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Lakhwani D, Vikarm Dhar Y, Singh S, Pandey A, Kumar Trivedi P, Hasan Asif M. Genome wide identification of MADS box gene family in Musa balbisiana and their divergence during evolution. Gene X 2022; 836:146666. [PMID: 35690281 DOI: 10.1016/j.gene.2022.146666] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/28/2022] Open
Abstract
MADS box gene family is transcription factor gene family that is involved in growth and development of eukaryotes. In plants the MADS box gene family is mainly associated with floral meristem identity and flower development, apart from being involved in nearly all the phases of plant growth. The MADS box gene family has also been shown to be involved during fruit development and ripening. In this study the MADS box gene family from Musa balbisiana was identified and the divergence of this gene family between Musa balbisiana and Musa acuminata studied. A total of 97 MADS box genes were identified from the genome of Musa balbisiana. Phylogenetic analysis showed that the MbMADS box genes were categorised into type I (α and γ; the β group was not distinguishable) and type II groups (MIKCc and MIKC* and MIKCc was further divided into 13 subfamilies). The typeII group has the largest number of genes and also showed the most expansion which could be correlated with the whole genome duplications. There were significant differences in the MADS box genes from Musa acuminata and Musa balbisiana during evolution that can be correlated with different floral phenotype and fruit ripening pattern. The divergence of the MADS RIN genes in Musa balbisiana as compared to Musa acuminata might play an important role in the slow ripening of Musa balbisiana fruits.
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Affiliation(s)
- Deepika Lakhwani
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India
| | - Yogeshwar Vikarm Dhar
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201 002, India
| | - Shikha Singh
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi 110 067, India
| | - Prabodh Kumar Trivedi
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201 002, India.
| | - Mehar Hasan Asif
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201 002, India.
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Changes in Homogalacturonan Metabolism in Banana Peel during Fruit Development and Ripening. Int J Mol Sci 2021; 23:ijms23010243. [PMID: 35008668 PMCID: PMC8745247 DOI: 10.3390/ijms23010243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/14/2023] Open
Abstract
Though numerous studies have focused on the cell wall disassembly of bananas during the ripening process, the modification of homogalacturonan (HG) during fruit development remains exclusive. To better understand the role of HGs in controlling banana fruit growth and ripening, RNA-Seq, qPCR, immunofluorescence labeling, and biochemical methods were employed to reveal their dynamic changes in banana peels during these processes. Most HG-modifying genes in banana peels showed a decline in expression during fruit development. Four polygalacturonase and three pectin acetylesterases showing higher expression levels at later developmental stages than earlier ones might be related to fruit expansion. Six out of the 10 top genes in the Core Enrichment Gene Set were HG degradation genes, and all were upregulated after softening, paralleled to the significant increase in HG degradation enzyme activities, decline in peel firmness, and the epitope levels of 2F4, CCRC-M38, JIM7, and LM18 antibodies. Most differentially expressed alpha-1,4-galacturonosyltransferases were upregulated by ethylene treatment, suggesting active HG biosynthesis during the fruit softening process. The epitope level of the CCRC-M38 antibody was positively correlated to the firmness of banana peel during fruit development and ripening. These results have provided new insights into the role of cell wall HGs in fruit development and ripening.
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Kaur K, Awasthi P, Tiwari S. Comparative transcriptome analysis of unripe and ripe banana (cv. Nendran) unraveling genes involved in ripening and other related processes. PLoS One 2021; 16:e0254709. [PMID: 34314413 PMCID: PMC8315498 DOI: 10.1371/journal.pone.0254709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/02/2021] [Indexed: 11/21/2022] Open
Abstract
Banana is one of the most important fruit crops consumed globally owing to its high nutritional value. Previously, we demonstrated that the ripe pulp of the banana cultivar (cv.) Nendran (AAB) contained a high amount of pro-vitamin A carotenoids. However, the molecular factors involved in the ripening process in Nendran fruit are unexplored. Hence, we commenced a transcriptome study by using the Illumina HiSeq 2500 at two stages i.e. unripe and ripe fruit-pulp of Nendran. Overall, 3474 up and 4727 down-regulated genes were obtained. A large number of identified transcripts were related to genes involved in ripening, cell wall degradation and aroma formation. Gene ontology analysis highlighted differentially expressed genes that play a key role in various pathways. These pathways were mainly linked to cellular, molecular and biological processes. The present transcriptome study also reveals a crucial role of up-regulated carotenoid biosynthesis pathway genes namely, lycopene beta cyclase and geranylgeranyl pyrophosphate synthase at the ripening stage. Genes related to the ripening and other processes like aroma and flavor were highly expressed in the ripe pulp. Expression of numerous transcription factor family genes was also identified. This study lays a path towards understanding the ripening, carotenoid accumulation and other related processes in banana.
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Affiliation(s)
- Karambir Kaur
- Department of Biotechnology, Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Ministry of Science and Technology (Government of India), Mohali, Punjab, India
| | - Praveen Awasthi
- Department of Biotechnology, Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Ministry of Science and Technology (Government of India), Mohali, Punjab, India
| | - Siddharth Tiwari
- Department of Biotechnology, Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Ministry of Science and Technology (Government of India), Mohali, Punjab, India
- * E-mail: ,
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Sun R, Gao L, Mi Z, Zheng Y, Li D. CnMADS1, a MADS transcription factor, positively modulates cell proliferation and lipid metabolism in the endosperm of coconut (Cocos nucifera L.). PLANTA 2020; 252:83. [PMID: 33040224 DOI: 10.1007/s00425-020-03490-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
The function of the first MADS-box transcription factor from endosperm of coconut, CnMADS1, was characterized via seed-specific overexpression in Arabidopsis seeds and further confirmed in protoplasts of coconut. Coconut (Cocos nucifera L.), which belongs to the palm family (Arecaceae), is one of the world's most useful economical tropical crops. However, few genes related to coconut endosperm development have been studied. In previous research, an AGAMOUS-like (AGL) MADS-box transcription factor, named CnMADS1, was identified in the endosperm of coconut through the SSH cDNA library. In this paper, functional characterization of the CnMADS1 gene was carried out by seed-specific overexpression in A. thaliana seeds and protoplasts of coconut. The results indicated that in the twelve independent T2 transgenic Arabidopsis lines with high overexpression of CnMADS1, the size of the mature seeds of transgenic plants was increased significantly (19.64% increase in the long axis and 8.6% increase in the short axis) compared to that of the wild-type seeds. Moreover, the total lipid content also increased significantly in mature seeds of transgenic plants. After comparing the expression of related genes in wild-type and transgenic plants and confirmation by EMSA, AtOSR1, a regulatory gene related to seed size, was proven to be significantly up-regulated by CnMADS1 in transgenic plants. Moreover, the transient transformation of protoplasts of coconut also proved that CnLECRK3 (the homologous gene of AtOSR1 in coconut) is up-regulated by the CnMADS1 gene in the same way. All these results indicated that a similar regulation mode existed in Arabidopsis and the endosperm of coconut and ultimately affected the yield and quality of coconut copra.
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Affiliation(s)
- RuHao Sun
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Li Gao
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Zhiqi Mi
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yusheng Zheng
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dongdong Li
- College of Tropical Crops, Hainan University, Hainan, 570228, China.
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Meng N, Wei Y, Gao Y, Yu K, Cheng J, Li XY, Duan CQ, Pan QH. Characterization of Transcriptional Expression and Regulation of Carotenoid Cleavage Dioxygenase 4b in Grapes. FRONTIERS IN PLANT SCIENCE 2020; 11:483. [PMID: 32457771 PMCID: PMC7227400 DOI: 10.3389/fpls.2020.00483] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/31/2020] [Indexed: 05/23/2023]
Abstract
Norisoprenoids are important aromatic volatiles contributing to the pleasant floral/fruity odor in grapes and wine. They are produced from carotenoids through the cleavage of carotenoid cleavage dioxygenases (CCDs). However, the underlying mechanisms regulating VvCCD expression remain poorly understood. In this study, we showed that VvCCD4b expression was positively correlated with the accumulation of β-damascenone, β-ionone, 6-methyl-5-hepten-2-one, geranylacetone, dihydroedulan I, and total norisoprenoids in developing grapes in two vintages from two regions. VvCCD4b was found to be principally expressed in flowers, mature leaves, and berries. Abscisic acid strongly induced the expression of this gene. Additionally, the present study preliminarily indicated that the activity of the VvCCD4b promoter was dropped under 37°C treatment and also responded to the illumination change. VvCCD4b was expressed in parallel with VvMADS4 in developing grape berries. The latter is a MADS family transcription factor and nucleus-localized protein that was captured by yeast one-hybrid. A dual-luciferase reporter assay in tobacco leaves revealed that VvMADS4 downregulated the activity of the VvCCD4b promoter. VvMADS4 overexpression in grape calli and Vitis quinquangularis Rehd. leaves repressed the VvCCD4b expression. In summary, this work demonstrates that VvCCD4b expression is positively correlated with the accumulation of norisoprenoids, and VvMADS4 is a potential negative regulator of VvCCD4b. Our results provide a new perspective for understanding the regulation of VvCCD4b expression and norisoprenoid accumulation in grapes.
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Affiliation(s)
- Nan Meng
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Yi Wei
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Yuan Gao
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Keji Yu
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Jing Cheng
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Xiang-Yi Li
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Chang-Qing Duan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Qiu-Hong Pan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing, China
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Vallarino JG, Merchante C, Sánchez‐Sevilla JF, de Luis Balaguer MA, Pott DM, Ariza MT, Casañal A, Posé D, Vioque A, Amaya I, Willmitzer L, Solano R, Sozzani R, Fernie AR, Botella MA, Giovannoni JJ, Valpuesta V, Osorio S. Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:929-943. [PMID: 31533196 PMCID: PMC7061862 DOI: 10.1111/pbi.13257] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 09/03/2019] [Accepted: 09/08/2019] [Indexed: 05/08/2023]
Abstract
FaMADS9 is the strawberry (Fragaria x ananassa) gene that exhibits the highest homology to the tomato (Solanum lycopersicum) RIN gene. Transgenic lines were obtained in which FaMADS9 was silenced. The fruits of these lines did not show differences in basic parameters, such as fruit firmness or colour, but exhibited lower Brix values in three of the four independent lines. The gene ontology MapMan category that was most enriched among the differentially expressed genes in the receptacles at the white stage corresponded to the regulation of transcription, including a high percentage of transcription factors and regulatory proteins associated with auxin action. In contrast, the most enriched categories at the red stage were transport, lipid metabolism and cell wall. Metabolomic analysis of the receptacles of the transformed fruits identified significant changes in the content of maltose, galactonic acid-1,4-lactone, proanthocyanidins and flavonols at the green/white stage, while isomaltose, anthocyanins and cuticular wax metabolism were the most affected at the red stage. Among the regulatory genes that were differentially expressed in the transgenic receptacles were several genes previously linked to flavonoid metabolism, such as MYB10, DIV, ZFN1, ZFN2, GT2, and GT5, or associated with the action of hormones, such as abscisic acid, SHP, ASR, GTE7 and SnRK2.7. The inference of a gene regulatory network, based on a dynamic Bayesian approach, among the genes differentially expressed in the transgenic receptacles at the white and red stages, identified the genes KAN1, DIV, ZFN2 and GTE7 as putative targets of FaMADS9. A MADS9-specific CArG box was identified in the promoters of these genes.
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Affiliation(s)
- José G. Vallarino
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - Catharina Merchante
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - José F. Sánchez‐Sevilla
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
- Genómica y BiotecnologíaCentro de MálagaInstituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA)MálagaSpain
| | - María Angels de Luis Balaguer
- Plant and Microbial Biology DepartmentNorth Carolina State UniversityRaleighNCUSA
- Present address:
Precision Biosciences, Inc.DurhamNCUSA
| | - Delphine M. Pott
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - María T. Ariza
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - Ana Casañal
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - David Posé
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - Amalia Vioque
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - Iraida Amaya
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
- Genómica y BiotecnologíaCentro de MálagaInstituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA)MálagaSpain
| | - Lothar Willmitzer
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Roberto Solano
- Departmento de Genética Molecular de PlantasCentro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Rosangela Sozzani
- Plant and Microbial Biology DepartmentNorth Carolina State UniversityRaleighNCUSA
- Biomathematics ProgramNorth Carolina State UniversityRaleighNCUSA
| | - Alisdair R. Fernie
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Miguel A. Botella
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant Research and USDA‐ARSRobert W. Holley CenterCornell University CampusIthacaNYUSA
| | - Victoriano Valpuesta
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
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Ectopic Expression of Litsea cubeba LcMADS20 Modifies Silique Architecture. G3-GENES GENOMES GENETICS 2019; 9:4139-4147. [PMID: 31615834 PMCID: PMC6893193 DOI: 10.1534/g3.119.400611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Litsea cubeba (Lour.) Pers. (mountain pepper, Lauraceae) is an important woody essential oil crop that produces fragrant oils in its fruits, especially in its peels. Identification of genes involved in the regulation of fruits and peel architecture is of economic significance for L. cubeba industry. It has been well known that the MADS-box genes are essential transcription factors that control flowers and fruits development. Here, we obtained 33 MADS-box genes first from the RNA-seq data in L. cubeba, and 27 of these genes were of the MIKC-type. LcMADS20, an AGAMOUS-like gene, was highly expressed in the developing stages of fruits, particularly at 85 days after full bloom. The ectopic expression of LcMADS20 in Arabidopsis resulted in not only curved leaves, early flowering and early full-opened inflorescences, but also shorter siliques and decreased percentage of peel thickness. Moreover, in the LcMADS20 transgenic Arabidopsis, the expression modes of several intrinsic ABC model class genes were influenced, among which the expression of FUL was significantly reduced and AP3, AG, and STK were significantly increased. This study systematically analyzed the MADS-box genes in L. cubeba at the transcriptional level and showed that LcMADS20 plays important roles in the regulation of fruit architecture.
