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Ma Z, Ma L, Zhou J. Applications of CRISPR/Cas genome editing in economically important fruit crops: recent advances and future directions. MOLECULAR HORTICULTURE 2023; 3:1. [PMID: 37789479 PMCID: PMC10515014 DOI: 10.1186/s43897-023-00049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 10/05/2023]
Abstract
Fruit crops, consist of climacteric and non-climacteric fruits, are the major sources of nutrients and fiber for human diet. Since 2013, CRISPR/Cas (Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-Associated Protein) genome editing system has been widely employed in different plants, leading to unprecedented progress in the genetic improvement of many agronomically important fruit crops. Here, we summarize latest advancements in CRISPR/Cas genome editing of fruit crops, including efforts to decipher the mechanisms behind plant development and plant immunity, We also highlight the potential challenges and improvements in the application of genome editing tools to fruit crops, including optimizing the expression of CRISPR/Cas cassette, improving the delivery efficiency of CRISPR/Cas reagents, increasing the specificity of genome editing, and optimizing the transformation and regeneration system. In addition, we propose the perspectives on the application of genome editing in crop breeding especially in fruit crops and highlight the potential challenges. It is worth noting that efforts to manipulate fruit crops with genome editing systems are urgently needed for fruit crops breeding and demonstration.
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Affiliation(s)
- Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lijing Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
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Hu XL, You C, Zhu K, Li X, Gong J, Ma H, Sun X. Nanopore long-read RNAseq reveals transcriptional variations in citrus species. FRONTIERS IN PLANT SCIENCE 2023; 13:1077797. [PMID: 36684788 PMCID: PMC9845879 DOI: 10.3389/fpls.2022.1077797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The number of studies on plant transcriptomes using ONT RNAseq technology is rapidly increasing in recent. It is a powerful method to decipher transcriptomic complexity, particularly alternative splicing (AS) event detection. Citrus plants are the most important widely grown fruit crops. Exploring different AS events in citrus contributes to transcriptome improvement and functional genome study. Here, we performed ONT RNAseq in 9 species (Atalantia buxifolia, Citrus clementina, C. grandis, C. ichangensis, C. reticulata, C. sinensis, Clausena lansium, Fortunella hindsii, and Poncirus trifoliata), accompanied with Illumina sequencing. Non-redundant full-length isoforms were identified between 41,957 and 76,974 per species. Systematic analysis including different types of isoforms, number of isoforms per gene locus, isoform distribution, ORFs and lncRNA prediction and functional annotation were performed mainly focused on novel isoforms, unraveling the capability of novel isoforms detection and characterization. For AS events prediction, A3, RI, and AF were overwhelming types across 9 species. We analyzed isoform similarity and evolutionary relationships in all species. We identified that multiple isoforms derived from orthologous single copy genes among different species were annotated as enzymes, nuclear-related proteins or receptors. Isoforms with extending sequences on 5', 3', or both compared with reference genome were filtered out to provide information for transcriptome improvement. Our results provide novel insight into comprehending complex transcriptomes in citrus and valuable information for further investigation on the function of genes with diverse isoforms.
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Affiliation(s)
- Xiao-Li Hu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Congjun You
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Kaikai Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xiaolong Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Jinli Gong
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
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3
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Song S, Liu H, Miao L, He L, Xie W, Lan H, Yu C, Yan W, Wu Y, Wen XP, Xu Q, Deng X, Chen C. Molecular cytogenetic map visualizes the heterozygotic genome and identifies translocation chromosomes in Citrus sinensis. J Genet Genomics 2023:S1673-8527(22)00283-1. [PMID: 36608932 DOI: 10.1016/j.jgg.2022.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023]
Abstract
Citrus sinensis is the most cultivated and economically valuable Citrus species in the world, whose genome has been assembled by three generation sequencings. However, chromosome recognition remains a problem due to the small size of chromosomes, and difficulty in differentiating between pseudo and real chromosomes because of a highly heterozygous genome. Here, we employ fluorescence in situ hybridization (FISH) with 9 chromosome painting probes, 30 oligo pools, and 8 repetitive sequences to visualize 18 chromosomes. Then, we develop an approach to identify each chromosome in one cell through single experiment of oligo-FISH and Chromoycin A3 (CMA) staining. By this approach, we construct a high-resolution molecular cytogenetic map containing the physical positions of CMA banding and 38 sequences of FISH including centromere regions, which enable us to visualize significant differences between homologous chromosomes. Based on the map, we locate several highly repetitive sequences on chromosomes and estimate sizes and copy numbers of each site. In particular, we discover the translocation regions of chromosomes 4 and 9 in C. sinensis "Valencia." The high-resolution molecular cytogenetic map will help improve understanding of sweet orange genome assembly and also provide a fundamental reference for investigating chromosome evolution and chromosome engineering for genetic improvement in Citrus.
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Affiliation(s)
- Shipeng Song
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hui Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Luke Miao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Li He
- National-local Joint Engineering Laboratory of Citrus Breeding and Cultivation/Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Wenzhao Xie
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Key Laboratory of Crop Genetics and Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hong Lan
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; Hubei Province Engineering Research Center of Legume Plants, College of Life Science, Jianghan University, Wuhan, Hubei 430056, China
| | - Changxiu Yu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenkai Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiao-Peng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering, College of Life Science, Guizhou University, Guiyang, Guizhou 550025, China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Chunli Chen
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Salonia F, Ciacciulli A, Pappalardo HD, Poles L, Pindo M, Larger S, Caruso P, Caruso M, Licciardello C. A dual sgRNA-directed CRISPR/Cas9 construct for editing the fruit-specific β-cyclase 2 gene in pigmented citrus fruits. FRONTIERS IN PLANT SCIENCE 2022; 13:975917. [PMID: 36582639 PMCID: PMC9792771 DOI: 10.3389/fpls.2022.975917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
CRISPR/Cas9 genome editing is a modern biotechnological approach used to improve plant varieties, modifying only one or a few traits of a specific variety. However, this technology cannot be easily used to improve fruit quality traits in citrus, due to the lack of knowledge of key genes, long juvenile stage, and the difficulty regenerating whole plants of specific varieties. Here, we introduce a genome editing approach with the aim of producing citrus plantlets whose fruits contain both lycopene and anthocyanins. Our method employs a dual single guide RNA (sgRNA)-directed genome editing approach to knockout the fruit-specific β-cyclase 2 gene, responsible for the conversion of lycopene to beta-carotene. The gene is targeted by two sgRNAs simultaneously to create a large deletion, as well as to induce point mutations in both sgRNA targets. The EHA105 strain of Agrobacterium tumefaciens was used to transform five different anthocyanin-pigmented sweet oranges, belonging to the Tarocco and Sanguigno varietal groups, and 'Carrizo' citrange, a citrus rootstock as a model for citrus transformation. Among 58 plantlets sequenced in the target region, 86% of them were successfully edited. The most frequent mutations were deletions (from -1 to -74 nucleotides) and insertions (+1 nucleotide). Moreover, a novel event was identified in six plantlets, consisting of the inversion of the region between the two sgRNAs. For 20 plantlets in which a single mutation occurred, we excluded chimeric events. Plantlets did not show an altered phenotype in vegetative tissues. To the best of our knowledge, this work represents the first example of the use of a genome editing approach to potentially improve qualitative traits of citrus fruit.
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Affiliation(s)
- Fabrizio Salonia
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Angelo Ciacciulli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Helena Domenica Pappalardo
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Lara Poles
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Trento with S. Michele all’ Adige, Trento, Italy
| | - Simone Larger
- Research and Innovation Centre, Trento with S. Michele all’ Adige, Trento, Italy
| | - Paola Caruso
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Marco Caruso
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Concetta Licciardello
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
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Ma H, Meng X, Xu K, Li M, Gmitter FG, Liu N, Gai Y, Huang S, Wang M, Wang M, Wang N, Xu H, Liu J, Sun X, Duan S. Highly efficient hairy root genetic transformation and applications in citrus. FRONTIERS IN PLANT SCIENCE 2022; 13:1039094. [PMID: 36388468 PMCID: PMC9647159 DOI: 10.3389/fpls.2022.1039094] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Highly efficient genetic transformation technology is greatly beneficial for crop gene function analysis and precision breeding. However, the most commonly used genetic transformation technology for woody plants, mediated by Agrobacterium tumefaciens, is time-consuming and inefficient, which limits its utility for gene function analysis. In this study, a simple, universal, and highly efficient genetic transformation technology mediated by A. rhizogenes K599 is described. This technology can be applied to multiple citrus genotypes, and only 2-8 weeks were required for the entire workflow. Genome-editing experiments were simultaneously conducted using 11 plasmids targeting different genomic positions and all corresponding transformants with the target knocked out were obtained, indicating that A. rhizogenes-mediated genome editing was highly efficient. In addition, the technology is advantageous for investigation of specific genes (such as ACD2) for obtaining "hard-to-get" transgenic root tissue. Furthermore, A. rhizogenes can be used for direct viral vector inoculation on citrus bypassing the requirement for virion enrichment in tobacco, which facilitates virus-induced gene silencing and virus-mediated gene expression. In summary, we established a highly efficient genetic transformation technology bypassing tissue culture in citrus that can be used for genome editing, gene overexpression, and virus-mediated gene function analysis. We anticipate that by reducing the cost, required workload, experimental period, and other technical obstacles, this genetic transformation technology will be a valuable tool for routine investigation of endogenous and exogenous genes in citrus.
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Affiliation(s)
- Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Xinyue Meng
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Kai Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Min Li
- China-USA Citrus Huanglongbing Joint Laboratory (A Joint Laboratory of The University of Florida’s Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Fred G. Gmitter
- Citrus Research and Education Center, Horticultural Sciences Department, University of Florida, Lake Alfred, FL, United States
| | - Ningge Liu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Suya Huang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Min Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Min Wang
- China-USA Citrus Huanglongbing Joint Laboratory (A Joint Laboratory of The University of Florida’s Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Nian Wang
- Citrus Research and Education Center, Horticultural Sciences Department, University of Florida, Lake Alfred, FL, United States
| | - Hairen Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Jinhua Liu
- Natural Medicine Institute of Zhejiang YangShengTang Co., LTD, Hangzhou, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Shuo Duan
- China-USA Citrus Huanglongbing Joint Laboratory (A Joint Laboratory of The University of Florida’s Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
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The Employment of Genera Vaccinium, Citrus, Olea, and Cynara Polyphenols for the Reduction of Selected Anti-Cancer Drug Side Effects. Nutrients 2022; 14:nu14081574. [PMID: 35458136 PMCID: PMC9025632 DOI: 10.3390/nu14081574] [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: 03/04/2022] [Revised: 04/02/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Cancer is one of the most widespread diseases globally and one of the leading causes of death. Known cancer treatments are chemotherapy, surgery, radiation therapy, targeted hormonal therapy, or a combination of these methods. Antitumor drugs, with different mechanisms, interfere with cancer growth by destroying cancer cells. However, anticancer drugs are dangerous, as they significantly affect both cancer cells and healthy cells. In addition, there may be the onset of systemic side effects perceived and mutagenicity, teratogenicity, and further carcinogenicity. Many polyphenolic extracts, taken on top of common anti-tumor drugs, can participate in the anti-proliferative effect of drugs and significantly reduce the side effects developed. This review aims to discuss the current scientific knowledge of the protective effects of polyphenols of the genera Vaccinium, Citrus, Olea, and Cynara on the side effects induced by four known chemotherapy, Cisplatin, Doxorubicin, Tamoxifen, and Paclitaxel. In particular, the summarized data will help to understand whether polyphenols can be used as adjuvants in cancer therapy, although further clinical trials will provide crucial information.
