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Ma X, Sheng L, Li F, Zhou T, Guo J, Chang Y, Yang J, Jin Y, Chen Y, Lu X. Seasonal drought promotes citrate accumulation in citrus fruit through the CsABF3-activated CsAN1-CsPH8 pathway. THE NEW PHYTOLOGIST 2024; 242:1131-1145. [PMID: 38482565 DOI: 10.1111/nph.19671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 02/12/2024] [Indexed: 04/12/2024]
Abstract
Plenty of rainfall but unevenly seasonal distribution happens regularly in southern China. Seasonal drought from summer to early autumn leads to citrus fruit acidification, but how seasonal drought regulates citrate accumulation remains unknown. Herein, we employed a set of physiological, biochemical, and molecular approaches to reveal that CsABF3 responds to seasonal drought stress and modulates citrate accumulation in citrus fruits by directly regulating CsAN1 and CsPH8. Here, we demonstrated that irreversible acidification of citrus fruits is caused by drought lasting for > 30 d during the fruit enlargement stage. We investigated the transcriptome characteristics of fruits affected by drought and corroborated the pivotal roles of a bHLH transcription factor (CsAN1) and a P3A-ATPase gene (CsPH8) in regulating citrate accumulation in response to drought. Abscisic acid (ABA)-responsive element binding factor 3 (CsABF3) was upregulated by drought in an ABA-dependent manner. CsABF3 activated CsAN1 and CsPH8 expression by directly and specifically binding to the ABA-responsive elements (ABREs) in the promoters and positively regulated citrate accumulation. Taken together, this study sheds new light on the regulatory module ABA-CsABF3-CsAN1-CsPH8 responsible for citrate accumulation under drought stress, which advances our understanding of quality formation of citrus fruit.
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Affiliation(s)
- Xiaochuan Ma
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- National Center for Citrus Improvement, 410128, Changsha, China
| | - Ling Sheng
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- National Center for Citrus Improvement, 410128, Changsha, China
| | - Feifei Li
- Institute of Horticulture, Hunan Academy of Agricultural Science, 410125, Changsha, China
| | - Tie Zhou
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- National Center for Citrus Improvement, 410128, Changsha, China
| | - Jing Guo
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- National Center for Citrus Improvement, 410128, Changsha, China
| | - Yuanyuan Chang
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- National Center for Citrus Improvement, 410128, Changsha, China
| | - Junfeng Yang
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- National Center for Citrus Improvement, 410128, Changsha, China
| | - Yan Jin
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- National Center for Citrus Improvement, 410128, Changsha, China
| | - Yuewen Chen
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- National Center for Citrus Improvement, 410128, Changsha, China
| | - Xiaopeng Lu
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- National Center for Citrus Improvement, 410128, Changsha, China
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Jin Y, Liao M, Li N, Ma X, Zhang H, Han J, Li D, Yang J, Lu X, Long G, Deng Z, Sheng L. Weighted gene coexpression correlation network analysis reveals the potential molecular regulatory mechanism of citrate and anthocyanin accumulation between postharvest 'Bingtangcheng' and 'Tarocco' blood orange fruit. BMC PLANT BIOLOGY 2023; 23:296. [PMID: 37268922 DOI: 10.1186/s12870-023-04309-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Organic acids and anthocyanins are the most important compounds for the flavor and nutritional quality of citrus fruit. However, there are few reports on the involvement of co-regulation of citrate and anthocyanin metabolism. Here, we performed a comparative transcriptome analysis to elucidate the genes and pathways involved in both citrate and anthocyanin accumulation in postharvest citrus fruit with 'Tarocco' blood orange (TBO; high accumulation) and 'Bingtangcheng' sweet orange (BTSO; low accumulation). RESULTS A robust core set of 825 DEGs were found to be temporally associated with citrate and anthocyanin accumulation throughout the storage period through transcriptome analysis. Further according to the results of weighted gene coexpression correlation network analysis (WGCNA), the turquoise and brown module was highly positively correlated with both of the content of citrate and anthocyanin, and p-type ATPase (PH8), phosphoenolpyruvate carboxylase kinase (PEPCK), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H) and glutathione S transferase (GST) were considered key structural genes. Moreover, MYB family transcription factor (PH4), Zinc finger PHD-type transcription factor (CHR4, HAC12), Zinc finger SWIM-type transcription factor (FAR1) and Zinc finger C3H1-type transcription factor (ATC3H64) were considered hub genes related to these structural genes. Further qRT-PCR analysis verified that these transcription factors were highly expressed in TBO fruit and their expression profiles were significantly positively correlated with the structural genes of citrate and anthocyanin metabolism as well as the content of citrate and anthocyanin content. CONCLUSIONS The findings suggest that the CHR4, FAR1, ATC3H64 and HAC12 may be the new transcription regulators participate in controlling the level of citrate and anthocyanin in postharvest TBO fruit in addition to PH4. These results may providing new insight into the regulation mechanism of citrate and anthocyanin accumulation in citrus fruit.