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Rego ECS, Pinheiro TDM, Antonino JD, Alves GSC, Cotta MG, Fonseca FCDA, Miller RNG. Stable reference genes for RT-qPCR analysis of gene expression in the Musa acuminata-Pseudocercospora musae interaction. Sci Rep 2019; 9:14592. [PMID: 31601872 PMCID: PMC6787041 DOI: 10.1038/s41598-019-51040-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 09/20/2019] [Indexed: 11/30/2022] Open
Abstract
Leaf pathogens are limiting factors in banana (Musa spp.) production, with Pseudocercospora spp. responsible for the important Sigatoka disease complex. In order to investigate cellular processes and genes involved in host defence responses, quantitative real-time PCR (RT-qPCR) is an analytical technique for gene expression quantification. Reliable RT-qPCR data, however, requires that reference genes for normalization of mRNA levels in samples are validated under the conditions employed for expression analysis of target genes. We evaluated the stability of potential reference genes ACT1, α-TUB, UBQ1, UBQ2, GAPDH, EF1α, APT and RAN. Total RNA was extracted from leaf tissues of Musa acuminata genotypes Calcutta 4 (resistant) and Cavendish Grande Naine (susceptible), both subjected to P. musae infection. Expression stability was determined with NormFinder, BestKeeper, geNorm and RefFinder algorithms. UBQ2 and RAN were the most stable across all M. acuminata samples, whereas when considering inoculated and non-inoculated leaf samples, APT and UBQ2 were appropriate for normalization in Calcutta 4, with RAN and α-TUB most stable in Cavendish Grande Naine. This first study of reference genes for relative quantification of target gene expression in the M. acuminata-P. musae interaction will enable reliable analysis of gene expression in this pathosystem, benefiting elucidation of disease resistance mechanisms.
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Affiliation(s)
- Erica Cristina Silva Rego
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Tatiana David Miranda Pinheiro
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Jose Dijair Antonino
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil.,Departamento de Agronomia-Entomologia, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros s/n, Dois Irmãos, 52171-900, Recife, PE, Brazil
| | - Gabriel Sergio Costa Alves
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Michelle Guitton Cotta
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Fernando Campos De Assis Fonseca
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Robert Neil Gerard Miller
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil.
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Xiao L, Li T, Jiang G, Jiang Y, Duan X. Cell wall proteome analysis of banana fruit softening using iTRAQ technology. J Proteomics 2019; 209:103506. [DOI: 10.1016/j.jprot.2019.103506] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 06/22/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
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10
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Combination of Transcriptomic, Proteomic, and Metabolomic Analysis Reveals the Ripening Mechanism of Banana Pulp. Biomolecules 2019; 9:biom9100523. [PMID: 31548496 PMCID: PMC6843284 DOI: 10.3390/biom9100523] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023] Open
Abstract
The banana is one of the most important fruits in the world. Bananas undergo a rapid ripening process after harvest, resulting in a short shelf. In this study, the mechanism underlying pulp ripening of harvested bananas was investigated using integrated transcriptomic, proteomic, and metabolomic analysis. Ribonucleic acid sequencing (RNA-Seq) revealed that a great number of genes related to transcriptional regulation, signal transduction, cell wall modification, and secondary metabolism were up-regulated during pulp ripening. At the protein level, 84 proteins were differentially expressed during pulp ripening, most of which were associated with energy metabolism, oxidation-reduction, cell wall metabolism, and starch degradation. According to partial least squares discriminant analysis, 33 proteins were identified as potential markers for separating different ripening stages of the fruit. In addition to ethylene’s central role, auxin signal transduction might be involved in regulating pulp ripening. Moreover, secondary metabolism, energy metabolism, and the protein metabolic process also played an important role in pulp ripening. In all, this study provided a better understanding of pulp ripening of harvested bananas.
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Wang P, Wang S, Chen Y, Xu X, Guang X, Zhang Y. Genome-wide Analysis of the MADS-Box Gene Family in Watermelon. Comput Biol Chem 2019; 80:341-350. [PMID: 31082717 DOI: 10.1016/j.compbiolchem.2019.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 12/24/2022]
Abstract
MADS-box genes comprise a family of transcription factors that function in the growth and development of plants. To obtain insights into their evolution in watermelon (Citrullus lanatus), we carried out a genome-wide analysis and identified 39 MADS-box genes. These genes were classified into MIKCc (25), MIKC*(3), Mα (5), Mβ (3), and Mγ (3) clades according to their phylogenetic relationship with Arabidopsis thaliana and Cucumis sativus; moreover, these 25 genes in the MIKC clade could be classified into 13 subfamilies, and the Flowering Locus C (FLC) subfamily is absent in watermelon. Analysis of the conserved gene motifs showed similar motifs among clades. Continuing chromosomal localizations analysis indicated that MADS-box genes were distributed across 11 chromosomes in watermelon, and these genes were conditioned to be differentially expressed during plant growth and development. This research provides information that will aid further investigations into the evolution of the MADS-box gene family in plants.
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Affiliation(s)
- Ping Wang
- School of Information & Computer, Anhui Agricultural University, Hefei 230036, China
| | - Songbo Wang
- College of Plant Protection, Hunan Agricultural University, Changsha 410000, China
| | - Yong Chen
- Science and Technology Department, State Tobacco Monopoly Administration, Beijing 100045, China
| | - Xiaomin Xu
- Department of Mathematics, University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xuanmin Guang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Youhua Zhang
- School of Information & Computer, Anhui Agricultural University, Hefei 230036, China.
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12
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Integrated Transcriptomic, Proteomic, and Metabolomics Analysis Reveals Peel Ripening of Harvested Banana under Natural Condition. Biomolecules 2019; 9:biom9050167. [PMID: 31052343 PMCID: PMC6572190 DOI: 10.3390/biom9050167] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 12/28/2022] Open
Abstract
Harvested banana ripening is a complex physiological and biochemical process, and there are existing differences in the regulation of ripening between the pulp and peel. However, the underlying molecular mechanisms governing peel ripening are still not well understood. In this study, we performed a combination of transcriptomic, proteomic, and metabolomics analysis on peel during banana fruit ripening. It was found that 5784 genes, 94 proteins, and 133 metabolites were differentially expressed or accumulated in peel during banana ripening. Those genes and proteins were linked to ripening-related processes, including transcriptional regulation, hormone signaling, cell wall modification, aroma synthesis, protein modification, and energy metabolism. The differentially expressed transcriptional factors were mainly ethylene response factor (ERF) and basic helix-loop-helix (bHLH) family members. Moreover, a great number of auxin signaling-related genes were up-regulated, and exogenous 3-indoleacetic acid (IAA) treatment accelerated banana fruit ripening and up-regulated the expression of many ripening-related genes, suggesting that auxin participates in the regulation of banana peel ripening. In addition, xyloglucan endotransglucosylase/hydrolase (XTH) family members play an important role in peel softening. Both heat shock proteins (Hsps) mediated-protein modification, and ubiqutin-protesome system-mediated protein degradation was involved in peel ripening. Furthermore, anaerobic respiration might predominate in energy metabolism in peel during banana ripening. Taken together, our study highlights a better understanding of the mechanism underlying banana peel ripening and provides a new clue for further dissection of specific gene functions.
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Cordenunsi-Lysenko BR, Nascimento JRO, Castro-Alves VC, Purgatto E, Fabi JP, Peroni-Okyta FHG. The Starch Is (Not) Just Another Brick in the Wall: The Primary Metabolism of Sugars During Banana Ripening. FRONTIERS IN PLANT SCIENCE 2019; 10:391. [PMID: 31001305 PMCID: PMC6454214 DOI: 10.3389/fpls.2019.00391] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/14/2019] [Indexed: 05/25/2023]
Abstract
The monocot banana fruit is one of the most important crops worldwide. As a typical climacteric fruit, the harvest of commercial bananas usually occurs when the fruit is physiologically mature but unripe. The universal treatment of green bananas with ethylene or ethylene-releasing compounds in order to accelerate and standardize the ripening of a bunch of bananas mimics natural maturation after increasing the exogenous production of ethylene. The trigger of autocatalytic ethylene production regulated by a dual positive feedback loop circuit derived from a NAC gene and three MADS genes results in metabolic processes that induce changes in the primary metabolism of bananas. These changes include pulp softening and sweetening which are sensorial attributes that determine banana postharvest quality. During fruit development, bananas accumulate large amounts of starch (between 15 and 35% w/w of their fresh weight, depending on the cultivar). Pulp softening and sweetening during banana ripening are attributed not only to changes in the activities of cell wall hydrolases but also to starch-to-sugar metabolism. Therefore, starch granule erosion and disassembling are key events that lead bananas to reach their optimal postharvest quality. The knowledge of the mechanisms that regulate sugar primary metabolism during banana ripening is fundamental to reduce postharvest losses and improve final product quality, though. Recent studies have shown that ethylene-mediated regulation of starch-degrading enzymes at transcriptional and translational levels is crucial for sugar metabolism in banana ripening. Furthermore, the crosstalk between ethylene and other hormones including indole-3-acetic acid and abscisic acid also influences primary sugar metabolism. In this review, we will describe the state-of-the-art sugar primary metabolism in bananas and discuss the recent findings that shed light on the understanding of the molecular mechanisms involved in the regulation of this metabolism during fruit ripening.
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Affiliation(s)
- Beatriz Rosana Cordenunsi-Lysenko
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), Research, Innovation and Dissemination Centers, São Paulo Research Foundation (CEPID-FAPESP), São Paulo, Brazil
- Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo, Brazil
| | - João Roberto Oliveira Nascimento
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), Research, Innovation and Dissemination Centers, São Paulo Research Foundation (CEPID-FAPESP), São Paulo, Brazil
- Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo, Brazil
| | - Victor Costa Castro-Alves
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), Research, Innovation and Dissemination Centers, São Paulo Research Foundation (CEPID-FAPESP), São Paulo, Brazil
| | - Eduardo Purgatto
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), Research, Innovation and Dissemination Centers, São Paulo Research Foundation (CEPID-FAPESP), São Paulo, Brazil
- Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo, Brazil
| | - João Paulo Fabi
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), Research, Innovation and Dissemination Centers, São Paulo Research Foundation (CEPID-FAPESP), São Paulo, Brazil
- Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo, Brazil
| | - Fernanda Helena Gonçalves Peroni-Okyta
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), Research, Innovation and Dissemination Centers, São Paulo Research Foundation (CEPID-FAPESP), São Paulo, Brazil
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14
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Lama K, Yadav S, Rosianski Y, Shaya F, Lichter A, Chai L, Dahan Y, Freiman Z, Peer R, Flaishman MA. The distinct ripening processes in the reproductive and non-reproductive parts of the fig syconium are driven by ABA. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:115-131. [PMID: 30239815 PMCID: PMC6305202 DOI: 10.1093/jxb/ery333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/14/2018] [Indexed: 05/18/2023]
Abstract
The common fig bears a unique closed inflorescence structure, the syconium, composed of small individual drupelets that develop from the ovaries, which are enclosed in a succulent receptacle of vegetative origin. The fig ripening process is traditionally classified as climacteric; however, recent studies have suggested that distinct mechanisms exist in its reproductive and non-reproductive parts. We analysed ABA and ethylene production, and expression of ABA-metabolism, ethylene-biosynthesis, MADS-box, NAC, and ethylene response-factor genes in inflorescences and receptacles of on-tree fruit treated with ABA, ethephon, fluridone, and nordihydroguaiaretic acid (NDGA). Exogenous ABA and ethephon accelerated fruit ripening and softening, whereas fluridone and NDGA had the opposite effect, delaying endogenous ABA and ethylene production compared to controls. Expression of the ABA-biosynthesis genes FcNCED2 and FcABA2, ethylene-biosynthesis genes FcACS4, FcACOL, and FcACO2, FcMADS8, 14, 15, FcNAC1, 2, 5, and FcERF9006 was up-regulated by exogenous ABA and ethephon. NDGA down-regulated FcNCED2 and FcABA2, whereas fluridone down-regulated FcABA2; both down-regulated the ethylene-related genes. These results demonstrate the key role of ABA in regulation of ripening by promoting ethylene production, as in the climacteric model plant tomato, especially in the inflorescence. However, increasing accumulation of endogenous ABA until full ripeness and significantly low expression of ethylene-biosynthesis genes in the receptacle suggests non-climacteric, ABA-dependent ripening in the vegetative-originated succulent receptacle part of the fruit.