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Mahmoud LM, Kaur P, Stanton D, Grosser JW, Dutt M. A cationic lipid mediated CRISPR/Cas9 technique for the production of stable genome edited citrus plants. PLANT METHODS 2022; 18:33. [PMID: 35303912 PMCID: PMC8932238 DOI: 10.1186/s13007-022-00870-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/05/2022] [Indexed: 05/09/2023]
Abstract
BACKGROUND The genetic engineering of crops has enhanced productivity in the face of climate change and a growing global population by conferring desirable genetic traits, including the enhancement of biotic and abiotic stress tolerance, to improve agriculture. The clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system has been found to be a promising technology for genomic editing. Protoplasts are often utilized for the development of genetically modified plants through in vitro integration of a recombinant DNA fragment into the plant genome. We targeted the citrus Nonexpressor of Pathogenesis-Related 3 (CsNPR3) gene, a negative regulator of systemic acquired resistance (SAR) that governs the proteasome-mediated degradation of NPR1 and developed a genome editing technique targeting citrus protoplast DNA to produce stable genome-edited citrus plants. RESULTS Here, we determined the best cationic lipid nanoparticles to deliver donor DNA and described a protocol using Lipofectamine™ LTX Reagent with PLUS Reagent to mediate DNA delivery into citrus protoplasts. A Cas9 construct containing a gRNA targeting the CsNPR3 gene was transfected into citrus protoplasts using the cationic lipid transfection agent Lipofectamine with or without polyethylene glycol (PEG, MW 6000). The optimal transfection efficiency for the encapsulation was 30% in Lipofectamine, 51% in Lipofectamine with PEG, and 2% with PEG only. Additionally, plasmid encapsulation in Lipofectamine resulted in the highest cell viability percentage (45%) compared with PEG. Nine edited plants were obtained and identified based on the T7EI assay and Sanger sequencing. The developed edited lines exhibited downregulation of CsNPR3 expression and upregulation of CsPR1. CONCLUSIONS Our results demonstrate that utilization of the cationic lipid-based transfection agent Lipofectamine is a viable option for the successful delivery of donor DNA and subsequent successful genome editing in citrus.
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Affiliation(s)
- Lamiaa M Mahmoud
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
- Pomology Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Prabhjot Kaur
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Daniel Stanton
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
| | - Jude W Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
| | - Manjul Dutt
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA.
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Wu YM, Ma YJ, Wang M, Zhou H, Gan ZM, Zeng RF, Ye LX, Zhou JJ, Zhang JZ, Hu CG. Mobility of FLOWERING LOCUS T protein as a systemic signal in trifoliate orange and its low accumulation in grafted juvenile scions. HORTICULTURE RESEARCH 2022; 9:uhac056. [PMID: 35702366 PMCID: PMC9186307 DOI: 10.1093/hr/uhac056] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/21/2022] [Indexed: 05/29/2023]
Abstract
The long juvenile period of perennial woody plants is a major constraint in breeding programs. FLOWERING LOCUS T (FT) protein is an important mobile florigen signal that induces plant flowering. However, whether FT can be transported in woody plants to shorten the juvenile period is unknown, and its transport mechanism remains unclear. In this study, trifoliate orange FT (ToFT) and Arabidopsis FT (AtFT, which has been confirmed to be transportable in Arabidopsis) as a control were transformed into tomato and trifoliate orange, and early flowering was induced in the transgenic plants. Long-distance and two-way (upward and downward) transmission of ToFT and AtFT proteins was confirmed in both tomato and trifoliate orange using grafting and western blot analysis. However, rootstocks of transgenic trifoliate orange could not induce flowering in grafted wild-type juvenile scions because of the low accumulation of total FT protein in the grafted scions. It was further confirmed that endogenous ToFT protein was reduced in trifoliate orange, and the accumulation of the transported ToFT and AtFT proteins was lower than that in grafted juvenile tomato scions. Furthermore, the trifoliate orange FT-INTERACTING PROTEIN1 homolog (ToFTIP1) was isolated by yeast two-hybrid analysis. The FTIP1 homolog may regulate FT transport by interacting with FT in tomato and trifoliate orange. Our findings suggest that FT transport may be conserved between the tomato model and woody plants. However, in woody plants, the transported FT protein did not accumulate in significant amounts in the grafted wild-type juvenile scions and induce the scions to flower.
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do Amaral M, Freitas ACO, Santos AS, Dos Santos EC, Ferreira MM, da Silva Gesteira A, Gramacho KP, Marinho-Prado JS, Pirovani CP. TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens. Sci Rep 2022; 12:698. [PMID: 35027639 PMCID: PMC8758671 DOI: 10.1038/s41598-021-04700-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/23/2021] [Indexed: 02/05/2023] Open
Abstract
Protease inhibitors (PIs) are important biotechnological tools of interest in agriculture. Usually they are the first proteins to be activated in plant-induced resistance against pathogens. Therefore, the aim of this study was to characterize a Theobroma cacao trypsin inhibitor called TcTI. The ORF has 740 bp encoding a protein with 219 amino acids, molecular weight of approximately 23 kDa. rTcTI was expressed in the soluble fraction of Escherichia coli strain Rosetta [DE3]. The purified His-Tag rTcTI showed inhibitory activity against commercial porcine trypsin. The kinetic model demonstrated that rTcTI is a competitive inhibitor, with a Ki value of 4.08 × 10-7 mol L-1. The thermostability analysis of rTcTI showed that 100% inhibitory activity was retained up to 60 °C and that at 70-80 °C, inhibitory activity remained above 50%. Circular dichroism analysis indicated that the protein is rich in loop structures and β-conformations. Furthermore, in vivo assays against Helicoverpa armigera larvae were also performed with rTcTI in 0.1 mg mL-1 spray solutions on leaf surfaces, which reduced larval growth by 70% compared to the control treatment. Trials with cocoa plants infected with Mp showed a greater accumulation of TcTI in resistant varieties of T. cacao, so this regulation may be associated with different isoforms of TcTI. This inhibitor has biochemical characteristics suitable for biotechnological applications as well as in resistance studies of T. cacao and other crops.
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Affiliation(s)
- Milena do Amaral
- Universidade Estadual de Santa Cruz, UESC, Rodovia Ilhéus-Itabuna, Km - 16, Ilhéus, BA, CEP 45662-900, Brazil
| | - Ana Camila Oliveira Freitas
- Universidade Estadual de Santa Cruz, UESC, Rodovia Ilhéus-Itabuna, Km - 16, Ilhéus, BA, CEP 45662-900, Brazil
| | - Ariana Silva Santos
- Universidade Estadual de Santa Cruz, UESC, Rodovia Ilhéus-Itabuna, Km - 16, Ilhéus, BA, CEP 45662-900, Brazil.
| | - Everton Cruz Dos Santos
- Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, RJ, 20230-130, Brazil
| | - Monaliza Macêdo Ferreira
- Universidade Estadual de Santa Cruz, UESC, Rodovia Ilhéus-Itabuna, Km - 16, Ilhéus, BA, CEP 45662-900, Brazil
| | | | - Karina Peres Gramacho
- Centro de Pesquisa do Cacau [CEPEC/CEPLAC] Molecular Plant Pathology Laboratory, Km 22 Rod. Ilhéus-Itabuna, Ilhéus, Bahia, 45600-970, Brazil
| | | | - Carlos Priminho Pirovani
- Universidade Estadual de Santa Cruz, UESC, Rodovia Ilhéus-Itabuna, Km - 16, Ilhéus, BA, CEP 45662-900, Brazil
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Hu B, Rao MJ, Deng X, Pandey SS, Hendrich C, Ding F, Wang N, Xu Q. Molecular signatures between citrus and Candidatus Liberibacter asiaticus. PLoS Pathog 2021; 17:e1010071. [PMID: 34882744 PMCID: PMC8659345 DOI: 10.1371/journal.ppat.1010071] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Citrus Huanglongbing (HLB), also known as citrus greening, is one of the most devastating citrus diseases worldwide. Candidatus Liberibacter asiaticus (CLas) is the most prevalent strain associated with HLB, which is yet to be cultured in vitro. None of the commercial citrus cultivars are resistant to HLB. The pathosystem of Ca. Liberibacter is complex and remains a mystery. In this review, we focus on the recent progress in genomic research on the pathogen, the interaction of host and CLas, and the influence of CLas infection on the transcripts, proteins, and metabolism of the host. We have also focused on the identification of candidate genes for CLas pathogenicity or the improvements of HLB tolerance in citrus. In the end, we propose potentially promising areas for mechanistic studies of CLas pathogenicity, defense regulators, and genetic improvement for HLB tolerance/resistance in the future.
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Affiliation(s)
- Bin Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Muhammad Junaid Rao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Sheo Shankar Pandey
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Connor Hendrich
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Fang Ding
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, China
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11
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Conti G, Xoconostle-Cázares B, Marcelino-Pérez G, Hopp HE, Reyes CA. Citrus Genetic Transformation: An Overview of the Current Strategies and Insights on the New Emerging Technologies. FRONTIERS IN PLANT SCIENCE 2021; 12:768197. [PMID: 34917104 PMCID: PMC8670418 DOI: 10.3389/fpls.2021.768197] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 05/04/2023]
Abstract
Citrus are among the most prevailing fruit crops produced worldwide. The implementation of effective and reliable breeding programs is essential for coping with the increasing demands of satisfactory yield and quality of the fruit as well as to deal with the negative impact of fast-spreading diseases. Conventional methods are time-consuming and of difficult application because of inherent factors of citrus biology, such as their prolonged juvenile period and a complex reproductive stage, sometimes presenting infertility, self-incompatibility, parthenocarpy, or polyembryony. Moreover, certain desirable traits are absent from cultivated or wild citrus genotypes. All these features are challenging for the incorporation of the desirable traits. In this regard, genetic engineering technologies offer a series of alternative approaches that allow overcoming the difficulties of conventional breeding programs. This review gives a detailed overview of the currently used strategies for the development of genetically modified citrus. We describe different aspects regarding genotype varieties used, including elite cultivars or extensively used scions and rootstocks. Furthermore, we discuss technical aspects of citrus genetic transformation procedures via Agrobacterium, regular physical methods, and magnetofection. Finally, we describe the selection of explants considering young and mature tissues, protoplast isolation, etc. We also address current protocols and novel approaches for improving the in vitro regeneration process, which is an important bottleneck for citrus genetic transformation. This review also explores alternative emerging transformation strategies applied to citrus species such as transient and tissue localized transformation. New breeding technologies, including cisgenesis, intragenesis, and genome editing by clustered regularly interspaced short palindromic repeats (CRISPR), are also discussed. Other relevant aspects comprising new promoters and reporter genes, marker-free systems, and strategies for induction of early flowering, are also addressed. We provided a future perspective on the use of current and new technologies in citrus and its potential impact on regulatory processes.