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Affiliation(s)
- Yan Jin
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Manyu Liao
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Na Li
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Xiaoqian Ma
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Huimin Zhang
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Jian Han
- Hunan Horticultural Research Institute, Changsha, CS, China
| | - Dazhi Li
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Junfeng Yang
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Xiaopeng Lu
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Guiyou Long
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Ziniu Deng
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China
| | - Ling Sheng
- National Center for Citrus Improvement Changsha, College of Horticulture, Hunan Agricultural University, Changsha, CS, China.
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Manzoor I, Samantara K, Bhat MS, Farooq I, Bhat KM, Mir MA, Wani SH. Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios. FRONTIERS IN PLANT SCIENCE 2023; 13:1048217. [PMID: 36743560 PMCID: PMC9893892 DOI: 10.3389/fpls.2022.1048217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/09/2022] [Indexed: 06/18/2023]
Abstract
Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.
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Affiliation(s)
- Ikra Manzoor
- Division of Fruit Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Kajal Samantara
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Momin Showkat Bhat
- Division of Floriculture and Landscape Architecture, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Iqra Farooq
- Field Station Bonera, Pulwama, Council of Industrial and Scientific Research (CSIR) Indian Institute of Integrative Medicine, J&K, Jammu, India
| | - Khalid Mushtaq Bhat
- Division of Fruit Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Mohammad Amin Mir
- Ambri Apple Research Centre, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shopian, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, Anantnag, India
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Qiu D, Zhu C, Fan R, Mao G, Wu P, Zeng J. Arsenic inhibits citric acid accumulation via downregulating vacuolar proton pump gene expression in citrus fruits. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114153. [PMID: 36252515 DOI: 10.1016/j.ecoenv.2022.114153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Citric acid content is a critical quality determinant in citrus (Citrus spp.) fruits. Although arsenic (As) can effectively reduce citric acid content to improve citrus fruit quality, it can have adverse environmental effects. The discovery of nontoxic substitutes is hampered by the incomplete elucidation of the underlying mechanisms of As action in citrus fruits. Metabolic, transcriptomic, and physiological analyses were employed to investigate As action on citric acid accumulation to discover the mechanisms of As action in citrus. The enzyme activity related to citrate biosynthesis was not inhibited and the content of the involved metabolites was not reduced in As-treated fruits. However, the proton pump genes CitPH5 and CitPH1 control the vacuolar citric acid accumulation and transcription factor genes CitTT8 and CitMYB5, which regulate CitPH5 and CitPH1, were downregulated. The oxidative stress-response genes were upregulated in As-treated fruits. The reactive oxygen species (ROS) treatment also downregulated CitTT8 and CitMYB5 in juice cells. The mitochondrial ROS production rate increased in As-treated fruits. AsIII was more potent in stimulating isolated mitochondria to overproduce ROS compared to AsV. Our results indicate that the As inhibition of citric acid accumulation may be primarily due to the transcriptional downregulation of CitPH5, CitPH1, CitTT8, and CitMYB5. As-induced oxidative stress signaling may operate upstream to downregulate these acid regulator genes. Mitochondrial thiol proteins may be the principal targets of As action in citrus fruits.