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Affiliation(s)
- Kumar Lama
- Institute of Plant Sciences, Agricultural Research Organization, Bet-Dagan, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sharawan Yadav
- Institute of Plant Sciences, Agricultural Research Organization, Bet-Dagan, Israel
| | - Yogev Rosianski
- Institute of Plant Sciences, Agricultural Research Organization, Bet-Dagan, Israel
| | - Felix Shaya
- Institute of Plant Sciences, Agricultural Research Organization, Bet-Dagan, Israel
| | - Amnon Lichter
- Institute of Postharvest and Food Sciences, Agricultural Research Organization, Bet-Dagan, Israel
| | - Lijuan Chai
- Institute of Plant Sciences, Agricultural Research Organization, Bet-Dagan, Israel
| | - Yardena Dahan
- Institute of Plant Sciences, Agricultural Research Organization, Bet-Dagan, Israel
| | - Zohar Freiman
- Institute of Plant Sciences, Agricultural Research Organization, Bet-Dagan, Israel
| | - Reut Peer
- Institute of Plant Sciences, Agricultural Research Organization, Bet-Dagan, Israel
| | - Moshe A Flaishman
- Institute of Plant Sciences, Agricultural Research Organization, Bet-Dagan, Israel
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15
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Yakir E, Zhangjun F, Sela N, Xu Y, Singh V, Dagar A, Joshi JR, Müller M, Munné-Bosch S, Giovannoni JJ, Vrebalov J, Friedman H. MaMADS2 repression in banana fruits modifies hormone synthesis and signalling pathways prior to climacteric stage. BMC PLANT BIOLOGY 2018; 18:267. [PMID: 30400866 PMCID: PMC6219179 DOI: 10.1186/s12870-018-1480-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 10/11/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND While the role of ethylene in fruit ripening has been widely studied, the contributions of additional plant hormones are less clear. Here we examined the interactions between the transcription factor MaMADS2-box which plays a major role in banana fruit ripening and hormonal regulation. Specifically, we used MaMADS2 repressed lines in transcriptome and hormonal analyses throughout ripening and assessed hormone and gene expression perturbations as compared to wild-type (WT) control fruit. RESULTS Our analyses revealed major differences in hormones levels and in expression of hormone synthesis and signaling genes mediated by MaMADS2 especially in preclimacteric pulp. Genes encoding ethylene biosynthesis enzymes had lower expression in the pulp of the repressed lines, consistent with reduced ethylene production. Generally, the expression of other hormone (auxin, gibberellins, abscisic acid, jasmonic acid and salicylic acid) response pathway genes were down regulated in the WT pulp prior to ripening, but remained high in MaMADS2 repressed lines. Hormone levels of abscisic acid were also higher, however, active gibberellin levels were lower and auxin levels were similar with MaMADS2 repression as compared to WT. Although abscisic level was higher in MaMADS2 repression, exogenous abscisic acid shortened the time to ethylene production and increased MaMADS2 mRNA accumulation in WT. Exogenous ethylene did not influence abscisic acid level. CRE - a cytokinin receptor, increased its expression during maturation in WT and was lower especially at prebreaker in the repressed line and zeatin level was lower at mature green of the repressed line in comparison to WT. CONCLUSIONS In addition to previously reported effects of MaMADS2 on ethylene, this transcription factor also influences other plant hormones, particularly at the pre-climacteric stage. The cytokinin pathway may play a previously unanticipated role via MaMADS2 in banana ripening. Finally, abscisic acid enhances MaMADS2 expression to promote ripening, but the transcription factor in turn auto inhibits ABA synthesis and signaling. Together, these results demonstrate a complex interaction of plant hormones and banana fruit ripening mediated by MaMADS2.
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Affiliation(s)
- Esther Yakir
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), The Volcani Center, P.O. Box 6, 50250 Bet Dagan, Israel
| | - Fei Zhangjun
- Boyce Thompson Institute for Plant Research and USDA-ARS Robert W. Holley Center, Tower Road, Cornell Campus, Ithaca, NY USA
| | - Noa Sela
- Plant Pathology and Weed Research, ARO, The Volcani Center, Bet Dagan, Israel
| | - Yimin Xu
- Boyce Thompson Institute for Plant Research and USDA-ARS Robert W. Holley Center, Tower Road, Cornell Campus, Ithaca, NY USA
| | - Vikram Singh
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), The Volcani Center, P.O. Box 6, 50250 Bet Dagan, Israel
| | - Anurag Dagar
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), The Volcani Center, P.O. Box 6, 50250 Bet Dagan, Israel
| | - Janak Raj Joshi
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), The Volcani Center, P.O. Box 6, 50250 Bet Dagan, Israel
| | - Maren Müller
- Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 645, E-08028 Barcelona, Spain
| | - Sergi Munné-Bosch
- Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 645, E-08028 Barcelona, Spain
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant Research and USDA-ARS Robert W. Holley Center, Tower Road, Cornell Campus, Ithaca, NY USA
| | - Julia Vrebalov
- Boyce Thompson Institute for Plant Research and USDA-ARS Robert W. Holley Center, Tower Road, Cornell Campus, Ithaca, NY USA
| | - Haya Friedman
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), The Volcani Center, P.O. Box 6, 50250 Bet Dagan, Israel
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16
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Genome-Wide Identification and Characterization of MADS-box Family Genes Related to Floral Organ Development and Stress Resistance in Hevea brasiliensis Müll. Arg. FORESTS 2018. [DOI: 10.3390/f9060304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Shima Y, Nakamura N, Kotake-Nara E, Kawasaki S, Toki S. Re-evaluation of the rin mutation and the role of RIN in the induction of tomato ripening. NATURE PLANTS 2017; 3:866-874. [PMID: 29085071 DOI: 10.1038/s41477-017-0041-5] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 09/29/2017] [Indexed: 05/18/2023]
Abstract
Tomato (Solanum lycopersicum) rin mutants completely fail to ripen: they do not produce red pigmentation, soften or induce an ethylene burst. Therefore, RIN has long been believed to function as a major regulator that is essential for the induction of ripening. Here, we provide evidence contradicting this concept of RIN function, showing induction of fruit ripening in the absence of RIN. A CRISPR/Cas9-mediated RIN-knockout mutation did not repress initiation of ripening and the mutant fruits showed moderate red colouring. Moreover, inactivation of the rin mutant allele partially restored the induction of ripening. Therefore, RIN is not required for the initiation of ripening and rin is not a null mutation, but rather is a gain-of-function mutation that produces a protein that actively represses ripening. Since the discovery of the rin mutant a half-century ago, many models have depicted RIN as indispensable for the induction of ripening; these models should be reconsidered in light of these results.
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Affiliation(s)
- Yasuhiro Ito
- Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
| | - Ayako Nishizawa-Yokoi
- Institute of Agrobiological Sciences, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Masafumi Mikami
- Institute of Agrobiological Sciences, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Yokohama, Kanagawa, 236-0027, Japan
| | - Yoko Shima
- Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Nobutaka Nakamura
- Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Eiichi Kotake-Nara
- Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Susumu Kawasaki
- Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Yokohama, Kanagawa, 236-0027, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Yokohama, Kanagawa, 244-0813, Japan
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18
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Wong YC, Teh HF, Mebus K, Ooi TEK, Kwong QB, Koo KL, Ong CK, Mayes S, Chew FT, Appleton DR, Kulaveerasingam H. Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm. BMC Genomics 2017; 18:470. [PMID: 28637447 DOI: 10.1186/s12864-017-3855-3857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 06/09/2017] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND The oil yield trait of oil palm is expected to involve multiple genes, environmental influences and interactions. Many of the underlying mechanisms that contribute to oil yield are still poorly understood. In this study, we used a microarray approach to study the gene expression profiles of mesocarp tissue at different developmental stages, comparing genetically related high- and low- oil yielding palms to identify genes that contributed to the higher oil-yielding palm and might contribute to the wider genetic improvement of oil palm breeding populations. RESULTS A total of 3412 (2001 annotated) gene candidates were found to be significantly differentially expressed between high- and low-yielding palms at at least one of the different stages of mesocarp development evaluated. Gene Ontologies (GO) enrichment analysis identified 28 significantly enriched GO terms, including regulation of transcription, fatty acid biosynthesis and metabolic processes. These differentially expressed genes comprise several transcription factors, such as, bHLH, Dof zinc finger proteins and MADS box proteins. Several genes involved in glycolysis, TCA, and fatty acid biosynthesis pathways were also found up-regulated in high-yielding oil palm, among them; pyruvate dehydrogenase E1 component Subunit Beta (PDH), ATP-citrate lyase, β- ketoacyl-ACP synthases I (KAS I), β- ketoacyl-ACP synthases III (KAS III) and ketoacyl-ACP reductase (KAR). Sucrose metabolism-related genes such as Invertase, Sucrose Synthase 2 and Sucrose Phosphatase 2 were found to be down-regulated in high-yielding oil palms, compared to the lower yield palms. CONCLUSIONS Our findings indicate that a higher carbon flux (channeled through down-regulation of the Sucrose Synthase 2 pathway) was being utilized by up-regulated genes involved in glycolysis, TCA and fatty acid biosynthesis leading to enhanced oil production in the high-yielding oil palm. These findings are an important stepping stone to understand the processes that lead to production of high-yielding oil palms and have implications for breeding to maximize oil production.
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Affiliation(s)
- Yick Ching Wong
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Huey Fang Teh
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Katharina Mebus
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Institute of Research Management & Monitoring (IPPP), Research Management & Innovation Comlex, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tony Eng Keong Ooi
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Qi Bin Kwong
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Ka Loo Koo
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Chuang Kee Ong
- European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Sean Mayes
- Plant and Crop Sciences, Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Fook Tim Chew
- Department of Biological Sciences, Faculty of Science, National University of Singapore, off Lower Kent Ridge Road, Singapore, 117543, Singapore
| | - David R Appleton
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Harikrishna Kulaveerasingam
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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19
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Wong YC, Teh HF, Mebus K, Ooi TEK, Kwong QB, Koo KL, Ong CK, Mayes S, Chew FT, Appleton DR, Kulaveerasingam H. Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm. BMC Genomics 2017. [PMID: 28637447 PMCID: PMC5480177 DOI: 10.1186/s12864-017-3855-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background The oil yield trait of oil palm is expected to involve multiple genes, environmental influences and interactions. Many of the underlying mechanisms that contribute to oil yield are still poorly understood. In this study, we used a microarray approach to study the gene expression profiles of mesocarp tissue at different developmental stages, comparing genetically related high- and low- oil yielding palms to identify genes that contributed to the higher oil-yielding palm and might contribute to the wider genetic improvement of oil palm breeding populations. Results A total of 3412 (2001 annotated) gene candidates were found to be significantly differentially expressed between high- and low-yielding palms at at least one of the different stages of mesocarp development evaluated. Gene Ontologies (GO) enrichment analysis identified 28 significantly enriched GO terms, including regulation of transcription, fatty acid biosynthesis and metabolic processes. These differentially expressed genes comprise several transcription factors, such as, bHLH, Dof zinc finger proteins and MADS box proteins. Several genes involved in glycolysis, TCA, and fatty acid biosynthesis pathways were also found up-regulated in high-yielding oil palm, among them; pyruvate dehydrogenase E1 component Subunit Beta (PDH), ATP-citrate lyase, β- ketoacyl-ACP synthases I (KAS I), β- ketoacyl-ACP synthases III (KAS III) and ketoacyl-ACP reductase (KAR). Sucrose metabolism-related genes such as Invertase, Sucrose Synthase 2 and Sucrose Phosphatase 2 were found to be down-regulated in high-yielding oil palms, compared to the lower yield palms. Conclusions Our findings indicate that a higher carbon flux (channeled through down-regulation of the Sucrose Synthase 2 pathway) was being utilized by up-regulated genes involved in glycolysis, TCA and fatty acid biosynthesis leading to enhanced oil production in the high-yielding oil palm. These findings are an important stepping stone to understand the processes that lead to production of high-yielding oil palms and have implications for breeding to maximize oil production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3855-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yick Ching Wong
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Huey Fang Teh
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Katharina Mebus
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Institute of Research Management & Monitoring (IPPP), Research Management & Innovation Comlex, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tony Eng Keong Ooi
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Qi Bin Kwong
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Ka Loo Koo
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Chuang Kee Ong
- European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Sean Mayes
- Plant and Crop Sciences, Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Fook Tim Chew
- Department of Biological Sciences, Faculty of Science, National University of Singapore, off Lower Kent Ridge Road, Singapore, 117543, Singapore
| | - David R Appleton
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Harikrishna Kulaveerasingam
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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Genome-wide analysis of banana MADS-box family closely related to fruit development and ripening. Sci Rep 2017; 7:3467. [PMID: 28615681 PMCID: PMC5471262 DOI: 10.1038/s41598-017-03897-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/05/2017] [Indexed: 11/08/2022] Open
Abstract
Proteins encoded by MADS-box genes are important transcription factors involved in the regulation of flowering plant growth and development. Currently, no systematic information exists regarding the MADS-box family in the important tropical fruit banana. Ninety-six MADS-box genes were identified from the banana (Pahang) A genome. Phylogenetic analysis indicated that Musa acuminata MCM1-AGAMOUS- DEFICIENS-SRF (MaMADS) could be divided into MIKCc, MIKC*, Mα/β and Mγ groups. MIKCc could be further divided into 11 subfamilies, which was further supported by conserved motif and gene structure analyses. Transcriptome analysis on the Feng Jiao (FJ) and BaXi Jiao (BX) banana cultivars revealed that MaMADS genes are differentially expressed in various organs, at different fruit development and ripening stages, indicating the involvement of these genes in fruit development and ripening processes. Interactive network analysis indicated that MaMADS24 and 49 not only interacted with MaMADS proteins themselves, but also interacted with hormone-response proteins, ethylene signal transduction and biosynthesis-related proteins, starch biosynthesis proteins and metabolism-related proteins. This systematic analysis identified candidate MaMADS genes related to fruit development and ripening for further functional characterization in plants, and also provided new insights into the transcriptional regulation of MaMADS genes, facilitating the future genetic manipulation of MADS-mediated fruit development and ripening.
