 36699853 PMCID: PMC9868706 DOI: 10.3389/fpls.2022.1029907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The leaves of Eucommia ulmoides contain various active compunds and nutritional components, and have successively been included as raw materials in the Chinese Pharmacopoeia, the Health Food Raw Material Catalogue, and the Feed Raw Material Catalogue. Core collections of E. ulmoides had been constructed from the conserved germplasm resources basing on molecular markers and morphological traits, however, the metabolite diversity and variation in this core population were little understood. Metabolite profiles of E. ulmoides leaves of 193 core collections were comprehensively characterized by GC-MS and LC-MS/MS based non-targeted metabolomics in present study. Totally 1,100 metabolites were identified and that belonged to 18 categories, and contained 120 active ingredients for traditional Chinese medicine (TCM) and 85 disease-resistant metabolites. Four leaf chemotypes of the core collections were established by integrated uses of unsupervised self-organizing map (SOM), supervised orthogonal partial least squares discriminant analysis (OPLS-DA) and random forest (RF) statistical methods, 30, 23, 43, and 23 chemomarkers were screened corresponding to the four chemotypes, respectively. The morphological markers for the chemotypes were obtained by weighted gene co-expression network analysis (WGCNA) between the chenomarkers and the morphological traits, with leaf length (LL), chlorophyll reference value (CRV), leaf dentate height (LDH), and leaf thickness (LT) corresponding to chemotypes I, II, III, and IV, respectively. Contents of quercetin-3-O-pentosidine, isoquercitrin were closely correlated to LL, leaf area (LA), and leaf perimeter (LP), suggesting the quercetin derivatives might influence the growth and development of E. ulmoides leaf shape.
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Affiliation(s)
- Yide Meng
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Qingxin Du
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Hongyan Du
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Qi Wang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Lu Wang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Lanying Du
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Panfeng Liu
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou, China
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Qing D, Zhou Y, Pan Y, Yang X, Li J, Zhou W, Liang H, Chen W, Chen L, Lu C, Dai G, Deng G. TMT-based quantitative proteomic analysis of indica rice cultivars reveals that novel components of the signaling pathways might play a role in grain length regulation. J Proteomics 2023; 270:104745. [PMID: 36220543 DOI: 10.1016/j.jprot.2022.104745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Grain length is one of the most important rice grain appearance components. To better understand the protein regulated by grain length in indica rice, the tandem mass tag (TMT) labeling combined with LC-MS/MS analysis was used for quantitative identification of differentially regulated proteins by comparing six long-grain cultivars (MeiB, LongfengB, YexiangB, FengtianB, WantaiB, and DingxiangB) to the short-grain cultivar BoB, respectively. A total of 6622 proteins were detected for quantitative analysis by comparing protein content of six long-grain cultivars to the short-grain cultivar, and 715 proteins were significantly regulated, consisting of 336 uniquely over-accumulated proteins and 355 uniquely down-accumulated proteins. KEGG pathway analysis revealed that most of accumulated proteins are involved in metabolic pathways, biosynthesis of secondary metabolites and phenylpropanoid biosynthesis. Four down-accumulated proteins maybe involved in the signaling pathways for grain length regulation. LC-PRM/MS quantitative analysis was used to analyze 10 differentially expressed proteins. The results were almost consistent with the TMT quantitative analysis. qRT-PCR analysis results showed that the transcription level was not always parallel to the protein content. This study identified many novel grain length accumulated proteins through the quantitative proteomics approach, providing candidate genes for further study of grain size regulatory mechanisms. SIGNIFICANCE: Rice grain length is one of the most important characteristics influencing appearance and yield. Six long-grain cultivars (MeiB, LongfengB, YexiangB, FengtianB, WantaiB, and DingxiangB obtained in Guangxi province of China from the 2000s to 2020s) and one short-grain cultivar (BoB obtained in Guangxi province of China in 1980s) were used for comparative analyses. Totally, 715 differentially expressed proteins (DEPs) were identified using TMT-base proteomic analysis. The numbers of DEPs increased as the grain length increased. 4 DEPs may be related to rice's signaling pathways for grain size regulation. A total of 85 DEPs regulated in at least four long-grain cultivars compared with the short-grain cultivar BoB, and 7 proteins were over-accumulated, and 3 proteins were down-accumulated in six long-grain cultivars. These findings provide valuable information to better understand the mechanisms of protein regulation by grain length in rice.
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Affiliation(s)
- Dongjin Qing
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Yan Zhou
- School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China; Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Nanning 530006, China; Key Laboratory of Guangxi Colleges, Universities for Food Safety and Pharmaceutical Analytical Chemistry, Nanning 530006, China
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Jingcheng Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Weiyong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Weiwei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Lei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Chunju Lu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Gaoxing Dai
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China.
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China.
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Huang J, Zhang G, Li Y, Lyu M, Zhang H, Zhang N, Chen R. Integrative genomic and transcriptomic analyses of a bud sport mutant 'Jinzao Wuhe' with the phenotype of large berries in grapevines. PeerJ 2023; 11:e14617. [PMID: 36620751 PMCID: PMC9817954 DOI: 10.7717/peerj.14617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023] Open
Abstract
Background Bud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. 'Jinzao Wuhe' is a bud sport of the elite cultivar 'Himord Seedless' with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear. Methods Whole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for 'Jinzao Wuhe' and its maternal plant 'Himord Seedless' were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation. Results In two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between 'Himord Seedless' and 'Jinzao Wuhe' harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine. Conclusion Our results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars.
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Affiliation(s)
- Jianquan Huang
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Guan Zhang
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China,College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Yanhao Li
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China,College of Horticulture and Gardening, Tianjin Agricultural University, Tianjin, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - He Zhang
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Na Zhang
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
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Wang T, Li XK, Liu X, Yang XQ, Li YJ, Hou BK. Rice glycosyltransferase gene UGT2 functions in salt stress tolerance under the regulation of bZIP23 transcription factor. PLANT CELL REPORTS 2023; 42:17-28. [PMID: 36224499 DOI: 10.1007/s00299-022-02933-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Rice glycosyltransferase gene UGT2 was identified to play a crucial role in salt tolerance. The transcription factor OsbZIP23 was demonstrated to regulate the UGT2 expression under stress conditions. UDP-glycosyltransferases (UGTs) play key roles in modulating plant responses to environmental challenges. In this study, we characterized a novel glycosyltransferase, UGT2, which plays an important role in salt stress responses in rice (Oryza sativa L). We found that seedlings overexpressing UGT2 exhibited better growth than wild type in shoot and root under hydroponic culture with salt stress treatments, while ugt2ko mutant lines suffered much more growth inhibition. When the soil-grown UGT2 transgenic plants were subjected to salt stress, we also found that ugt2ko mutant lines were severely withered and most of them died, while the overexpression lines grew well and had higher survival rate. Compared with wild-type plants, UGT2 overexpression greatly increased the expression levels of the reactive oxygen species scavenging genes and stress-responsive genes. Furthermore, the upstream regulatory mechanism of the UGT2 gene was identified and we found that a bZIP transcription factor, OsbZIP23, can bind to the UGT2 promoter and enhance the UGT2 transcription levels. This work reveals that OsbZIP23-UGT2 module may play a major role in regulating the salt stress tolerance in rice.
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Affiliation(s)
- Ting Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, 261000, China
| | - Xing-Kun Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Xi Liu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Xian-Qin Yang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Yan-Jie Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Bing-Kai Hou
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China.
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Shrestha S, Mahat J, Shrestha J, K.C. M, Paudel K. Influence of high-temperature stress on rice growth and development. A review. Heliyon 2022; 8:e12651. [PMID: 36643304 PMCID: PMC9834771 DOI: 10.1016/j.heliyon.2022.e12651] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/14/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
High-temperature stress (HS) has become an alarming threat to the global food system. Rice, an important crop that supports almost half of the global population, is vulnerable to heat stress. Under the influence of HS, it shows various physiological and morphological symptoms that increase spikelet sterility, reduce grain yield, and even cause total crop failure. HS affects growth and yield in two ways: hindrance in the process of pollination and fertilization and reduction of the grain weight. The former is caused by (i) distortion of floral organs, (ii) tapetum degeneration, (iii) low pollen protein concentration, (iv) decline in pollen viability, (v) reduction in dehiscence of anther, (vi) low pollen dispersal, (vii) decrease in number of pollens on stigma, (viii) reduction in pollen grain germination, (ix) hindrance in extension of pollen tubes, and (x) shrinkage of stigma which ultimately cause spikelet infertility. The latter is caused by (i)reduced photosynthetic rate, (ii) a boost in senescence of functional leaves, (iii) reduction of biological synthesis of starch, (iv)reduced starch augmentation, (v) shrunk duration of grain filling, and (vi) declined grain weight which ultimately reduce the grain yield. However, some agronomic and breeding approaches have been adopted for developing thermo-resistant cultivars but the success is limited. In this paper, we have summarized the the morpho-physiological and molecular response of plant to HS, and a few possible management strategies.
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Um TY, Hong SY, Han JS, Jung KH, Moon S, Choi BS, Basnet P, Chung YS, Lee SW, Yang WT, Kim DH. Gibberellic acid sensitive dwarf encodes an ARPC2 subunit that mediates gibberellic acid biosynthesis, effects to grain yield in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1027688. [PMID: 36618614 PMCID: PMC9813395 DOI: 10.3389/fpls.2022.1027688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The plant hormone gibberellic acid (GA) is important for plant growth and productivity. Actin-related proteins (ARPs) also play central roles in plant growth, including cell elongation and development. However, the relationships between ARPs and GA signaling and biosynthesis are not fully understood. Here, we isolated OsGASD, encoding an ARP subunit from rice (Oryza sativa), using the Ac/Ds knockout system. The osgasd knockout (Ko) mutation reduced GA3 content in shoots as well as plant growth and height. However, GA application restored the plant height of the osgasd Ko mutant to a height similar to that of the wild type (WT). Rice plants overexpressing OsGASD (Ox) showed increased plant height and grain yield compared to the WT. Transcriptome analysis of flag leaves of OsGASD Ox and osgasd Ko plants revealed that OsGASD regulates cell development and the expression of elongation-related genes. These observations suggest that OsGASD is involved in maintaining GA homeostasis to regulate plant development, thereby affecting rice growth and productivity.