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Affiliation(s)
- Gabriela Conti
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
- Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Beatriz Xoconostle-Cázares
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Gabriel Marcelino-Pérez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Horacio Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
- Laboratorio de Agrobiotecnología, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular (FBMC), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Carina A. Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Buenos Aires, Argentina
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12
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Different Host Plants Distinctly Influence the Feeding Ability of the Brown Citrus Aphid Toxoptera citricida. INSECTS 2021; 12:insects12100864. [PMID: 34680633 PMCID: PMC8538693 DOI: 10.3390/insects12100864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 12/04/2022]
Abstract
Simple Summary The brown citrus aphid, Toxoptera citricida, is an important pest of citrus and causes serious damage in the main production areas. Host plant resistance is an environmentally friendly method to manage aphid infestations and is becoming increasingly important as aphids develop greater resistance to insecticides. The aim of this study was to assess T. citricida resistance on seven widespread and common hosts using electropenetrography combined with a population development test. We showed that the feeding parameters of the brown citrus aphid differed significantly depending on the host plants. Toxoptera citricida spent more time in the pathway stage and less time in the phloem stage on Eureka, while the opposite was observed on Yuzu and Rough Lemon. Measurements of population development of aphids showed that on the Eureka, aphids developed more slowly. Our data suggest that different host plants distinctly influence the ability of T. citricida to feed. The brown citrus aphid did not prefer to feed on Eureka Lemon compared to the other six host plants. Abstract Piercing–sucking insects are important crop pests, and an understanding of their feeding behavior and population development plays a crucial role in studying insect population dynamics and crop resistance. In our study, we examined the probing behavior of the brown citrus aphid, Toxoptera citricida, using electropenetrography and assessed its population development after 8 days on seven host plants: Yuzu, Citrus junos Sieb. ex Tanaka; Rough Lemon, C. jambhiri Lush.; ‘Luofu’ kumquat, Fortunella margarita Swingle; ‘Olinda’ valencia orange, C. sinensis (L.) Osbeck; ‘Yanxiwanlu’ Ponkan, C. reticulata Blanco; ‘Rohde Red’ valencia orange, C. sinensis; and ‘Eureka’ lemon, C. limon (L.) Osbeck. The results demonstrated that probing by the brown citrus aphid differed significantly according to the target hosts. Toxoptera citricida produced significantly more pathway activities on Eureka than on Rough Lemon and Yuzu. Toxoptera citricida spent more time from the first probe to first salivation into phloem sieve elements on Eureka compared to Yuzu. In addition, the total duration of ingestion from sieve cells of each aphid in the phloem-feeding phase was shortest on Eureka, and this was significantly shorter than that on Yuzu, Rough Lemon, Luofu, and Olinda. The population number of T. citricida on Eureka after 8 days was significantly lower than that on the other hosts. Overall, Eureka was found to have obvious resistance to T. citricida, whereas Yuzu and Rough Lemon were susceptible host plants. These results provide a theoretical basis for exploring aphid-resistant fruit tree resources using resistant varieties.
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13
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Wang L, Huang Y, Liu Z, He J, Jiang X, He F, Lu Z, Yang S, Chen P, Yu H, Zeng B, Ke L, Xie Z, Larkin RM, Jiang D, Ming R, Buckler ES, Deng X, Xu Q. Somatic variations led to the selection of acidic and acidless orange cultivars. NATURE PLANTS 2021; 7:954-965. [PMID: 34140668 DOI: 10.1038/s41477-021-00941-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Somatic variations are a major source of genetic diversification in asexual plants, and underpin clonal evolution and the breeding of asexual crops. Sweet orange is a model species for studying somatic variation because it reproduces asexually through apomixis and is propagated asexually through grafting. To dissect the genomic basis of somatic variation, we de novo assembled a reference genome of sweet orange with an average of three gaps per chromosome and a N50 contig of 24.2 Mb, as well as six diploid genomes of somatic mutants of sweet oranges. We then sequenced 114 somatic mutants with an average genome coverage of 41×. Categorization of the somatic variations yielded insights into the single-nucleotide somatic mutations, structural variations and transposable element (TE) transpositions. We detected 877 TE insertions, and found TE insertions in the transporter or its regulatory genes associated with variation in fruit acidity. Comparative genomic analysis of sweet oranges from three diversity centres supported a dispersal from South China to the Mediterranean region and to the Americas. This study provides a global view on the somatic variations, the diversification and dispersal history of sweet orange and a set of candidate genes that will be useful for improving fruit taste and flavour.
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Affiliation(s)
- Lun Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yue Huang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - ZiAng Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jiaxian He
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaolin Jiang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Fa He
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Zhihao Lu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shuizhi Yang
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha, P. R. China
| | - Peng Chen
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha, P. R. China
| | - Huiwen Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Bin Zeng
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha, P. R. China
| | - Lingjun Ke
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Dong Jiang
- Citrus Research Institute, Southwest University, Chongqing, P. R. China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Edward S Buckler
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China.
- Hubei Hongshan Laboratory, Wuhan, China.
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14
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Citrus Cell Suspension Culture Establishment, Maintenance, Efficient Transformation and Regeneration to Complete Transgenic Plant. PLANTS 2021; 10:plants10040664. [PMID: 33808465 PMCID: PMC8066040 DOI: 10.3390/plants10040664] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 11/25/2022]
Abstract
Agrobacterium-mediated transformation of epicotyl segment has been used in Citrus transgenic studies. The approach suffers, however, from limitations such as occasionally seed unavailability, the low transformation efficiency of juvenile tissues and the high frequency of chimeric plants. Therefore, a suspension cell culture system was established and used to generate transgenic plants in this study to overcome the shortcomings. The embryonic calli were successfully developed from undeveloped ovules of the three cultivars used in this study, “Sweet orange”-Egyptian cultivar (Citrus sinensis), “Shatangju” (Citrus reticulata) and “W. Murcott” (Citrus reticulata), on three different solid media. Effects of media, genotypes and ages of ovules on the induction of embryonic calli were also investigated. The result showed that the ovules’ age interferes with the callus production more significantly than media and genotypes. The 8 to 10 week-old ovules were found to be the best materials. A cell suspension culture system was established in an H+H liquid medium. Transgenic plants were obtained from Agrobacterium-mediated transformation of cell suspension as long as eight weeks subculture intervals. A high transformation rate (~35%) was achieved by using our systems, confirming BASTA selection and later on by PCR confirmation. The results demonstrated that transformation of cell suspension should be more useful for the generation of non-chimeric transgenic Citrus plants. It was also shown that our cell suspension culture procedure was efficient in maintaining the vigor and regeneration potential of the cells.
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15
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Zayed A, Badawy MT, Farag MA. Valorization and extraction optimization of Citrus seeds for food and functional food applications. Food Chem 2021; 355:129609. [PMID: 33799261 DOI: 10.1016/j.foodchem.2021.129609] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/07/2021] [Accepted: 03/10/2021] [Indexed: 12/13/2022]
Abstract
Valorization of food byproducts has attracted recently considerable attention. Citrus fruits provide considerable non-edible residues reach 80% in juice production. They are considered agri-wastes to comprise peel, pulp and seeds. Previous investigations have focused on peel and pulp to recover value-added products. The review presents for the first-time phytochemical composition of Citrus seeds' products, i.e., oil and extracts. Fatty acids, phytosterols and tocopherols amounted as the major bioactives in Citrus seeds, in addition to limonoids, dietary fibers and flavonoids. Besides their nutritional values, these chemicals have promising applications including production of biodiesel, food enhancers and antioxidants, especially from mandarin and grapefruit seeds. Optimum conditions of the different Citrus seeds' valorization are discussed to improve extraction yield and lessen environmental hazards of solvent extraction. This review presents the best utilization practices for one of the largest cultivated fruit seeds worldwide and its different applications.
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Affiliation(s)
- Ahmed Zayed
- Pharmacognosy Department, College of Pharmacy, Tanta University, El-guish Street, 31527 Tanta, Egypt; Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663 Kaiserslautern, Germany
| | - Marwa T Badawy
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr el Aini St., P.B. 11562 Cairo, Egypt; Chemistry Department, School of Sciences & Engineering, The American University in Cairo, New Cairo 11835, Egypt.
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16
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De Novo Transcriptome Sequencing of Rough Lemon Leaves ( Citrus jambhiri Lush.) in Response to Plenodomus tracheiphilus Infection. Int J Mol Sci 2021; 22:ijms22020882. [PMID: 33477297 PMCID: PMC7830309 DOI: 10.3390/ijms22020882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/17/2022] Open
Abstract
Mal secco is one of the most severe diseases of citrus, caused by the necrotrophic fungus Plenodomus tracheiphilus. With the main aim of identifying candidate genes involved in the response of citrus plants to "Mal secco", we performed a de novo transcriptome analysis of rough lemon seedlings subjected to inoculation of P. tracheiphilus. The analysis of differential expressed genes (DEGs) highlighted a sharp response triggered by the pathogen as a total of 4986 significant DEGs (2865 genes up-regulated and 2121 down-regulated) have been revealed. The analysis of the most significantly enriched KEGG pathways indicated that a crucial role is played by genes involved in "Plant hormone signal transduction", "Phenylpropanoid biosynthesis", and "Carbon metabolism". The main findings of this work are that under fungus challenge, the rough lemon genes involved both in the light harvesting and the photosynthetic electron flow were significantly down-regulated, thus probably inducing a shortage of energy for cellular functions. Moreover, the systemic acquired resistance (SAR) was activated through the induced salicylic acid cascade. Interestingly, RPM1 interacting protein 4, an essential positive regulator of plant defense, and BIR2, which is a negative regulator of basal level of immunity, have been identified thus representing useful targets for molecular breeding.
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17
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Peng Z, Bredeson JV, Wu GA, Shu S, Rawat N, Du D, Parajuli S, Yu Q, You Q, Rokhsar DS, Gmitter FG, Deng Z. A chromosome-scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance, cold tolerance and genome evolution in Citrus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1215-1232. [PMID: 32985030 PMCID: PMC7756384 DOI: 10.1111/tpj.14993] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/17/2020] [Indexed: 05/19/2023]
Abstract
Trifoliate orange (Poncirus trifoliata), a deciduous close relative of evergreen Citrus, has important traits for citrus production, including tolerance/resistance to citrus greening disease (Huanglongbing, HLB) and other major diseases, and cold tolerance. It has been one of the most important rootstocks, and one of the most valuable sources of resistance and tolerance genes for citrus. Here we present a high-quality, chromosome-scale genome assembly of P. trifoliata. The 264.9-Mb assembly contains nine chromosomal pseudomolecules with 25 538 protein-coding genes, covering 97.2% of the estimated gene space. Comparative analyses of P. trifoliata and nine Citrus genomes revealed 605 species-specific genes and six rapidly evolving gene families in the P. trifoliata genome. Poncirus trifoliata has evolved specific adaptation in the C-repeat/DREB binding factor (CBF)-dependent and CBF-independent cold signaling pathways to tolerate cold. We identified candidate genes within quantitative trait loci for HLB tolerance, and at the loci for resistance to citrus tristeza virus and citrus nematode. Genetic diversity analysis of Poncirus accessions and Poncirus/Citrus hybrids shows a narrow genetic base in the US germplasm collection, and points to the importance of collecting and preserving more natural genetic variation. Two phenotypically divergent Poncirus accessions are found to be clonally related, supporting a previous conjecture that dwarf Flying Dragon originated as a mutant of a non-dwarfing type. The high-quality genome reveals features and evolutionary insights of Poncirus, and it will serve as a valuable resource for genetic, genomic and molecular research and manipulation in citrus.
