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Yi Z, Sharif R, Gulzar S, Huang Y, Ning T, Zhan H, Meng Y, Xu C. Changes in hemicellulose metabolism in banana peel during fruit development and ripening. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109025. [PMID: 39142014 DOI: 10.1016/j.plaphy.2024.109025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 08/16/2024]
Abstract
Hemicellulose is key in determining the fate of plant cell wall in almost all growth and developmental stages. Nevertheless, there is limited knowledge regarding its involvement in the development and ripening of banana fruit. This study investigated changes in the temporal-spatial distribution of various hemicellulose components, hemicellulose content, activities of the main hydrolysis enzymes, and transcription level of the main hemicellulose-related gene families in banana peels. Both hemicellulose and xylan contents were positively correlated to the fruit firmness observed in our previous study. On the contrary, the xylanase activity was negatively correlated to xylan content and the fruit firmness. The vascular bundle cells, phloem, and cortex of bananas are abundant in xyloglucan, xylan, and mannan contents. Interestingly, the changes in the signal intensity of the CCRC-M104 antibody recognizing non-XXXG type xyloglucan are positively correlated to hemicellulose content. According to RNA-Seq analysis, xyloglucan and xylan-related genes were highly active in the early stages of growth, and the expression of MaMANs and MaXYNs increased as the fruit ripened. The abundance of plant hormonal and growth-responsive cis-acting elements was detected in the 2 kb upstream region of hemicellulose-related gene families. Interaction between hemicellulose and cell wall-specific proteins and MaKCBP1/2, MaCKG1, and MaHKL1 was found. The findings shed light on cell wall hemicellulose's role in banana fruit development and ripening, which could improve nutrition, flavor, and reduce postharvest fruit losses.
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Affiliation(s)
- Zan Yi
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Shazma Gulzar
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yongxin Huang
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Tong Ning
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Huiling Zhan
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yue Meng
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Chunxiang Xu
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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Bianchetti R, Ali A, Gururani M. Abscisic acid and ethylene coordinating fruit ripening under abiotic stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 349:112243. [PMID: 39233143 DOI: 10.1016/j.plantsci.2024.112243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Fleshy fruit metabolism is intricately influenced by environmental changes, yet the hormonal regulations underlying these responses remain poorly elucidated. ABA and ethylene, pivotal in stress responses across plant vegetative tissues, play crucial roles in triggering fleshy fruit ripening. Their actions are intricately governed by complex mechanisms, influencing key aspects such as nutraceutical compound accumulation, sugar content, and softening parameters. Both hormones are essential orchestrators of significant alterations in fruit development in response to stressors like drought, salt, and temperature fluctuations. These alterations encompass colour development, sugar accumulation, injury mitigation, and changes in cell-wall degradation and ripening progression. This review provides a comprehensive overview of recent research progress on the roles of ABA and ethylene in responding to drought, salt, and temperature stress, as well as the molecular mechanisms controlling ripening in environmental cues. Additionally, we propose further studies aimed at genetic manipulation of ABA and ethylene signalling, offering potential strategies to enhance fleshy fruit resilience in the face of future climate change scenarios.
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Affiliation(s)
- Ricardo Bianchetti
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Amjad Ali
- Department of Sustainable Crop Production, Università Cattolica Del Sacro Cuore, Via Emilia Parmense 84, Piacenza 29122, Italy
| | - Mayank Gururani
- Biology department, College of Science, UAE University, P.O.Box 15551, Al Ain, United Arab Emirates.
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Yue Q, Yang X, Cheng P, He J, Shen W, Li Y, Ma F, Niu C, Guan Q. Heterologous Overexpression of Apple MdKING1 Promotes Fruit Ripening in Tomato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2848. [PMID: 37571003 PMCID: PMC10421076 DOI: 10.3390/plants12152848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/29/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023]
Abstract
Fruit ripening is governed by a complex regulatory network, and ethylene plays an important role in this process. MdKING1 is a γ subunit of SNF1-related protein kinases (SnRKs), but the function was unclear. Here, we characterized the role of MdKING1 during fruit ripening, which can promote fruit ripening through the ethylene pathway. Our findings reveal that MdKING1 has higher expression in early-ripening cultivars than late-ripening during the early stage of apple fruit development, and its transcription level significantly increased during apple fruit ripening. Overexpression of MdKING1 (MdKING1 OE) in tomatoes could promote early ripening of fruits, with the increase in ethylene content and the loss of fruit firmness. Ethylene inhibitor treatment could delay the fruit ripening of both MdKING1 OE and WT fruits. However, MdKING1 OE fruits turned fruit ripe faster, with an increase in carotenoid content compared with WT. In addition, the expression of genes involved in ethylene biosynthesis (SlACO1, SlACS2, and SlACS4), carotenoid biosynthesis (SlPSY1 and SlGgpps2a), and fruit firmness regulation (SlPG2a, SlPL, and SlCEL2) was also increased in the fruits of MdKING1 OE plants. In conclusion, our results suggest that MdKING1 plays a key role in promoting tomato fruit ripening, thus providing a theoretical basis for apple fruit quality improvement by genetic engineering in the future.