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Affiliation(s)
- Tae Young Um
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea
| | - So Yeon Hong
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Ji Sung Han
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Ki Hong Jung
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Sunok Moon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Beom-Soon Choi
- Research Institute, NBIT Co., Ltd., Chuncheon, Republic of Korea
| | - Prakash Basnet
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea
| | - Young Soo Chung
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Seon Woo Lee
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Won Tae Yang
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Doh Hoon Kim
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
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Weng H, Yan J, Guo L, Chen H. Integrated transcriptomic and metabolomic analyses of the molecular mechanisms of two highland barley genotypes with pyroxsulam responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1030578. [PMID: 36618617 PMCID: PMC9812518 DOI: 10.3389/fpls.2022.1030578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Highland barley is one of the few crops that can be grown at high elevations, making it a key resource within the Tibet Plateau. Weeds are a significant threat to highland barley production, and new herbicides and tolerant barley varieties are needed to control this ever-growing problem. A better understanding of existing herbicide resistance mechanisms is therefore needed. In this study, transcriptomic and metabolomic analyses were used to identify molecular and physiological changes in two highland barley genotypes with differing sensitivities to the herbicide pyroxsulam. We identified several stress-responsive metabolites, including flavonoids and antioxidants, which accumulated to significantly higher levels in the pyroxsulam-resistant genotype. Additionally, we found key genes in both the flavonoid biosynthesis pathway and the antioxidant system that were up-regulated in pyroxsulam-resistant barley. This work significantly expands on the current understanding of the molecular mechanisms underlying differing pyroxsulam tolerance among barley genotypes and provides several new avenues to explore for breeding or engineering tolerant barley.
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Du S, Cai Y, Qiu S, Hao Y, Tian K, Zou Z, Luo L. Metabolic Profiling of Oryza sativa L. Triggered by Chilling Stress Using Ultraperformance Liquid Chromatography Coupled with Quadrupole/Time-of-Flight Mass Spectrometry (UPLC-QTOF-MS) with Transcriptome Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15703-15714. [PMID: 36473722 DOI: 10.1021/acs.jafc.2c05949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Low temperature, a major abiotic stress, often causes molecular changes in crops, which leads to metabolic disturbances and probably affects crop yield. In this study, chilling stress induced distinct metabolic profiles associated with transcriptome regulation, exhibiting great metabolic differences between Qiutianxiaoting (japonica) and 93-11 (indica). In total, 41 and 58 differential metabolites were screened and identified in Qiutianxiaoting and 93-11, respectively. Five key metabolites were screened in response to chilling stress, which were involved or related to different metabolic pathways. Moreover, starch and sucrose metabolism, aminoacyl-tRNA biosynthesis, and phenylpropanoid biosynthesis were significantly enriched in Qiutianxiaoting to maintain cellular homeostasis. Aminoacyl-tRNA biosynthesis and antioxidation metabolism were significantly enriched in 93-11, but disorders of the metabolome and transcriptome occurred at recovery stage. The results could provide some useful information for in-depth understanding of cold-resistant mechanisms, as well as reference for the selection and breeding of rice varieties.
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Affiliation(s)
- Shangguang Du
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
- School of Life Sciences, Nanchang Normal University, Nanchang 330031, China
| | - Yali Cai
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Shengrong Qiu
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Yingbin Hao
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Kaili Tian
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Zhengrong Zou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Liping Luo
- College of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Life Sciences, Nanchang University, Nanchang 330031, China
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Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean ( Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms). Genes (Basel) 2022; 13:genes13122350. [PMID: 36553617 PMCID: PMC9777823 DOI: 10.3390/genes13122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/26/2022] [Accepted: 12/09/2022] [Indexed: 12/16/2022] Open
Abstract
Seed size is an important yield and quality-determining trait in higher plants and is also crucial to their evolutionary fitness. In African yam bean (AYB), seed size varies widely among different accessions. However, the genetic basis of such variation has not been adequately documented. A genome-wide marker-trait association study was conducted to identify genomic regions associated with four seed size traits (seed length, seed width, seed thickness, and 100-seed weight) in a panel of 195 AYB accessions. A total of 5416 SNP markers were generated from the diversity array technology sequence (DArTseq) genotype-by-sequencing (GBS)- approach, in which 2491 SNPs were retained after SNP quality control and used for marker-trait association analysis. Significant phenotypic variation was observed for the traits. Broad-sense heritability ranged from 50.0% (seed width) to 66.4% (seed length). The relationships among the traits were positive and significant. Genome-wide association study (GWAS) using the general linear model (GLM) and the mixed linear model (MLM) approaches identified 12 SNP markers significantly associated with seed size traits across the six test environments. The 12 makers explained 6.5-10.8% of the phenotypic variation. Two markers (29420334|F|0-52:C>G-52:C>G and 29420736|F|0-57:G>T-57:G>T) with pleiotropic effects associated with seed width and seed thickness were found. A candidate gene search identified five significant markers (100026424|F|0-37:C>T-37:C>T, 100041049|F|0-42:G>C-42:G>C, 100034480|F|0-31:C>A-31:C>A, 29420365|F|0-55:C>G-55:C>G, and 29420736|F|0-57:G>T-57:G>T) located close to 43 putative genes whose encoding protein products are known to regulate seed size traits. This study revealed significant makers not previously reported for seed size in AYB and could provide useful information for genomic-assisted breeding in AYB.
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Daldoul S, Hanzouli F, Hamdi Z, Chenenaoui S, Wetzel T, Nick P, Mliki A, Gargouri M. The root transcriptome dynamics reveals new valuable insights in the salt-resilience mechanism of wild grapevine ( Vitis vinifera subsp . sylvestris). FRONTIERS IN PLANT SCIENCE 2022; 13:1077710. [PMID: 36570937 PMCID: PMC9780605 DOI: 10.3389/fpls.2022.1077710] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/16/2022] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Most of elite cultivated grapevine varieties (Vitis vinifera L.), conventionally grafted on rootstocks, are becoming more and more affected by climate changes, such as increase of salinity. Therefore, we revisited the valuable genetic resources of wild grapevines (V. sylvestris) to elaborate strategies for a sustainable viticulture. METHODS Here, we compared physiological and biochemical responses of two salt-tolerant species: a wild grapevine genotype "Tebaba" from our previous studies and the conventional rootstock "1103 Paulsen". Interestingly, our physio-biochemical results showed that under 150mM NaCl, "Tebaba" maintains higher leaf osmotic potential, lower Na+/K+ ratio and a significant peaked increase of polyphenol content at the first 8h of salinity stress. This behavior allowed to hypothesis a drastic repatterning of metabolism in "Tebaba's" roots following a biphasic response. In order to deepen our understanding on the "Tebaba" salt tolerance mechanism, we investigated a time-dependent transcriptomic analysis covering three sampling times, 8h, 24h and 48h. RESULTS The dynamic analysis indicated that "Tebaba" root cells detect and respond on a large scale within 8h to an accumulation of ROS by enhancing a translational reprogramming process and inducing the transcripts of glycolytic metabolism and flavonoids biosynthesis as a predominate non-enzymatic scavenging process. Afterwards, there is a transition to a largely gluconeogenic stage followed by a combined response mechanism based on cell wall remodeling and lignin biosynthesis with an efficient osmoregulation between 24 and 48 h. DISCUSSION This investigation explored for the first time in depth the established cross-talk between the physiological, biochemical and transcriptional regulators contributing to propose a hypothetical model of the dynamic salt mechanism tolerance of wild grapevines. In summary, these findings allowed further understanding of the genetic regulation mechanism of salt-tolerance in V. sylvestris and identified specific candidate genes valuable for appropriate breeding strategies.
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Affiliation(s)
- Samia Daldoul
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Faouzia Hanzouli
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Zohra Hamdi
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Synda Chenenaoui
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
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Wu TY, Krishnamoorthi S, Boonyaves K, Al-Darabsah I, Leong R, Jones AM, Ishizaki K, Liao KL, Urano D. G protein controls stress readiness by modulating transcriptional and metabolic homeostasis in Arabidopsis thaliana and Marchantia polymorpha. MOLECULAR PLANT 2022; 15:1889-1907. [PMID: 36321200 DOI: 10.1016/j.molp.2022.10.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
The core G protein signaling module, which consists of Gα and extra-large Gα (XLG) subunits coupled with the Gβγ dimer, is a master regulator of various stress responses. In this study, we compared the basal and salt stress-induced transcriptomic, metabolomic and phenotypic profiles in Gα, Gβ, and XLG-null mutants of two plant species, Arabidopsis thaliana and Marchantia polymorpha, and showed that G protein mediates the shift of transcriptional and metabolic homeostasis to stress readiness status. We demonstrated that such stress readiness serves as an intrinsic protection mechanism against further stressors through enhancing the phenylpropanoid pathway and abscisic acid responses. Furthermore, WRKY transcription factors were identified as key intermediates of G protein-mediated homeostatic shifts. Statistical and mathematical model comparisons between A. thaliana and M. polymorpha revealed evolutionary conservation of transcriptional and metabolic networks over land plant evolution, whereas divergence has occurred in the function of plant-specific atypical XLG subunit. Taken together, our results indicate that the shifts in transcriptional and metabolic homeostasis at least partially act as the mechanisms of G protein-coupled stress responses that are conserved between two distantly related plants.
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Affiliation(s)
- Ting-Ying Wu
- Temasek Life Sciences Laboratory, Singapore, Singapore.
| | | | - Kulaporn Boonyaves
- Temasek Life Sciences Laboratory, Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Isam Al-Darabsah
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada
| | - Richalynn Leong
- Temasek Life Sciences Laboratory, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Alan M Jones
- Departments of Biology and Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Kang-Ling Liao
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada.
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
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Xiang YH, Yu JJ, Liao B, Shan JX, Ye WW, Dong NQ, Guo T, Kan Y, Zhang H, Yang YB, Li YC, Zhao HY, Yu HX, Lu ZQ, Lin HX. An α/β hydrolase family member negatively regulates salt tolerance but promotes flowering through three distinct functions in rice. MOLECULAR PLANT 2022; 15:1908-1930. [PMID: 36303433 DOI: 10.1016/j.molp.2022.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/09/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Ongoing soil salinization drastically threatens crop growth, development, and yield worldwide. It is therefore crucial that we improve salt tolerance in rice by exploiting natural genetic variation. However, many salt-responsive genes confer undesirable phenotypes and therefore cannot be effectively applied to practical agricultural production. In this study, we identified a quantitative trait locus for salt tolerance from the African rice species Oryza glaberrima and named it as Salt Tolerance and Heading Date 1 (STH1). We found that STH1 regulates fatty acid metabolic homeostasis, probably by catalyzing the hydrolytic degradation of fatty acids, which contributes to salt tolerance. Meanwhile, we demonstrated that STH1 forms a protein complex with D3 and a vital regulatory factor in salt tolerance, OsHAL3, to regulate the protein abundance of OsHAL3 via the 26S proteasome pathway. Furthermore, we revealed that STH1 also serves as a co-activator with the floral integrator gene Heading date 1 to balance the expression of the florigen gene Heading date 3a under different circumstances, thus coordinating the regulation of salt tolerance and heading date. Notably, the allele of STH1 associated with enhanced salt tolerance and high yield is found in some African rice accessions but barely in Asian cultivars. Introgression of the STH1HP46 allele from African rice into modern rice cultivars is a desirable approach for boosting grain yield under salt stress. Collectively, our discoveries not only provide conceptual advances on the mechanisms of salt tolerance and synergetic regulation between salt tolerance and flowering time but also offer potential strategies to overcome the challenges resulted from increasingly serious soil salinization that many crops are facing.