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Affiliation(s)
- Diyang Qiu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Congyi Zhu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Ruiyi Fan
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Genlin Mao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Pingzhi Wu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Jiwu Zeng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
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Borredá C, Perez-Roman E, Talon M, Terol J. Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression. BMC PLANT BIOLOGY 2022; 22:123. [PMID: 35300613 PMCID: PMC8928680 DOI: 10.1186/s12870-022-03509-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/03/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break. RESULTS Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions. CONCLUSION In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.
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Affiliation(s)
- Carles Borredá
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Estela Perez-Roman
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
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6
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Mathiazhagan M, Chidambara B, Hunashikatti LR, Ravishankar KV. Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content. Genes (Basel) 2021; 12:1881. [PMID: 34946829 PMCID: PMC8701245 DOI: 10.3390/genes12121881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.
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Affiliation(s)
| | | | | | - Kundapura V. Ravishankar
- Division of Basic Sciences, ICAR Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru 560089, India; (M.M.); (B.C.); (L.R.H.)
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Li S, Cerri M, Strazzer P, Li Y, Spelt C, Bliek M, Vandenbussche M, Martínez-Calvó E, Lai B, Reale L, Koes R, Quattrocchio FM. An ancient RAB5 governs the formation of additional vacuoles and cell shape in petunia petals. Cell Rep 2021; 36:109749. [PMID: 34592147 DOI: 10.1016/j.celrep.2021.109749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/11/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022] Open
Abstract
Homologous ("canonical") RAB5 proteins regulate endosomal trafficking to lysosomes in animals and to the central vacuole in plants. Epidermal petal cells contain small vacuoles (vacuolinos) that serve as intermediate stations for proteins on their way to the central vacuole. Here, we show that transcription factors required for vacuolino formation in petunia induce expression of RAB5a. RAB5a defines a previously unrecognized clade of canonical RAB5s that is evolutionarily and functionally distinct from ARA7-type RAB5s, which act in trafficking to the vacuole. Loss of RAB5a reduces cell height and abolishes vacuolino formation, which cannot be rescued by the ARA7 homologs, whereas constitutive RAB5a (over)expression alters the conical cell shape and promotes homotypic vacuolino fusion, resulting in oversized vacuolinos. These findings provide a rare example of how gene duplication and neofunctionalization increased the complexity of membrane trafficking during evolution and suggest a mechanism by which cells may form multiple vacuoles with distinct content and function.
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Affiliation(s)
- Shuangjiang Li
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Martina Cerri
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Pamela Strazzer
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Yanbang Li
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Cornelis Spelt
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Mattijs Bliek
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Enric Martínez-Calvó
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Biao Lai
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Lara Reale
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Ronald Koes
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands.
| | - Francesca M Quattrocchio
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
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Feng G, Wu J, Xu Y, Lu L, Yi H. High-spatiotemporal-resolution transcriptomes provide insights into fruit development and ripening in Citrus sinensis. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1337-1353. [PMID: 33471410 PMCID: PMC8313135 DOI: 10.1111/pbi.13549] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 05/02/2023]
Abstract
Citrus fruit has a unique structure with soft leathery peel and pulp containing vascular bundles and several segments with many juice sacs. The function and morphology of each fruit tissue are different. Therefore, analysis at the organ-wide or mixed-tissue level inevitably obscures many tissue-specific phenomena. High-throughput RNA sequencing was used to profile Citrus sinensis fruit development based on four fruit tissue types and six development stages from young fruits to ripe fruits. Using a coexpression network analysis, modules of coexpressed genes and hub genes of tissue-specific networks were identified. Of particular, importance is the discovery of the regulatory network of phytohormones during citrus fruit development and ripening. A model was proposed to illustrate how ABF2 mediates the ABA signalling involved in sucrose transport, chlorophyll degradation, auxin homoeostasis, carotenoid and ABA biosynthesis, and cell wall metabolism during citrus fruit development. Moreover, we depicted the detailed spatiotemporal expression patterns of the genes involved in sucrose and citric acid metabolism in citrus fruit and identified several key genes that may play crucial roles in sucrose and citric acid accumulation in the juice sac, such as SWEET15 and CsPH8. The high spatial and temporal resolution of our data provides important insights into the molecular networks underlying citrus fruit development and ripening.