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Tranbarger TJ, Fooyontphanich K, Roongsattham P, Pizot M, Collin M, Jantasuriyarat C, Suraninpong P, Tragoonrung S, Dussert S, Verdeil JL, Morcillo F. Transcriptome Analysis of Cell Wall and NAC Domain Transcription Factor Genes during Elaeis guineensis Fruit Ripening: Evidence for Widespread Conservation within Monocot and Eudicot Lineages. FRONTIERS IN PLANT SCIENCE 2017; 8:603. [PMID: 28487710 PMCID: PMC5404384 DOI: 10.3389/fpls.2017.00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/03/2017] [Indexed: 05/13/2023]
Abstract
The oil palm (Elaeis guineensis), a monocotyledonous species in the family Arecaceae, has an extraordinarily oil rich fleshy mesocarp, and presents an original model to examine the ripening processes and regulation in this particular monocot fruit. Histochemical analysis and cell parameter measurements revealed cell wall and middle lamella expansion and degradation during ripening and in response to ethylene. Cell wall related transcript profiles suggest a transition from synthesis to degradation is under transcriptional control during ripening, in particular a switch from cellulose, hemicellulose, and pectin synthesis to hydrolysis and degradation. The data provide evidence for the transcriptional activation of expansin, polygalacturonase, mannosidase, beta-galactosidase, and xyloglucan endotransglucosylase/hydrolase proteins in the ripening oil palm mesocarp, suggesting widespread conservation of these activities during ripening for monocotyledonous and eudicotyledonous fruit types. Profiling of the most abundant oil palm polygalacturonase (EgPG4) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) transcripts during development and in response to ethylene demonstrated both are sensitive markers of ethylene production and inducible gene expression during mesocarp ripening, and provide evidence for a conserved regulatory module between ethylene and cell wall pectin degradation. A comprehensive analysis of NAC transcription factors confirmed at least 10 transcripts from diverse NAC domain clades are expressed in the mesocarp during ripening, four of which are induced by ethylene treatment, with the two most inducible (EgNAC6 and EgNAC7) phylogenetically similar to the tomato NAC-NOR master-ripening regulator. Overall, the results provide evidence that despite the phylogenetic distance of the oil palm within the family Arecaceae from the most extensively studied monocot banana fruit, it appears ripening of divergent monocot and eudicot fruit lineages are regulated by evolutionarily conserved molecular physiological processes.
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Affiliation(s)
| | - Kim Fooyontphanich
- Institut de Recherche pour le Développement, IRD, UMR DIADEMontpellier, France
| | | | - Maxime Pizot
- Institut de Recherche pour le Développement, IRD, UMR DIADEMontpellier, France
| | - Myriam Collin
- Institut de Recherche pour le Développement, IRD, UMR DIADEMontpellier, France
| | | | - Potjamarn Suraninpong
- Department of Plant Science, Institute of Agricultural Technology, Walailak UniversityNakhon Si Thammarat, Thailand
| | - Somvong Tragoonrung
- Genome Institute, National Center for Genetic Engineering and BiotechnologyPathumthani, Thailand
| | - Stéphane Dussert
- Institut de Recherche pour le Développement, IRD, UMR DIADEMontpellier, France
| | - Jean-Luc Verdeil
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAPMontpellier, France
| | - Fabienne Morcillo
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR DIADEMontpellier, France
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22
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Kuang JF, Chen JY, Liu XC, Han YC, Xiao YY, Shan W, Tang Y, Wu KQ, He JX, Lu WJ. The transcriptional regulatory network mediated by banana (Musa acuminata) dehydration-responsive element binding (MaDREB) transcription factors in fruit ripening. THE NEW PHYTOLOGIST 2017; 214:762-781. [PMID: 28044313 DOI: 10.1111/nph.14389] [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] [Received: 01/29/2016] [Accepted: 11/16/2016] [Indexed: 05/24/2023]
Abstract
Fruit ripening is a complex, genetically programmed process involving the action of critical transcription factors (TFs). Despite the established significance of dehydration-responsive element binding (DREB) TFs in plant abiotic stress responses, the involvement of DREBs in fruit ripening is yet to be determined. Here, we identified four genes encoding ripening-regulated DREB TFs in banana (Musa acuminata), MaDREB1, MaDREB2, MaDREB3, and MaDREB4, and demonstrated that they play regulatory roles in fruit ripening. We showed that MaDREB1-MaDREB4 are nucleus-localized, induced by ethylene and encompass transcriptional activation activities. We performed a genome-wide chromatin immunoprecipitation and high-throughput sequencing (ChIP-Seq) experiment for MaDREB2 and identified 697 genomic regions as potential targets of MaDREB2. MaDREB2 binds to hundreds of loci with diverse functions and its binding sites are distributed in the promoter regions proximal to the transcriptional start site (TSS). Most of the MaDREB2-binding targets contain the conserved (A/G)CC(G/C)AC motif and MaDREB2 appears to directly regulate the expression of a number of genes involved in fruit ripening. In combination with transcriptome profiling (RNA sequencing) data, our results indicate that MaDREB2 may serve as both transcriptional activator and repressor during banana fruit ripening. In conclusion, our study suggests a hierarchical regulatory model of fruit ripening in banana and that the MaDREB TFs may act as transcriptional regulators in the regulatory network.
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Affiliation(s)
- Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xun-Cheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yan-Chao Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yun-Yi Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Ke-Qiang Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jun-Xian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
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23
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Li L, Wang X, Zhang X, Guo M, Liu T. Unraveling the target genes of RIN transcription factor during tomato fruit ripening and softening. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:991-1000. [PMID: 27247090 DOI: 10.1002/jsfa.7825] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 05/08/2016] [Accepted: 05/25/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The RIN transcription factor is one of the MADS box family members and predominantly controls fruit ripening. In this study, effort was made to demonstrate the regulation network of RIN transcription factor during tomato fruit ripening and softening. Novel RIN target genes were identified by proteomics, electrophoresis mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) analysis. RESULTS Over 700 protein spots were achieved by two-dimensional gel electrophoresis, and 42 proteins were successfully identified. Among them, 1-aminocyclopropane-1-carboxylate oxidase (LeACO4, ethylene synthesis, spot 3) and α-galactosidase-like isoform 2 (α-Gal, cell wall metabolism, spot 26) exhibited varied expression levels in different tomato fruits. Particularly high expression levels of LeACO4 and α-Gal were observed in wild type but not in the rin mutant. Additionally, CArG box, a RIN-binding site, was discovered in the promoter regions of both LeACO4 and α-Gal genes, suggesting that RIN possibly directly regulates their transcriptions, and this assumption was further confirmed by EMSA and ChIP assay. CONCLUSION Functional annotations of RIN target genes demonstrated the specific role of RIN in the process of fruit ripening and softening, especially in cell wall degradation and ethylene biosynthesis. This study will further illuminate the mechanism of tomato ripening and softening. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Ling Li
- College of Food Science and Biotechnology, Tianjin Agricultural University, No. 22 Jinjing Road, Tianjin, 300384, China
- Tianjin Engineering Research Center of Agricultural Products Processing, No. 22 Jinjing Road, Tianjin, 300384, China
| | - Xiaoguang Wang
- Institute of Microbiology Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Xinhua Zhang
- School of Agricultural Engineering & Food Science, Shandong University of Technology, No. 266 Xincun West Road, Zibo, 255049, China
| | - Mei Guo
- College of Food Science and Biotechnology, Tianjin Agricultural University, No. 22 Jinjing Road, Tianjin, 300384, China
- Tianjin Engineering Research Center of Agricultural Products Processing, No. 22 Jinjing Road, Tianjin, 300384, China
| | - Tieling Liu
- College of Food Science and Biotechnology, Tianjin Agricultural University, No. 22 Jinjing Road, Tianjin, 300384, China
- Tianjin Engineering Research Center of Agricultural Products Processing, No. 22 Jinjing Road, Tianjin, 300384, China
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Zhang S, Lu S, Yi S, Han H, Liu L, Zhang J, Bao M, Liu G. Functional conservation and divergence of five SEPALLATA-like genes from a basal eudicot tree, Platanus acerifolia. PLANTA 2017; 245:439-457. [PMID: 27833998 DOI: 10.1007/s00425-016-2617-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 11/03/2016] [Indexed: 06/06/2023]
Abstract
MAIN CONCLUSION Five SEP -like genes were cloned and identified from Platanus acerifolia through the analysis of expression profiles, protein-protein interaction patterns, and transgenic phenotypes, which suggested that they play conservative and diverse functions in floral initiation and development, fruit development, bud growth, and dormancy. SEPALLATA (SEP) genes have been well characterized in core eudicots and some monocots, and they play important and diverse roles in plant development, including flower meristem initiation, floral organ identity, and fruit development and ripening. However, the knowledge on the function and evolution of SEP-like genes in basal eudicot species is very limited. Here, we cloned and identified five SEP-like genes from London plane (Platanus acerifolia), a basal eudicot tree that is widely used for landscaping in cities. Sequence alignment and phylogenetic analysis indicated that three genes (PlacSEP1.1, PlacSEP1.2, and PlacSEP1.3) belong to the SEP1/2/4 clade, while the other two genes (PlacSEP3.1 and PlacSEP3.2) are grouped into the SEP3 clade. Quantitative real-time PCR (qRT-PCR) analysis showed that all PlacSEPs, except PlacSEP1.1 and PlacSEP1.2, were expressed during the male and female inflorescence initiation, and throughout the flower and fruit development process. PlacSEP1.2 gene expression was only detected clearly in female inflorescence at April. PlacSEP1.3 and PlacSEP3.1 were also expressed, although relatively weak, in vegetative buds of adult trees. No evident PlacSEPs transcripts were detected in various organs of juvenile trees. Overexpression of PlacSEPs in Arabidopsis and tobacco plants resulted in different phenotypic alterations. 35S:PlacSEP1.1, 35S:PlacSEP1.3, and 35S:PlacSEP3.2 transgenic Arabidopsis plants showed evident early flowering, with less rosette leaves but more cauline leaves, while 35S:PlacSEP1.2 and PlacSEP3.1 transgenic plants showed no visible phenotypic changes. 35S:PlacSEP1.1 and 35S:PlacSEP3.2 transgenic Arabidopsis plants also produced smaller and curled leaves. Overexpression of PlacSEP1.1 and PlacSEP3.1 in tobacco resulted in the early flowering and producing more lateral branches. Yeast two-hybrid analysis indicated that PlacSEPs proteins can form homo- or hetero-dimers with the Platanus APETALA1 (AP1)/FRUITFULL (FUL), B-, C-, and D-class MADS-box proteins in different interacting patterns and intensities. Our results suggest that the five PlacSEP genes may play important and divergent roles during floral initiation and development, as well as fruit development, by collaborating with FUL, B-, C-, and D-class MADS-box genes in London plane; PlacSEP1.3 and PlacSEP3.1 genes might also involve in vegetative bud growth and dormancy. The results provide valuable data for us to understand the functional evolution of SEP-like genes in basal eudicot species.