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Affiliation(s)
- You-Huang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Jun Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ben Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Hai Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Chao Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Huai-Yu Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Xiao Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; University of the Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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Wu Y, Li X, Zhang J, Zhao H, Tan S, Xu W, Pan J, Yang F, Pi E. ERF subfamily transcription factors and their function in plant responses to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1042084. [PMID: 36531407 PMCID: PMC9748296 DOI: 10.3389/fpls.2022.1042084] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/09/2022] [Indexed: 06/09/2023]
Abstract
Ethylene Responsive Factor (ERF) subfamily comprise the largest number of proteins in the plant AP2/ERF superfamily, and have been most extensively studied on the biological functions. Members of this subfamily have been proven to regulate plant resistances to various abiotic stresses, such as drought, salinity, chilling and some other adversities. Under these stresses, ERFs are usually activated by mitogen-activated protein kinase induced phosphorylation or escape from ubiquitin-ligase enzymes, and then form complex with nucleic proteins before binding to cis-element in promoter regions of stress responsive genes. In this review, we will discuss the phylogenetic relationships among the ERF subfamily proteins, summarize molecular mechanism how the transcriptional activity of ERFs been regulated and how ERFs of different subgroup regulate the transcription of stress responsive genes, such as high-affinity K+ transporter gene PalHKT1;2, reactive oxygen species related genes LcLTP, LcPrx, and LcRP, flavonoids synthesis related genes FtF3H and LhMYBSPLATTER, etc. Though increasing researches demonstrate that ERFs are involved in various abiotic stresses, very few interact proteins and target genes of them have been comprehensively annotated. Hence, future research prospects are described on the mechanisms of how stress signals been transited to ERFs and how ERFs regulate the transcriptional expression of stress responsive genes.
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Wang SL, Zhang ZH, Fan YY, Huang DR, Yang YL, Zhuang JY, Zhu YJ. Control of Grain Weight and Size in Rice (Oryza sativa L.) by OsPUB3 Encoding a U-Box E3 Ubiquitin Ligase. RICE (NEW YORK, N.Y.) 2022; 15:58. [PMID: 36418747 PMCID: PMC9684364 DOI: 10.1186/s12284-022-00604-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Grain weight and size, mostly determined by grain length, width and thickness, are crucial traits affecting grain quality and yield in rice. A quantitative trait locus controlling grain length and width in rice, qGS1-35.2, was previously fine-mapped in a 57.7-kb region on the long arm of chromosome 1. In this study, OsPUB3, a gene encoding a U-box E3 ubiquitin ligase, was validated as the causal gene for qGS1-35.2. The effects were confirmed firstly by using CRISPR/Cas9-based mutagenesis and then through transgenic complementation of a Cas9-free knock-out (KO) mutant. Two homozygous KO lines were produced, each having a 1-bp insertion in OsPUB3 which caused frameshift mutation and premature termination. Compared with the recipient and a transgenic-negative control, both mutants showed significant decreases in grain weight and size. In transgenic complementation populations derived from four independent T0 plants, grain weight of transgenic-positive plants was significantly higher than transgenic-negative plants, coming with increased grain length and a less significant decrease in grain width. Based on data documented in RiceVarMap V2.0, eight haplotypes were classified according to six single-nucleotide polymorphisms (SNPs) found in the OsPUB3 coding region of 4695 rice accessions. Significant differences on grain size traits were detected between the three major haplotypes, Hap1, Hap2 and Hap3 that jointly occupy 98.6% of the accessions. Hap3 having the largest grain weight and grain length but intermediate grain width exhibits a potential for simultaneously improving grain yield and quality. In another set of 257 indica rice cultivars tested in our study, Hap1 and Hap2 remained to be the two largest groups. Their differences on grain weight and size were significant in the background of non-functional gse5, but non-significant in the background of functional GSE5, indicating a genetic interaction between OsPUB3 and GSE5. Cloning of OsPUB3 provides a new gene resource for investigating the regulation of grain weight and size.
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Affiliation(s)
- Shi-Lin Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhen-Hua Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - De-Run Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yao-Long Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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Shomali A, Das S, Arif N, Sarraf M, Zahra N, Yadav V, Aliniaeifard S, Chauhan DK, Hasanuzzaman M. Diverse Physiological Roles of Flavonoids in Plant Environmental Stress Responses and Tolerance. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223158. [PMID: 36432887 PMCID: PMC9699315 DOI: 10.3390/plants11223158] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 05/27/2023]
Abstract
Flavonoids are characterized as the low molecular weight polyphenolic compounds universally distributed in planta. They are a chemically varied group of secondary metabolites with a broad range of biological activity. The increasing amount of evidence has demonstrated the various physiological functions of flavonoids in stress response. In this paper, we provide a brief introduction to flavonoids' biochemistry and biosynthesis. Then, we review the recent findings on the alternation of flavonoid content under different stress conditions to come up with an overall picture of the mechanism of involvement of flavonoids in plants' response to various abiotic stresses. The participation of flavonoids in antioxidant systems, flavonoid-mediated response to different abiotic stresses, the involvement of flavonoids in stress signaling networks, and the physiological response of plants under stress conditions are discussed in this review. Moreover, molecular and genetic approaches to tailoring flavonoid biosynthesis and regulation under abiotic stress are addressed in this review.
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Affiliation(s)
- Aida Shomali
- Photosynthesis Laboratory, Department of Horticulture, University of Tehran, Tehran 33916-53755, Iran
| | - Susmita Das
- Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Calcutta, Kolkata 700019, India
| | - Namira Arif
- D. D. Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, India
- Faculty of Environmental Studies, Dehli School of Journalism, University of Delhi, Delhi 110007, India
| | - Mohammad Sarraf
- Department of Horticultural Science, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz 61357-43311, Iran
| | - Noreen Zahra
- Department of Botany, Government College for Women University, Faisalabad 38000, Pakistan
| | - Vaishali Yadav
- Department of Botany, Multanimal Modi College Modinagar, Ghaziabad 201204, India
| | - Sasan Aliniaeifard
- Photosynthesis Laboratory, Department of Horticulture, University of Tehran, Tehran 33916-53755, Iran
| | - Devendra Kumar Chauhan
- D. D. Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, India
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh
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Developing Genetic Engineering Techniques for Control of Seed Size and Yield. Int J Mol Sci 2022; 23:ijms232113256. [PMID: 36362043 PMCID: PMC9655546 DOI: 10.3390/ijms232113256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops' genetic and molecular aspects in balancing seed size and yield.
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Jiang H, Guo D, Liu Y, Zhu L, Xie F, Xie L. RNA-Seq combined with population-level analysis reveals important candidate genes related to seed size in flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1015399. [PMID: 36388602 PMCID: PMC9641021 DOI: 10.3389/fpls.2022.1015399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Seed size is a key determinant of crop yields. Understanding the regulatory mechanisms of seed size is beneficial for improving flax seed yield. In this study, the development of large flax seeds lagged behind that of small seeds, and 1,751 protein-coding genes were differentially expressed in early seeds, torpedo-stage embryos, and endosperms of CIli2719 and Z11637 using RNA sequencing. Homologous alignment revealed that 129 differentially expressed genes (DEGs) in flax were homologous with 71 known seed size-related genes in Arabidopsis thaliana and rice (Oryza sativa L.). These DEGs controlled seed size through multiple processes and factors, among which phytohormone pathways and transcription factors were the most important. Moreover, 54 DEGs were found to be associated with seed size and weight in a DEG-based association study. Nucleotide diversity (π) analysis of seed size-related candidate DEGs by homologous alignment and association analysis showed that the π values decreased significantly during flax acclimation from oil to fiber flax, suggesting that some seed size-related candidate genes were selected in this acclimation process. These results provide important resources and genetic foundation for further research on seed size regulation and seed improvement in flax.
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Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat ( Triticum aestivum L.). Genes (Basel) 2022; 13:genes13101906. [PMID: 36292791 PMCID: PMC9601369 DOI: 10.3390/genes13101906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
Plant cell metabolism inevitably forms an important drought-responsive mechanism, which halts crop productivity. Globally, more than 30% of the total harvested area was affected by dehydration. RNA-seq technology has enabled biologists to identify stress-responsive genes in relatively quick times. However, one shortcoming of this technology is the inconsistent data generation compared to other parts of the world. So, we have tried, here, to generate a consensus by analyzing meta-transcriptomic data available in the public microarray database GEO NCBI. In this way, the aim was set, here, to identify stress genes commonly identified as differentially expressed (p < 0.05) then followed by downstream analyses. The search term “Drought in wheat” resulted in 233 microarray experiments from the GEO NCBI database. After discarding empty datasets containing no expression data, the large-scale meta-transcriptome analytics and one sample proportional test were carried out (Bonferroni adjusted p < 0.05) to reveal a set of 11 drought-responsive genes on a global scale. The annotation of these genes revealed that the transcription factor activity of RNA polymerase II and sequence-specific DNA-binding mechanism had a significant role during the drought response in wheat. Similarly, the primary root differentiation zone annotations, controlled by TraesCS5A02G456300 and TraesCS7B02G243600 genes, were found as top-enriched terms (p < 0.05 and Q < 0.05). The resultant standard drought genes, glycosyltransferase; Arabidopsis thaliana KNOTTED-like; bHLH family protein; Probable helicase MAGATAMA 3; SBP family protein; Cytochrome c oxidase subunit 2; Trihelix family protein; Mic1 domain-containing protein; ERF family protein; HD-ZIP I protein; and ERF family protein, are important in terms of their worldwide proved link with stress. From a future perspective, this study could be important in a breeding program contributing to increased crop yield. Moreover, the wheat varieties could be identified as drought-resistant/sensitive based on the nature of gene expression levels.
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Li Y, Yang Z, Zhang Y, Guo J, Liu L, Wang C, Wang B, Han G. The roles of HD-ZIP proteins in plant abiotic stress tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1027071. [PMID: 36311122 PMCID: PMC9598875 DOI: 10.3389/fpls.2022.1027071] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 05/31/2023]
Abstract
Homeodomain leucine zipper (HD-ZIP) proteins are plant-specific transcription factors that contain a homeodomain (HD) and a leucine zipper (LZ) domain. The highly conserved HD binds specifically to DNA and the LZ mediates homodimer or heterodimer formation. HD-ZIP transcription factors control plant growth, development, and responses to abiotic stress by regulating downstream target genes and hormone regulatory pathways. HD-ZIP proteins are divided into four subclasses (I-IV) according to their sequence conservation and function. The genome-wide identification and expression profile analysis of HD-ZIP proteins in model plants such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have improved our understanding of the functions of the different subclasses. In this review, we mainly summarize and discuss the roles of HD-ZIP proteins in plant response to abiotic stresses such as drought, salinity, low temperature, and harmful metals. HD-ZIP proteins mainly mediate plant stress tolerance by regulating the expression of downstream stress-related genes through abscisic acid (ABA) mediated signaling pathways, and also by regulating plant growth and development. This review provides a basis for understanding the roles of HD-ZIP proteins and potential targets for breeding abiotic stress tolerance in plants.