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Affiliation(s)
- Guizhi Feng
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Juxun Wu
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Yanhui Xu
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Liqing Lu
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Hualin Yi
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
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9
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Fu H, Zeng T, Zhao Y, Luo T, Deng H, Meng C, Luo J, Wang C. Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses. Genes (Basel) 2021; 12:genes12030449. [PMID: 33801035 PMCID: PMC8004015 DOI: 10.3390/genes12030449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022] Open
Abstract
Green chrysanthemums are difficult to breed but have high commercial value. The molecular basis for the green petal color in chrysanthemum is not fully understood. This was investigated in the present study by RNA sequencing analysis of white and green ray florets collected at three stages of flower development from the F1 progeny of the cross between Chrysanthemum × morifolium “Lüdingdang” with green-petaled flowers and Chrysanthemum vistitum with white-petaled flowers. The chlorophyll content was higher and chloroplast degradation was slower in green pools than in white pools at each developmental stage. Transcriptome analysis revealed that genes that were differentially expressed between the two pools were enriched in pathways related to chlorophyll metabolism and photosynthesis. We identified the transcription factor genes CmCOLa, CmCOLb, CmERF, and CmbHLH as regulators of the green flower color in chrysanthemum by differential expression analysis and weighted gene co-expression network analysis. These findings can guide future efforts to improve the color palette of chrysanthemum flowers through genetic engineering.
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Zhang Y, Ye J, Liu C, Xu Q, Long L, Deng X. Citrus PH4-Noemi regulatory complex is involved in proanthocyanidin biosynthesis via a positive feedback loop. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1306-1321. [PMID: 31728522 PMCID: PMC7031078 DOI: 10.1093/jxb/erz506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/06/2019] [Indexed: 05/21/2023]
Abstract
Proanthocyanidins (PAs; or condensed tannins) are a major class of flavonoids that contribute to citrus fruit quality. However, the molecular mechanism responsible for PA biosynthesis and accumulation in citrus remains unclear. Here, we identify a PH4-Noemi regulatory complex that regulates proanthocyanidin biosynthesis in citrus. Overexpression of PH4 or Noemi in citrus calli activated the expression of PA biosynthetic genes and significantly increased the PA content. Interestingly, Noemi was also shown to be up-regulated in CsPH4-overexpressing lines compared with wild-type calli. Simultaneously, CsPH4 partially complemented the PA-deficient phenotype of the Arabidopsis tt2 mutant and promoted PA accumulation in the wild-type. Further analysis revealed that CsPH4 interacted with Noemi, and together these proteins synergistically activated the expression of PA biosynthetic genes by directly binding to the MYB-recognizing elements (MRE) of the promoters of these genes. Moreover, CsPH4 could directly bind to the promoter of Noemi and up-regulate the expression of this gene. These findings explain how the CsPH4-Noemi regulatory complex contributes to the activation of PA biosynthetic genes via a positive feedback loop and provide new insights into the molecular mechanisms underlying PA biosynthesis, which can be effectively employed for metabolic engineering to improve citrus fruit quality.
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Affiliation(s)
- Yin Zhang
- 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
| | - Chaoyang Liu
- 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
| | - Lichang Long
- Agriculture Bureau of Hongjiang City, Hongjiang, Hunan, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
- Correspondence:
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11
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Dong T, Xiong B, Huang S, Liao L, Qiu X, Sun G, He Y, Duan C, Wang X, Zhang X, Li S, Zhu J, Wang Z. Investigation of the cause of reduced sugar content in Kiyomi tangor fruit of Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) rootstock. Sci Rep 2019; 9:19263. [PMID: 31848437 PMCID: PMC6917820 DOI: 10.1038/s41598-019-55957-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/30/2019] [Indexed: 12/24/2022] Open
Abstract
Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) (Cj) rootstock is effective in Citrus production; however, when Cj rootstock was used, sugar content in Kiyomi tangor fruit was significantly lower than that in the fruit produced using Poncirus trifoliata (L.) Raf. rootstock (Pt). Therefore, using K. tangor, we explored the cause of this difference, determining sugar accumulation, sucrose-metabolism enzyme activities, and gene expression. Before ripening, sugar content in fruits with Cj rootstock was significantly lower than that in fruits with Pt rootstock, due to low fructose and sucrose content. Sucrose phosphate synthase (SPS) activity of Pt was higher than that of Cj in the early growth stage (at 90–210 days after anthesis), however it was opposite at 240–300 days after anthesis. Additionally, neutral invertase (NI) activity of Pt was higher than that of Cj. Gene expression in Pt was higher than that in Cj, but is was essentially the same at maturity. SPS and NI activities and CitSPS1 expression were positively correlated with sucrose, fructose, and glucose content, but CSCW1 expression was negatively correlated with the sugars. Overall, the weak flavour of K. tangor fruit with Cj rootstock was regulated by the sucrose metabolism-related enzymes and gene expression.