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Affiliation(s)
- Qianyu Yue
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, China;
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Xinyue Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Pengda Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Wenyun Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Yixuan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Chundong Niu
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, China;
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Qingmei Guan
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, China;
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
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Campos NA, Colombié S, Moing A, Cassan C, Amah D, Swennen R, Gibon Y, Carpentier SC. From fruit growth to ripening in plantain: a careful balance between carbohydrate synthesis and breakdown. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4832-4849. [PMID: 35512676 PMCID: PMC9366326 DOI: 10.1093/jxb/erac187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/04/2022] [Indexed: 06/14/2023]
Abstract
In this study, we aimed to investigate for the first time different fruit development stages in plantain banana in order gain insights into the order of appearance and dominance of specific enzymes and fluxes. We examined fruit development in two plantain banana cultivars during the period between 2-12 weeks after bunch emergence using high-throughput proteomics, quantification of major metabolites, and analyses of metabolic fluxes. Starch synthesis and breakdown are processes that take place simultaneously. During the first 10 weeks fruits accumulated up to 48% of their dry weight as starch, and glucose 6-phosphate and fructose were important precursors. We found a unique amyloplast transporter and hypothesize that it facilitates the import of fructose. We identified an invertase originating from the Musa balbisiana genome that would enable carbon flow back to growth and starch synthesis and maintain a high starch content even during ripening. Enzymes associated with the initiation of ripening were involved in ethylene and auxin metabolism, starch breakdown, pulp softening, and ascorbate biosynthesis. The initiation of ripening was cultivar specific, with faster initiation being particularly linked to the 1-aminocyclopropane-1-carboxylate oxidase and 4-alpha glucanotransferase disproportionating enzymes. Information of this kind is fundamental to determining the optimal time for picking the fruit in order to reduce post-harvest losses, and has potential applications for breeding to improve fruit quality.
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Affiliation(s)
| | - Sophie Colombié
- INRAE, Fruit Biology and Pathology, Université De Bordeaux, UMR 1332, 33140 Villenave d’Ornon, France
| | - Annick Moing
- INRAE, Fruit Biology and Pathology, Université De Bordeaux, UMR 1332, 33140 Villenave d’Ornon, France
| | - Cedric Cassan
- INRAE, Fruit Biology and Pathology, Université De Bordeaux, UMR 1332, 33140 Villenave d’Ornon, France
| | - Delphine Amah
- IITA, Crop Breeding, Ibadan 200001, Oyo State, Nigeria
| | - Rony Swennen
- Biosystems Department, KULeuven, 3001 Leuven, Belgium
- IITA, Crop Breeding, PO Box 7878, Kampala, Uganda
| | - Yves Gibon
- INRAE, Fruit Biology and Pathology, Université De Bordeaux, UMR 1332, 33140 Villenave d’Ornon, France
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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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Choi HR, Baek MW, Jeong CS, Tilahun S. Comparative Transcriptome Analysis of Softening and Ripening-Related Genes in Kiwifruit Cultivars Treated with Ethylene. Curr Issues Mol Biol 2022; 44:2593-2613. [PMID: 35735618 PMCID: PMC9221576 DOI: 10.3390/cimb44060177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
This work presents the transcriptome analysis of green ‘Hayward’ (Actinidia deliciosa) and gold ‘Haegeum’ (Actinidia chinensis) kiwifruit cultivars after treatment with ethylene for three days at 25 °C. Illumina high-throughput sequencing platform was used to sequence total mRNAs and the transcriptome gene set was constructed by de novo assembly. A total of 1287 and 1724 unigenes were differentially expressed during the comparison of ethylene treatment with control in green ‘Hayward’ and gold ‘Haegeum’, respectively. From the differentially expressed unigenes, 594 and 906 were upregulated, and 693 and 818 were downregulated in the green and gold kiwifruit cultivars, respectively, when treated with ethylene. We also identified a list of genes that were expressed commonly and exclusively in the green and gold kiwifruit cultivars treated with ethylene. Several genes were expressed differentially during the ripening of kiwifruits, and their cumulative effect brought about the softening- and ripening-related changes. This work also identified and categorized genes related to softening and other changes during ripening. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) identified in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR) to validate the reliability of the expression profiles obtained from RNA-Seq. The data obtained from the present study will add to the information available on the molecular mechanisms of the effects of ethylene during the ripening of kiwifruits. This study will also provide resources for further studies of the genes related to ripening, helping kiwifruit breeders and postharvest technologists to improve ripening quality.
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Affiliation(s)
- Han Ryul Choi
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Interdisciplinary Program in Smart Agriculture, Kangwon National Uinversity, Chuncheon 24341, Korea
| | - Min Woo Baek
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Interdisciplinary Program in Smart Agriculture, Kangwon National Uinversity, Chuncheon 24341, Korea
| | - Cheon Soon Jeong
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Interdisciplinary Program in Smart Agriculture, Kangwon National Uinversity, Chuncheon 24341, Korea
- Correspondence: (C.S.J.); (S.T.); Tel.: +82-033-250-6409 (C.S.J.)
| | - Shimeles Tilahun
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea; (H.R.C.); (M.W.B.)
- Agriculture and Life Science Research Institute, Kangwon National University, Chuncheon 24341, Korea
- Department of Horticulture and Plant Sciences, Jimma University, Jimma 378, Ethiopia
- Correspondence: (C.S.J.); (S.T.); Tel.: +82-033-250-6409 (C.S.J.)