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Zhao Y, Zhai G, Li X, Tao H, Li L, He Y, Zhang X, Wang F, Hong G, Zhu Y. Metabolomics Reveals Nutritional Diversity among Six Coarse Cereals and Antioxidant Activity Analysis of Grain Sorghum and Sweet Sorghum. Antioxidants (Basel) 2022; 11:antiox11101984. [PMID: 36290708 PMCID: PMC9598553 DOI: 10.3390/antiox11101984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/29/2022] Open
Abstract
Coarse cereals are rich in dietary fiber, B vitamins, minerals, secondary metabolites, and other bioactive components, which exert numerous health benefits. To better understand the diversity of metabolites in different coarse cereals, we performed widely targeted metabolic profiling analyses of six popular coarse cereals, millet, coix, buckwheat, quinoa, oat, and grain sorghum, of which 768 metabolites are identified. Moreover, quinoa and buckwheat showed significantly different metabolomic profiles compared with other coarse cereals. Analysis of the accumulation patterns of common nutritional metabolites among six coarse cereals, we found that the accumulation of carbohydrates follows a conserved pattern in the six coarse cereals, while those of amino acids, vitamins, flavonoids, and lipids were complementary. Furthermore, the species-specific metabolites in each coarse cereal were identified, and the neighbor-joining tree for the six coarse cereals was constructed based on the metabolome data. Since sorghum contains more species-specific metabolites and occupies a unique position on the neighbor-joining tree, the metabolite differences between grain sorghum 654 and sweet sorghum LTR108 were finally compared specifically, revealing that LTR108 contained more flavonoids and had higher antioxidant activity than 654. Our work supports an overview understanding of nutrient value in different coarse cereals, which provides the metabolomic evidence for the healthy diet. Additionally, the superior antioxidant activity of sweet sorghum provides clues for its targeted uses.
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Affiliation(s)
- Yao Zhao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Guowei Zhai
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xuetong Li
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Han Tao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Linying Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Yuqing He
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Xueying Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Fulin Wang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Gaojie Hong
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
- Correspondence: (G.H.); (Y.Z.)
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence: (G.H.); (Y.Z.)
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Yu A, Jiang X, Sun Y, Hu Q, Zhu X, Kang J, Chen L, Liu L, Hao L, Yang Q, Long R, Li M. Genome-wide identification, characterization, and expression analysis of UDP-glycosyltransferase genes associated with secondary metabolism in alfalfa ( Medicago sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1001206. [PMID: 36254261 PMCID: PMC9568668 DOI: 10.3389/fpls.2022.1001206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Uridine diphosphate glycosyltransferases (UGTs) are enzymes that catalyze glycosylation modifications and play an essential role in regulating plant metabolism. Alfalfa (Medicago sativa L.) is the most important legume in the world due to its high yields and protein content; however, the UGT genes in alfalfa have not yet been studied. Identifying UGT genes with metabolic roles in alfalfa is essential for identifying and modifying genetic traits that are relevant to yield and quality. In this study, 90 of the 239 UGT genes identified from the alfalfa "Zhongmu No. 1" genome database were found to be related to secondary metabolism, and a series of gene family characterization analyses were conducted on each. The results demonstrated that all 90 UGT genes were unevenly distributed on eight chromosomes with few introns and that tandem duplications were the crucial driving force expanding the UGT family in alfalfa. Notably, the 90 UGT genes can be clustered into ten evolutionary groups which contain specific PSPG motifs, and genes in these ten groups have specific tissue expressions. This suggests that the UGT genes in each group could have similar glycosylation roles corresponding to analogous secondary metabolites in alfalfa. Additionally, multiple cis-acting elements found in MsUGT promoter regions, such as phytohormone and flavonoids, indicate that 90 UGT members could be induced by these features, which are also related to secondary metabolism. Therefore, our study identified 90 UGT members inten evolutionary groups that are likely related to glycosylation modifications with secondary metabolites in alfalfa. These findings help uncover pivotal regulatory mechanisms associated with secondary metabolism in plant yield and quality and contribute to genetic modification and breeding in alfalfa and other plant species.
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Affiliation(s)
- Andong Yu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xueqian Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Qiannan Hu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xiaoxi Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Liu
- Bayannur Institute of Agricultural and Animal Husbandry Sciences, Inner Mongolia, China
| | - Linfeng Hao
- Bayannur Institute of Agricultural and Animal Husbandry Sciences, Inner Mongolia, China
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Li ZH, Wang SL, Zhu YJ, Fan YY, Huang DR, Zhu AK, Zhuang JY, Liang Y, Zhang ZH. Control of Grain Shape and Size in Rice by Two Functional Alleles of OsPUB3 in Varied Genetic Background. PLANTS (BASEL, SWITZERLAND) 2022; 11:2530. [PMID: 36235396 PMCID: PMC9571118 DOI: 10.3390/plants11192530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Grain shape and size are key determinants of grain appearance quality and yield in rice. In our previous study, a grain shape QTL, qGS1-35.2, was fine-mapped using near-isogenic lines (NILs) derived from a cross between Zhenshan 97 (ZS97) and Milyang 46 (MY46). One annotated gene, OsPUB3, was found to be the most likely candidate gene. Here, knockout and overexpression experiments were performed to investigate the effects of OsPUB3 on grain shape and size. Four traits were tested, including grain length, grain width, grain weight, and the ratio of grain length to width. Knockout of OsPUB3 in NILZS97, NILMY46, and another rice cultivar carrying the OsPUB3MY46 allele all caused decreases in grain width and weight and increases in the ratio of grain length to width. Results also showed that the magnitude of the mutational effects varied depending on the target allele and the genetic background. Moreover, it was found that NILZS97 and NILMY46 carried different functional alleles of OsPUB3, causing differences in grain shape rather than grain weight. In the overexpression experiment, significant differences between transgenic-positive and transgenic-negative plants were detected in all four traits. These results indicate that OsPUB3 regulates grain shape and size through a complex mechanism and is a good target for deciphering the regulatory network of grain shape. This gene could be used to improve grain appearance quality through molecular breeding as well.
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Affiliation(s)
- Zhu-Hao Li
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shi-Lin Wang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - De-Run Huang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ai-Ke Zhu
- Nanchong Academy of Agricultural Sciences, Nanchong 637000, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Yan Liang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhen-Hua Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
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Heat Stress Decreases Rice Grain Weight: Evidence and Physiological Mechanisms of Heat Effects Prior to Flowering. Int J Mol Sci 2022; 23:ijms231810922. [PMID: 36142833 PMCID: PMC9504709 DOI: 10.3390/ijms231810922] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/02/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Heat stress during the preflowering panicle initiation stage seriously decreases rice grain weight in an invisible way and has not been given enough attention. The current review aims to (i) specify the heat effects on rice grain weight during the panicle initiation stage compared with the most important grain-filling stage; and (ii) discuss the physiological mechanisms of the decreased rice grain weight induced by heat during panicle initiation in terms of assimilate supply and phytohormone regulation, which are key physiological processes directly regulating rice grain weight. We emphasize that the effect of heat during the panicle initiation stage on rice grain weight is more serious than that during the grain-filling stage. Heat stress during the panicle initiation stage induces alterations in endogenous phytohormones, leading to the inhibition of the photosynthesis of functional leaves (source) and the formation of vascular bundles (flow), thus reducing the accumulation and transport of nonstructural carbohydrates and the growth of lemmata and paleae. The disruptions in the “flow” and restrictions in the preanthesis “source” tissue reduce grain size directly and decrease grain plumpness indirectly, resulting in a reduction in the final grain weight, which could be the direct physiological causes of the lower rice grain weight induced by heat during the panicle initiation stage. We highlight the seriousness of preflowering heat stress on rice grain weight, which can be regarded as an invisible disaster. The physiological mechanisms underlying the lower grain weight induced by heat during panicle initiation show a certain novelty because they distinguish this stage from the grain-filling stage. Additionally, a number of genes that control grain size through phytohormones have been summarized, but their functions have not yet been fully tested under heat conditions, except for the Grain Size and Abiotic stress tolerance 1 (GSA1) and BRASSINOSTEROID INSENSITIVE1 (OsBRI1) genes, which are reported to respond rapidly to heat stress. The mechanisms of reduced rice grain weight induced by heat during the panicle initiation stage should be studied in more depth in terms of molecular pathways.
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Kuang L, Shen Q, Chen L, Ye L, Yan T, Chen ZH, Waugh R, Li Q, Huang L, Cai S, Fu L, Xing P, Wang K, Shao J, Wu F, Jiang L, Wu D, Zhang G. The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies. PLANT COMMUNICATIONS 2022; 3:100333. [PMID: 35643085 PMCID: PMC9482977 DOI: 10.1016/j.xplc.2022.100333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/24/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The tribe Triticeae provides important staple cereal crops and contains elite wild species with wide genetic diversity and high tolerance to abiotic stresses. Sea barleygrass (Hordeum marinum Huds.), a wild Triticeae species, thrives in saline marshlands and is well known for its high tolerance to salinity and waterlogging. Here, a 3.82-Gb high-quality reference genome of sea barleygrass is assembled de novo, with 3.69 Gb (96.8%) of its sequences anchored onto seven chromosomes. In total, 41 045 high-confidence (HC) genes are annotated by homology, de novo prediction, and transcriptome analysis. Phylogenetics, non-synonymous/synonymous mutation ratios (Ka/Ks), and transcriptomic and functional analyses provide genetic evidence for the divergence in morphology and salt tolerance among sea barleygrass, barley, and wheat. The large variation in post-domestication genes (e.g. IPA1 and MOC1) may cause interspecies differences in plant morphology. The extremely high salt tolerance of sea barleygrass is mainly attributed to low Na+ uptake and root-to-shoot translocation, which are mainly controlled by SOS1, HKT, and NHX transporters. Agrobacterium-mediated transformation and CRISPR/Cas9-mediated gene editing systems were developed for sea barleygrass to promote its utilization for exploration and functional studies of hub genes and for the genetic improvement of cereal crops.