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Affiliation(s)
- Tiantian Dong
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bo Xiong
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shengjia Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ling Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xia Qiu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Guochao Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yunzhenzi He
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Changwen Duan
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaojia Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xu Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Sichen Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jin Zhu
- Sichuan Horticultural Crop Extension Station, 610041, Sichuan, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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12
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Shi CY, Hussain SB, Yang H, Bai YX, Khan MA, Liu YZ. CsPH8, a P-type proton pump gene, plays a key role in the diversity of citric acid accumulation in citrus fruits. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110288. [PMID: 31623791 DOI: 10.1016/j.plantsci.2019.110288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
Citric acid homeostasis patterns and its content are diversified among the fruits of citrus cultivars, but the cause remained unclear. In this study we showed that changes of citric acid content were highly associated with the expression profiles of a P-type proton pump gene (CsPH8) in the fruits of six citrus cultivars; moreover, analysis of 21 different fruit samples indicated that the correlation coefficient between titratable acid content and CsPH8 transcript level was 0.5837 with a significant level (P < 0.05). Overexpression of CsPH8 in acidless pumelo juice sacs, strawberry fruit, and tomato fruit significantly increased the titratable acid or citric acid content besides the gene transcript level. On another hand, RNA interference of CsPH8 in acidic pumelo juice sacs significantly decreased the CsPH8 transcript level and the titratable acid or citric acid content as well. In addition, severe drought significantly increased the CsPH8 transcript level besides the titratable acid content. Taken together, these findings address the function of CsPH8 in citrus vacuolar acidification, confirm that CsPH8 plays a key role in the variation of citric acid content, and supported that the acid fluctuation influenced by drought, is at least partly due to the change of CsPH8 transcript level.
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Affiliation(s)
- Cai-Yun Shi
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, PR China; College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Syed Bilal Hussain
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, PR China; College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Huan Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, PR China; College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ying-Xin Bai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, PR China; College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Muhammad Abbas Khan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, PR China; College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yong-Zhong Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, PR China; College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China.
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Feng G, Wu J, Yi H. Global tissue-specific transcriptome analysis of Citrus sinensis fruit across six developmental stages. Sci Data 2019; 6:153. [PMID: 31434903 PMCID: PMC6704135 DOI: 10.1038/s41597-019-0162-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022] Open
Abstract
Citrus sinensis fruit is a type of nonclimacteric fruit that mainly consists of four tissues: the epicarp, albedo, segment membrane and juice sac. The fruit quality is determined by the characteristics of these four tissues. However, our knowledge of the molecular processes that occur in these four tissues during citrus fruit development and ripening is limited. Tissue-specific transcriptomes provide a comprehensive and detailed molecular regulatory network of citrus fruit development and ripening. In our study, we collected four types of tissue from C. sinensis fruits at six developmental stages. A total of 72 libraries were constructed from 24 samples (each sample had three replicates), and the transcriptomes were sequenced by an Illumina HiSeq 4000. The comprehensive analyses of the transcriptomes from the four tissues and six developmental stages presented here provide a valuable resource for the discovery of the molecular networks underlying citrus fruit development and ripening.