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Affiliation(s)
- Sisi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shunjiao Lu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, 571737, China
| | - Shuangshuang Yi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, 571737, China
| | - Hongji Han
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lei Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Guofeng Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Li L, Guo M, Wang X, Zhang X, Liu T. Effects and Mechanism of 1-Methylcyclopropene and Ethephon on Softening in Ailsa Craig Tomato Fruit. J FOOD PROCESS PRES 2016. [DOI: 10.1111/jfpp.12883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ling Li
- College of Food Science and Biotechnology; Tianjin Agricultural University; No. 22 Jinjing Road Tianjin 300384 China
| | - Mei Guo
- College of Food Science and Biotechnology; Tianjin Agricultural University; No. 22 Jinjing Road Tianjin 300384 China
| | - Xiaoguang Wang
- Institute of Microbiology Chinese Academy of Sciences; No. 1 Beichen West Road Chaoyang District Beijing 100101 China
| | - Xinhua Zhang
- School of Agricultural Engineering and Food Science; Shandong University of Technology; No. 266 Xincun West Road Zibo 255049 China
| | - Tieling Liu
- College of Food Science and Biotechnology; Tianjin Agricultural University; No. 22 Jinjing Road Tianjin 300384 China
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26
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Elitzur T, Yakir E, Quansah L, Zhangjun F, Vrebalov J, Khayat E, Giovannoni JJ, Friedman H. Banana MaMADS Transcription Factors Are Necessary for Fruit Ripening and Molecular Tools to Promote Shelf-Life and Food Security. PLANT PHYSIOLOGY 2016; 171:380-91. [PMID: 26956665 PMCID: PMC4854685 DOI: 10.1104/pp.15.01866] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/28/2016] [Indexed: 05/18/2023]
Abstract
Genetic solutions to postharvest crop loss can reduce cost and energy inputs while increasing food security, especially for banana (Musa acuminata), which is a significant component of worldwide food commerce. We have functionally characterized two banana E class (SEPALLATA3 [SEP3]) MADS box genes, MaMADS1 and MaMADS2, homologous to the tomato (Solanum lycopersicum) RIN-MADS ripening gene. Transgenic banana plants repressing either gene (via antisense or RNA interference [RNAi]) were created and exhibited specific ripening delay and extended shelf-life phenotypes, including delayed color development and softening. The delay in fruit ripening is associated with a delay in climacteric respiration and reduced synthesis of the ripening hormone ethylene; in the most severe repressed lines, no ethylene was produced and ripening was most delayed. Unlike tomato rin mutants, banana fruits of all transgenic repression lines responded to exogenous ethylene by ripening normally, likely due to incomplete transgene repression and/or compensation by other MADS box genes. Our results show that, although MADS box ripening gene necessity is conserved across diverse taxa (monocots to dicots), unlike tomato, banana ripening requires at least two necessary members of the SEPALLATA MADS box gene group, and either can serve as a target for ripening control. The utility of such genes as tools for ripening control is especially relevant in important parthenocarpic crops such as the vegetatively propagated and widely consumed Cavendish banana, where breeding options for trait improvement are severely limited.
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Affiliation(s)
- Tomer Elitzur
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Esther Yakir
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Lydia Quansah
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Fei Zhangjun
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Julia Vrebalov
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Eli Khayat
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - James J Giovannoni
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Haya Friedman
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
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Feng BH, Han YC, Xiao YY, Kuang JF, Fan ZQ, Chen JY, Lu WJ. The banana fruit Dof transcription factor MaDof23 acts as a repressor and interacts with MaERF9 in regulating ripening-related genes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2263-75. [PMID: 26889012 PMCID: PMC4809287 DOI: 10.1093/jxb/erw032] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The DNA binding with one finger (Dof) proteins, a family of plant-specific transcription factors, are involved in a variety of plant biological processes. However, little information is available on their involvement in fruit ripening. We have characterized 25 MaDof genes from banana fruit (Musa acuminata), designated as MaDof1-MaDof25 Gene expression analysis in fruit subjected to different ripening conditions revealed that MaDofs were differentially expressed during different stages of ripening. MaDof10, 23, 24, and 25 were ethylene-inducible and nuclear-localized, and their transcript levels increased during fruit ripening. Moreover, yeast two-hybrid and bimolecular fluorescence complementation analyses demonstrated a physical interaction between MaDof23 and MaERF9, a potential regulator of fruit ripening reported in a previous study. We determined that MaDof23 is a transcriptional repressor, whereas MaERF9 is a transcriptional activator. We suggest that they might act antagonistically in regulating 10 ripening-related genes, including MaEXP1/2/3/5, MaXET7, MaPG1, MaPME3, MaPL2, MaCAT, and MaPDC, which are associated with cell wall degradation and aroma formation. Taken together, our findings provide new insight into the transcriptional regulation network controlling banana fruit ripening.
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Affiliation(s)
- Bi-hong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China College of Agriculture, GuangXi University, Nanning 530004, PR China
| | - Yan-chao Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Yun-yi Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian-fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Zhong-qi Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian-ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Wang-jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
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28
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Feng X, An Y, Zheng J, Sun M, Wang L. Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1. FRONTIERS IN PLANT SCIENCE 2016; 7:1615. [PMID: 27872628 PMCID: PMC5098116 DOI: 10.3389/fpls.2016.01615] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/12/2016] [Indexed: 05/20/2023]
Abstract
Skin color is a key quality attribute of fruits and how to improve fruit coloration has long been a major concern. 5-Aminolevulinic acid (ALA), a natural plant growth regulator, can significantly increase anthocyanin accumulation in fruit skin and therefore effectively improve coloration of many fruits, including apple. However, the molecular mechanism how ALA stimulates anthocyanin accumulation in fruit skin remains unknown. Here, we investigated the impact of ALA on apple skin at the protein and mRNA levels. A total of 85 differentially expressed proteins in apple skins between ALA and water treatment (control) were identified by complementary gel-based and gel-free separation techniques. Most of these differentially expressed proteins were up-regulated by ALA. Function analysis suggested that 87.06% of the ALA-responsive proteins were associated with fruit ripening. To further screen ALA-responsive regulators, we constructed a subtracted cDNA library (tester: ALA treatment; driver: control) and obtained 104 differentially expressed unigenes, of which 38 unigenes were indicators for the fruit ripening-related genes. The differentially changed proteins and transcripts did not correspond well at an individual level, but showed similar regulated direction in function at the pathway level. Among the identified fruit ripening-related genes, the expression of MdMADS1, a developmental transcription regulator of fruit ripening, was positively correlated with expression of anthocyanin biosynthetic genes (MdCHS, MdDFR, MdLDOX, and MdUFGT) in apple skin under ALA treatment. Moreover, overexpression of MdMADS1 enhanced anthocyanin content in transformed apple calli, which was further enhanced by ALA. The anthocyanin content in MdMADS1-silenced calli was less than that in the control with ALA treatment, but higher than that without ALA treatment. These results indicated that MdMADS1 is involved in ALA-induced anthocyanin accumulation. In addition, anthocyanin-related verification in apple calli suggested that the regulation of MdMADS1 on anthocyanin biosynthesis was partially independent of fruit ripening process. Taken together, our findings provide insight into the mechanism how ALA regulates anthocyanin accumulation and add new information on transcriptase regulators of fruit coloration.
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Affiliation(s)
- Xinxin Feng
- College of Horticulture, Nanjing Agricultural University Nanjing, China
| | - Yuyan An
- College of Horticulture, Nanjing Agricultural University Nanjing, China
| | - Jie Zheng
- College of Horticulture, Nanjing Agricultural University Nanjing, China
| | - Miao Sun
- College of Horticulture, Nanjing Agricultural University Nanjing, China
| | - Liangju Wang
- College of Horticulture, Nanjing Agricultural University Nanjing, China
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McAtee PA, Richardson AC, Nieuwenhuizen NJ, Gunaseelan K, Hoong L, Chen X, Atkinson RG, Burdon JN, David KM, Schaffer RJ. The hybrid non-ethylene and ethylene ripening response in kiwifruit (Actinidia chinensis) is associated with differential regulation of MADS-box transcription factors. BMC PLANT BIOLOGY 2015; 15:304. [PMID: 26714876 PMCID: PMC4696264 DOI: 10.1186/s12870-015-0697-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/21/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ripening in tomato is predominantly controlled by ethylene, whilst in fruit such as grape, it is predominantly controlled by other hormones. The ripening response of many kiwifruit (Actinidia) species is atypical. The majority of ripening-associated fruit starch hydrolysis, colour change and softening occurs in the apparent absence of ethylene production (Phase 1 ripening) whilst Phase 2 ripening requires autocatalytic ethylene production and is associated with further softening and an increase in aroma volatiles. RESULTS To dissect the ripening response in the yellow-fleshed kiwifruit A. chinensis ('Hort16A'), a two dimensional developmental stage X ethylene response time study was undertaken. As fruit progressed through maturation and Phase 1 ripening, fruit were treated with different concentrations of propylene and ethylene. At the start of Phase 1 ripening, treated fruit responded to ethylene, and were capable of producing endogenous ethylene. As the fruit progressed through Phase 1 ripening, the fruit became less responsive to ethylene and endogeneous ethylene production was partially repressed. Towards the end of Phase 1 ripening the fruit were again able to produce high levels of ethylene. Progression through Phase 1 ripening coincided with a developmental increase in the expression of the ethylene-unresponsive MADS-box FRUITFUL-like gene (FUL1). The ability to respond to ethylene however coincided with a change in expression of another MADS-box gene SEPALLATA4/RIPENING INHIBITOR-like (SEP4/RIN). The promoter of SEP4/RIN was shown to be transactivated by EIN3-like transcription factors, but unlike tomato, not by SEP4/RIN itself. Transient over-expression of SEP4/RIN in kiwifruit caused an increase in ethylene production. CONCLUSIONS These results suggest that the non-ethylene/ethylene ripening response observed in kiwifruit is a hybrid of both the tomato and grape ripening progression, with Phase 1 being akin to the RIN/ethylene inhibitory response observed in grape and Phase 2 akin to the RIN-associated autocatalytic ethylene response observed in tomato.
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Affiliation(s)
- Peter A McAtee
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | | | - Niels J Nieuwenhuizen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Kularajathevan Gunaseelan
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Ling Hoong
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Xiuyin Chen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Ross G Atkinson
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Jeremy N Burdon
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Karine M David
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Robert J Schaffer
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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Liu J, Liu L, Li Y, Jia C, Zhang J, Miao H, Hu W, Wang Z, Xu B, Jin Z. Role for the banana AGAMOUS-like gene MaMADS7 in regulation of fruit ripening and quality. PHYSIOLOGIA PLANTARUM 2015; 155:217-231. [PMID: 25980771 DOI: 10.1111/ppl.12348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/21/2015] [Accepted: 04/20/2015] [Indexed: 05/29/2023]
Abstract
MADS-box transcription factors play important roles in organ development. In plants, most studies on MADS-box genes have mainly focused on flower development and only a few concerned fruit development and ripening. A new MADS-box gene named MaMADS7 was isolated from banana fruit by rapid amplification of cDNA ends (RACE) based on a MADS-box fragment obtained from a banana suppression subtractive hybridization (SSH) cDNA library. MaMADS7 is an AGAMOUS-like MADS-box gene that is preferentially expressed in the ovaries and fruits and in tobacco its protein product localizes to the nucleus. This study found that MaMADS7 expression can be induced by exogenous ethylene. Ectopic expression of MaMADS7 in tomato resulted in broad ripening phenotypes. The expression levels of seven ripening and quality-related genes, ACO1, ACS2, E4, E8, PG, CNR and PSY1 in MaMADS7 transgenic tomato fruits were greatly increased while the expression of the AG-like MADS-box gene TAGL1 was suppressed. Compared with the control, the contents of β-carotene, lycopene, ascorbic acid and organic acid in transformed tomato fruits were increased, while the contents of glucose and fructose were slightly decreased. MaMADS7 interacted with banana 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase gene 1 (MaACO1) and tomato phytoene synthase gene (LePSY1) promoters. Our results indicated that MaMADS7 plays an important role in initiating endogenous ethylene biosynthesis and fruit ripening.
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Affiliation(s)
- Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Lin Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yujia Li
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Wei Hu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, China
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Bi F, Meng X, Ma C, Yi G. Identification of miRNAs involved in fruit ripening in Cavendish bananas by deep sequencing. BMC Genomics 2015; 16:776. [PMID: 26462563 PMCID: PMC4603801 DOI: 10.1186/s12864-015-1995-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/06/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are a family of non-coding small RNAs that play an important regulatory role in various biological processes. Previous studies have reported that miRNAs are closely related to the ripening process in model plants. However, the miRNAs that are closely involved in the banana fruit ripening process remain unknown. METHODS Here, we investigated the miRNA populations from banana fruits in response to ethylene or 1-MCP treatment using a deep sequencing approach and bioinformatics analysis combined with quantitative RT-PCR validation. RESULTS A total of 125 known miRNAs and 26 novel miRNAs were identified from three libraries. MiRNA profiling of bananas in response to ethylene treatment compared with 1-MCP treatment showed differential expression of 82 miRNAs. Furthermore, the differentially expressed miRNAs were predicted to target a total of 815 target genes. Interestingly, some targets were annotated as transcription factors and other functional proteins closely involved in the development and the ripening process in other plant species. Analysis by qRT-PCR validated the contrasting expression patterns between several miRNAs and their target genes. CONCLUSIONS The miRNAome of the banana fruit in response to ethylene or 1-MCP treatment were identified by high-throughput sequencing. A total of 82 differentially expressed miRNAs were found to be closely associated with the ripening process. The miRNA target genes encode transcription factors and other functional proteins, including SPL, APETALA2, EIN3, E3 ubiquitin ligase, β-galactosidase, and β-glucosidase. These findings provide valuable information for further functional research of the miRNAs involved in banana fruit ripening.