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Backiyarani S, Anuradha C, Thangavelu R, Chandrasekar A, Renganathan B, Subeshkumar P, Giribabu P, Muthusamy M, Uma S. Genome-wide identification, characterization of expansin gene family of banana and their expression pattern under various stresses. 3 Biotech 2022; 12:101. [PMID: 35463044 PMCID: PMC8960517 DOI: 10.1007/s13205-021-03106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/28/2021] [Indexed: 11/01/2022] Open
Abstract
Expansin, a cell wall-modifying gene family, has been well characterized and its role in biotic and abiotic stress resistance has been proven in many monocots, but not yet studied in banana, a unique model crop. Banana is one of the staple food crops in developing countries and its production is highly influenced by various biotic and abiotic factors. Characterizing the expansin genes of the ancestor genome (M. acuminata and M. balbisiana) of present day cultivated banana will enlighten their role in growth and development, and stress responses. In the present study, 58 (MaEXPs) and 55 (MbaEXPs) putative expansin genes were identified in A and B genome, respectively, and were grouped in four subfamilies based on phylogenetic analysis. Gene structure and its duplications revealed that EXPA genes are highly conserved and are under negative selection whereas the presence of more number of introns in other subfamilies revealed that they are diversifying. Expression profiling of expansin genes showed a distinct expression pattern for biotic and abiotic stress conditions. This study revealed that among the expansin subfamilies, EXPAs contributed significantly towards stress-resistant mechanism. The differential expression of MaEXPA18 and MaEXPA26 under drought stress conditions in the contrasting cultivar suggested their role in drought-tolerant mechanism. Most of the MaEXPA genes are differentially expressed in the root lesion nematode contrasting cultivars which speculated that this expansin subfamily might be the susceptible factor. The downregulation of MaEXPLA6 in resistant cultivar during Sigatoka leaf spot infection suggested that by suppressing this gene, resistance may be enhanced in susceptible cultivar. Further, in-depth studies of these genes will lead to gain insight into their role in various stress conditions in banana. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-021-03106-x.
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Affiliation(s)
- Suthanthiram Backiyarani
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Chelliah Anuradha
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Raman Thangavelu
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Arumugam Chandrasekar
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Baratvaj Renganathan
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Parasuraman Subeshkumar
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Palaniappan Giribabu
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Muthusamy Muthusamy
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), RDA, Jeonju, 54874 Korea
| | - Subbaraya Uma
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
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Parijadi AAR, Yamamoto K, Ikram MMM, Dwivany FM, Wikantika K, Putri SP, Fukusaki E. Metabolome Analysis of Banana (Musa acuminata) Treated With Chitosan Coating and Low Temperature Reveals Different Mechanisms Modulating Delayed Ripening. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.835978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Banana (Musa acuminata) is one of the most important crop plants consumed in many countries. However, the commercial value decreases during storage and transportation. To maintain fruit quality, postharvest technologies have been developed. Storage at low temperature is a common method to prolong the shelf life of food products, especially during transportation and distribution. Another emerging approach is the use of chitosan biopolymer as an edible coating, which can extend the shelf life of fruit by preventing moisture and aroma loss, and inhibiting oxygen penetration into the plant tissue. Gas chromatography-mass spectrometry metabolite profiling of the banana ripening process was performed to clarify the global metabolism changes in banana after chitosan coating or storage at low temperature. Both postharvest treatments were effective in delaying banana ripening. Interestingly, principal component analysis and orthogonal projection to latent structure regression analysis revealed significant differences of both treatments in the metabolite changes, indicating that the mechanism of prolonging the banana shelf life may be different. Chitosan (1.25% w/v) treatment stored for 11 days resulted in a distinct accumulation of 1-aminocyclopropane-1-carboxylic acid metabolite, an important precursor of ethylene that is responsible for the climacteric fruit ripening process. Low temperature (LT, 14 ± 1°C) treatment stored for 9 days resulted in higher levels of putrescine, a polyamine that responds to plant stress, at the end of ripening days. The findings clarify how chitosan delays fruit ripening and provides a deeper understanding of how storage at low temperature affects banana metabolism. The results may aid in more effective development of banana postharvest strategies.
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Jia C, Wang Z, Wang J, Miao H, Zhang J, Xu B, Liu J, Jin Z, Liu J. Genome-Wide Analysis of the Banana WRKY Transcription Factor Gene Family Closely Related to Fruit Ripening and Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050662. [PMID: 35270130 PMCID: PMC8912484 DOI: 10.3390/plants11050662] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/14/2022] [Accepted: 02/24/2022] [Indexed: 05/11/2023]
Abstract
WRKY transcription factors (TFs) play an important role in plant responses to biotic and abiotic stress as well as in plant growth and development. In the present study, bioinformatics methods were used to identify members of the WRKY transcription factor family in the Musa acuminata (DH-Pahang) genome (version 2). A total of 164 MaWRKYs were identified and phylogenetic analysis showed that MaWRKYs could be categorized into three subfamilies. Overall, the 162 MaWRKYs were distributed on 11 chromosomes, and 2 genes were not located on the chromosome. There were 31 collinear genes from segmental duplication and 7 pairs of genes from tandem duplication. RNA-sequencing was used to analyze the expression profiles of MaWRKYs in different fruit development, ripening stages, under various abiotic and biotic stressors. Most of the MaWRKYs showed a variety of expression patterns in the banana fruit development and ripening stages. Some MaWRKYs responded to abiotic stress, such as low temperature, drought, and salt stress. Most differentially expressed MaWRKYs were downregulated during banana's response to Foc TR4 infection, which plays an important role in physiological regulation to stress. Our findings indicate that MaWRKY21 directly binds to the W-box of the MaICS promoter to decrease MaICS transcription and then reduce the enzyme activity. These studies have improved our understanding of the molecular basis for the development and stress resistance of an important banana variety.