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Affiliation(s)
- Guizhi Feng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Juxun Wu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Hualin Yi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
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De Ollas C, Morillón R, Fotopoulos V, Puértolas J, Ollitrault P, Gómez-Cadenas A, Arbona V. Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:427. [PMID: 31057569 PMCID: PMC6477659 DOI: 10.3389/fpls.2019.00427] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
The Mediterranean basin is especially sensitive to the adverse outcomes of climate change and especially to variations in rainfall patterns and the incidence of extremely high temperatures. These two concurring adverse environmental conditions will surely have a detrimental effect on crop performance and productivity that will be particularly severe on woody crops such as citrus, olive and grapevine that define the backbone of traditional Mediterranean agriculture. These woody species have been traditionally selected for traits such as improved fruit yield and quality or alteration in harvesting periods, leaving out traits related to plant field performance. This is currently a crucial aspect due to the progressive and imminent effects of global climate change. Although complete genome sequence exists for sweet orange (Citrus sinensis) and clementine (Citrus clementina), olive tree (Olea europaea) and grapevine (Vitis vinifera), the development of biotechnological tools to improve stress tolerance still relies on the study of the available genetic resources including interspecific hybrids, naturally occurring (or induced) polyploids and wild relatives under field conditions. To this respect, post-genomic era studies including transcriptomics, metabolomics and proteomics provide a wide and unbiased view of plant physiology and biochemistry under adverse environmental conditions that, along with high-throughput phenotyping, could contribute to the characterization of plant genotypes exhibiting physiological and/or genetic traits that are correlated to abiotic stress tolerance. The ultimate goal of precision agriculture is to improve crop productivity, in terms of yield and quality, making a sustainable use of land and water resources under adverse environmental conditions using all available biotechnological tools and high-throughput phenotyping. This review focuses on the current state-of-the-art of biotechnological tools such as high throughput -omics and phenotyping on grapevine, citrus and olive and their contribution to plant breeding programs.
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Affiliation(s)
- Carlos De Ollas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Raphaël Morillón
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, France
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Jaime Puértolas
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Patrick Ollitrault
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), San-Giuliano, France
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
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15
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Strazzer P, Spelt CE, Li S, Bliek M, Federici CT, Roose ML, Koes R, Quattrocchio FM. Hyperacidification of Citrus fruits by a vacuolar proton-pumping P-ATPase complex. Nat Commun 2019; 10:744. [PMID: 30808865 PMCID: PMC6391481 DOI: 10.1038/s41467-019-08516-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 01/08/2019] [Indexed: 11/09/2022] Open
Abstract
The sour taste of Citrus fruits is due to the extreme acidification of vacuoles in juice vesicle cells via a mechanism that remained elusive. Genetic analysis in petunia identified two vacuolar P-ATPases, PH1 and PH5, which determine flower color by hyperacidifying petal cell vacuoles. Here we show that Citrus homologs, CitPH1 and CitPH5, are expressed in sour lemon, orange, pummelo and rangpur lime fruits, while their expression is strongly reduced in sweet-tasting “acidless” varieties. Down-regulation of CitPH1 and CitPH5 is associated with mutations that disrupt expression of MYB, HLH and/or WRKY transcription factors homologous to those activating PH1 and PH5 in petunia. These findings address a long-standing enigma in cell biology and provide targets to engineer or select for taste in Citrus and other fruits. The sour taste of citrus fruit results from the extremely low pH of juice vesicle cell vacuoles. Here the authors provide genetic evidence that a vacuolar P-type ATPase, that is known to determine flower color in petunia via vacuolar acidification, is also responsible for extreme acidification in citrus.