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Affiliation(s)
- Liuhui Kuang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Qiufang Shen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Liyang Chen
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Lingzhen Ye
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia
| | - Robbie Waugh
- The James Hutton Institute, Dundee DD2 5DA, UK; The Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK; School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Qi Li
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Lu Huang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Liangbo Fu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Pengwei Xing
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jiari Shao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Feibo Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Dezhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Guoping Zhang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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Lian C, Lan J, Zhang B, Yang H, Guo K, Li J, Chen S. Molecular Cloning and Functional Analysis of IrUGT86A1-like Gene in Medicinal Plant Isodon rubescens (Hemsl.) Hara. Life (Basel) 2022; 12:life12091334. [PMID: 36143372 PMCID: PMC9503823 DOI: 10.3390/life12091334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
The synthesis of secondary metabolites in plants often includes glycosylation modifications. Often, the final step of constructing plant secondary metabolites is completed by glycosylation transferases, which are also involved in many cell processes. In this study, a UDP-glycosyltransferase gene (UGT) was amplified from Isodon rubescens (Hemsl.) Hara with RT-PCR and named IrUGT86A1-like (GenBank: MZ913258). Here, we found that IrUGT86A1-like gene is 1450 bp in length and encodes for 479 amino acids. Bioinformatics analysis revealed that IrUGT86A1-like is a stable and hydrophilic protein, located in the cytoplasm with a transmembrane domain. Phylogenetic analysis showed that IrUGT86A1-like protein has the closest genetic relationship with the UDP-glycosyltransferase 86A1-like protein (XP_042054241.1) of Salvia splendens. RT-qPCR analysis demonstrated that the expression of IrUGT86A1-like gene varied in different tissues; leaves had the highest expression followed by flowers, stems, and roots had the lowest expression. This expression trend is similar to the distribution of oridonin content in different tissues of I. rubescens. Additionally, IrUGT86A1-like gene was found to be positively enhanced by NaCl and MeJA treatment, and in contrast was down-regulated by ABA treatment. Finally, the prokaryotic expression vector pEASY®-Blunt E1-IrUGT86A1 was successfully used to express about 53 KD of IrUGT86A1-like protein. This research builds a foundation for further investigation on the function of this gene in the synthesis and modification of secondary metabolites.
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Khan H, Krishnappa G, Kumar S, Mishra CN, Krishna H, Devate NB, Rathan ND, Parkash O, Yadav SS, Srivastava P, Biradar S, Kumar M, Singh GP. Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.). Front Genet 2022; 13:982589. [PMID: 36092913 PMCID: PMC9458894 DOI: 10.3389/fgene.2022.982589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
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Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Gopalareddy Krishnappa
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Hari Krishna
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Om Parkash
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonu Singh Yadav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Suma Biradar
- University of Agricultural Sciences, Dharwad, India
| | - Monu Kumar
- ICAR-Indian Agricultural Research Institute, Jharkhand, India
| | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
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Ge L, Guo H, Li X, Tang M, Guo C, Bao H, Huang L, Yi Y, Cui Y, Chen L. OsSIDP301, a Member of the DUF1644 Family, Negatively Regulates Salt Stress and Grain Size in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:863233. [PMID: 35968081 PMCID: PMC9366248 DOI: 10.3389/fpls.2022.863233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
As a major environmental factor, salt stress substantially retards growth and reduces the productivity of rice (Oryza sativa). Members of the DUF1644 family, "the domains of unknown function 1644 motif" are predicted to play an essential regulatory role in response to abiotic stress. However, the specific molecular mechanisms of most members of this family remain elusive. Here, we report that the OsSIDP301 (stress-induced DUF1644 protein) was induced by salt stress and abscisic acid (ABA). We found that overexpression of OsSIDP301 (OE) in plants conferred salt hypersensitivity and reduced grain size, whereas plants with OsSIDP301 RNA interference (RNAi) exhibited salt tolerance and increased grain size in rice. OsSIDP301 determines salt stress tolerance by modulating genes involved in the salt-response and ABA signaling pathways. Further studies suggest that OsSIDP301 regulates grain size by influencing cell expansion in spikelet hulls. Moreover, OsSIDP301 interacts with OsBUL1 COMPLEX1 (OsBC1), which positively regulates grain size in rice. Our findings reveal that OsSIDP301 functions as a negative regulator of salt stress and grain size, and repressing its expression represents a promising strategy for improving salt stress tolerance and yield in rice.
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Affiliation(s)
- Li Ge
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hongming Guo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiu Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ming Tang
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Chiming Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Han Bao
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Linjuan Huang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yin Yi
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
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Luo Z, Zhou Z, Li Y, Tao S, Hu ZR, Yang JS, Cheng X, Hu R, Zhang W. Transcriptome-based gene regulatory network analyses of differential cold tolerance of two tobacco cultivars. BMC PLANT BIOLOGY 2022; 22:369. [PMID: 35879667 PMCID: PMC9316383 DOI: 10.1186/s12870-022-03767-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 07/20/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND Cold is one of the main abiotic stresses that severely affect plant growth and development, and crop productivity as well. Transcriptional changes during cold stress have already been intensively studied in various plant species. However, the gene networks involved in the regulation of differential cold tolerance between tobacco varieties with contrasting cold resistance are quite limited. RESULTS Here, we conducted multiple time-point transcriptomic analyses using Tai tobacco (TT, cold susceptibility) and Yan tobacco (YT, cold resistance) with contrasting cold responses. We identified similar DEGs in both cultivars after comparing with the corresponding control (without cold treatment), which were mainly involved in response to abiotic stimuli, metabolic processes, kinase activities. Through comparison of the two cultivars at each time point, in contrast to TT, YT had higher expression levels of the genes responsible for environmental stresses. By applying Weighted Gene Co-Expression Network Analysis (WGCNA), we identified two main modules: the pink module was similar while the brown module was distinct between the two cultivars. Moreover, we obtained 100 hub genes, including 11 important transcription factors (TFs) potentially involved in cold stress, 3 key TFs in the brown module and 8 key TFs in the pink module. More importantly, according to the genetic regulatory networks (GRNs) between TFs and other genes or TFs by using GENIE3, we identified 3 TFs (ABI3/VP1, ARR-B and WRKY) mainly functioning in differential cold responses between two cultivars, and 3 key TFs (GRAS, AP2-EREBP and C2H2) primarily involved in cold responses. CONCLUSION Collectively, our study provides valuable resources for transcriptome- based gene network studies of cold responses in tobacco. It helps to reveal how key cold responsive TFs or other genes are regulated through network. It also helps to identify the potential key cold responsive genes for the genetic manipulation of tobacco cultivars with enhanced cold tolerance in the future.
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Affiliation(s)
- Zhenyu Luo
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Zhicheng Zhou
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Yangyang Li
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Zheng-Rong Hu
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Jia-Shuo Yang
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China.
| | - Risheng Hu
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China.
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China.
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Wang H, Feng X, Zhang Y, Wei D, Zhang Y, Jin Q, Cai Y. PbUGT72AJ2-Mediated Glycosylation Plays an Important Role in Lignin Formation and Stone Cell Development in Pears (Pyrus bretschneideri). Int J Mol Sci 2022; 23:ijms23147893. [PMID: 35887241 PMCID: PMC9318811 DOI: 10.3390/ijms23147893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 12/04/2022] Open
Abstract
Glycosylation is necessary for many processes of plant secondary metabolism. It can maintain plant homeostasis and is of great significance to normal plant growth and development. At present, the significance of glycosylation for lignin biosynthesis has been proven in some plants, but it has not yet been reported in pears. We used in situ hybridization, in vitro expression, substrate catalysis, transgenic Arabidopsisthaliana, and transient transformation of pear fruit in our investigation, which was predicated on the identification of a gene PbUGT72AJ2 that may be involved in lignin monolignol glycosylation according to our previous work. These results revealed that PbUGT72AJ2 transcripts were localized to some pulp cell walls, lignin deposition, and stone cell areas of pear fruit. The recombinant PbUGT72AJ2-pGEX4T-1 protein had activity against coniferyl alcohol and sinapyl alcohol, and its catalytic efficiency against coniferyl alcohol was higher than that against sinapyl alcohol. When PbUGT72AJ2 was transferred into Arabidopsisthaliana mutants, it was found that some characteristics of Arabidopsisthalianaugt72e3 mutants were restored. In Arabidopsisthaliana, overexpression of PbUGT72AJ2 enhanced the contents of coniferin and syringin, whereas lignification did not change significantly. Transient transformation of pear fruit showed that when PbUGT72AJ2 in pear fruit was silenced by RNA interference, the content of lignin and stone cells in pear fruit increased, whereas the gene PbUGT72AJ2 was overexpressed in pear fruit, and there was almost no change in the pear fruit compared with the control. Lignin deposition in pear fruit was closely related to stone cell development. In this study, we proved that PbUGT72AJ2 plays an important role in lignin deposition and stone cell development in pear fruit, which provides a molecular biological basis for improving pear fruit quality at the molecular level.
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Affiliation(s)
- Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Xiaofeng Feng
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yingjie Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Dongyi Wei
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yang Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
- Correspondence:
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Pal G, Bakade R, Deshpande S, Sureshkumar V, Patil SS, Dawane A, Agarwal S, Niranjan V, PrasannaKumar MK, Vemanna RS. Transcriptomic responses under combined bacterial blight and drought stress in rice reveal potential genes to improve multi-stress tolerance. BMC PLANT BIOLOGY 2022; 22:349. [PMID: 35850621 PMCID: PMC9290298 DOI: 10.1186/s12870-022-03725-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/29/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND The unprecedented drought and frequent occurrence of pathogen infection in rice is becoming more due to climate change. Simultaneous occurrence of stresses lead to more crop loss. To cope up multiple stresses, the durable resistant cultivars needs to be developed, by identifying relevant genes from combined biotic and abiotic stress exposed plants. RESULTS We studied the effect of drought stress, bacterial leaf blight disease causing Xanthomonas oryzae pv. oryzae (Xoo) pathogen infection and combined stress in contrasting BPT5204 and TN1 rice genotypes. Mild drought stress increased Xoo infection irrespective of the genotype. To identify relevant genes that could be used to develop multi-stress tolerant rice, RNA sequencing from individual drought, pathogen and combined stresses in contrasting genotypes has been developed. Many important genes are identified from resistant genotype and diverse group of genes are differentially expressed in contrasting genotypes under combined stress. Further, a meta-analysis from individual drought and Xoo pathogen stress from public domain data sets narrowed- down candidate differentially expressed genes. Many translation associated genes are differentially expressed suggesting their extra-ribosomal function in multi-stress adaptation. Overexpression of many of these genes showed their relevance in improving stress tolerance in rice by different scientific groups. In combined stress, many downregulated genes also showed their relevance in stress adaptation when they were over-expressed. CONCLUSIONS Our study identifies many important genes, which can be used as molecular markers and targets for genetic manipulation to develop durable resistant rice cultivars. Strategies should be developed to activate downregulated genes, to improve multi-stress tolerance in plants.