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Affiliation(s)
- Ze Peng
- Department of Environmental HorticultureGulf Coast Research and Education CenterUniversity of FloridaIFAS14625 County Road 672WimaumaFL33598USA
| | - Jessen V. Bredeson
- Molecular and Cell Biology DepartmentUniversity of California, BerkeleyBerkeleyCA94720USA
| | - Guohong A. Wu
- US Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron RoadBerkeleyCA94720USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron RoadBerkeleyCA94720USA
| | - Nidhi Rawat
- Department of Environmental HorticultureGulf Coast Research and Education CenterUniversity of FloridaIFAS14625 County Road 672WimaumaFL33598USA
| | - Dongliang Du
- Citrus Research and Education CenterUniversity of Florida, IFAS700 Experiment Station RdLake AlfredFL33850USA
| | - Saroj Parajuli
- Department of Environmental HorticultureGulf Coast Research and Education CenterUniversity of FloridaIFAS14625 County Road 672WimaumaFL33598USA
| | - Qibin Yu
- Citrus Research and Education CenterUniversity of Florida, IFAS700 Experiment Station RdLake AlfredFL33850USA
| | - Qian You
- Department of Environmental HorticultureGulf Coast Research and Education CenterUniversity of FloridaIFAS14625 County Road 672WimaumaFL33598USA
| | - Daniel S. Rokhsar
- Molecular and Cell Biology DepartmentUniversity of California, BerkeleyBerkeleyCA94720USA
- US Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron RoadBerkeleyCA94720USA
| | - Frederick G. Gmitter
- Citrus Research and Education CenterUniversity of Florida, IFAS700 Experiment Station RdLake AlfredFL33850USA
| | - Zhanao Deng
- Department of Environmental HorticultureGulf Coast Research and Education CenterUniversity of FloridaIFAS14625 County Road 672WimaumaFL33598USA
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18
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Gao J, Arthurs S, Mao R. Asymmetric Interaction between Aphis spiraecola and Toxoptera citricida on Sweet Orange Induced by Pre-Infestation. INSECTS 2020; 11:insects11070414. [PMID: 32635348 PMCID: PMC7411604 DOI: 10.3390/insects11070414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 05/31/2023]
Abstract
Indirect interactions between herbivorous insects that share the same host have been focused on insects feeding on herbaceous plants, while few studies investigate similar interactions on woody plants. We investigated performance and feeding behavior of two citrus aphids, Aphis spiraecola Patch and Toxoptera citricida Kirkaldy, on sweet orange as affected by prior infestation of conspecifics and heterospecifics. Results showed that pre-infestation-induced interactions between A. spiraecola and T. citricida were asymmetric, with A. spiraecola gaining more fitness. In detail, pre-infestation by A. spiraecola decreased adult weight, enhanced survival rate and accelerated phloem sap acceptance of conspecifics. However, A. spiraecola pre-infestation did not affect performance or feeding behavior of T. citricida. In another infestation sequence, the pre-infestation of T. citricida did not affect conspecifics, but positively affected heterospecifics, indicated as a decreased pre-reproductive period, enhanced survival rate, adult weight, fecundity, and feeding efficiency, i.e., faster access and acceptance of phloem sap, and longer phloem sap ingestion duration. Furthermore, we found A. spiraecola pre-infestation enhanced amino acid concentration, amino acid to sugar ratio, activated salicylic acid and jasmonic acid marker gene expression, while T. citricida pre-infestation only depressed jasmonic acid marker gene expression. Changes in nutrient and phytohormone-dependent defense probably underlie the asymmetric effect.
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Affiliation(s)
- Jing Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou 510260, China;
| | | | - Runqian Mao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou 510260, China;
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19
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Ali M, Cheng H, Soomro M, Shuyan L, Bilal Tufail M, Nazir MF, Feng X, Zhang Y, Dongyun Z, Limin L, Wang Q, Song G. Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii. Genes (Basel) 2020; 11:genes11050472. [PMID: 32357512 PMCID: PMC7290383 DOI: 10.3390/genes11050472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/15/2020] [Accepted: 04/19/2020] [Indexed: 12/17/2022] Open
Abstract
Cotton is one of the major industrial crops that supply natural fibers and oil for industries. This study was conducted to understand the mechanism of delayed gland morphogenesis in seeds of Gossypium bickii. In this study, we compared glandless seeds of G. bickii with glanded seeds of Gossypium arboreum. High-throughput sequencing technology was used to explore and classify the expression patterns of gland-related genes in seeds and seedlings of cotton plants. Approximately 131.33 Gigabases of raw data from 12 RNA sequencing samples with three biological replicates were generated. A total of 7196 differentially-expressed genes (DEGs) were identified in all transcriptome data. Among them, 3396 genes were found up-regulated and 3480 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were performed to identify different functions between genes unique to glandless imbibed seeds and glanded seedlings. Co-expression network analysis revealed four modules that were identified as highly associated with the development of glandless seeds. Here the hub genes in each module were identified by weighted gene co-expression network analysis (WGCNA). In total, we have selected 13 genes involved in transcription factors, protein and MYB-related functions, that were differentially expressed in transcriptomic data and validated by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). These selected genes may play an important role for delayed gland morphogenesis. Our study provides comprehensive insight into the key genes related to glandless traits of seeds and plants, and can be further exploited by functional and molecular studies.
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Affiliation(s)
- Mushtaque Ali
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Mahtab Soomro
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Li Shuyan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Muhammad Bilal Tufail
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Mian Faisal Nazir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Xiaoxu Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
- Plant Genetics, Gambloux Agro Bio Tech, University of Liege, 5030 Gambloux, Belgium
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Zuo Dongyun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Lv Limin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.A.); (H.C.); (M.S.); (L.S.); (M.B.T.); (M.F.N.); (X.F.); (Y.Z.); (Z.D.); (L.L.); (Q.W.)
- Correspondence: ; Tel.: +86-3722562377
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20
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Kawahara Y, Endo T, Omura M, Teramoto Y, Itoh T, Fujii H, Shimada T. Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding. BREEDING SCIENCE 2020; 70:200-211. [PMID: 32523402 PMCID: PMC7272249 DOI: 10.1270/jsbbs.19097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/16/2019] [Indexed: 06/11/2023]
Abstract
Citrus species are some of the most valuable and widely consumed fruits globally. The genome sequences of representative citrus (e.g., Citrus clementina, C. sinensis, C. grandis) species have been released but the research base for mandarin molecular breeding is still poor. We assembled the genomes of Citrus unshiu and Poncirus trifoliata, two important species for citrus industry in Japan, using hybrid de novo assembly of Illumina and PacBio sequence data, and developed the Mikan Genome Database (MiGD). The assembled genome sizes of C. unshiu and P. trifoliata are 346 and 292 Mb, respectively, similar to those of citrus species in public databases; they are predicted to possess 41,489 and 34,333 protein-coding genes in their draft genome sequences, with 9,642 and 8,377 specific genes when compared to C. clementina, respectively. MiGD is an integrated database of genome annotation, genetic diversity, and Cleaved Amplified Polymorphic Sequence (CAPS) marker information, with these contents being mutually linked by genes. MiGD facilitates access to genome sequences of interest from previously reported linkage maps through CAPS markers and obtains polymorphism information through the multiple genome browser TASUKE. The genomic resources in MiGD (https://mikan.dna.affrc.go.jp) could provide valuable information for mandarin molecular breeding in Japan.
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Affiliation(s)
- Yoshihiro Kawahara
- National Agriculture and Food Research Organization Advanced Analysis Center, Tsukuba, Ibaraki 305-8602, Japan
- National Agriculture and Food Research Organization Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
| | - Tomoko Endo
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Mitsuo Omura
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422-8529, Japan
| | - Yumiko Teramoto
- IMSBIO Co., Ltd., Owl Tower 6F, 4-21-1, Higashi-ikebukuro, Toshima-ku, Tokyo 170-0013, Japan
| | - Takeshi Itoh
- National Agriculture and Food Research Organization Advanced Analysis Center, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Fujii
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Takehiko Shimada
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
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21
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Zhou J, Li D, Wang G, Wang F, Kunjal M, Joldersma D, Liu Z. Application and future perspective of CRISPR/Cas9 genome editing in fruit crops. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020. [PMID: 30791200 DOI: 10.1111/jipb.1279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Fruit crops, including apple, orange, grape, banana, strawberry, watermelon, kiwifruit and tomato, not only provide essential nutrients for human life but also contribute to the major agricultural output and economic growth of many countries and regions in the world. Recent advancements in genome editing provides an unprecedented opportunity for the genetic improvement of these agronomically important fruit crops. Here, we summarize recent reports of applying CRISPR/Cas9 to fruit crops, including efforts to reduce disease susceptibility, change plant architecture or flower morphology, improve fruit quality traits, and increase fruit yield. We discuss challenges facing fruit crops as well as new improvements and platforms that could be used to facilitate genome editing in fruit crops, including dCas9-base-editing to introduce desirable alleles and heat treatment to increase editing efficiency. In addition, we highlight what we see as potentially revolutionary development ranging from transgene-free genome editing to de novo domestication of wild relatives. Without doubt, we now see only the beginning of what will eventually be possible with the use of the CRISPR/Cas9 toolkit. Efforts to communicate with the public and an emphasis on the manipulation of consumer-friendly traits will be critical to facilitate public acceptance of genetically engineered fruits with this new technology.
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Affiliation(s)
- Junhui Zhou
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Dongdong Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
- Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, Hangzhou, 310058, China
| | - Guoming Wang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fuxi Wang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Merixia Kunjal
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Dirk Joldersma
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
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22
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Zhou J, Li D, Wang G, Wang F, Kunjal M, Joldersma D, Liu Z. Application and future perspective of CRISPR/Cas9 genome editing in fruit crops. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:269-286. [PMID: 30791200 PMCID: PMC6703982 DOI: 10.1111/jipb.12793] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/18/2019] [Indexed: 05/24/2023]
Abstract
Fruit crops, including apple, orange, grape, banana, strawberry, watermelon, kiwifruit and tomato, not only provide essential nutrients for human life but also contribute to the major agricultural output and economic growth of many countries and regions in the world. Recent advancements in genome editing provides an unprecedented opportunity for the genetic improvement of these agronomically important fruit crops. Here, we summarize recent reports of applying CRISPR/Cas9 to fruit crops, including efforts to reduce disease susceptibility, change plant architecture or flower morphology, improve fruit quality traits, and increase fruit yield. We discuss challenges facing fruit crops as well as new improvements and platforms that could be used to facilitate genome editing in fruit crops, including dCas9-base-editing to introduce desirable alleles and heat treatment to increase editing efficiency. In addition, we highlight what we see as potentially revolutionary development ranging from transgene-free genome editing to de novo domestication of wild relatives. Without doubt, we now see only the beginning of what will eventually be possible with the use of the CRISPR/Cas9 toolkit. Efforts to communicate with the public and an emphasis on the manipulation of consumer-friendly traits will be critical to facilitate public acceptance of genetically engineered fruits with this new technology.
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Affiliation(s)
- Junhui Zhou
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Dongdong Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
- Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, Hangzhou 310058, China
| | - Guoming Wang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology
Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Fuxi Wang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Merixia Kunjal
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Dirk Joldersma
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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23
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Klimek-Szczykutowicz M, Szopa A, Ekiert H. Citrus limon (Lemon) Phenomenon-A Review of the Chemistry, Pharmacological Properties, Applications in the Modern Pharmaceutical, Food, and Cosmetics Industries, and Biotechnological Studies. PLANTS 2020; 9:plants9010119. [PMID: 31963590 PMCID: PMC7020168 DOI: 10.3390/plants9010119] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/02/2020] [Accepted: 01/14/2020] [Indexed: 12/17/2022]
Abstract
This review presents important botanical, chemical and pharmacological characteristics of Citrus limon (lemon)—a species with valuable pharmaceutical, cosmetic and culinary (healthy food) properties. A short description of the genus Citrus is followed by information on the chemical composition, metabolomic studies and biological activities of the main raw materials obtained from C. limon (fruit extract, juice, essential oil). The valuable biological activity of C. limon is determined by its high content of phenolic compounds, mainly flavonoids (e.g., diosmin, hesperidin, limocitrin) and phenolic acids (e.g., ferulic, synapic, p-hydroxybenzoic acids). The essential oil is rich in bioactive monoterpenoids such as D-limonene, β-pinene, γ-terpinene. Recently scientifically proven therapeutic activities of C. limon include anti-inflammatory, antimicrobial, anticancer and antiparasitic activities. The review pays particular attention, with references to published scientific research, to the use of C. limon in the food industry and cosmetology. It also addresses the safety of use and potential phototoxicity of the raw materials. Lastly, the review emphasizes the significance of biotechnological studies on C. limon.