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Affiliation(s)
- Fangcheng Bi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, 510640, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
| | - Xiangchun Meng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, 510640, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
| | - Chao Ma
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet Dagan, 50250, Israel.
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, 510640, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
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Leng X, Fang J, Pervaiz T, Li Y, Wang X, Liu D, Zhu X, Fang J. Characterization of Expression Patterns of Grapevine MicroRNA Family Members using MicroRNA Rapid Amplification of Complementary DNA Ends. THE PLANT GENOME 2015; 8:eplantgenome2014.10.0069. [PMID: 33228326 DOI: 10.3835/plantgenome2014.10.0069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/11/2015] [Indexed: 06/11/2023]
Abstract
Grapevine (Vitis vinifera L.), with important nutritional values and health benefits, is one of the most economically fruit crop worldwide. In the present study, real-time quantitative polymerase chain reaction (qRT-PCR) and microRNA rapid amplification of cDNA ends (miR-RACE) techniques were used to characterize the expression and diversification patterns of various grapevine microRNAs (Vv-miRNAs) and their family members in grapevine. Based on our results, eight different grapevine miRNAs (miR159, miR164, miR167, miR172, miR319, miR393, miR396, and miR398) and their family members were expressed in different tissues at various developmental stages. The qRT-PCR results showed that the expression levels of Vv-miRNAs during grapevine development were dynamic. Furthermore, based on miR-RACE analysis and polymerase chain reaction (PCR) product sequencing results, different members within the same miRNA family were also expressed at different levels. Comparing the spatiotemporal expression levels of different members in the same miRNA family indicated that some miRNA families might have a key miRNA member that played the prominent role in regulation of their subsequent common target genes. In conclusion, our results showed that miR-RACE is a powerful technique to analyze the expression patterns of different members in the same miRNA family in terms of reverse-transcription (RT) efficiency and specificity. The findings of the expression diversification among Vv-miRNA family members and the existence of some Vv-miRNAs playing the key role could add to our understanding about the regulatory role of miRNAs in grapevine.
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Affiliation(s)
- Xiangpeng Leng
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
| | - Jinxiang Fang
- Chinese Medicine Hospital in Linyi City, Jiefang Rd. 211, Linyi, 276003, P.R. China
| | - Tariq Pervaiz
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
| | - Yu Li
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
| | - Xiaomin Wang
- Institute of Botany, Jiangsu Province and the Chinese Academy of Sciences, P.O. Box1435, No.1 Qianhu Houcun, Zhongshanmen Wai, Nanjing, 210014, P.R. China
| | - Dan Liu
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
| | - Xudong Zhu
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural Univ., Tongwei Rd. 6, Nanjing, 210095, P.R. China
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Saladié M, Cañizares J, Phillips MA, Rodriguez-Concepcion M, Larrigaudière C, Gibon Y, Stitt M, Lunn JE, Garcia-Mas J. Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties. BMC Genomics 2015; 16:440. [PMID: 26054931 PMCID: PMC4460886 DOI: 10.1186/s12864-015-1649-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 05/20/2015] [Indexed: 11/14/2022] Open
Abstract
Background In climacteric fruit-bearing species, the onset of fruit ripening is marked by a transient rise in respiration rate and autocatalytic ethylene production, followed by rapid deterioration in fruit quality. In non-climacteric species, there is no increase in respiration or ethylene production at the beginning or during fruit ripening. Melon is unusual in having climacteric and non-climacteric varieties, providing an interesting model system to compare both ripening types. Transcriptomic analysis of developing melon fruits from Védrantais and Dulce (climacteric) and Piel de sapo and PI 161375 (non-climacteric) varieties was performed to understand the molecular mechanisms that differentiate the two fruit ripening types. Results Fruits were harvested at 15, 25, 35 days after pollination and at fruit maturity. Transcript profiling was performed using an oligo-based microarray with 75 K probes. Genes linked to characteristic traits of fruit ripening were differentially expressed between climacteric and non-climacteric types, as well as several transcription factor genes and genes encoding enzymes involved in sucrose catabolism. The expression patterns of some genes in PI 161375 fruits were either intermediate between. Piel de sapo and the climacteric varieties, or more similar to the latter. PI 161375 fruits also accumulated some carotenoids, a characteristic trait of climacteric varieties. Conclusions Simultaneous changes in transcript abundance indicate that there is coordinated reprogramming of gene expression during fruit development and at the onset of ripening in both climacteric and non-climacteric fruits. The expression patterns of genes related to ethylene metabolism, carotenoid accumulation, cell wall integrity and transcriptional regulation varied between genotypes and was consistent with the differences in their fruit ripening characteristics. There were differences between climacteric and non-climacteric varieties in the expression of genes related to sugar metabolism suggesting that they may be potential determinants of sucrose content and post-harvest stability of sucrose levels in fruit. Several transcription factor genes were also identified that were differentially expressed in both types, implicating them in regulation of ripening behaviour. The intermediate nature of PI 161375 suggested that classification of melon fruit ripening behaviour into just two distinct types is an over-simplification, and that in reality there is a continuous spectrum of fruit ripening behaviour. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1649-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Montserrat Saladié
- IRTA, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain. .,Present address: School of Chemistry and Biochemistry, Biochemistry and Molecular Biology, The University of Western Australia, Crawley, WA, 6009, Australia.
| | - Joaquin Cañizares
- COMAV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València (UPV), Camino de Vera s/n, Valencia, 46022, Spain.
| | - Michael A Phillips
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Manuel Rodriguez-Concepcion
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Christian Larrigaudière
- IRTA, Parc Científic i Tecnològic Agroalimentari, Parc de Gardeny, Edifici Fruitcentre, Lleida, 25003, Spain.
| | - Yves Gibon
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany. .,Present address: INRA Bordeaux, University of Bordeaux, UMR1332 Fruit Biology and Pathology, Villenave d'Ornon, F-33883, France.
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany.
| | - John Edward Lunn
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany.
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
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Freiman ZE, Rosianskey Y, Dasmohapatra R, Kamara I, Flaishman MA. The ambiguous ripening nature of the fig (Ficus carica L.) fruit: a gene-expression study of potential ripening regulators and ethylene-related genes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3309-24. [PMID: 25956879 PMCID: PMC4449545 DOI: 10.1093/jxb/erv140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The traditional definition of climacteric and non-climacteric fruits has been put into question. A significant example of this paradox is the climacteric fig fruit. Surprisingly, ripening-related ethylene production increases following pre- or postharvest 1-methylcyclopropene (1-MCP) application in an unexpected auto-inhibitory manner. In this study, ethylene production and the expression of potential ripening-regulator, ethylene-synthesis, and signal-transduction genes are characterized in figs ripening on the tree and following preharvest 1-MCP application. Fig ripening-related gene expression was similar to that in tomato and apple during ripening on the tree, but only in the fig inflorescence-drupelet section. Because the pattern in the receptacle is different for most of the genes, the fig drupelets developed inside the syconium are proposed to function as parthenocarpic true fruit, regulating ripening processes for the whole accessory fruit. Transcription of a potential ripening regulator, FcMADS8, increased during ripening on the tree and was inhibited following 1-MCP treatment. Expression patterns of the ethylene-synthesis genes FcACS2, FcACS4, and FcACO3 could be related to the auto-inhibition reaction of ethylene production in 1-MCP-treated fruit. Along with FcMADS8 suppression, gene expression analysis revealed upregulation of FcEBF1, and downregulation of FcEIL3 and several FcERFs by 1-MCP treatment. This corresponded with the high storability of the treated fruit. One FcERF was overexpressed in the 1-MCP-treated fruit, and did not share the increasing pattern of most FcERFs in the tree-ripened fig. This demonstrates the potential of this downstream ethylene-signal-transduction component as an ethylene-synthesis regulator, responsible for the non-climacteric auto-inhibition of ethylene production in fig.
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Affiliation(s)
- Zohar E Freiman
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel
| | - Yogev Rosianskey
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel
| | - Rajeswari Dasmohapatra
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel
| | - Itzhak Kamara
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel
| | - Moshe A Flaishman
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel
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Liu J, Zhang J, Hu W, Miao H, Zhang J, Jia C, Wang Z, Xu B, Jin Z. Banana Ovate family protein MaOFP1 and MADS-box protein MuMADS1 antagonistically regulated banana fruit ripening. PLoS One 2015; 10:e0123870. [PMID: 25886169 PMCID: PMC4401719 DOI: 10.1371/journal.pone.0123870] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/23/2015] [Indexed: 12/30/2022] Open
Abstract
The ovate family protein named MaOFP1 was identified in banana (Musa acuminata L.AAA) fruit by a yeast two-hybrid (Y2H) method using the banana MADS-box gene MuMADS1 as bait and a 2 day postharvest (DPH) banana fruit cDNA library as prey. The interaction between MuMADS1 and MaOFP1 was further confirmed by Y2H and Bimolecular Fluorescence Complementation (BiFC) methods, which showed that the MuMADS1 K domain interacted with MaOFP1. Real-time quantitative PCR evaluation of MuMADS1 and MaOFP1 expression patterns in banana showed that they are highly expressed in 0 DPH fruit, but present in low levels in the stem, which suggests that simultaneous but different expression patterns exist for both MuMADS1 and MaOFP1 in different tissues and developing fruits. Meanwhile, MuMADS1 and MaOFP1 expression was highly stimulated and greatly suppressed, respectively, by exogenous ethylene. In contrast, MaOFP1 expression was highly stimulated while MuMADS1 was greatly suppressed by the ethylene competitor 1-methylcyclopropene (1-MCP). These results indicate that MuMADS1 and MaOFP1 are antagonistically regulated by ethylene and might play important roles in postharvest banana fruit ripening.
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Affiliation(s)
- Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jing Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Wei Hu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- * E-mail: (BX); (ZJ)
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- * E-mail: (BX); (ZJ)
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Identification of microRNAs and target genes in the fruit and shoot tip of Lycium chinense: a traditional Chinese medicinal plant. PLoS One 2015; 10:e0116334. [PMID: 25587984 PMCID: PMC4294688 DOI: 10.1371/journal.pone.0116334] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/05/2014] [Indexed: 11/19/2022] Open
Abstract
Although Lycium chinense (goji berry) is an important traditional Chinese medicinal plant, little genome information is available for this plant, particularly at the small-RNA level. Recent findings indicate that the evolutionary role of miRNAs is very important for a better understanding of gene regulation in different plant species. To elucidate small RNAs and their potential target genes in fruit and shoot tissues, high-throughput RNA sequencing technology was used followed by qRT-PCR and RLM 5’-RACE experiments. A total of 60 conserved miRNAs belonging to 31 families and 30 putative novel miRNAs were identified. A total of 62 significantly differentially expressed miRNAs were identified, of which 15 (14 known and 1 novel) were shoot-specific, and 12 (7 known and 5 novel) were fruit-specific. Additionally, 28 differentially expressed miRNAs were recorded as up-regulated in fruit tissues. The predicted potential targets were involved in a wide range of metabolic and regulatory pathways. GO (Gene Ontology) enrichment analysis and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database revealed that “metabolic pathways” is the most significant pathway with respect to the rich factor and gene numbers. Moreover, five miRNAs were related to fruit maturation, lycopene biosynthesis and signaling pathways, which might be important for the further study of fruit molecular biology. This study is the first, to detect known and novel miRNAs, and their potential targets, of L. chinense. The data and findings that are presented here might be a good source for the functional genomic study of medicinal plants and for understanding the links among diversified biological pathways.
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Asif MH, Lakhwani D, Pathak S, Gupta P, Bag SK, Nath P, Trivedi PK. Transcriptome analysis of ripe and unripe fruit tissue of banana identifies major metabolic networks involved in fruit ripening process. BMC PLANT BIOLOGY 2014; 14:316. [PMID: 25442405 PMCID: PMC4263013 DOI: 10.1186/s12870-014-0316-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/04/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Banana is one of the most important crop plants grown in the tropics and sub-tropics. It is a climacteric fruit and undergoes ethylene dependent ripening. Once ripening is initiated, it proceeds at a fast rate making postharvest life short, which can result in heavy economic losses. During the fruit ripening process a number of physiological and biochemical changes take place and thousands of genes from various metabolic pathways are recruited to produce a ripe and edible fruit. To better understand the underlying mechanism of ripening, we undertook a study to evaluate global changes in the transcriptome of the fruit during the ripening process. RESULTS We sequenced the transcriptomes of the unripe and ripe stages of banana (Musa accuminata; Dwarf Cavendish) fruit. The transcriptomes were sequenced using a 454 GSFLX-Titanium platform that resulted in more than 7,00,000 high quality (HQ) reads. The assembly of the reads resulted in 19,410 contigs and 92,823 singletons. A large number of the differentially expressed genes identified were linked to ripening dependent processes including ethylene biosynthesis, perception and signalling, cell wall degradation and production of aromatic volatiles. In the banana fruit transcriptomes, we found transcripts included in 120 pathways described in the KEGG database for rice. The members of the expansin and xyloglucan transglycosylase/hydrolase (XTH) gene families were highly up-regulated during ripening, which suggests that they might play important roles in the softening of the fruit. Several genes involved in the synthesis of aromatic volatiles and members of transcription factor families previously reported to be involved in ripening were also identified. CONCLUSIONS A large number of differentially regulated genes were identified during banana fruit ripening. Many of these are associated with cell wall degradation and synthesis of aromatic volatiles. A large number of differentially expressed genes did not align with any of the databases and might be novel genes in banana. These genes can be good candidates for future studies to establish their role in banana fruit ripening. The datasets developed in this study will help in developing strategies to manipulate banana fruit ripening and reduce post harvest losses.