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Affiliation(s)
- Garima Pal
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | - Rahul Bakade
- Department of Plant Pathology, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India
| | - Sanjay Deshpande
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | - V Sureshkumar
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | - Swathi S Patil
- Department of Plant Pathology, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India
| | - Akashata Dawane
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | - Subham Agarwal
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | - Vidya Niranjan
- Department of Biotechnology, R.V. Engineering College, Bengaluru, 560059, India
| | - M K PrasannaKumar
- Department of Plant Pathology, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India
| | - Ramu S Vemanna
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India.
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Li C, Guan H, Jing X, Li Y, Wang B, Li Y, Liu X, Zhang D, Liu C, Xie X, Zhao H, Wang Y, Liu J, Zhang P, Hu G, Li G, Li S, Sun D, Wang X, Shi Y, Song Y, Jiao C, Ross-Ibarra J, Li Y, Wang T, Wang H. Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding. NATURE PLANTS 2022; 8:750-763. [PMID: 35851624 DOI: 10.1038/s41477-022-01190-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. Here we assembled 1,604 historically utilized maize inbred lines belonging to various female heterotic groups (FHGs) and male heterotic groups (MHGs), and conducted phenotyping and genomic sequencing analyses. We found that the FHGs and MHGs have undergone both convergent and divergent changes for different sets of agronomic traits. Using genome-wide selection scans and association analyses, we identified a large number of candidate genes that contributed to the improvement of agronomic traits of the FHGs and MHGs. Moreover, we observed increased genetic differentiation between the FHGs and MHGs across the breeding eras, and we found a positive correlation between increasing heterozygosity levels in the differentiated genes and heterosis in hybrids. Furthermore, we validated the function of two selected genes and a differentiated gene. This study provides insights into the genomic basis of modern hybrid maize breeding.
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Affiliation(s)
- Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honghui Guan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Jing
- Novogene Bioinformatics Institute, Beijing, China
| | - Yaoyao Li
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Liu
- Institute of Food Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xiaoqing Xie
- Institute of Food Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haiyan Zhao
- Institute of Maize Research, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yanbo Wang
- Institute of Maize Research, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jingbao Liu
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Panpan Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Guanghui Hu
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guoliang Li
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Suiyan Li
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Dequan Sun
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xiaoming Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA, USA.
- Center for Population Biology and Genome Center, University of California, Davis, CA, USA.
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Haiyang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
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Ao B, Han Y, Wang S, Wu F, Zhang J. Genome-Wide Analysis and Profile of UDP-Glycosyltransferases Family in Alfalfa (Medicago sativa L.) under Drought Stress. Int J Mol Sci 2022; 23:ijms23137243. [PMID: 35806246 PMCID: PMC9266349 DOI: 10.3390/ijms23137243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/23/2022] [Indexed: 12/04/2022] Open
Abstract
Drought stress is one of the major constraints that decreases global crop productivity. Alfalfa, planted mainly in arid and semi-arid areas, is of crucial importance in sustaining the agricultural system. The family 1 UDP-glycosyltransferases (UGT) is indispensable because it takes part in the regulation of plant growth and stress resistance. However, a comprehensive insight into the participation of the UGT family in adaptation of alfalfa to drought environments is lacking. In the present study, a genome-wide analysis and profiling of the UGT in alfalfa were carried out. A total of 409 UGT genes in alfalfa (MsUGT) were identified and they are clustered into 13 groups. The expression pattern of MsUGT genes were analyzed by RNA-seq data in six tissues and under different stresses. The quantitative real-time PCR verification genes suggested the distinct role of the MsUGT genes under different drought stresses and abscisic acid (ABA) treatment. Furthermore, the function of MsUGT003 and MsUGT024, which were upregulated under drought stress and ABA treatment, were characterized by heterologous expression in yeast. Taken together, this study comprehensively analyzed the UGT gene family in alfalfa for the first time and provided useful information for improving drought tolerance and in molecular breeding of alfalfa.
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85
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Ghosh S, Zhang S, Azam M, Agyenim-Boateng KG, Qi J, Feng Y, Li Y, Li J, Li B, Sun J. Identification of Genomic Loci and Candidate Genes Related to Seed Tocopherol Content in Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:1703. [PMID: 35807655 PMCID: PMC9269242 DOI: 10.3390/plants11131703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Soybean seeds are primary sources of natural tocopherols used by the food and pharmaceutical industries, owing to their beneficial impacts on human health. Selection for higher tocopherol contents in seeds along with other desirable traits is an important goal in soybean breeding. In order to identify the genomic loci and candidate genes controlling tocopherol content in soybean seeds, the bulked-segregant analysis technique was performed using a natural population of soybean consisting of 1525 accessions. We constructed the bulked-segregant analysis based on 98 soybean accessions that showed extreme phenotypic variation for the target trait, consisting of 49 accessions with extremely-high and 49 accessions with extremely-low tocopherol content. A total of 144 variant sites and 109 predicted genes related to tocopherol content were identified, in which a total of 83 genes were annotated by the gene ontology functions. Furthermore, 13 enriched terms (p < 0.05) were detected, with four of them found to be highly enriched: response to lipid, response to abscisic acid, transition metal ion transmembrane transporter activity, and double-stranded DNA binding. Especially, six candidate genes were detected at 41.8−41.9 Mb genomic hotspots on chromosome 5 based on ANNOtate VARiation analysis. Among the genes, only Glyma.05G243400 carried a non-synonymous mutation that encodes a “translation elongation factor EF1A or initiation factor IF2gamma family protein” was identified. The haplotype analysis confirmed that Glyma.05G243400 exhibited highly significant variations in terms of tocopherol content across multiple experimental locations, suggesting that it can be the key candidate gene regulating soybean seed tocopherols. The present findings provide novel gene resources related to seed tocopherols for further validation by genome editing, functional characterization, and genetic improvement targeting enhanced tocopherol composition in soybean molecular breeding.
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Affiliation(s)
- Suprio Ghosh
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
- Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh
| | - Shengrui Zhang
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Muhammad Azam
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Kwadwo Gyapong Agyenim-Boateng
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Jie Qi
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Yue Feng
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Yecheng Li
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Jing Li
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Bin Li
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Junming Sun
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
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Analysis of Related Metabolites Affecting Taste Values in Rice under Different Nitrogen Fertilizer Amounts and Planting Densities. Foods 2022; 11:foods11101508. [PMID: 35627078 PMCID: PMC9141971 DOI: 10.3390/foods11101508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 02/07/2023] Open
Abstract
The aim of this study was to explore the differences in metabolites related to rice quality formation under different nitrogen (N) fertilizers and planting densities. In this study, Yangnongxiang 28 was used as the experimental material with the following conditions: high nitrogen and low density (HNLD; high nitrogen: 360 kg·hm−2, low density: the row spacing of rice plants was 16 cm × 30 cm), medium nitrogen and medium density (MNMD; medium nitrogen: 270 kg·hm−2, medium density: the row spacing of rice plants was 13 cm × 30 cm), and low nitrogen and high density (LNHD; low nitrogen: 270 kg·hm−2, high density: the row spacing of rice plants was 10 cm × 30 cm). The rice quality indexes, including the processing quality, amylose content, and taste value, were compared under different treatments, and we analyzed their relationship with the metabolites. The results show that the milled rice rate of HNLD was 13.85% and was 1.89% higher than that of LNHD and MNMD, respectively. The head milled rice rate of HNLD was 32.45% and 6.39% higher than that of LNHD and MNMD, respectively. The milled rice rate and head milled rice rate of HNLD and MNMD were significantly higher than those of LNHD. This study identified 22 differential metabolites (DMs) in HNLD and LNHD, 38 DMs in HNLD and MNMD, and 23 DMs in LNHD and MNMD. Most of the identified differential metabolites were lipid metabolites, which were mainly enriched in the lipid metabolic pathways and amino acid metabolic pathways. The correlation analysis showed that the lipid metabolite physapubescin was significantly negatively correlated with the taste value. The lipid metabolites 2-undecen-1-ol, lucidenic acid F, and 8-deoxy-11,13-dihydroxygrosheimin were significantly positively correlated with the taste value. Lipids may be important substances that lead to differences in taste under different nitrogen fertilizer and density treatments.
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Behr M, Speeckaert N, Kurze E, Morel O, Prévost M, Mol A, Mahamadou Adamou N, Baragé M, Renaut J, Schwab W, El Jaziri M, Baucher M. Leaf necrosis resulting from downregulation of poplar glycosyltransferase UGT72A2. TREE PHYSIOLOGY 2022; 42:1084-1099. [PMID: 34865151 DOI: 10.1093/treephys/tpab161] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Reactive species (RS) causing oxidative stress are unavoidable by-products of various plant metabolic processes, such as photosynthesis, respiration or photorespiration. In leaves, flavonoids scavenge RS produced during photosynthesis and protect plant cells against deleterious oxidative damages. Their biosynthesis and accumulation are therefore under tight regulation at the cellular level. Glycosylation has emerged as an essential biochemical reaction in the homeostasis of various specialized metabolites such as flavonoids. This article provides a functional characterization of the Populus tremula x P. alba (poplar) UGT72A2 coding for a UDP-glycosyltransferase that is localized in the chloroplasts. Compared with the wild type, transgenic poplar lines with decreased expression of UGT72A2 are characterized by reduced growth and oxidative damages in leaves, as evidenced by necrosis, higher content of glutathione and lipid peroxidation products as well as diminished soluble peroxidase activity and NADPH to NADP+ ratio under standard growing conditions. They furthermore display lower pools of phenolics, anthocyanins and total flavonoids but higher proanthocyanidins content. Promoter analysis revealed the presence of cis-elements involved in photomorphogenesis, chloroplast biogenesis and flavonoid biosynthesis. The UGT72A2 is regulated by the poplar MYB119, a transcription factor known to regulate the flavonoid biosynthesis pathway. Phylogenetic analysis and molecular docking suggest that UGT72A2 could glycosylate flavonoids; however, the actual substrate(s) was not consistently evidenced with either in vitro assays nor analyses of glycosylated products in leaves of transgenic poplar overexpressing or downregulated for UGT72A2. This article provides elements highlighting the importance of flavonoid glycosylation regarding protection against oxidative stress in poplar leaves and raises new questions about the link between this biochemical reaction and regulation of the redox homeostasis system.