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Affiliation(s)
- Pamela Strazzer
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Cornelis E Spelt
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Shuangjiang Li
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Mattijs Bliek
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Claire T Federici
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Ronald Koes
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
| | - Francesca M Quattrocchio
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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Liu X, Lin C, Ma X, Tan Y, Wang J, Zeng M. Functional Characterization of a Flavonoid Glycosyltransferase in Sweet Orange ( Citrus sinensis). FRONTIERS IN PLANT SCIENCE 2018; 9:166. [PMID: 29497429 PMCID: PMC5818429 DOI: 10.3389/fpls.2018.00166] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/30/2018] [Indexed: 05/06/2023]
Abstract
Fruits of sweet orange (Citrus sinensis), a popular commercial Citrus species, contain high concentrations of flavonoids beneficial to human health. These fruits predominantly accumulate O-glycosylated flavonoids, in which the disaccharides [neohesperidose (rhamnosyl-α-1,2-glucose) or rutinose (rhamnosyl-α-1,6-glucose)] are linked to the flavonoid aglycones through the 3- or 7-hydroxyl sites. The biotransformation of the flavonoid aglycones into O-rutinosides or O-neohesperidosides in the Citrus plants usually consists of two glycosylation reactions involving a series of uridine diphosphate-sugar dependent glycosyltransferases (UGTs). Although several genes encoding flavonoid UGTs have been functionally characterized in the Citrus plants, full elucidation of the flavonoid glycosylation process remains elusive. Based on the available genomic and transcriptome data, we isolated a UGT with a high expression level in the sweet orange fruits that possibly encodes a flavonoid glucosyltransferase and/or rhamnosyltransferase. Biochemical analyses revealed that a broad range of flavonoid substrates could be glucosylated at their 3- and/or 7-hydrogen sites by the recombinant enzyme, including hesperetin, naringenin, diosmetin, quercetin, and kaempferol. Furthermore, overexpression of the gene could significantly increase the accumulations of quercetin 7-O-rhamnoside, quercetin 7-O-glucoside, and kaempferol 7-O-glucoside, implying that the enzyme has flavonoid 7-O-glucosyltransferase and 7-O-rhamnosyltransferase activities in vivo.
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Affiliation(s)
- Xiaogang Liu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| | - Cailing Lin
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xiaodi Ma
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Yan Tan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Jiuzhao Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Ming Zeng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
- *Correspondence: Ming Zeng,
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Qiao L, Cao M, Zheng J, Zhao Y, Zheng ZL. Gene coexpression network analysis of fruit transcriptomes uncovers a possible mechanistically distinct class of sugar/acid ratio-associated genes in sweet orange. BMC PLANT BIOLOGY 2017; 17:186. [PMID: 29084509 PMCID: PMC5663102 DOI: 10.1186/s12870-017-1138-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/22/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND The ratio of sugars to organic acids, two of the major metabolites in fleshy fruits, has been considered the most important contributor to fruit sweetness. Although accumulation of sugars and acids have been extensively studied, whether plants evolve a mechanism to maintain, sense or respond to the fruit sugar/acid ratio remains a mystery. In a prior study, we used an integrated systems biology tool to identify a group of 39 acid-associated genes from the fruit transcriptomes in four sweet orange varieties (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). RESULTS We reanalyzed the prior sweet orange fruit transcriptome data, leading to the identification of 72 genes highly correlated with the fruit sugar/acid ratio. The majority of these sugar/acid ratio-related genes are predicted to be involved in regulatory functions such as transport, signaling and transcription or encode enzymes involved in metabolism. Surprisingly, only three of these sugar/acid ratio-correlated genes are weakly correlated with sugar level and none of them overlaps with the acid-associated genes. Weighted Gene Coexpression Network Analysis (WGCNA) has revealed that these genes belong to four modules, Blue, Grey, Brown and Turquoise, with the former two modules being unique to the sugar/acid ratio control. CONCLUSION Our results indicate that orange fruits contain a possible mechanistically distinct class of genes that may potentially be involved in maintaining fruit sugar/acid ratios and/or responding to the cellular sugar/acid ratio status. Therefore, our analysis of orange transcriptomes provides an intriguing insight into the potentially novel genetic or molecular mechanisms controlling the sugar/acid ratio in fruits.