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Affiliation(s)
- Mehar Hasan Asif
- />CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- />Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
| | - Deepika Lakhwani
- />CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- />Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
| | - Sumya Pathak
- />CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
| | - Parul Gupta
- />CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
| | - Sumit K Bag
- />CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- />Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
| | - Pravendra Nath
- />CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
| | - Prabodh Kumar Trivedi
- />CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- />Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
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Li X, Fan T, Song J, Sun W, Xia K, Liao J, Zhang M. Functional conservation and divergence of four ginger AP1/AGL9 MADS-box genes revealed by analysis of their expression and protein-protein interaction, and ectopic expression of AhFUL gene in Arabidopsis. PLoS One 2014; 9:e114134. [PMID: 25461565 PMCID: PMC4252096 DOI: 10.1371/journal.pone.0114134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/03/2014] [Indexed: 11/28/2022] Open
Abstract
Alpinia genus are known generally as ginger-lilies for showy flowers in the ginger family, Zingiberaceae, and their floral morphology diverges from typical monocotyledon flowers. However, little is known about the functions of ginger MADS-box genes in floral identity. In this study, four AP1/AGL9 MADS-box genes were cloned from Alpinia hainanensis, and protein-protein interactions (PPIs) and roles of the four genes in floral homeotic conversion and in floral evolution are surveyed for the first time. AhFUL is clustered to the AP1 lineage, AhSEP4 and AhSEP3b to the SEP lineage, and AhAGL6-like to the AGL6 lineage. The four genes showed conserved and divergent expression patterns, and their encoded proteins were localized in the nucleus. Seven combinations of PPI (AhFUL-AhSEP4, AhFUL-AhAGL6-like, AhFUL-AhSEP3b, AhSEP4-AhAGL6-like, AhSEP4-AhSEP3b, AhAGL6-like-AhSEP3b, and AhSEP3b-AhSEP3b) were detected, and the PPI patterns in the AP1/AGL9 lineage revealed that five of the 10 possible combinations are conserved and three are variable, while conclusions cannot yet be made regarding the other two. Ectopic expression of AhFUL in Arabidopsis thaliana led to early flowering and floral organ homeotic conversion to sepal-like or leaf-like. Therefore, we conclude that the four A. hainanensis AP1/AGL9 genes show functional conservation and divergence in the floral identity from other MADS-box genes.
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Affiliation(s)
- Xiumei Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Fan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juanjuan Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Wei Sun
- Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing, 100700, China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jingping Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Ba LJ, Shan W, Xiao YY, Chen JY, Lu WJ, Kuang JF. A ripening-induced transcription factor MaBSD1 interacts with promoters of MaEXP1/2 from banana fruit. PLANT CELL REPORTS 2014; 33:1913-20. [PMID: 25097074 DOI: 10.1007/s00299-014-1668-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 07/29/2014] [Indexed: 06/03/2023]
Abstract
KEY MESSAGE The ripening-induced MaBSD1 acts as a transcriptional activator, and might be involved in banana fruit ripening partly through directly activating the expression of two ripening-associated genes, MaEXP1/2. BSD (BTF2-like transcription factors, synapse-associated proteins and DOS2-like proteins) transcription factors are characterized by a typical BSD domain. However, little information is available concerning their possible roles in plant growth and development, especially in fruit ripening. In the present study, one BSD gene, designated as MaBSD1, was isolated from banana fruit. MaBSD1 has an open reading frame (ORF) of 921 bp which encodes a polypeptide of 306 amino acid residues with molecular weight of 34.80 kDa, and isoelectric point (pI) of 4.54. Subcellular localization and transcriptional activation assays showed that MaBSD1 was localized in both the nucleus and cytoplasm and possessed transcriptional activity. RT-qPCR and promoter activity analysis indicated that MaBSD1 was ethylene and ripening inducible, and the accumulation of MaBSD1 transcript was correlated well with the evolution of ethylene production and ripening process. Moreover, transient assay showed that MaBSD1 could activate the expression of two cell wall modification-related genes, MaEXP1/2, via directly interacting with their promoters. Together, these data suggest that ripening-induced MaBSD1 acts as a transcriptional activator and might be associated with banana fruit ripening, at least partially through directly activating the expression of MaEXP1/2, expanding the limited information concerning the BSD transcription factor in relation to fruit ripening.
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Affiliation(s)
- Liang-Jie Ba
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
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Moyle RL, Koia JH, Vrebalov J, Giovannoni J, Botella JR. The pineapple AcMADS1 promoter confers high level expression in tomato and Arabidopsis flowering and fruiting tissues, but AcMADS1 does not complement the tomato LeMADS-RIN (rin) mutant. PLANT MOLECULAR BIOLOGY 2014; 86:395-407. [PMID: 25139231 DOI: 10.1007/s11103-014-0236-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 08/04/2014] [Indexed: 06/03/2023]
Abstract
A previous EST study identified a MADS box transcription factor coding sequence, AcMADS1, that is strongly induced during non-climacteric pineapple fruit ripening. Phylogenetic analyses place the AcMADS1 protein in the same superclade as LeMADS-RIN, a master regulator of fruit ripening upstream of ethylene in climacteric tomato. LeMADS-RIN has been proposed to be a global ripening regulator shared among climacteric and non-climacteric species, although few functional homologs of LeMADS-RIN have been identified in non-climacteric species. AcMADS1 shares 67 % protein sequence similarity and a similar expression pattern in ripening fruits as LeMADS-RIN. However, in this study AcMADS1 was not able to complement the tomato rin mutant phenotype, indicating AcMADS1 may not be a functionally conserved homolog of LeMADS-RIN or has sufficiently diverged to be unable to act in the context of the tomato network of interacting proteins. The AcMADS1 promoter directed strong expression of the GUS reporter gene to fruits and developing floral organs in tomato and Arabidopsis thaliana, suggesting AcMADS1 may play a role in flower development as well as fruitlet ripening. The AcMADS1 promoter provides a useful molecular tool for directing transgene expression, particularly where up-regulation in developing flowers and fruits is desirable.
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Affiliation(s)
- Richard L Moyle
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, 4072, Australia,
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Cherian S, Figueroa CR, Nair H. 'Movers and shakers' in the regulation of fruit ripening: a cross-dissection of climacteric versus non-climacteric fruit. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4705-22. [PMID: 24994760 DOI: 10.1093/jxb/eru280] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fruit ripening is a complex and highly coordinated developmental process involving the expression of many ripening-related genes under the control of a network of signalling pathways. The hormonal control of climacteric fruit ripening, especially ethylene perception and signalling transduction in tomato has been well characterized. Additionally, great strides have been made in understanding some of the major regulatory switches (transcription factors such as RIPENING-INHIBITOR and other transcriptional regulators such as COLOURLESS NON-RIPENING, TOMATO AGAMOUS-LIKE1 and ETHYLENE RESPONSE FACTORs), that are involved in tomato fruit ripening. In contrast, the regulatory network related to non-climacteric fruit ripening remains poorly understood. However, some of the most recent breakthrough research data have provided several lines of evidences for abscisic acid- and sucrose-mediated ripening of strawberry, a non-climacteric fruit model. In this review, we discuss the most recent research findings concerning the hormonal regulation of fleshy fruit ripening and their cross-talk and the future challenges taking tomato as a climacteric fruit model and strawberry as a non-climacteric fruit model. We also highlight the possible contribution of epigenetic changes including the role of plant microRNAs, which is opening new avenues and great possibilities in the fields of fruit-ripening research and postharvest biology.
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Affiliation(s)
- Sam Cherian
- Faculty of Integrative Sciences and Technology, Quest International University Perak, Jalan Raja Permaisuri Bainun, 30250 Ipoh, Perak Darul Ridzuan, Malaysia
| | - Carlos R Figueroa
- Faculty of Forest Sciences and Biotechnology Center, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile
| | - Helen Nair
- Faculty of Integrative Sciences and Technology, Quest International University Perak, Jalan Raja Permaisuri Bainun, 30250 Ipoh, Perak Darul Ridzuan, Malaysia
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Karlova R, Chapman N, David K, Angenent GC, Seymour GB, de Maagd RA. Transcriptional control of fleshy fruit development and ripening. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4527-41. [PMID: 25080453 DOI: 10.1093/jxb/eru316] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fleshy fruits have evolved to be attractive to frugivores in order to enhance seed dispersal, and have become an indispensable part of the human diet. Here we review the recent advances in the understanding of transcriptional regulation of fleshy fruit development and ripening with a focus on tomato. While aspects of fruit development are probably conserved throughout the angiosperms, including the model plant Arabidopsis thaliana, it is shown that the likely orthologues of Arabidopsis genes have distinct functions in fleshy fruits. The model for the study of fleshy fruit development is tomato, because of the availability of single gene mutants and transgenic knock-down lines. In other species, our knowledge is often incomplete or absent. Tomato fruit size and shape are co-determined by transcription factors acting during formation of the ovary. Other transcription factors play a role in fruit chloroplast formation, and upon ripening impact quality aspects such as secondary metabolite content. In tomato, the transcription factors NON-RIPENING (NOR), COLORLESS NON-RIPENING (CNR), and RIPENING INHIBITOR (MADS-RIN) in concert with ethylene signalling regulate ripening, possibly in response to a developmental switch. Additional components include TOMATO AGAMOUS-LIKE1 (TAGL1), APETALA2a (AP2a), and FRUITFULL (FUL1 and FUL2). The links between this highly connected regulatory network and downstream effectors modulating colour, texture, and flavour are still relatively poorly understood. Intertwined with this network is post-transcriptional regulation by fruit-expressed microRNAs targeting several of these transcription factors. This important developmental process is also governed by changes in DNA methylation levels and possibly chromatin remodelling.
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Affiliation(s)
- Rumyana Karlova
- Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands Laboratory of Molecular Biology, Wageningen University, 6700 ET Wageningen, The Netherlands
| | - Natalie Chapman
- Plant and Crop Science Division, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Karine David
- University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University, 6700 ET Wageningen, The Netherlands Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
| | - Graham B Seymour
- Plant and Crop Science Division, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Ruud A de Maagd
- Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands Chair group Bioinformatics, Wageningen University, 6700 ET Wageningen, The Netherlands
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Pacheco-Sánchez MA, Contreras-Vergara CA, Hernandez-Navarro E, Yepiz-Plascencia G, Martínez-Téllez MA, Casas-Flores S, Arvizu-Flores AA, Islas-Osuna MA. Molecular modeling and expression analysis of a MADS-box cDNA from mango (Mangifera indica L.). 3 Biotech 2014; 4:357-365. [PMID: 28324472 PMCID: PMC4145620 DOI: 10.1007/s13205-013-0162-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/30/2013] [Indexed: 12/18/2022] Open
Abstract
MADS-box genes are a large family of transcription factors initially discovered for their role during development of flowers and fruits. The MADS-box transcription factors from animals have been studied by X-ray protein crystallography but those from plants remain to be studied. In this work, a MADS-box cDNA from mango encoding a protein of 254 residues was obtained and compared. Based on phylogenetic analysis, it is proposed that the MADS-box transcription factor expressed in mango fruit (MiMADS1) belongs to the SEP clade of MADS-box proteins. MiMADS1 mRNA steady-state levels did not changed during mango fruit development and were up-regulated, when mango fruits reached physiological maturity as assessed by qRT-PCR. Thus, MiMADS1 could have a role during development and ripening of this fruit. The theoretical structural model of MiMADS1 showed the DNA-binding domain folding bound to a double-stranded DNA. Therefore, MiMADS1 is an interesting model for understanding DNA-binding for transcriptional regulation.