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Affiliation(s)
- Marc Behr
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Nathanael Speeckaert
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Elisabeth Kurze
- Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany
| | - Oriane Morel
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Martine Prévost
- Unité de recherche Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, Bruxelles, Belgium
| | - Adeline Mol
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Nassirou Mahamadou Adamou
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
- Laboratoire de Biotechnologie Végétale et Amélioration des Plantes (LABAP), Université Abdou Moumouni de Niamey, Niamey, Niger
| | - Moussa Baragé
- Laboratoire de Biotechnologie Végétale et Amélioration des Plantes (LABAP), Université Abdou Moumouni de Niamey, Niamey, Niger
| | - Jenny Renaut
- Luxembourg Institute of Science and Technology, 4422 Belvaux, Luxembourg
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany
| | - Mondher El Jaziri
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Marie Baucher
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
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Ding Y, Qiu X, Luo H, Huang L, Guo J, Yu B, Sudini H, Pandey M, Kang Y, Liu N, Zhou X, Chen W, Chen Y, Wang X, Huai D, Yan L, Lei Y, Jiang H, Varshney R, Liu K, Liao B. Comprehensive evaluation of Chinese peanut mini-mini core collection and QTL mapping for aflatoxin resistance. BMC PLANT BIOLOGY 2022; 22:207. [PMID: 35448951 PMCID: PMC9027753 DOI: 10.1186/s12870-022-03582-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Aflatoxin contamination caused by Aspergillus fungi has been a serious factor affecting food safety of peanut (Arachis hypogaea L.) because aflatoxins are highly harmful for human and animal health. As three mechanisms of resistance to aflatoxin in peanut including shell infection resistance, seed infection resistance and aflatoxin production resistance exist among naturally evolved germplasm stocks, it is highly crucial to pyramid these three resistances for promoting peanut industry development and protecting consumers' health. However, less research effort has been made yet to investigate the differentiation and genetic relationship among the three resistances in diversified peanut germplasm collections. RESULTS In this study, the Chinese peanut mini-mini core collection selected from a large basic collection was systematically evaluated for the three resistances against A. flavus for the first time. The research revealed a wide variation among the diversified peanut accessions for all the three resistances. Totally, 14 resistant accessions were identified, including three with shell infection resistance, seven with seed infection resistance and five with aflatoxin production resistance. A special accession, Zh.h1312, was identified with both seed infection and aflatoxin production resistance. Among the five botanic types of A. hypogaea, the var. vulgaris (Spanish type) belonging to subspecies fastigiata is the only one which possessed all the three resistances. There was no close correlation between shell infection resistance and other two resistances, while there was a significant positive correlation between seed infection and toxin production resistance. All the three resistances had a significant negative correlation with pod or seed size. A total of 16 SNPs/InDels associated with the three resistances were identified through genome-wide association study (GWAS). Through comparative analysis, Zh.h1312 with seed infection resistance and aflatoxin production resistance was also revealed to possess all the resistance alleles of associated loci for seed infection index and aflatoxin content. CONCLUSIONS This study provided the first comprehensive understanding of differentiation of aflatoxin resistance in diversified peanut germplasm collection, and would further contribute to the genetic enhancement for resistance to aflatoxin contamination.
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Affiliation(s)
- Yingbin Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
- National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xike Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Hari Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Manish Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Rajeev Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Kede Liu
- National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
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Huang F, Jiang Y, Chen T, Li H, Fu M, Wang Y, Xu Y, Li Y, Zhou Z, Jia L, Ouyang Y, Yao W. New Data and New Features of the FunRiceGenes (Functionally Characterized Rice Genes) Database: 2021 Update. RICE (NEW YORK, N.Y.) 2022; 15:23. [PMID: 35438356 PMCID: PMC9018921 DOI: 10.1186/s12284-022-00569-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/06/2022] [Indexed: 05/06/2023]
Abstract
As a major food crop and model organism, rice has been mostly studied with the largest number of functionally characterized genes among all crops. We previously built the funRiceGenes database including ~ 2800 functionally characterized rice genes and ~ 5000 members of different gene families. Since being published, the funRiceGenes database has been accessed by more than 54,400 users with over 540,000 pageviews. The funRiceGenes database has been continuously updated with newly cloned rice genes and newly published literature, based on the progress of rice functional genomics studies. Up to Nov 2021, ~ 4100 functionally characterized rice genes and ~ 6000 members of different gene families were collected in funRiceGenes, accounting for 22.3% of the 39,045 annotated protein-coding genes in the rice genome. Here, we summarized the update of the funRiceGenes database with new data and new features in the last 5 years.
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Affiliation(s)
- Fangfang Huang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingru Jiang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Tiantian Chen
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haoran Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mengjia Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yazhou Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yufang Xu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yang Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhengfu Zhou
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Lihua Jia
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
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90
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Li D, Lu X, Zhu Y, Pan J, Zhou S, Zhang X, Zhu G, Shang Y, Huang S, Zhang C. The multi-omics basis of potato heterosis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:671-687. [PMID: 34963038 DOI: 10.1111/jipb.13211] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Heterosis is a fundamental biological phenomenon characterized by the superior performance of hybrids over their parents. Although tremendous progress has been reported in seed crops, the molecular mechanisms underlying heterosis in clonally propagated crops are largely unknown. Potato (Solanum tuberosum L.) is the most important tuber crop and an ongoing revolution is transforming potato from a clonally propagated tetraploid crop into a seed-propagated diploid hybrid potato. In our previous study, we developed the first generation of highly homozygous inbred lines of potato and hybrids with strong heterosis. Here, we integrated transcriptome, metabolome, and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages. We found that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation. Flower color, male fertility, and starch and sucrose metabolism showed obvious gene dominant complementation in hybrids, and hybrids devoted more energy to primary metabolism for rapid growth. In addition, we identified ~2 700 allele-specific expression genes at each stage, which likely function in potato heterosis and might be regulated by CHH allele-specific methylation level. Our multi-omics analysis provides insight into heterosis in potato and facilitates the exploitation of heterosis in potato breeding.
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Affiliation(s)
- Dawei Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Xiaoyue Lu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Yanhui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Jun Pan
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Shaoqun Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Xinyan Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Guangtao Zhu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Sanwen Huang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Chunzhi Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
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91
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Wang J, Li J, Li Z, Liu B, Zhang L, Guo D, Huang S, Qian W, Guo L. Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions. HORTICULTURE RESEARCH 2022; 9:uhac021. [PMID: 35184175 PMCID: PMC9071379 DOI: 10.1093/hr/uhac021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/05/2022] [Accepted: 01/24/2022] [Indexed: 05/25/2023]
Abstract
Longan (Dimocarpus longan) is a subtropical fruit best known for its nutritious fruit and regarded as a precious tonic and traditional medicine since ancient times. High-quality chromosome-scale genome assembly is valuable for functional genomic study and genetic improvement of longan. Here, we report a chromosome-level reference genome sequence for longan cultivar JDB with an assembled genome of 455.5 Mb in size anchored to fifteen chromosomes, representing a significant improvement of contiguity (contig N50 = 12.1 Mb, scaffold N50 = 29.5 Mb) over a previous draft assembly. A total of 40 420 protein-coding genes were predicted in D. longan genome. Synteny analysis suggests longan shares the widespread gamma event with core eudicots, but has no other whole genome duplications. Comparative genomics showed that D. longan genome experienced significant expansions of gene families related to phenylpropanoid biosynthesis and UDP-glucosyltransferase. Deep genome sequencing analysis of longan cultivars identified longan biogeography as a major contributing factor for genetic diversity, and revealed a clear population admixture and introgression among cultivars of different geographic origins, postulating a likely migration trajectory of longan overall confirmed by existing historical records. Finally, genome-wide association studies (GWAS) of longan cultivars identified quantitative trait loci (QTL) for six different fruit quality traits and revealed a shared QTL containing three genes for total soluble solid and seed weight. The chromosome-level reference genome assembly, annotation and population genetic resource for D. longan will facilitate the molecular studies and breeding of desirable longan cultivars in the future.
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Affiliation(s)
- Jing Wang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jianguang Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zaiyuan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bo Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lili Zhang
- Weifang Institute of Technology, Weifang, China
| | - Dongliang Guo
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shilian Huang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wanqiang Qian
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Li Guo
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
- Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
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92
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Quality analysis of Euryales Semen from different origins and varieties based on untargeted metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1191:123114. [DOI: 10.1016/j.jchromb.2022.123114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/12/2021] [Accepted: 01/06/2022] [Indexed: 11/17/2022]
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93
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Xue P, Chen YY, Wen XX, Wang BF, Yang QQ, Gong K, Kang YW, Sun LP, Yu P, Cao LY, Zhang YX, Zhan XD, Cheng SH. Dissection of Closely Linked Quantitative Trait Locis Controlling Grain Size in Rice. FRONTIERS IN PLANT SCIENCE 2022; 12:804444. [PMID: 35126429 PMCID: PMC8810522 DOI: 10.3389/fpls.2021.804444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Grain size is a key constituent of grain weight and appearance in rice. However, insufficient attention has been paid to the small-effect quantitative trait loci (QTLs) on the grain size. In the present study, residual heterozygous populations were developed for mapping two genetically linked small-effect QTLs for grain size. After the genotyping and the phenotyping of five successive generations, qGS7.1 was dissected into three QTLs and two were selected for further analysis. The qTGW7.2a was finally mapped into a 21.10 kb interval containing four annotated candidate genes. Transcript levels assay showed that the expression of the candidates LOC_Os07g39490 and the LOC_Os07g39500 were significantly reduced in the NIL-qTGW7.2aBG1 . The cytological observation indicated that qTGW7.2a regulated the grain width through controlling the cell expansion. Using the same strategy, qTGW7.2b was fine-mapped into a 52.71 kb interval containing eight annotated candidate genes, showing a significant effect on the grain length and width with opposite allelic directions, but little on the grain weight. Our study provides new genetic resources for yield improvement and for fine-tuning of grain size in rice.
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Affiliation(s)
- Pao Xue
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yu-yu Chen
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Department of Resource and Environment, Moutai Institute, Renhuai, China
| | - Xiao-xia Wen
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Bei-fang Wang
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qin-qin Yang
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ke Gong
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yi-wei Kang
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lian-ping Sun
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ping Yu
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li-yong Cao
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ying-xin Zhang
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiao-deng Zhan
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shi-hua Cheng
- Zhejiang Key Laboratory of Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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94
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Wu Z, Zhang X, Chang G, Yang J, Wan J, Wang F, Tao D, Zhou J, Shang L, Xu P, Yu D. Natural alleles of a uridine 5'-diphospho-glucosyltransferase gene responsible for differential endosperm development between upland rice and paddy rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:135-148. [PMID: 34742166 DOI: 10.1111/jipb.13184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Traditional upland rice generally exhibits insufficient grains resulting from abnormal endosperm development compared to paddy rice. However, the underlying molecular mechanism of this trait is poorly understood. Here, we cloned the uridine 5'-diphospho (UDP)-glucosyltransferase gene EDR1 (Endosperm Development in Rice) responsible for differential endosperm development between upland rice and paddy rice by performing quantitative trait loci analysis and map-based cloning. EDR1 was highly expressed in developing seeds during grain filling. Natural variations in EDR1 significantly reduced the UDP-glucosyltransferase activity of EDR1YZN compared to EDR1YD1 , resulting in abnormal endosperm development in the near-isogenic line, accompanied by insufficient grains and changes in grain quality. By analyzing the distribution of the two alleles EDR1YD1 and EDR1YZN among diverse paddy rice and upland rice varieties, we discovered that EDR1 was conserved in upland rice, but segregated in paddy rice. Further analyses of grain chalkiness in the alleles of EDR1YD1 and EDR1YZN varieties indicated that rice varieties harboring EDR1YZN and EDR1YD1 preferentially showed high chalkiness, and low chalkiness, respectively. Taken together, these results suggest that the UDP-glucosyltransferase gene EDR1 is an important determinant controlling differential endosperm development between upland rice and paddy rice.