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Affiliation(s)
- Caihong Jia
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China;
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
| | - 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; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jingyi 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; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
| | - 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; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, 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; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
| | - 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; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
| | - 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; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (J.L.); (Z.J.); (J.L.)
| | - 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; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
- Correspondence: (J.L.); (Z.J.); (J.L.)
| | - Jihong Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China;
- Correspondence: (J.L.); (Z.J.); (J.L.)
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10
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Song Z, Lai X, Yao Y, Qin J, Ding X, Zheng Q, Pang X, Chen W, Li X, Zhu X. F-box protein EBF1 and transcription factor ABI5-like regulate banana fruit chilling-induced ripening disorder. PLANT PHYSIOLOGY 2022; 188:1312-1334. [PMID: 34791491 PMCID: PMC8825429 DOI: 10.1093/plphys/kiab532] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/16/2021] [Indexed: 05/03/2023]
Abstract
Cold stress adversely affects plant production, both qualitatively and quantitatively. Banana (Musa acuminata) is sensitive to cold stress and suffers chilling injury (CI) when stored under 11°C, causing abnormal fruit softening. However, the mechanism underlying the abnormal fruit softening due to CI remains obscure. This study uncovered the coordinated transcriptional mechanism of ethylene F-box (EBF1) protein and abscisic acid-insensitive 5 (ABI5)-like protein in regulating chilling-induced softening disorders of Fenjiao banana. Cold stress severely inhibited the transcript and protein levels of EBF1, ABI5-like, and fruit softening-related genes. The ABI5-like protein bound to the promoters of key starch and cell wall degradation-related genes such as β-amylase 8 (BAM8), pectate lyase 8 (PL8), and β-D-xylosidase23-like (XYL23-like) and activated their activities. EBF1 physically interacted with ABI5-like and enhanced the transcriptional activity of the key starch and cell wall degradation-related genes but did not ubiquitinate or degrade ABI5-like protein. This promoted fruit ripening and ameliorated fruit CI in a manner similar to the effect of exogenous abscisic acid treatment. The ectopic and transient overexpression of EBF1 and ABI5-like genes in tomato (Solanum lycopersicum) and Fenjiao banana accelerated fruit ripening and softening by promoting ethylene production, starch and cell wall degradation, and decreasing fruit firmness. EBF1 interacted with EIL4 but did not ubiquitinate or degrade EIL4, which is inconsistent with the typical role of EBF1/2 in Arabidopsis (Arabidopsis thaliana). These results collectively highlight that the interaction of EBF1 and ABI5-like controls starch and cell wall metabolism in banana, which is strongly inhibited by chilling stress, leading to fruit softening and ripening disorder.
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Affiliation(s)
- Zunyang Song
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xiuhua Lai
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yulin Yao
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jiajia Qin
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xiaochun Ding
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Qiuli Zheng
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xuequn Pang
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Weixin Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xueping Li
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyang Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Author for communication:
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11
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Pradeepkumara N, Sharma PK, Munshi AD, Behera TK, Bhatia R, Kumari K, Singh J, Jaiswal S, Iquebal MA, Arora A, Rai A, Kumar D, Bhattacharya RC, Dey SS. Fruit transcriptional profiling of the contrasting genotypes for shelf life reveals the key candidate genes and molecular pathways regulating post-harvest biology in cucumber. Genomics 2022; 114:110273. [PMID: 35092817 DOI: 10.1016/j.ygeno.2022.110273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Cucumber fruits are perishable in nature and become unfit for market within 2-3 days of harvesting. A natural variant, DC-48 with exceptionally high shelf life was developed and used to dissect the genetic architecture and molecular mechanism for extended shelf life through RNA-seq for first time. A total of 1364 DEGs were identified and cell wall degradation, chlorophyll and ethylene metabolism related genes played key role. Polygalacturunase (PG), Expansin (EXP) and xyloglucan were down regulated determining fruit firmness and retention of fresh green colour was mainly attributed to the low expression level of the chlorophyll catalytic enzymes (CCEs). Gene regulatory networks revealed the hub genes and cross-talk associated with wide variety of the biological processes. Large number of SSRs (21524), SNPs (545173) and InDels (126252) identified will be instrumental in cucumber improvement. A web genomic resource, CsExSLDb developed will provide a platform for future investigation on cucumber post-harvest biology.
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Affiliation(s)
- N Pradeepkumara
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Parva Kumar Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A D Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jogendra Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ajay Arora
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - R C Bhattacharya
- ICAR-National Institute of Plant Biotechnology, New Delhi, India
| | - S S Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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12
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Chen MZ, Zhong XM, Lin HS, Qin XM. Combined Transcriptome and Metabolome Analysis of Musa nana Laur. Peel Treated With UV-C Reveals the Involvement of Key Metabolic Pathways. Front Genet 2022; 12:792991. [PMID: 35154246 PMCID: PMC8830439 DOI: 10.3389/fgene.2021.792991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
An increasing attention is being given to treat fruits with ultraviolet C (UV-C) irradiation to extend shelf-life, senescence, and protection from different diseases during storage. However, the detailed understanding of the pathways and key changes in gene expression and metabolite accumulation related to UV-C treatments are yet to be explored. This study is a first attempt to understand such changes in banana peel irradiated with UV-C. We treated Musa nana Laur. with 0.02 KJ/m2 UV-C irradiation for 0, 4, 8, 12, 15, and 18 days and studied the physiological and quality indicators. We found that UV-C treatment reduces weight loss and decay rate, while increased the accumulation of total phenols and flavonoids. Similarly, our results demonstrated that UV-C treatment increases the activity of defense and antioxidant system related enzymes. We observed that UV-C treatment for 8 days is beneficial for M. nana peels. The peels of M. nana treated with UV-C for 8 days were then subjected to combined transcriptome and metabolome analysis. In total, there were 425 and 38 differentially expressed genes and accumulated metabolites, respectively. We found that UV-C treatment increased the expression of genes in secondary metabolite biosynthesis related pathways. Concomitant changes in the metabolite accumulation were observed. Key pathways that were responsive to UV-C irradiation include flavonoid biosynthesis, phenylpropanoid bios6ynthesis, plant-pathogen interaction, MAPK signaling (plant), and plant hormone signal transduction pathway. We concluded that UV-C treatment imparts beneficial effects on banana peels by triggering defense responses against disease, inducing expression of flavonoid and alkaloid biosynthesis genes, and activating phytohormone and MAPK signaling pathways.