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24
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Salonia F, Ciacciulli A, Poles L, Pappalardo HD, La Malfa S, Licciardello C. New Plant Breeding Techniques in Citrus for the Improvement of Important Agronomic Traits. A Review. FRONTIERS IN PLANT SCIENCE 2020; 11:1234. [PMID: 32922420 PMCID: PMC7456868 DOI: 10.3389/fpls.2020.01234] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/28/2020] [Indexed: 05/18/2023]
Abstract
New plant breeding techniques (NPBTs) aim to overcome traditional breeding limits for fruit tree species, in order to obtain new varieties with improved organoleptic traits and resistance to biotic and abiotic stress, and to maintain fruit quality achieved over centuries by (clonal) selection. Knowledge on the gene(s) controlling a specific trait is essential for the use of NPBTs, such as genome editing and cisgenesis. In the framework of the international scientific community working on fruit tree species, including citrus, NPBTs have mainly been applied to address pathogen threats. Citrus could take advantage of NPBTs because of its complex species biology (seedlessness, apomixis, high heterozygosity, and long juvenility phase) and aptitude for in vitro manipulation. To our knowledge, genome editing in citrus via transgenesis has successful for induced resistance to Citrus bacterial canker in sweet orange and grapefruit using the resistance gene CsLOB1. In the future, NPBTs will also be used to improve fruit traits, making them healthier. The regeneration of plants following the application of NPBTs is a bottleneck, making it necessary to optimize the efficiency of current protocols. The strengths and weaknesses of using explants from young in vitro plantlets, and from mature plants, will be discussed. Other major issues addressed in this review are related to the requirement for marker-free systems and shortening the long juvenility phase. This review aims to summarize methods and approaches available in the literature that are suitable to citrus, focusing on the principles observed before the use of NPBTs.
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Affiliation(s)
- Fabrizio Salonia
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Angelo Ciacciulli
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Lara Poles
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | | | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
- *Correspondence: Stefano La Malfa, ; Concetta Licciardello,
| | - Concetta Licciardello
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- *Correspondence: Stefano La Malfa, ; Concetta Licciardello,
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25
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Ferrasa A, Murata MM, Cofre TDCG, Cavallini JS, Peron G, Julião MHM, Belasque J, Ferreira H, Ferro MIT, Leite RP, Penha HA, Carvalho FMS, Varani AM, Herai RH, Ferro JA. CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5979747. [PMID: 33181825 PMCID: PMC7904050 DOI: 10.1093/database/baaa081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/05/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023]
Abstract
Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the CitrusKB knowledge base. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable resource of information on citrus and their interaction with the citrus canker bacterium X. citri. CitrusKB provides tools for a user-friendly web interface to let users search and analyse a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease, with controls and infected plants at different stages of infection by the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue over time by the incorporation of novel annotations and analysis tools. We expect that CitrusKB may substantially contribute to the field of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.
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Affiliation(s)
- Adriano Ferrasa
- Departamento de Informática, Universidade Estadual de Ponta Grossa (UEPG), Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, PR, Brazil.,Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), R. Imaculada Conceição, 1155, 80215-901, Curitiba, PR, Brazil
| | - Mayara M Murata
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil.,Diretoria de PÓs-Graduação Stricto Sensu, Universidade Norte do Paraná (UNOPAR), Av. Paris, 675, 86041-100, Londrina, PR, Brazil
| | - Teresa D C G Cofre
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Juliana S Cavallini
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Gustavo Peron
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Maria H M Julião
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo (USP), Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil
| | - Henrique Ferreira
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Av. 24-A, 1515, 13506-900, Rio Claro, SP, Brazil
| | - Maria Inês T Ferro
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Rui P Leite
- Instituto Agronômico do Paraná (IAPAR), Londrina, Rod. Celso Garcia Cid, km 375, 86047-902, Londrina, PR, Brazil
| | - Helen A Penha
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil.,Inprenha Biotecnologia e Desenvolvimento Avançado LTDA, Fazenda Lagoinha, Estrada Velha de Taquaritinga, Km 04, 14870-970, Jaboticabal, SP, Brazil
| | - Flávia M S Carvalho
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Alessandro M Varani
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Roberto H Herai
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), R. Imaculada Conceição, 1155, 80215-901, Curitiba, PR, Brazil
| | - Jesus A Ferro
- Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
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26
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Long Q, Xie Y, He Y, Li Q, Zou X, Chen S. Abscisic Acid Promotes Jasmonic Acid Accumulation and Plays a Key Role in Citrus Canker Development. FRONTIERS IN PLANT SCIENCE 2019; 10:1634. [PMID: 31921273 PMCID: PMC6934002 DOI: 10.3389/fpls.2019.01634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/20/2019] [Indexed: 05/06/2023]
Abstract
Antagonism between jasmonic acid (JA) and salicylic acid (SA) plays pivotal roles in the fine-tuning of plant immunity against pathogen infection. In this study, we compared the phytohormonal responses to Xanthomonas citri subsp. citri (Xcc) between the citrus canker-susceptible (S) cultivar Wanjincheng orange (Citrus sinensis Osbeck) and -resistant (R) cultivar Jindan (Fortunella crassifolia Swingle). Upon Xcc infection, SA and JA were strongly induced in Jindan (R) and Wanjincheng orange (S), respectively, and JA appeared to contribute to citrus disease susceptibility by antagonizing SA-mediated effective defenses. A homologous gene encoding the allene oxide synthase (AOS) 1-2 enzyme, which catalyzes the first committed step in JA biosynthesis, was specifically upregulated in Wanjincheng orange (S) but not in Jindan (R). A promoter sequence analysis showed that abscisic acid (ABA)-responsive elements are enriched in the AOS1-2 of Wanjincheng orange (S) but not in Jindan (R). Accordingly, ABA treatments could induce AOS1-2 expression and JA accumulation, leading to enhanced citrus disease susceptibility in Wanjincheng orange (S), while the synthesis inhibitor sodium tungstate had the opposite effects. Moreover, ABA was specifically induced by Xcc infection in Wanjincheng orange (S) but not in Jindan (R). Thus, Xcc appeared to hijack host ABA biosynthesis to promote JA accumulation, which in turn suppressed effectual SA-mediated defenses to favor disease development in citrus. Our findings provide new insights into the molecular mechanisms underlying the differential citrus-canker resistance in citrus cultivars, and a new strategy for the biotechnological improvement of citrus canker resistance was discussed.
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Affiliation(s)
| | | | | | | | - Xiuping Zou
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
| | - Shanchun Chen
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
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27
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Citrus Taste Modification Potentials by Genetic Engineering. Int J Mol Sci 2019; 20:ijms20246194. [PMID: 31817978 PMCID: PMC6940753 DOI: 10.3390/ijms20246194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 12/22/2022] Open
Abstract
Citrus fruits are mainly consumed as fresh fruit and processed juice products. They serve as nutritional and a tasty diet in our daily life. However, the formidable bitterness and delayed bitterness significantly impact the citrus industry attributable to the two major bitter compounds naringin and limonin. The extremely sour and acidic also negatively affects the sensory quality of citrus products. Citrus breeding programs have developed different strategies to improve citrus quality and a wealth of studies have aimed to uncover the genetic and biochemical basis of citrus flavor. In this minireview, we outline the major genes characterized to be involved in pathways shaping the sweet, bitter, or sour taste in citrus, and discuss briefly about the possible approaches to modify citrus taste by genetic engineering.
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28
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Yuan J, Wang J, Yu J, Meng F, Zhao Y, Li J, Sun P, Sun S, Zhang Z, Liu C, Wei C, Guo H, Li X, Duan X, Shen S, Xie Y, Hou Y, Zhang J, Shehzad T, Wang X. Alignment of Rutaceae Genomes Reveals Lower Genome Fractionation Level Than Eudicot Genomes Affected by Extra Polyploidization. FRONTIERS IN PLANT SCIENCE 2019; 10:986. [PMID: 31447866 PMCID: PMC6691040 DOI: 10.3389/fpls.2019.00986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Owing to their nutritional and commercial values, the genomes of several citrus plants have been sequenced, and the genome of one close relative in the Rutaceae family, atalantia (Atalantia buxifolia), has also been sequenced. Here, we show a family-level comparative analysis of Rutaceae genomes. By using grape as the outgroup and checking cross-genome gene collinearity, we systematically performed a hierarchical and event-related alignment of Rutaceae genomes, and produced a gene list defining homologous regions based on ancestral polyploidization or speciation. We characterized genome fractionation resulting from gene loss or relocation, and found that erosion of gene collinearity could largely be described by a geometric distribution. Moreover, we found that well-assembled Rutaceae genomes retained significantly more genes (65-82%) than other eudicots affected by recursive polyploidization. Additionally, we showed divergent evolutionary rates among Rutaceae plants, with sweet orange evolving faster than others, and by performing evolutionary rate correction, re-dated major evolutionary events during their evolution. We deduced that the divergence between the Rutaceae family and grape occurred about 81.15-91.74 million years ago (mya), while the split between citrus and atalantia plants occurred <10 mya. In addition, we showed that polyploidization led to a copy number expansion of key gene families contributing to the biosynthesis of vitamin C. Overall, the present effort provides an important comparative genomics resource and lays a foundation to understand the evolution and functional innovation of Rutaceae genomes.
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Affiliation(s)
- Jiaqing Yuan
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuhao Zhao
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jing Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Pengchuan Sun
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Sangrong Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Zhikang Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chao Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xueqian Duan
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shaoqi Shen
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yangqin Xie
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yue Hou
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jin Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
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A sweet orange mutant impaired in carotenoid biosynthesis and reduced ABA levels results in altered molecular responses along peel ripening. Sci Rep 2019; 9:9813. [PMID: 31285504 PMCID: PMC6614452 DOI: 10.1038/s41598-019-46365-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/27/2019] [Indexed: 11/08/2022] Open
Abstract
Citrus fruit ripening is a complex process involving biochemical, physiological and molecular events that differ between the flesh and the peel of the fruit. We characterized sweet orange peel maturation by means of a comparative transcriptomic analysis between Navelate orange (Citrus sinensis L. Osbeck) and its mutant fruit Pinalate, which presents a severe blockage at early steps of the carotenoid biosynthetic pathway and consequently reduced ABA levels. Peel ripening involved the decrease of the photosynthetic activity and the transmembrane transport processes, as well as the buildup of starch and cuticular waxes and the cell wall modification. In addition, a number of biotic and abiotic stress responses, including the defense response, and the response to blue light, water deprivation and abscisic acid stimulus were modulated in a ripening-stage specific manner. The regulation of energy-related processes and secondary metabolism pathways was attenuated in Pinalate, while the molecular mechanisms underlying stress responses displayed dependency on ABA levels. These results indicate that ABA is a key signal inducing stress responses along orange peel ripening, which might determine the fruit postharvest performance.
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Goldenberg L, Zohar M, Kirshinbaum L, Yaniv Y, Doron-Faigenboim A, Porat R, Carmi N, Isaacson T. Biochemical and Molecular Factors Governing Peel-Color Development in 'Ora' and 'Shani' Mandarins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:4800-4807. [PMID: 30973717 DOI: 10.1021/acs.jafc.9b00669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To identify factors governing peel-color development in mandarins, we examined carotenoid content and composition and the expression of carotenoid-related genes during four stages of ripening (i.e., green, breaker, yellow, and orange) in two varieties: 'Ora', which has orange fruit, and 'Shani', which has orange-reddish fruit. The two varieties had different carotenoid compositions, and 'Shani' had a significantly higher level of total carotenoid pigments. 'Shani' was rich in the deep orange β-cryptoxanthin and the orange-reddish β-citraurin, whereas 'Ora' was rich in the orange violaxanthin. RNA-Seq analysis revealed significantly greater expression of the carotenoid-biosynthesis genes PSY, βLCY, βCHX, and CCD4b, as well as MEP-pathway genes and several ethylene-biosynthesis and -signaling genes in 'Shani' fruit. In contrast, the expression levels of genes involved in the synthesis of α-branch carotenoids (i.e., εLCY and εCHX) and ZEP, which is involved in the formation of violaxanthin, were significantly higher in the 'Ora' fruit.