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Affiliation(s)
- Zihao Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, the Chinese Academy of Sciences, Kunming, 650223, China
| | - Xiao Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, the Chinese Academy of Sciences, Kunming, 650223, China
| | - Guimei Chang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, the Chinese Academy of Sciences, Kunming, 650223, China
| | - Jun Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, the Chinese Academy of Sciences, Kunming, 650223, China
| | - Jinpeng Wan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, the Chinese Academy of Sciences, Kunming, 650223, China
| | - Feijun Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, the Chinese Academy of Sciences, Kunming, 650223, China
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Lianguang Shang
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Mengla, 666303, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, the Chinese Academy of Sciences, Kunming, 650223, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agricultural and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China
| | - Diqiu Yu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, the Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
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95
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Bano N, Fakhrah S, Nayak SP, Bag SK, Mohanty CS. Identification of miRNA and their target genes in Cestrum nocturnum L. and Cestrum diurnum L. in stress responses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:31-49. [PMID: 35221570 PMCID: PMC8847519 DOI: 10.1007/s12298-022-01127-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/14/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules and products of primary miRNAs that regulate the target gene expression. Homology-based approaches were employed to identify miRNAs and their targets in Cestrum nocturnum L. and Cestrum diurnum L. A total of 32 and 12 miRNA candidates were identified in C. nocturnum and C. diurnum. These miRNAs belong to 26 and 10 miRNA families and regulate 1024 and 1007 target genes in C. nocturnum, and C. diurnum, respectively. The functional roles of these miRNAs have not been earlier elucidated in Cestrum. MiR815a, miR849, miR1089 and miR172 have a strong propensity to target genes controlling phytochrome-interacting factor 1 (PIF1), ubiquitin-specific protease 12 (UBP12), leucine-rich repeat (LRR) protein kinase and GAI, RGA, SCR (GRAS) family transcription factor in C. nocturnum. While miR5205a, miR1436 and miR530 regulate PATATIN-like protein 6 (PLP6), PHD finger transcription factor and myb domain protein 48 (MYB48) in C. diurnum. Overall, these miRNAs have regulatory responses in biotic and abiotic stresses in both plant species. Eight putative miRNAs and their target genes were selected for qRT-PCR validation. The validated results suggested the importance of miR815a, miR849, miR5205a, miR1089, miR172, miR1436, and miR530 in exerting control over stress responses in C. nocturnum and C. diurnum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01127-1.
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Affiliation(s)
- Nasreen Bano
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shafquat Fakhrah
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh 226007 India
| | - Sagar Prasad Nayak
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Sumit Kumar Bag
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Chandra Sekhar Mohanty
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Lucknow, India
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96
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Zuo ZW, Zhang ZH, Huang DR, Fan YY, Yu SB, Zhuang JY, Zhu YJ. Control of Thousand-Grain Weight by OsMADS56 in Rice. Int J Mol Sci 2021; 23:ijms23010125. [PMID: 35008551 PMCID: PMC8745348 DOI: 10.3390/ijms23010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Grain weight and size are important traits determining grain yield and influencing grain quality in rice. In a previous study, a quantitative trait locus controlling thousand-grain weight (TGW) in rice, qTGW10-20.8, was mapped in a 70.7 kb region on chromosome 10. Validation of the candidate gene for qTGW10-20.8, OsMADS56 encoding a MADS-box transcription factor, was performed in this study. In a near-isogenic line (NIL) population segregated only at the OsMADS56 locus, NILs carrying the OsMADS56 allele of IRBB52 were 1.9% and 2.9% lower in TGW than NILs carrying the OsMADS56 allele of Teqing in 2018 and 2020, respectively. Using OsMADS56 knock-out mutants and overexpression transgenic plants, OsMADS56 was validated as the causal gene for qTGW10-20.8. Compared with the recipients, the TGW of the knock-out mutants was reduced by 6.0-15.0%. In these populations, decreased grain weight and size were associated with a reduction in the expression of OsMADS56. In transgenic populations of OsMADS56 driven by a strong constitutive promoter, grain weight and size of the positive plants were significantly higher than those of the negative plants. Haplotype analysis showed that the Teqing-type allele of OsMADS56 is the major type presented in cultivated rice and used in variety improvement. Cloning of OsMADS56 provides a new gene resource to improve grain weight and size through molecular design breeding.
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Affiliation(s)
- Zi-Wei Zuo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Zhen-Hua Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
| | - De-Run Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
| | - Si-Bin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
- Correspondence: (J.-Y.Z.); (Y.-J.Z.); Tel.: +86-571-6337-0369 (J.-Y.Z.); +86-571-6337-0364 (Y.-J.Z.)
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
- Correspondence: (J.-Y.Z.); (Y.-J.Z.); Tel.: +86-571-6337-0369 (J.-Y.Z.); +86-571-6337-0364 (Y.-J.Z.)
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97
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Zhang X, Zhang M, Zhao T, Deng B. Phosphate availability regulates flavonoid accumulation associated with photosynthetic carbon partitioning in Cyclocarya paliurus. PHYSIOLOGIA PLANTARUM 2021; 173:1956-1966. [PMID: 34435673 DOI: 10.1111/ppl.13539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/15/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Cyclocarya paliurus has traditionally been used as medicine and functional food. This study aims at investigating the flavonoid accumulation in C. paliurus dependent on phosphate (Pi) availability and its potential association with internal carbon partitioning. One-year-old seedlings of C. paliurus were planted in four different Pi levels. Low Pi resulted in low phosphorus content within plants, while the nitrogen content increased. Further analysis revealed that the surplus carbon pool was greater and was allocated to N-metabolism and carbohydrate synthesis under low Pi conditions, as shown by the higher levels of free amino acids, starch, and soluble sugars. Low Pi availability also induced higher enzymatic activities of shikimate dehydrogenase (SDH) and flavonoid 3-hydoxylase (FHT), and higher flavonoid accumulation in leaves. Our results indicated that the surplus carbon induced by low-Pi levels can increase flavonoid synthesis in seedlings of C. paliurus. In addition, growth and biomass accumulation were increased by the elevated Pi levels. As a result, the highest flavonoid yield per plant was obtained under relative low Pi conditions. This study can provide the basis for developing new agricultural practices to maintain high yield while still keeping the quality of medicinal plants and crops.
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Affiliation(s)
- Xiaoyan Zhang
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Mengjia Zhang
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Tingting Zhao
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Bo Deng
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
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98
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Plant metabolism paves the way for breeding crops with high nutritional value and stable yield. SCIENCE CHINA. LIFE SCIENCES 2021; 64:2202-2205. [PMID: 34536206 DOI: 10.1007/s11427-021-2004-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
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The Role of Membrane Transporters in Plant Growth and Development, and Abiotic Stress Tolerance. Int J Mol Sci 2021; 22:ijms222312792. [PMID: 34884597 PMCID: PMC8657488 DOI: 10.3390/ijms222312792] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
The proteins of membrane transporters (MTs) are embedded within membrane-bounded organelles and are the prime targets for improvements in the efficiency of water and nutrient transportation. Their function is to maintain cellular homeostasis by controlling ionic movements across cellular channels from roots to upper plant parts, xylem loading and remobilization of sugar molecules from photosynthesis tissues in the leaf (source) to roots, stem and seeds (sink) via phloem loading. The plant's entire source-to-sink relationship is regulated by multiple transporting proteins in a highly sophisticated manner and driven based on different stages of plant growth and development (PG&D) and environmental changes. The MTs play a pivotal role in PG&D in terms of increased plant height, branches/tiller numbers, enhanced numbers, length and filled panicles per plant, seed yield and grain quality. Dynamic climatic changes disturbed ionic balance (salt, drought and heavy metals) and sugar supply (cold and heat stress) in plants. Due to poor selectivity, some of the MTs also uptake toxic elements in roots negatively impact PG&D and are later on also exported to upper parts where they deteriorate grain quality. As an adaptive strategy, in response to salt and heavy metals, plants activate plasma membranes and vacuolar membrane-localized MTs that export toxic elements into vacuole and also translocate in the root's tips and shoot. However, in case of drought, cold and heat stresses, MTs increased water and sugar supplies to all organs. In this review, we mainly review recent literature from Arabidopsis, halophytes and major field crops such as rice, wheat, maize and oilseed rape in order to argue the global role of MTs in PG&D, and abiotic stress tolerance. We also discussed gene expression level changes and genomic variations within a species as well as within a family in response to developmental and environmental cues.
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100
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Kumar S, Singh VP, Saini DK, Sharma H, Saripalli G, Kumar S, Balyan HS, Gupta PK. Meta-QTLs, ortho-MQTLs, and candidate genes for thermotolerance in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:69. [PMID: 37309361 PMCID: PMC10236124 DOI: 10.1007/s11032-021-01264-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Meta-QTL analysis for thermotolerance in wheat was conducted to identify robust meta-QTLs (MQTLs). In this study, 441 QTLs related to 31 heat-responsive traits were projected on the consensus map with 50,310 markers. This exercise resulted in the identification of 85 MQTLs with confidence interval (CI) ranging from 0.11 to 34.9 cM with an average of 5.6 cM. This amounted to a 2.96-fold reduction relative to the mean CI (16.5 cM) of the QTLs used. Seventy-seven (77) of these MQTLs were also compared and verified with the results of recent genome-wide association studies (GWAS). The 85 MQTLs included seven MQTLs that are particularly useful for breeding purposes (we called them breeders' MQTLs). Seven ortho-MQTLs between wheat and rice genomes were also identified using synteny and collinearity. The MQTLs were used for the identification of 1,704 candidate genes (CGs). In silico expression analysis of these CGs permitted identification of 182 differentially expressed genes (DEGs), which included 36 high confidence CGs with known functions previously reported to be important for thermotolerance. These high confidence CGs encoded proteins belonging to the following families: protein kinase, WD40 repeat, glycosyltransferase, ribosomal protein, SNARE associated Golgi protein, GDSL lipase/esterase, SANT/Myb domain, K homology domain, etc. Thus, the present study resulted in the identification of MQTLs (including breeders' MQTLs), ortho-MQTLs, and underlying CGs, which could prove useful not only for molecular breeding for the development of thermotolerant wheat cultivars but also for future studies focused on understanding the molecular basis of thermotolerance. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01264-7.
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Affiliation(s)
- Sourabh Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Vivudh Pratap Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab India
| | - Hemant Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
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