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Affiliation(s)
- Ming-zhong Chen
- College of Food Science and Technology, and Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Ocean University, Zhanjiang, China
- Yangjiang Polytechnic, Yangjiang, China
| | | | - Hai-Sheng Lin
- College of Food Science and Technology, and Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Ocean University, Zhanjiang, China
| | - Xiao-Ming Qin
- College of Food Science and Technology, and Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Ocean University, Zhanjiang, China
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13
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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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14
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Mathiazhagan M, Chidambara B, Hunashikatti LR, Ravishankar KV. Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content. Genes (Basel) 2021; 12:1881. [PMID: 34946829 PMCID: PMC8701245 DOI: 10.3390/genes12121881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.
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Affiliation(s)
| | | | | | - Kundapura V. Ravishankar
- Division of Basic Sciences, ICAR Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru 560089, India; (M.M.); (B.C.); (L.R.H.)
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15
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Peng K, Tian Y, Sun X, Song C, Ren Z, Bao Y, Xing J, Li Y, Xu Q, Yu J, Zhang D, Cang J. tae-miR399- UBC24 Module Enhances Freezing Tolerance in Winter Wheat via a CBF Signaling Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13398-13415. [PMID: 34729981 DOI: 10.1021/acs.jafc.1c04316] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Although the regulation of Pi homeostasis by miR399 has been studied in various plant species, its underlying molecular mechanism in response to freezing stress is still poorly understood. In this work, we found that the expression of tae-miR399 and its target gene TaUBC24 in the tillering nodes of the strong cold-resistant winter wheat cultivar Dongnongdongmai1 (Dn1) was not only significantly altered after severe winters but also responsive to short-term freezing stress. TaUBC24 physically interacted with TaICE1. Enhanced freezing tolerance was observed for tae-miR399-overexpressing Arabidopsis lines. Under freezing stress, overexpression of tae-miR399 ultimately decreased the expression of AtUBC24, inhibiting the degradation of AtICE1, which increased the expression of genes involved in the CBF signaling pathway and starch metabolism and promoted the activities of antioxidant enzymes. These results will improve our understanding of the molecular mechanism through which the miR399-UBC24 module plays a cardinal role in regulating plant freezing stress tolerance through mediation of downstream pathways.
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Affiliation(s)
- Kankan Peng
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Yu Tian
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Xianze Sun
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Chunhua Song
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Zhipeng Ren
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Yuzhuo Bao
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Jinpu Xing
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Yuanshan Li
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Qinghua Xu
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Jing Yu
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Da Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Jing Cang
- College of Life Science, Northeast Agricultural University, Harbin 150030, P.R. China
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Liu J, Liu M, Wang J, Zhang J, Miao H, Wang Z, Jia C, Zhang J, Xu B, Jin Z. Transcription factor MaMADS36 plays a central role in regulating banana fruit ripening. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7078-7091. [PMID: 34282447 DOI: 10.1093/jxb/erab341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Bananas are model fruits for studying starch conversion and climactericity. Starch degradation and ripening are two important biological processes that occur concomitantly in banana fruit. Ethylene biosynthesis and postharvest fruit ripening processes, i.e. starch degradation, fruit softening, and sugar accumulation, are highly correlated and thus could be controlled by a common regulatory switch. However, this switch has not been identified. In this study, we transformed red banana (Musa acuminata L.) with sense and anti-sense constructs of the MaMADS36 transcription factor gene (also MuMADS1, Ma05_g18560.1). Analysis of these lines showed that MaMADS36 interacts with 74 other proteins to form a co-expression network and could act as an important switch to regulate ethylene biosynthesis, starch degradation, softening, and sugar accumulation. Among these target genes, musa acuminata beta-amylase 9b (MaBAM9b, Ma05_t07800.1), which encodes a starch degradation enzyme, was selected to further investigate the regulatory mechanism of MaMADS36. Our findings revealed that MaMADS36 directly binds to the CA/T(r)G box of the MaBAM9b promoter to increase MaBAM9b transcription and, in turn, enzyme activity and starch degradation during ripening. These results will further our understanding of the fine regulatory mechanisms of MADS-box transcription factors in regulating fruit ripening, which can be applied to breeding programs to improve fruit shelf-life.