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Affiliation(s)
- Magda A Pacheco-Sánchez
- Plant Molecular Biology Lab, Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera a la Victoria Km 0.6, Apartado Postal 1735, 83304, Hermosillo, Sonora, Mexico
| | - Carmen A Contreras-Vergara
- Plant Molecular Biology Lab, Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera a la Victoria Km 0.6, Apartado Postal 1735, 83304, Hermosillo, Sonora, Mexico
| | - Eduardo Hernandez-Navarro
- Plant Molecular Biology Lab, Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera a la Victoria Km 0.6, Apartado Postal 1735, 83304, Hermosillo, Sonora, Mexico
| | - Gloria Yepiz-Plascencia
- Plant Molecular Biology Lab, Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera a la Victoria Km 0.6, Apartado Postal 1735, 83304, Hermosillo, Sonora, Mexico
| | - Miguel A Martínez-Téllez
- Plant Molecular Biology Lab, Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera a la Victoria Km 0.6, Apartado Postal 1735, 83304, Hermosillo, Sonora, Mexico
| | - Sergio Casas-Flores
- División de Biología Molecular, IPICYT, Camino a la Presa San José No. 2055, Lomas 4a sección, 78216, San Luis Potosí, Mexico
| | - Aldo A Arvizu-Flores
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Blvd. Rosales S/N, 83000, Hermosillo, Sonora, Mexico
| | - Maria A Islas-Osuna
- Plant Molecular Biology Lab, Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera a la Victoria Km 0.6, Apartado Postal 1735, 83304, Hermosillo, Sonora, Mexico.
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Hubert O, Piral G, Galas C, Baurens FC, Mbéguié-A-Mbéguié D. Changes in ethylene signaling and MADS box gene expression are associated with banana finger drop. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 223:99-108. [PMID: 24767119 DOI: 10.1016/j.plantsci.2014.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/25/2014] [Accepted: 03/05/2014] [Indexed: 06/03/2023]
Abstract
Banana finger drop was examined in ripening banana harvested at immature (iMG), early (eMG) and late mature green (lMG) stages, with contrasting ripening rates and ethylene sensitivities. Concomitantly, 11 ethylene signal transduction components (ESTC) and 6 MADS box gene expressions were comparatively studied in median (control zone, CZ) and pedicel rupture (drop zone DZ) areas in peel tissue. iMG fruit did not ripen or develop finger drop while eMG and lMG fruits displayed a similar finger drop pattern. Several ESTC and MADS box gene mRNAs were differentially induced in DZ and CZ and sequentially in eMG and lMG fruits. MaESR2, 3 and MaEIL1, MaMADS2 and MaMADS5 had a higher mRNA level in eMG and acted earlier, whereas MaERS1, MaCTR1, MaEIL3/AB266319, MaEIL4/AB266320 and MaEIL5/AB266321, MaMADS4 and to a lesser extent MaMADS2 and 5 acted later in lMG. In this fruit, MaERS1 and 3, MaCTR1, MaEIL3, 4 and MaEIL5/AB266321, and MaMADS4 were enhanced by finger drop, suggesting their specific involvement in this process. MaEIL1, MaMADS1 and 3, induced at comparable levels in DZ and CZ, are probably related to the overall fruit ripening process. These findings led us to consider that developmental cues are the predominant finger drop regulation factor.
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Affiliation(s)
- O Hubert
- CIRAD, UMR QUALISUD, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; CIRAD, UMR QUALISUD, F-34398 Montpellier, France.
| | - G Piral
- CIRAD, UMR QUALISUD, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; CIRAD, UMR QUALISUD, F-34398 Montpellier, France.
| | - C Galas
- INRA, UMR QUALITROP, F-97170 Petit-Bourg, Guadeloupe, France.
| | - F-C Baurens
- CIRAD, UMR AGAP/SEG, F-34398 Montpellier, France.
| | - D Mbéguié-A-Mbéguié
- CIRAD, UMR QUALISUD, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; CIRAD, UMR QUALISUD, F-34398 Montpellier, France.
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Pan ZJ, Chen YY, Du JS, Chen YY, Chung MC, Tsai WC, Wang CN, Chen HH. Flower development of Phalaenopsis orchid involves functionally divergent SEPALLATA-like genes. THE NEW PHYTOLOGIST 2014; 202:1024-1042. [PMID: 24571782 PMCID: PMC4288972 DOI: 10.1111/nph.12723] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 01/02/2014] [Indexed: 05/20/2023]
Abstract
The Phalaenopsis orchid produces complex flowers that are commercially valuable, which has promoted the study of its flower development. E-class MADS-box genes, SEPALLATA (SEP), combined with B-, C- and D-class MADS-box genes, are involved in various aspects of plant development, such as floral meristem determination, organ identity, fruit maturation, seed formation and plant architecture. Four SEP-like genes were cloned from Phalaenopsis orchid, and the duplicated PeSEPs were grouped into PeSEP1/3 and PeSEP2/4. All PeSEPs were expressed in all floral organs. PeSEP2 expression was detectable in vegetative tissues. The study of protein-protein interactions suggested that PeSEPs may form higher order complexes with the B-, C-, D-class and AGAMOUS LIKE6-related MADS-box proteins to determine floral organ identity. The tepal became a leaf-like organ when PeSEP3 was silenced by virus-induced silencing, with alterations in epidermis identity and contents of anthocyanin and chlorophyll. Silencing of PeSEP2 had minor effects on the floral phenotype. Silencing of the E-class genes PeSEP2 and PeSEP3 resulted in the downregulation of B-class PeMADS2-6 genes, which indicates an association of PeSEP functions and B-class gene expression. These findings reveal the important roles of PeSEP in Phalaenopsis floral organ formation throughout the developmental process by the formation of various multiple protein complexes.
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Affiliation(s)
- Zhao-Jun Pan
- Department of Life Sciences, National Cheng Kung UniversityTainan, 701, Taiwan
| | - You-Yi Chen
- Institute of Tropical Plant Sciences, National Cheng Kung UniversityTainan, 701, Taiwan
| | - Jian-Syun Du
- Department of Life Sciences, National Cheng Kung UniversityTainan, 701, Taiwan
| | - Yun-Yu Chen
- Institute of Ecology and Evolutionary Biology, National Taiwan UniversityTaipei, 106, Taiwan
| | - Mei-Chu Chung
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, 115, Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung UniversityTainan, 701, Taiwan
- Orchid Research Center, National Cheng Kung UniversityTainan, 701, Taiwan
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan UniversityTaipei, 106, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung UniversityTainan, 701, Taiwan
- Orchid Research Center, National Cheng Kung UniversityTainan, 701, Taiwan
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Dong T, Chen G, Tian S, Xie Q, Yin W, Zhang Y, Hu Z. A non-climacteric fruit gene CaMADS-RIN regulates fruit ripening and ethylene biosynthesis in climacteric fruit. PLoS One 2014; 9:e95559. [PMID: 24751940 PMCID: PMC3994064 DOI: 10.1371/journal.pone.0095559] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 03/28/2014] [Indexed: 11/19/2022] Open
Abstract
MADS-box genes have been reported to play a major role in the molecular circuit of developmental regulation. Especially, SEPALLATA (SEP) group genes play a central role in the developmental regulation of ripening in both climacteric and non-climacteric fruits. However, the mechanisms underlying the regulation of SEP genes to non-climacteric fruits ripening are still unclear. Here a SEP gene of pepper, CaMADS-RIN, has been cloned and exhibited elevated expression at the onset of ripening of pepper. To further explore the function of CaMADS-RIN, an overexpressed construct was created and transformed into ripening inhibitor (rin) mutant tomato plants. Broad ripening phenotypes were observed in CaMADS-RIN overexpressed rin fruits. The accumulation of carotenoid and expression of PDS and ZDS were enhanced in overexpressed fruits compared with rin mutant. The transcripts of cell wall metabolism genes (PG, EXP1 and TBG4) and lipoxygenase genes (TomloxB and TomloxC) accumulated more abundant compared to rin mutant. Besides, both ethylene-dependent genes including ACS2, ACO1, E4 and E8 and ethylene-independent genes such as HDC and Nor were also up-regulated in transgenic fruits at different levels. Moreover, transgenic fruits showed approximately 1–3 times increase in ethylene production compared with rin mutant fruits. Yeast two-hybrid screen results indicated that CaMADS-RIN could interact with TAGL1, FUL1 and itself respectively as SlMADS-RIN did in vitro. These results suggest that CaMADS-RIN affects fruit ripening of tomato both in ethylene-dependent and ethylene-independent aspects, which will provide a set of significant data to explore the role of SEP genes in ripening of non-climacteric fruits.
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Affiliation(s)
- Tingting Dong
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Guoping Chen
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Shibing Tian
- The Institute of Vegetable Research, Chongqing Academy of Agricultural Sciences, Chongqing, People’s Republic of China
| | - Qiaoli Xie
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Wencheng Yin
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Yanjie Zhang
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Zongli Hu
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
- * E-mail:
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Dreni L, Kater MM. MADS reloaded: evolution of the AGAMOUS subfamily genes. THE NEW PHYTOLOGIST 2014; 201:717-732. [PMID: 24164649 DOI: 10.1111/nph.12555] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/02/2013] [Indexed: 05/03/2023]
Abstract
AGAMOUS subfamily proteins are encoded by MADS-box family genes. They have been shown to play key roles in the determination of reproductive floral organs such as stamens, carpels and ovules. However, they also play key roles in ensuring a fixed number of floral organs by controlling floral meristem determinacy. Recently, an enormous amount of sequence data for nonmodel species have become available together with functional data on AGAMOUS subfamily members in many species. Here, we give a detailed overview of the most important information about this interesting gene subfamily and provide new insights into its evolution.
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Affiliation(s)
- Ludovico Dreni
- Department of Biosciences, Università degli Studi di Milano, via Celoria 26, 20133, Milan, Italy
| | - Martin M Kater
- Department of Biosciences, Università degli Studi di Milano, via Celoria 26, 20133, Milan, Italy
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Ortiz R, Swennen R. From crossbreeding to biotechnology-facilitated improvement of banana and plantain. Biotechnol Adv 2014; 32:158-69. [DOI: 10.1016/j.biotechadv.2013.09.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 12/30/2022]
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49
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Acri-Nunes-Miranda R, Mondragón-Palomino M. Expression of paralogous SEP-, FUL-, AG- and STK-like MADS-box genes in wild-type and peloric Phalaenopsis flowers. FRONTIERS IN PLANT SCIENCE 2014; 5:76. [PMID: 24659990 PMCID: PMC3950491 DOI: 10.3389/fpls.2014.00076] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/17/2014] [Indexed: 05/05/2023]
Abstract
The diverse flowers of Orchidaceae are the result of several major morphological transitions, among them the most studied is the differentiation of the inner median tepal into the labellum, a perianth organ key in pollinator attraction. Type A peloria lacking stamens and with ectopic labella in place of inner lateral tepals are useful for testing models on the genes specifying these organs by comparing their patterns of expression between wild-type and peloric flowers. Previous studies focused on DEFICIENS- and GLOBOSA-like MADS-box genes because of their conserved role in perianth and stamen development. The "orchid code" model summarizes this work and shows in Orchidaceae there are four paralogous lineages of DEFICIENS/AP3-like genes differentially expressed in each floral whorl. Experimental tests of this model showed the conserved, higher expression of genes from two specific DEF-like gene lineages is associated with labellum development. The present study tests whether eight MADS-box candidate SEP-, FUL-, AG-, and STK-like genes have been specifically duplicated in the Orchidaceae and are also differentially expressed in association with the distinct flower organs of Phalaenopsis hyb. "Athens." The gene trees indicate orchid-specific duplications. In a way analogous to what is observed in labellum-specific DEF-like genes, a two-fold increase in the expression of SEP3-like gene PhaMADS7 was measured in the labellum-like inner lateral tepals of peloric flowers. The overlap between SEP3-like and DEF-like genes suggests both are associated with labellum specification and similar positional cues determine their domains of expression. In contrast, the uniform messenger levels of FUL-like genes suggest they are involved in the development of all organs and their expression in the ovary suggests cell differentiation starts before pollination. As previously reported AG-like and STK-like genes are exclusively expressed in gynostemium and ovary, however no evidence for transcriptional divergence was found in the stage investigated. Gene expression suggests a developmental regulatory system based on the combined activity of duplicate MADS-box genes. We discuss its feasibility based on documented protein interactions and patterns of expression.
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Affiliation(s)
| | - Mariana Mondragón-Palomino
- *Correspondence: Mariana Mondragón-Palomino, Department of Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany e-mail:
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50
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Gapper NE, Giovannoni JJ, Watkins CB. Understanding development and ripening of fruit crops in an 'omics' era. HORTICULTURE RESEARCH 2014; 1:14034. [PMID: 26504543 PMCID: PMC4596339 DOI: 10.1038/hortres.2014.34] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 05/21/2014] [Accepted: 05/28/2014] [Indexed: 05/17/2023]
Abstract
Next generation sequencing has revolutionized plant biology. Not only has our understanding of plant metabolism advanced using model systems and modern chromatography, but application of 'omics'-based technology has been widely extended to non-model systems as costs have plummeted and efficiency increased. As a result, important fundamental questions relating to important horticultural crops are being answered, and novel approaches with application to industry are in progress. Here we review recent research advances on development and ripening of fruit crops, how next generation sequencing approaches are driving this advance and the emerging future landscape.
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Affiliation(s)
- Nigel E Gapper
- Department of Horticulture, Cornell University, Ithaca, NY 14853, USA
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
- mailto:
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
- Plant, Soil, and Nutrition Laboratory, US Department of Agriculture/Agriculture Research Service, Ithaca, NY 14853, USA
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