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Affiliation(s)
- Livnat Goldenberg
- Department of Postharvest Science of Fresh Produce , ARO, The Volcani Center , P.O. Box 15159, Rishon LeZion 7505101 , Israel
- Faculty of Agricultural, Food and Environmental Quality Sciences , Hebrew University of Jerusalem , Rehovot 76100 , Israel
| | - Matat Zohar
- Newe Ya'ar Research Center , ARO , Ramat Yishay 30095 , Israel
| | - Lina Kirshinbaum
- Biology and DNA Laboratory, Division of Identification and Forensic Science , Israel Police , Jerusalem , Israel
| | - Yossi Yaniv
- Department of Fruit Tree Crops , ARO, The Volcani Center , P.O. Box 15159, Rishon LeZion 7505101 , Israel
| | - Adi Doron-Faigenboim
- Department of Genomics and Bioinformatics , ARO, the Volcani Center , P.O. Box 15159, Rishon LeZion 7505101 , Israel
| | - Ron Porat
- Department of Postharvest Science of Fresh Produce , ARO, The Volcani Center , P.O. Box 15159, Rishon LeZion 7505101 , Israel
| | - Nir Carmi
- Department of Fruit Tree Crops , ARO, The Volcani Center , P.O. Box 15159, Rishon LeZion 7505101 , Israel
| | - Tal Isaacson
- Newe Ya'ar Research Center , ARO , Ramat Yishay 30095 , Israel
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Zheng X, Tang Y, Ye J, Pan Z, Tan M, Xie Z, Chai L, Xu Q, Fraser PD, Deng X. SLAF-Based Construction of a High-Density Genetic Map and Its Application in QTL Mapping of Carotenoids Content in Citrus Fruit. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:994-1002. [PMID: 30589260 DOI: 10.1021/acs.jafc.8b05176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Carotenoids are important antioxidant components in the human diet. To develop carotenoid-rich agricultural products by genetic intervention, understanding the genetic basis of carotenoids variation is essential. In this study, we constructed a high-density integrated genetic map with 3817 molecular markers using specific locus amplified fragment (SLAF) sequencing from a C. reticulata × P. trifoliata F1 pseudotestcross population. A total of 17 significant quantitative trait loci (QTLs) distributed on Chromosomes (Chr) 2, 3, 5, 6, and 9 were detected to determine the carotenoid variation in the population. In particular, three QTL colocalizations for multiple carotenoid constituents were observed on Chr 2, 3, and 9, one of which was located on Chr2:34,654,608-35430715 accounted for 20.1-25.4% of the variation of luteoxanthin, auroxanthin, lutein, violaxanthin, and total carotenoid content. Overall, this study provides a genetic foundation for marker-assisted selection (MAS) breeding of nutritionally enhanced citrus fruit.
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Affiliation(s)
- Xiongjie Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Yuqing Tang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Meilian Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway , University of London , Egham, Surrey TW20 0EX , United Kingdom
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
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Phytohormone participation during Citrus sinensis non-host response to Xanthomonas campestris pv. vesicatoria. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.plgene.2018.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Wang L, He F, Huang Y, He J, Yang S, Zeng J, Deng C, Jiang X, Fang Y, Wen S, Xu R, Yu H, Yang X, Zhong G, Chen C, Yan X, Zhou C, Zhang H, Xie Z, Larkin RM, Deng X, Xu Q. Genome of Wild Mandarin and Domestication History of Mandarin. MOLECULAR PLANT 2018; 11:1024-1037. [PMID: 29885473 DOI: 10.1016/j.molp.2018.06.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 05/19/2023]
Abstract
Mandarin (Citrus reticulata) is one of the most important citrus crops worldwide. Its domestication is believed to have occurred in South China, which has been one of the centers of mandarin cultivation for four millennia. We collected natural wild populations of mandarin around the Nanling region and cultivated landraces in the vicinity. We found that the citric acid level was dramatically reduced in cultivated mandarins. To understand genetic basis of mandarin domestication, we de novo assembled a draft genome of wild mandarin and analyzed a set of 104 citrus genomes. We found that the Mangshan mandarin is a primitive type and that two independent domestication events have occurred, resulting in two groups of cultivated mandarins (MD1 and MD2) in the North and South Nanling Mountains, respectively. Two bottlenecks and two expansions of effective population size were identified for the MD1 group of cultivated mandarins. However, in the MD2 group there was a long and continuous decrease in the population size. MD1 and MD2 mandarins showed different patterns of interspecific introgression from cultivated pummelo species. We identified a region of high divergence in an aconitate hydratase (ACO) gene involved in the regulation of citrate content, which was possibly under selection during the domestication of mandarin. This study provides concrete genetic evidence for the geographical origin of extant wild mandarin populations and sheds light on the domestication and evolutionary history of mandarin.
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Affiliation(s)
- Lun Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Fa He
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yue Huang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jiaxian He
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Shuizhi Yang
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, P.R. China
| | - Jiwu Zeng
- Fruit Tree Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Chongling Deng
- Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin 541000, P.R. China
| | - Xiaolin Jiang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yiwen Fang
- Institute of Citrus Science Research of Ganzhou City, Ganzhou 341000, P.R. China
| | - Shaohua Wen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Rangwei Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Huiwen Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xiaoming Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Guangyan Zhong
- Fruit Tree Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Chuanwu Chen
- Fruit Tree Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Xiang Yan
- Institute of Citrus Science Research of Ganzhou City, Ganzhou 341000, P.R. China
| | - Changfu Zhou
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, P.R. China
| | - Hongyan Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, P.R. China.
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Páscoa RN, Moreira S, Lopes JA, Sousa C. Citrus species and hybrids depicted by near- and mid-infrared spectroscopy. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:3953-3961. [PMID: 29385231 DOI: 10.1002/jsfa.8918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/12/2018] [Accepted: 01/21/2018] [Indexed: 06/07/2023]
Abstract
BACKGROUND Citrus trees are among the most cultivated plants in the world, with a high economic impact. The wide sexual compatibility among relatives gave rise to a large number of hybrids that are difficult to discriminate. This work sought to explore the ability of infrared spectroscopy to discriminate among Citrus species and/or hybrids and to contribute to the elucidation of its relatedness. RESULTS Adult leaves of 18 distinct Citrus plants were included in this work. Near- and mid-infrared (NIR and FTIR) spectra were acquired from leaves after harvesting and a drying period of 1 month. Spectra were modelled by principal component analysis and partial least squares discriminant analysis. Both techniques revealed a high discrimination potential (78.5-95.9%), being the best results achieved with NIR spectroscopy and air-dried leaves (95.9%). CONCLUSION Infrared spectroscopy was able to successfully discriminate several Citrus species and/or hybrids. Our results contributed also to enhance insights regarding the studied Citrus species and/or hybrids. Despite the benefit of including additional samples, the results herein obtained clearly pointed infrared spectroscopy as a reliable technique for Citrus species and/or hybrid discrimination. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Ricardo Nmj Páscoa
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Silvana Moreira
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - João A Lopes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Clara Sousa
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Chávez-Dulanto PN, Rey B, Ubillús C, Rázuri V, Bazán R, Sarmiento J. Foliar application of macro- and micronutrients for pest-mites control in citrus crops. Food Energy Secur 2018. [DOI: 10.1002/fes3.132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
| | - Benjamín Rey
- Servicios Especiales de Formulación Industrial SERFI; Lima Peru
| | | | | | - Rubén Bazán
- Faculty of Agronomy; Universidad Nacional Agraria La Molina; Lima Peru
| | - Jorge Sarmiento
- Faculty of Agronomy; Universidad Nacional Agraria La Molina; Lima Peru
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Shimizu T, Kitajima A, Nonaka K, Yoshioka T, Ohta S, Goto S, Toyoda A, Fujiyama A, Mochizuki T, Nagasaki H, Kaminuma E, Nakamura Y. Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes. PLoS One 2016; 11:e0166969. [PMID: 27902727 PMCID: PMC5130255 DOI: 10.1371/journal.pone.0166969] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/07/2016] [Indexed: 01/07/2023] Open
Abstract
Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy-Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.
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Affiliation(s)
- Tokurou Shimizu
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
- * E-mail:
| | - Akira Kitajima
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, Japan
| | - Keisuke Nonaka
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Terutaka Yoshioka
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Satoshi Ohta
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Shingo Goto
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Comparative Genomics laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- National Institute of Genetics, Comparative Genomics laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takako Mochizuki
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hideki Nagasaki
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Eli Kaminuma
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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Magalhães DM, Scholte LLS, Silva NV, Oliveira GC, Zipfel C, Takita MA, De Souza AA. LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects. BMC Genomics 2016; 17:623. [PMID: 27515968 PMCID: PMC4982124 DOI: 10.1186/s12864-016-2930-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/12/2016] [Indexed: 11/17/2022] Open
Abstract
Background Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of plant RLKs. The functions of most LRR-RLKs have remained undiscovered, and a few that have been experimentally characterized have been shown to have important roles in growth and development as well as in defense responses. Although RLK subfamilies have been previously studied in many plants, no comprehensive study has been performed on this gene family in Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (sweet orange). In addition, we used large-scale phylogenetic approaches to elucidate the evolutionary relationships of the LRR-RLKs and further narrowed the analysis to the LRR-XII group, which contains several previously described cell surface immune receptors. Results We built integrative protein signature databases for Citrus clementina and Citrus sinensis using all predicted protein sequences obtained from whole genomes. A total of 300 and 297 proteins were identified as LRR-RLKs in C. clementina and C. sinensis, respectively. Maximum-likelihood phylogenetic trees were estimated using Arabidopsis LRR-RLK as a template and they allowed us to classify Citrus LRR-RLKs into 16 groups. The LRR-XII group showed a remarkable expansion, containing approximately 150 paralogs encoded in each Citrus genome. Phylogenetic analysis also demonstrated the existence of two distinct LRR-XII clades, each one constituted mainly by RD and non-RD kinases. We identified 68 orthologous pairs from the C. clementina and C. sinensis LRR-XII genes. In addition, among the paralogs, we identified a subset of 78 and 62 clustered genes probably derived from tandem duplication events in the genomes of C. clementina and C. sinensis, respectively. Conclusions This work provided the first comprehensive evolutionary analysis of the LRR-RLKs in Citrus. A large expansion of LRR-XII in Citrus genomes suggests that it might play a key role in adaptive responses in host-pathogen co-evolution, related to the perennial life cycle and domestication of the citrus crop species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2930-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diogo M Magalhães
- Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.,Departamento de Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Larissa L S Scholte
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Nicholas V Silva
- Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil
| | - Guilherme C Oliveira
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil.,Instituto Tecnológico Vale - ITV, Belém, Pará, Brazil
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Marco A Takita
- Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil
| | - Alessandra A De Souza
- Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.