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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, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Mengting Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Horticulture, Hainan University, Haikou, China
| | - Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 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, 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, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 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, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 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, 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, 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, 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, China
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17
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Yang Y, Jiang M, Feng J, Wu C, Shan W, Kuang J, Chen J, Hu Z, Lu W. Transcriptome analysis of low-temperature-affected ripening revealed MYB transcription factors-mediated regulatory network in banana fruit. Food Res Int 2021; 148:110616. [PMID: 34507760 DOI: 10.1016/j.foodres.2021.110616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
Low temperature leads to abnormal ripening and poor quality of the harvested banana fruit, which is an urgent problem limiting the development of industry in China. To comprehensively understand the mechanism underlying low-temperature-affected ripening, we performed comparative RNA-Seq analysis of ethylene-induced ripening of banana fruit after 3 days of pre-storage at 7 °C and 22 °C. A total of 986 differentially expressed genes (DEGs) were identified in both RT-0 d versus RT-3 d, LT-0 d versus LT-3 d, RT-0 d versus LT-0 d and RT-3 d versus LT-3 d, and the RNA-Seq outputs of 15 randomly selective DEGs were verified using qRT-PCR. Among the 986 DEGs obtained in the four groups, 9 MYB genes (MaMYB75/281/219/4/151/156/3/37 and MaMYB3R1) and 32 genes related to carotenoid biosynthesis (MaPSY1/2a), flavor formation (MaLOX6, MaADH7, MaAAT1), sucrose transport (MaSUS2/4), ethylene production (MaSAM1, MaACO9/10/12, MaACS1/12), starch degradation (MaAMY1A/1B, MaPHS1/2, MaMEX2, MapGlcT1) and cell wall degradation (MaPG3/X1, MaPME25/41, MaXTH5/7/22/23/25, MaEXP2/20/A1/A15) were characterized. Combining transcription factor binding site (TFBS) analysis as well as cis-acting element analysis, the regulatory network of low-temperature-affected ripening mediated by MYBs were constructed. The data generated in this study may unravel the transcriptional regulatory network of MYBs associated with low-temperature-affected ripening and provide a solid foundation for future studies.
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Affiliation(s)
- Yingying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Mengge Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jintao Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Chaojie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, 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/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jianfei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jianye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zhuoyan Hu
- College of Food Science, South China Agricultural University, Guangzhou 510642, China.
| | - Wangjin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
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18
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Cárcamo de la Concepción M, Sargent DJ, Šurbanovski N, Colgan RJ, Moretto M. De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars 'Bluecrop' and 'Legacy' at harvest and following post-harvest storage. PLoS One 2021; 16:e0255139. [PMID: 34339434 PMCID: PMC8328333 DOI: 10.1371/journal.pone.0255139] [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: 04/06/2021] [Accepted: 07/12/2021] [Indexed: 11/19/2022] Open
Abstract
Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, 'Bluecrop' and 'Legacy', at harvest, three weeks storage in a non-modified environment at 4 °C and after three weeks storage at 4 °C followed by three days at 21 °C, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality. De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for 'Bluecrop' and 'Legacy' respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 290 unigenes were up-regulated in 'Legacy' only, 685 were up-regulated in 'Bluecrop', 252 were up-regulated in both cultivars and 948 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes. In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.
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Affiliation(s)
| | - Daniel James Sargent
- Natural Resources Institute, University of Greenwich, Chatham, Kent, United Kingdom
- NIAB EMR, East Malling, Kent, United Kingdom
| | | | - Richard John Colgan
- Natural Resources Institute, University of Greenwich, Chatham, Kent, United Kingdom
- * E-mail:
| | - Marco Moretto
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, Italy
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19
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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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20
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Kuang J, Wu C, Guo Y, Walther D, Shan W, Chen J, Chen L, Lu W. Deciphering transcriptional regulators of banana fruit ripening by regulatory network analysis. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:477-489. [PMID: 32920977 PMCID: PMC7955892 DOI: 10.1111/pbi.13477] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/31/2020] [Indexed: 05/19/2023]
Abstract
Fruit ripening is a critical phase in the production and marketing of fruits. Previous studies have indicated that fruit ripening is a highly coordinated process, mainly regulated at the transcriptional level, in which transcription factors play essential roles. Thus, identifying key transcription factors regulating fruit ripening as well as their associated regulatory networks promises to contribute to a better understanding of fruit ripening. In this study, temporal gene expression analyses were performed to investigate banana fruit ripening with the aim to discern the global architecture of gene regulatory networks underlying fruit ripening. Eight time points were profiled covering dynamic changes of phenotypes, the associated physiology and levels of known ripening marker genes. Combining results from a weighted gene co-expression network analysis (WGCNA) as well as cis-motif analysis and supported by EMSA, Y1H, tobacco-, banana-transactivation experimental results, the regulatory network of banana fruit ripening was constructed, from which 25 transcription factors were identified as prime candidates to regulate the ripening process by modulating different ripening-related pathways. Our study presents the first global view of the gene regulatory network involved in banana fruit ripening, which may provide the basis for a targeted manipulation of fruit ripening to attain higher banana and loss-reduced banana commercialization.