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Affiliation(s)
- Liang Qiao
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Minghao Cao
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Jian Zheng
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
| | - Yihong Zhao
- Division of Biostatistics, Department of Child and Adolescent Psychiatry, New York University Langone Medical Center, New York, NY 10016 USA
| | - Zhi-Liang Zheng
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712 China
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY 10468 USA
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Xu L, Yang P, Feng Y, Xu H, Cao Y, Tang Y, Yuan S, Liu X, Ming J. Spatiotemporal Transcriptome Analysis Provides Insights into Bicolor Tepal Development in Lilium "Tiny Padhye". FRONTIERS IN PLANT SCIENCE 2017; 8:398. [PMID: 28392796 PMCID: PMC5364178 DOI: 10.3389/fpls.2017.00398] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/08/2017] [Indexed: 05/24/2023]
Abstract
The bicolor Asiatic hybrid lily cultivar "Tiny Padhye" is an attractive variety because of its unique color pattern. During its bicolor tepal development, the upper tepals undergo a rapid color change from green to white, while the tepal bases change from green to purple. However, the molecular mechanisms underlying these changes remain largely uncharacterized. To systematically investigate the dynamics of the lily bicolor tepal transcriptome during development, we generated 15 RNA-seq libraries from the upper tepals (S2-U) and basal tepals (S1-D, S2-D, S3-D, and S4-D) of Lilium "Tiny Padhye." Utilizing the Illumina platform, a total of 295,787 unigenes were obtained from 713.12 million high-quality paired-end reads. A total of 16,182 unigenes were identified as differentially expressed genes during tepal development. Using Kyoto Encyclopedia of Genes and Genomes pathway analysis, candidate genes involved in the anthocyanin biosynthetic pathway (61 unigenes), and chlorophyll metabolic pathway (106 unigenes) were identified. Further analyses showed that most anthocyanin biosynthesis genes were transcribed coordinately in the tepal bases, but not in the upper tepals, suggesting that the bicolor trait of "Tiny Padhye" tepals is caused by the transcriptional regulation of anthocyanin biosynthetic genes. Meanwhile, the high expression level of chlorophyll degradation genes and low expression level of chlorophyll biosynthetic genes resulted in the absence of chlorophylls from "Tiny Padhye" tepals after flowering. Transcription factors putatively involved in the anthocyanin biosynthetic pathway and chlorophyll metabolism in lilies were identified using a weighted gene co-expression network analysis and their possible roles in lily bicolor tepal development were discussed. In conclusion, these extensive transcriptome data provide a platform for elucidating the molecular mechanisms of bicolor tepals in lilies and provide a basis for similar research in other closely related species.
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Affiliation(s)
- Leifeng Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Panpan Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
- Department of Ornamental Plants, College of Landscape Architecture, Nanjing Forestry UniversityNanjing, China
| | - Yayan Feng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Hua Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yuwei Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yuchao Tang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Suxia Yuan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xinyan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jun Ming
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
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Sheng L, Shen D, Yang W, Zhang M, Zeng Y, Xu J, Deng X, Cheng Y. GABA Pathway Rate-Limit Citrate Degradation in Postharvest Citrus Fruit Evidence from HB Pumelo (Citrus grandis) × Fairchild (Citrus reticulata) Hybrid Population. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1669-1676. [PMID: 28150945 DOI: 10.1021/acs.jafc.6b05237] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Organic acids are a major index of fresh fruit marketing properties. However, the genetic effects on the organic acid level in postharvest citrus fruit still remain unknown. Here, we used the fruits of about 40 lines in a hybrid population (high-acid "HB Pumelo" × low-acid "Fairchild") to analyze the organic acid metabolism of postharvest citrus fruit. A transgressive content of titratable acid (TA) was observed, which was attributed to citrate accumulation. High- and low-acid fruits (No. 130, 168 and No. 080, 181, respectively) were chosen for further study. Gene expression analysis on citrate metabolism showed that the high accumulation of citrate could be attributed to the low activity of γ-aminobutyric acid (GABA) shunt, and was partially due to the block of tricarboxylic acid (TCA) cycle by low mitochondrial aconitase (m-ACO) expression. TA level was significantly negatively correlated with weight loss in fruits during postharvest storage, implying a close relationship between organic acid and water metabolism.
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Affiliation(s)
- Ling Sheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, PR China, College of Horticulture and Forestry Science, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Dandan Shen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, PR China, College of Horticulture and Forestry Science, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Wei Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, PR China, College of Horticulture and Forestry Science, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Mingfei Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, PR China, College of Horticulture and Forestry Science, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Yunliu Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, PR China, College of Horticulture and Forestry Science, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Juan Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, PR China, College of Horticulture and Forestry Science, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, PR China, College of Horticulture and Forestry Science, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Yunjiang Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, PR China, College of Horticulture and Forestry Science, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
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