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Narula K, Ghosh S, Aggarwal PR, Sinha A, Chakraborty N, Chakraborty S. Comparative Proteomics of Oxalate Downregulated Tomatoes Points toward Cross Talk of Signal Components and Metabolic Consequences during Post-harvest Storage. FRONTIERS IN PLANT SCIENCE 2016; 7:1147. [PMID: 27555852 PMCID: PMC4977721 DOI: 10.3389/fpls.2016.01147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
Fruits of angiosperms evolved intricate regulatory machinery for sensorial attributes and storage quality after harvesting. Organic acid composition of storage organs forms the molecular and biochemical basis of organoleptic and nutritional qualities with metabolic specialization. Of these, oxalic acid (OA), determines the post-harvest quality in fruits. Tomato (Solanum lycopersicum) fruit has distinctive feature to undergo a shift from heterotrophic metabolism to carbon assimilation partitioning during storage. We have earlier shown that decarboxylative degradation of OA by FvOXDC leads to acid homeostasis besides increased fungal tolerance in E8.2-OXDC tomato. Here, we elucidate the metabolic consequences of oxalate down-regulation and molecular mechanisms that determine organoleptic features, signaling and hormonal regulation in E8.2-OXDC fruit during post-harvest storage. A comparative proteomics approach has been applied between wild-type and E8.2-OXDC tomato in temporal manner. The MS/MS analyses led to the identification of 32 and 39 differentially abundant proteins associated with primary and secondary metabolism, assimilation, biogenesis, and development in wild-type and E8.2-OXDC tomatoes, respectively. Next, we interrogated the proteome data using correlation network analysis that identified significant functional hubs pointing toward storage related coinciding processes through a common mechanism of function and modulation. Furthermore, physiochemical analyses exhibited reduced oxalic acid content with concomitant increase in citric acid, lycopene and marginal decrease in malic acid in E8.2-OXDC fruit. Nevertheless, E8.2-OXDC fruit maintained an optimal pH and a steady state acid pool. These might contribute to reorganization of pectin constituent, reduced membrane leakage and improved fruit firmness in E8.2-OXDC fruit with that of wild-type tomato during storage. Collectively, our study provides insights into kinetically controlled protein network, identified regulatory module for pathway formulation and provide basis toward understanding the context of storage quality maintenance as a consequence of oxalate downregulation in the sink organ.
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Antoine S, Pailly O, Gibon Y, Luro F, Santini J, Giannettini J, Berti L. Short- and long-term effects of carbohydrate limitation on sugar and organic acid accumulation during mandarin fruit growth. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:3906-3914. [PMID: 26694637 DOI: 10.1002/jsfa.7594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 12/14/2015] [Accepted: 12/17/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND The physiological roles of organic acids in fruit cells are not fully understood, especially in citrus, whereas the decline in titratable acidity during ripening shown by many citrus fruits is due to the utilization of citric acid. We induced carbohydrate depletion by removing source leaves at two key periods in mandarin development (early and full citric acid accumulation). Then, we assessed the resulting changes in the short term (within 48 h) and long term (several weeks until ripening). RESULTS Control mature fruits were characterized by elevated fresh weight, large diameters and high quantities of malic acid, citric acid and sucrose. At the same stage, fruits subjected to early or late defoliation had higher glucose, fructose, citric acid concentrations and lower sucrose concentrations. They differed only in their malic acid concentrations, which were higher in early defoliation fruits and similar in late defoliation fruits when compared to control fruits. Finally, fruits subjected to late defoliation were characterized by high proline and γ-aminobutyric acid concentrations, and low fructose and glucose concentrations. CONCLUSION We have shown that short- and long-term carbohydrate limitation modifies sugar and organic acid metabolism during mandarin fruit growth. © 2015 Society of Chemical Industry.
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Affiliation(s)
- Sandrine Antoine
- UMR AGAP Corse, station INRA, F-20230, San Giuliano, France
- CNRS, UMR 6134 SPE, Laboratoire Biochimie et Biologie Moléculaire du Végétal, F-20250, Corte, France
| | - Olivier Pailly
- Unité Expérimentale Citrus - INRA, F-20230, San Giuliano, France
| | - Yves Gibon
- Institut National de la Recherche Agronomique and, Université de Bordeaux, Unité Mixte de Recherche 1332, Biologie du Fruit et Pathologie, F-33883, Villenave d'Ornon, France
- Plateforme Métabolome-Fluxome Bordeaux, BP 81, F-33140, Villenave d'Ornon, France
| | - François Luro
- UMR AGAP Corse, station INRA, F-20230, San Giuliano, France
| | - Jérémie Santini
- CNRS, UMR 6134 SPE, Laboratoire Biochimie et Biologie Moléculaire du Végétal, F-20250, Corte, France
| | - Jean Giannettini
- CNRS, UMR 6134 SPE, Laboratoire Biochimie et Biologie Moléculaire du Végétal, F-20250, Corte, France
| | - Liliane Berti
- CNRS, UMR 6134 SPE, Laboratoire Biochimie et Biologie Moléculaire du Végétal, F-20250, Corte, France
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Ayadi M, Hanana M, Kharrat N, Merchaoui H, Marzoug RB, Lauvergeat V, Rebaï A, Mzid R. The WRKY Transcription Factor Family in Citrus: Valuable and Useful Candidate Genes for Citrus Breeding. Appl Biochem Biotechnol 2016; 180:516-543. [PMID: 27193354 DOI: 10.1007/s12010-016-2114-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/05/2016] [Indexed: 11/28/2022]
Abstract
WRKY transcription factors belong to a large family of plant transcriptional regulators whose members have been reported to be involved in a wide range of biological roles including plant development, adaptation to environmental constraints and response to several diseases. However, little or poor information is available about WRKY's in Citrus. The recent release of completely assembled genomes sequences of Citrus sinensis and Citrus clementina and the availability of ESTs sequences from other citrus species allowed us to perform a genome survey for Citrus WRKY proteins. In the present study, we identified 100 WRKY members from C. sinensis (51), C. clementina (48) and Citrus unshiu (1), and analyzed their chromosomal distribution, gene structure, gene duplication, syntenic relation and phylogenetic analysis. A phylogenetic tree of 100 Citrus WRKY sequences with their orthologs from Arabidopsis has distinguished seven groups. The CsWRKY genes were distributed across all ten sweet orange chromosomes. A comprehensive approach and an integrative analysis of Citrus WRKY gene expression revealed variable profiles of expression within tissues and stress conditions indicating functional diversification. Thus, candidate Citrus WRKY genes have been proposed as potentially involved in fruit acidification, essential oil biosynthesis and abiotic/biotic stress tolerance. Our results provided essential prerequisites for further WRKY genes cloning and functional analysis with an aim of citrus crop improvement.
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Affiliation(s)
- M Ayadi
- Laboratory of Extremophile Plants. Center of Biotechnology of Borj-Cédria (CBBC), BP 901, Hammam-lif, 2050, Tunisia. .,Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Road, P.O. Box 1177, 3018, Sfax, Tunisia.
| | - M Hanana
- Laboratory of Extremophile Plants. Center of Biotechnology of Borj-Cédria (CBBC), BP 901, Hammam-lif, 2050, Tunisia
| | - N Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Road, P.O. Box 1177, 3018, Sfax, Tunisia
| | - H Merchaoui
- Laboratory of Extremophile Plants. Center of Biotechnology of Borj-Cédria (CBBC), BP 901, Hammam-lif, 2050, Tunisia
| | - R Ben Marzoug
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Road, P.O. Box 1177, 3018, Sfax, Tunisia
| | - V Lauvergeat
- Unit 'Ecophysiology and Grape Functional Genomics' Institute of Vine and Wine Sciences, INRA Bordeaux-Aquitaine, 210 Chemin de Leysotte - CS 50008, 33882, Villenave d'Ornon Cedex, France
| | - A Rebaï
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Road, P.O. Box 1177, 3018, Sfax, Tunisia
| | - R Mzid
- Laboratory of Extremophile Plants. Center of Biotechnology of Borj-Cédria (CBBC), BP 901, Hammam-lif, 2050, Tunisia
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Omura M, Shimada T. Citrus breeding, genetics and genomics in Japan. BREEDING SCIENCE 2016; 66:3-17. [PMID: 27069387 PMCID: PMC4780800 DOI: 10.1270/jsbbs.66.3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/09/2015] [Indexed: 05/03/2023]
Abstract
Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering.
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Affiliation(s)
- Mitsuo Omura
- Faculty of Agriculture, Shizuoka University,
836 Ohya, Suruga, Shizuoka, Shizuoka 422-8529,
Japan
| | - Takehiko Shimada
- Citrus Research Division, NARO Institute of Fruit Tree Science,
485-6 Okitsunakacho, Shimizu, Shizuoka, Shizuoka 424-0292,
Japan
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Abstract
A range of leaf symptoms, including blotchy mottle, yellowing, and small, upright leaves with a variety of chlorotic patterns resembling those induced by zinc deficiencies, are associated with huanglongbing (HLB, yellow shoot disease), a worldwide destructive citrus disease. HLB is presumably caused by the phloem-limited fastidious prokaryotic α-proteobacterium ‘Candidatus Liberibacter spp.’ Previous studies focused on the proteome and transcriptome analyses of citrus 5 to 35 weeks after ‘Ca. L. spp.’ inoculation. In this study, gene expression profiles were analyzed from mandarin Citrus reticulate Blanco cv. jiaogan leaves after a 2 year infection with ‘Ca. L. asiaticus’. The Affymetrix microarray analysis explored 2,017 differentially expressed genes. Of the 1,364 genes had known functions, 938 (46.5%) were up-regulated. Genes related to photosynthesis, carbohydrate metabolic, and structure were mostly down-regulated, with rates of 92.7%, 61.0%, and 80.2%, respectively. Genes associated with oxidation-reduction and transport were mostly up-regulated with the rates of 75.0% and 64.6%, respectively. Our data analyses implied that the infection of ‘Ca. L. asiaticus’ could alter hormone crosstalk, inducing the jasmine acid pathway and depressing the ethylene and salicylic acid pathways in the citrus host. This study provides an enhanced insight into the host response of citrus to ‘Ca. L. asiaticus’ infection at a two-years infection stage.
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Huang XS, Zhang Q, Zhu D, Fu X, Wang M, Zhang Q, Moriguchi T, Liu JH. ICE1 of Poncirus trifoliata functions in cold tolerance by modulating polyamine levels through interacting with arginine decarboxylase. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3259-74. [PMID: 25873670 PMCID: PMC4449543 DOI: 10.1093/jxb/erv138] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
ICE1 (Inducer of CBF Expression 1) encodes a MYC-like basic helix-loop-helix transcription factor that acts as a central regulator of cold response. In this study, we elucidated the function and underlying mechanisms of PtrICE1 from trifoliate orange [Poncirus trifoliata (L.) Raf.]. PtrICE1 was upregulated by cold, dehydration, and salt, with the greatest induction under cold conditions. PtrICE1 was localized in the nucleus and could bind to a MYC-recognizing sequence. Ectopic expression of PtrICE1 in tobacco and lemon conferred enhanced tolerance to cold stresses at either chilling or freezing temperatures. Yeast two-hybrid screening revealed that 21 proteins belonged to the PtrICE1 interactome, in which PtADC (arginine decarboxylase) was confirmed as a bona fide protein interacting with PtrICE1. Transcript levels of ADC genes in the transgenic lines were slightly elevated under normal growth condition but substantially increased under cold conditions, consistent with changes in free polyamine levels. By contrast, accumulation of the reactive oxygen species, H2O2 and O2 (-), was appreciably alleviated in the transgenic lines under cold stress. Higher activities of antioxidant enzymes, such as superoxide dismutase and catalase, were detected in the transgenic lines under cold conditions. Taken together, these results demonstrated that PtrICE1 plays a positive role in cold tolerance, which may be due to modulation of polyamine levels through interacting with the ADC gene.
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Affiliation(s)
- Xiao-San Huang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Qinghua Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dexin Zhu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xingzheng Fu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Min Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Qian Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Takaya Moriguchi
- National Institute of Fruit Tree Science, Tsukuba 305-8605, Japan
| | - Ji-Hong Liu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
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Guo F, Yu H, Xu Q, Deng X. Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis). BMC PLANT BIOLOGY 2015; 15:44. [PMID: 25849782 PMCID: PMC4352283 DOI: 10.1186/s12870-015-0435-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/22/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND The external colour of fruit is a crucial quality feature, and the external coloration of most citrus fruits is due to the accumulation of carotenoids. The molecular regulation of carotenoid biosynthesis and accumulation in pericarp is limited due to the lack of mutant. In this work, an orange-pericarp mutant (MT) which showed altered pigmentation in the pericarp was used to identify genes potentially related to the regulation of carotenoid accumulation in the pericarp. RESULTS High Performance Liquid Chromatography (HPLC) analysis revealed that the pericarp from MT fruits had a 10.5-fold increase of β-carotene content over that of the Wild Type (WT). Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of all downstream carotenogenic genes was lower in MT than in WT, suggesting that down-regulation is critical for the β-carotene increase in the MT pericarp. RNA-seq analysis of the transcriptome revealed extensive changes in the MT gene expression level, with 168 genes down-regulated and 135 genes up-regulated. Gene ontology (GO) and KEGG pathway analyses indicated seven reliable metabolic pathways are altered in the mutant, including carbon metabolism, starch and sucrose metabolism and biosynthesis of amino acids. The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp. CONCLUSIONS This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo. Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.