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Affiliation(s)
- Jian‐Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China)Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and VegetablesCollege of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Chao‐Jie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China)Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and VegetablesCollege of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Yu‐Fan Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China)Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and VegetablesCollege of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Dirk Walther
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China)Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and VegetablesCollege of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian‐Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China)Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and VegetablesCollege of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Lin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China)Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and VegetablesCollege of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Wang‐Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China)Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and VegetablesCollege of HorticultureSouth China Agricultural UniversityGuangzhouChina
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21
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Ma M, Yuan Y, Cheng C, Zhang Y, Yang S. The MdXTHB gene is involved in fruit softening in 'Golden Del. Reinders' (Malus pumila). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:564-572. [PMID: 32672847 DOI: 10.1002/jsfa.10668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Fruit softening is a major determinant of commercial value and shelf life. A transcriptomic analysis of 'Golden Delicious' and 'Golden Del. Reinders' (a bud mutation of 'Golden Delicious' that readily softens) apple fruit was conducted during storage. RESULTS A comparative analysis of the obtained expression profiles of fruit between two cultivars identified 1345 upregulated and 3475 downregulated differentially expressed genes (DEGs). The DEGs identified were associated with cellular processes and carbohydrate metabolism and were especially enriched in cell-wall-related genes. Among the cell-wall-related genes, the xyloglucan endotransglucosylase/hydrolases (XTH) gene MdXTHB was significantly upregulated and exhibited high expression levels in 'Golden Del. Reinders' fruit, which had a lower level of firmness relative to 'Golden Delicious'. Overexpression of MdXTHB in both 'Golden Delicious' and 'Fuji', which typically maintain high levels of firmness in storage, exhibited faster rates of softening and an earlier peak of ethylene production than empty-vector-infiltrated fruit did. CONCLUSION The results of this study indicate that MdXTHB potentially promotes apple fruit softening by degrading the fruit cell wall. This result is also useful to designing further experiments on the molecular regulation of fruit softening in apple. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Mengmeng Ma
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yongbing Yuan
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Chenxia Cheng
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yong Zhang
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Shaolan Yang
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China
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22
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Ma D, Dong S, Zhang S, Wei X, Xie Q, Ding Q, Xia R, Zhang X. Chromosome-level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis). Mol Ecol Resour 2020; 21:955-968. [PMID: 33325619 DOI: 10.1111/1755-0998.13310] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/30/2022]
Abstract
Passion fruit, native to tropical America, is an agriculturally, economically and ornamentally important fruit plant that is well known for its acid pulp, rich aroma and distinctive flavour. Here, we present a chromosome-level genome assembly of passion fruit by incorporating PacBio long HiFi reads and Hi-C technology. The assembled reference genome is 1.28 Gb size with a scaffold N50 of 126.4 Mb and 99.22% sequences anchored onto nine pseudochromosomes. This genome is highly repetitive, accounting for 86.61% of the assembled genome. A total of 39,309 protein-coding genes were predicted with 93.48% of those being functionally annotated in the public databases. Genome evolution analysis revealed a core eudicot-common γ whole-genome triplication event and a more recent whole-genome duplication event, possibly contributing to the expansion of certain gene families. The 33 rapidly expanded gene families were significantly enriched in the pathways of isoflavone biosynthesis, galactose metabolism, diterpene biosynthesis and fatty acid metabolism, which might be responsible for the formation of featured flavours in the passion fruit. Transcriptome analysis revealed that genes related to ester and ethylene biosynthesis were significantly upregulated in the mature fruit and the expression levels of those genes were consistent with the accumulation of volatile lipid compounds. The passion fruit genome analysis improves our understanding of the genome evolution of this species and sheds new lights into the molecular mechanism of aroma biosynthesis in passion fruit.
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Affiliation(s)
- Dongna Ma
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Shanshan Dong
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Shengcheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiuqing Wei
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangzhou, China
| | - Qiansu Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China.,Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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23
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Stankov S, Fidan H, Petkova Z, Stoyanova M, Petkova N, Stoyanova A, Semerdjieva I, Radoukova T, Zheljazkov VD. Comparative Study on the Phytochemical Composition and Antioxidant Activity of Grecian Juniper ( Juniperus excelsa M. Bieb) Unripe and Ripe Galbuli. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091207. [PMID: 32942594 PMCID: PMC7570073 DOI: 10.3390/plants9091207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
Grecian juniper (Juniperus excelsa M. Bieb.) is an evergreen tree and a rare plant found in very few locations in southern Bulgaria. The aim of this study was to evaluate the phytochemical content and antioxidant potential of J. excelsa unripe and ripe galbuli from three different locations in Bulgaria. The essential oil content ranged between 1.9% and 5.1%, while the lipid fraction yield was between 4.5% and 9.1%. The content of total chlorophyll was 185.4-273.4 μg/g dw. The total carotenoid content ranged between 41.7 and 50.4 μg/g dw of ripe galbuli, and protein content was between 13.6% and 16.4%. Histidine (5.5 and 8.0 mg/g content range) and lysine (4.0 and 6.1 mg/g) were the major essential amino acids. The antioxidant potential of the 95% and 70% ethanol extracts was analyzed using four different methods. A positive correlation between the antioxidant potential and phenolic content of the galbuli was found. The results obtained in this study demonstrated the differences in phytochemical composition and antioxidant capacity of J. excelsa galbuli as a function of maturity stage and collection locality.
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Affiliation(s)
- Stanko Stankov
- Department of Nutrition and Tourism, University of Food Technologies, 26 Maritza, 4002 Plovdiv, Bulgaria; (S.S.); (H.F.)
| | - Hafize Fidan
- Department of Nutrition and Tourism, University of Food Technologies, 26 Maritza, 4002 Plovdiv, Bulgaria; (S.S.); (H.F.)