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Affiliation(s)
- Fei Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
| | - Huiwen Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
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Inactivation, aggregation, secondary and tertiary structural changes of germin-like protein in Satsuma mandarine with high polyphenol oxidase activity induced by ultrasonic processing. Biophys Chem 2014; 197:18-24. [PMID: 25522206 DOI: 10.1016/j.bpc.2014.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 10/24/2022]
Abstract
The inhibition of Polyphenol oxidase (PPO) in plants has been widely researched for their important roles in browning reaction. A newly found germin-like protein (GLP) with high PPO activity in Satsuma mandarine was inactivated by low-frequency high-intensity ultrasonic (20 kHz) processing. The effects of ultrasound on PPO activity and structure of GLP were investigated using dynamic light scattering (DLS) analysis, transmission electron microscopy (TEM), circular dichroism (CD) spectral measurement and fluorescence spectral measurement. The lowest PPO activity achieved was 27.4% following ultrasonication for 30 min at 400 W. DLS analysis showed ultrasound caused both aggregation and dissociation of GLP particles. TEM images also demonstrated protein aggregation phenomena. CD spectra exhibited a certain number of loss in α-helix structure content. Fluorescence spectra showed remarkable increase in fluorescence intensity with tiny blue-shift following ultrasonication. In conclusion, ultrasound applied in this study induced structural changes of GLP and eventually inactivated PPO activity.
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Pinheiro TT, Figueira A, Latado RR. Early-flowering sweet orange mutant 'x11' as a model for functional genomic studies of Citrus. BMC Res Notes 2014; 7:511. [PMID: 25108567 PMCID: PMC4267115 DOI: 10.1186/1756-0500-7-511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 08/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There had been many reports on genetic transformation of Citrus for functional genomic studies but few included genes associated with flower or fruit traits. A major reason for this might derive from the extensive juvenile stage of Citrus plants when regenerated from juvenile explants (epicotyls, cotyledon or calli), which delays the observation of the resulting phenotype. Alternatives include the use of explants from adult tissues, which sometimes may be recalcitrant to regeneration or transformation, or of early-flowering genotypes. However, there is no report about the use of early-flowering sweet orange mutants for functional genomic studies. RESULTS Here, we propose a sweet orange spontaneous early-flowering mutant, named 'x11', as a platform for Citrus functional genomic studies, particularly for genes associated with flower or fruit traits. We report a procedure for efficient regeneration and transformation using epicotyl segment explants of 'x11' and Agrobacterium tumefaciens as a proof-of-concept. The average transformation efficiency was 18.6%, but reached 29.6% in the best protocol tested. Among 270 positive shoots, five were in vitro micrografted and acclimatized, followed by evaluation of transgene expression by quantitative amplification of reversed transcripts (RT-qPCR) and determination of the number of copies inserted. Four of these plants, containing from one to four copies of the transgene, exhibited the first flowers within three months after ex vitro establishment, and the other, two months later, regardless of the period of the year. Flowers of transgenic plants displayed fertile pollen and gynoecium, with self-pollination inducing fruit development with seeds. Histochemical staining for β-glucuronidase activity using stem segments, flowers and fruits from 5 to 7 month-old acclimatized transgenic plants confirmed the constitutive transgene expression in these organs. CONCLUSION The 'x11' sweet orange is suitable for functional genomics studies with a satisfactory transformation rate, and it can be considered a good model for functional genomic studies in commercial sweet oranges, for traits related to flower and fruit.
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Affiliation(s)
- Thaísa Tessutti Pinheiro
- />Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP 13400-970 Brazil
- />Centro de Citricultura “Sylvio Moreira”, Instituto Agronômico, CP 04, Cordeirópolis, SP 13490-970 Brazil
| | - Antonio Figueira
- />Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP 13400-970 Brazil
| | - Rodrigo Rocha Latado
- />Centro de Citricultura “Sylvio Moreira”, Instituto Agronômico, CP 04, Cordeirópolis, SP 13490-970 Brazil
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Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astúa J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 2014; 32:656-62. [PMID: 24908277 PMCID: PMC4113729 DOI: 10.1038/nbt.2906] [Citation(s) in RCA: 335] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/14/2014] [Indexed: 01/21/2023]
Abstract
Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
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Affiliation(s)
- G. Albert Wu
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Simon Prochnik
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jerry Jenkins
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Jerome Salse
- INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France
| | - Uffe Hellsten
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | - Javier Terol
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Kamel Jabbari
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | | | | | | | - Andrea Zuccolo
- Istituto di Genomica Applicata, Udine, Italy
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jarrod Chapman
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Francisco R. Tadeo
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Leandro H. Estornell
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Juan V. Muñoz-Sanz
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Victoria Ibanez
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Amparo Herrero-Ortega
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Pablo Aleza
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | | | | | - Dominique Brunel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- INRA, US EPGV_1279, Evry, France
| | | | - Chunxian Chen
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - William G. Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Brian Desany
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Chinnappa Kodira
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Mohammed Mohiuddin
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Tim Harkins
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Karin Fredrikson
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Paul Burns
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alexandre Lomsadze
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark Borodovsky
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Giuseppe Reforgiato
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy
| | - Juliana Freitas-Astúa
- Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil
- Embrapa Cassava and Fruits, Cruz das Almas, BA, Brazil
| | - Francis Quetier
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | - Mikeal Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | - Jeremy Schmutz
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy
| | | | - Manuel Talon
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Olivier Jaillon
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | | | - Frederick Gmitter
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - Daniel Rokhsar
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Division of Genetics, Genomics, and Development, University of California, Berkeley, CA, USA
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48
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Jia H, Wang N. Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One 2014; 9:e93806. [PMID: 24710347 PMCID: PMC3977896 DOI: 10.1371/journal.pone.0093806] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 03/06/2014] [Indexed: 12/27/2022] Open
Abstract
Genetic modification, including plant breeding, has been widely used to improve crop yield and quality, as well as to increase disease resistance. Targeted genome engineering is expected to contribute significantly to future varietal improvement, and genome editing technologies using zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9/single guide RNA (sgRNA) have already been successfully used to genetically modify plants. However, to date, there has been no reported use of any of the current genome editing approaches in sweet orange, an important fruit crop. In this study, we first developed a novel tool, Xcc-facilitated agroinfiltration, for enhancing transient protein expression in sweet orange leaves. We then successfully employed Xcc-facilitated agroinfiltration to deliver Cas9, along with a synthetic sgRNA targeting the CsPDS gene, into sweet orange. DNA sequencing confirmed that the CsPDS gene was mutated at the target site in treated sweet orange leaves. The mutation rate using the Cas9/sgRNA system was approximately 3.2 to 3.9%. Off-target mutagenesis was not detected for CsPDS-related DNA sequences in our study. This is the first report of targeted genome modification in citrus using the Cas9/sgRNA system-a system that holds significant promise for the study of citrus gene function and for targeted genetic modification.
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Affiliation(s)
- Hongge Jia
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, Florida, United States of America
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, Florida, United States of America
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49
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Podda A, Simili M, Del Carratore R, Mouhaya W, Morillon R, Maserti BE. Expression profiling of two stress-inducible genes encoding for miraculin-like proteins in citrus plants under insect infestation or salinity stress. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:45-54. [PMID: 24001970 DOI: 10.1016/j.jplph.2013.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/01/2013] [Accepted: 08/01/2013] [Indexed: 06/02/2023]
Abstract
The expression of two genes, namely Mir1 and Mir3 and the abundance of their encoded proteins, the putative miraculin-like proteins, MLP1 and MLP3, showing similarity to the Kunitz family of protease inhibitors, were monitored in the leaves of the citrus variety, 'Clementine' after Tetranychus urticae infestation and elicitor treatments, or in the leaves of three other diploid citrus: 'Willow leaf', 'Cleopatra' mandarins and 'Trifoliate' orange, as well as their respective doubled diploids and the allotetraploid somatic hybrid 'FLHORAG1' under salt stress. RT-PCR and 2-DE indicated that Mir1 and Mir3 and their products were present at low-basal expression in all citrus genotypes. Both genes and products were induced in the 'Clementine' leaves infested by T. urticae, but a contrasting profile was observed under elicitor treatments. Under salt stress, the two genes showed an expression pattern contrasting each other and depending on the genotypes. 'Cleopatra' mandarin, 'Trifoliate' orange and 'FLHORAG1' presented overexpression of Mir3 and MLP3 and decreased levels of Mir1 and MPL1. The opposite behaviour was found in 'Willow leaf' mandarin. The positive correlation of the expression profile of the two genes with that of a gene encoding a putative apoplastic cysteine protease (CysP) might suggest a possible interaction of the respective encoded proteins during the response to biotic stress. Under salt stress, CysP and Mir 1 showed a similar expression pattern but only at transcript level. The possible occurrence of post-translational CysP regulation is discussed.
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Affiliation(s)
- A Podda
- CNR-IBF, Istituto di Biofisica, Dipartimento di Scienze fisiche e tecnologie della materia, Italy
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50
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Perdiguero P, Collada C, Soto Á. Novel dehydrins lacking complete K-segments in Pinaceae. The exception rather than the rule. FRONTIERS IN PLANT SCIENCE 2014; 5:682. [PMID: 25520734 PMCID: PMC4251312 DOI: 10.3389/fpls.2014.00682] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/15/2014] [Indexed: 05/13/2023]
Abstract
Dehydrins are thought to play an essential role in the plant response, acclimation and tolerance to different abiotic stresses, such as cold and drought. These proteins contain conserved and repeated segments in their amino acid sequence, used for their classification. Thus, dehydrins from angiosperms present different repetitions of the segments Y, S, and K, while gymnosperm dehydrins show A, E, S, and K segments. The only fragment present in all the dehydrins described to date is the K-segment. Different works suggest the K-segment is involved in key protective functions during dehydration stress, mainly stabilizing membranes. In this work, we describe for the first time two Pinus pinaster proteins with truncated K-segments and a third one completely lacking K-segments, but whose sequence homology leads us to consider them still as dehydrins. qRT-PCR expression analysis show a significant induction of these dehydrins during a severe and prolonged drought stress. By in silico analysis we confirmed the presence of these dehydrins in other Pinaceae species, breaking the convention regarding the compulsory presence of K-segments in these proteins. The way of action of these unusual dehydrins remains unrevealed.
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Affiliation(s)
- Pedro Perdiguero
- GENFOR Grupo de Investigación en Genética y Fisiología Forestal, Universidad Politécnica de MadridMadrid, Spain
- Unidad Mixta de Genómica y Ecofisiología ForestalINIA/UPM, Madrid, Spain
| | - Carmen Collada
- GENFOR Grupo de Investigación en Genética y Fisiología Forestal, Universidad Politécnica de MadridMadrid, Spain
- Unidad Mixta de Genómica y Ecofisiología ForestalINIA/UPM, Madrid, Spain
| | - Álvaro Soto
- GENFOR Grupo de Investigación en Genética y Fisiología Forestal, Universidad Politécnica de MadridMadrid, Spain
- Unidad Mixta de Genómica y Ecofisiología ForestalINIA/UPM, Madrid, Spain
- *Correspondence: Álvaro Soto, GENFOR Grupo de Investigación en Genética y Fisiología Forestal, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, E-28040 Madrid, Spain e-mail:
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