| | - Zhana Petkova
- Department of Chemical Technology, University of Plovdiv Paisii Hilendarski, 24 Tzar Asen, 4000 Plovdiv, Bulgaria;
| | - Magdalena Stoyanova
- Department of Analytical Chemistry and Physicochemistry, University of Food Technologies, 26 Maritza, 4002 Plovdiv, Bulgaria;
| | - Nadezhda Petkova
- Department of Organic Chemistry and Inorganic Chemistry, University of Food Technologies, 26 Maritza, 4002 Plovdiv, Bulgaria;
| | - Albena Stoyanova
- Department of Technology of Fats, Essential Oils, Perfumery and Cosmetics, University of Food Technologies, 26 Maritza, 4002 Plovdiv, Bulgaria;
| | - Ivanka Semerdjieva
- Department of Botany and Agrometeorology, Agricultural University, 12 Mendleev12, 4000 Plovdiv, Bulgaria;
| | - Tzenka Radoukova
- Department of Botany and Methods of Biology Teaching, University of Plovdiv Paisii Hilendarski, 24 Tzar Asen, 4000 Plovdiv, Bulgaria;
| | - Valtcho D. Zheljazkov
- Crop and Soil Science Department, Oregon State University, 3050 SW Campus Way, 109 Crop Science Building, Corvallis, OR 97331, USA
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24
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Wu S, Cao G, Adil MF, Tu Y, Wang W, Cai B, Zhao D, Shamsi IH. Changes in water loss and cell wall metabolism during postharvest withering of tobacco (Nicotiana tabacum L.) leaves using tandem mass tag-based quantitative proteomics approach. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 150:121-132. [PMID: 32142985 DOI: 10.1016/j.plaphy.2020.02.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/11/2020] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Withering is an important biological process accompanied by dehydration and cell wall metabolism in postharvest plant organs during curing/processing and storage. However, dynamics involved in cell wall metabolism and resultant water loss during withering in postharvest tobacco leaves is not well-documented. Here, tandem mass tag (TMT)-based quantitative proteomic analysis in postharvest tobacco leaves (cultivar K326) under different withering conditions was performed. In total, 11,556 proteins were detected, among which 496 differentially abundant proteins (DAPs) were identified. To elucidate the withering mechanism of tobacco leaves, 27 DAPs associated with cell wall metabolism were screened. In particular, pectin acetylesterases, glucan endo-1,3-beta-glucosidases, xyloglucan endotransglucosylase/hydrolase, alpha-xylosidase 1-like, probable galactinol-sucrose galactosyltransferases, endochitinase A, chitotriosidase-1-like and expansin were the key proteins responsible for the withering of postharvest tobacco leaves. These DAPs were mainly involved in pectin metabolism, cellulose, hemicellulose and galactose metabolism, amino sugar and nucleotide sugar metabolism as well as cell wall expansion. Furthermore, relative water content and softness values were significantly and positively correlated. Thus, dehydration and cell wall metabolism were crucial for tobacco leaf withering under different conditions. Nine candidate DAPs were confirmed by parallel reaction monitoring (PRM) technique. These results provide new insights into the withering mechanism underlying postharvest physiological regulatory networks in plants/crops.
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Affiliation(s)
- Shengjiang Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Center for Research & Development of Fine Chemicals, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, PR China; Guizhou Academy of Tobacco Science, Guiyang, 550081, PR China
| | - Gaoyi Cao
- College of Agronomy & Resources and Environment, Tianjin Agricultural University, Tianjin, 300384, PR China
| | - Muhammad Faheem Adil
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou, 310058, PR China
| | - Yonggao Tu
- Guizhou Academy of Tobacco Science, Guiyang, 550081, PR China
| | - Wei Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Center for Research & Development of Fine Chemicals, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, PR China; Guizhou Academy of Agricultural Sciences, Guiyang, 550006, PR China
| | - Bin Cai
- Hainan Cigar Research Institute, Hainan Provincial Branch of China National Tobacco Corporation, Haikou, 571100, PR China
| | - Degang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Center for Research & Development of Fine Chemicals, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, PR China; Guizhou Academy of Agricultural Sciences, Guiyang, 550006, PR China.
| | - Imran Haider Shamsi
- Department of Agronomy, College of Agriculture and Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University, Hangzhou, 310058, PR China.
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25
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Yang YY, Shan W, Kuang JF, Chen JY, Lu WJ. Four HD-ZIPs are involved in banana fruit ripening by activating the transcription of ethylene biosynthetic and cell wall-modifying genes. PLANT CELL REPORTS 2020; 39:351-362. [PMID: 31784771 DOI: 10.1007/s00299-019-02495-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/20/2019] [Indexed: 05/20/2023]
Abstract
Four MaHDZs are possibly involved in banana fruit ripening by activating the transcription of genes related to ethylene biosynthesis and cell wall degradation, such as MaACO5, MaEXP2, MaEXPA10, MaPG4 and MaPL4. The homeodomain-leucine zipper (HD-ZIP) proteins represent plant-specific transcription factors, which contribute to various plant physiological processes. However, little information is available regarding the association of HD-ZIPs with banana fruit ripening. In this study, we identified a total of 96 HD-ZIP genes in banana genome, which were divided into four different groups consisting of 35, 31, 9 and 21 members in the I, II, III and IV subfamilies, respectively. The expression patterns of MaHDZ genes during fruit ripening showed that MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were significantly up-regulated in the ripening stage and thus suggested to be potential regulators of banana fruit ripening. Furthermore, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were found to localize exclusively in the nucleus and exhibit transcriptional activation capacities. Importantly, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 stimulated the transcription of several ripening-related genes including MaACO5 related to ethylene biosynthesis, MaEXP2, MaEXPA10, MaPG4 and MaPL4 were associated with cell wall degradation, through directly binding to their promoters. Taken together, our findings expand the functions of HD-ZIP transcription factors and identify four MaHDZs likely involved in regulating banana fruit ripening by activating the expression of genes related to ethylene biosynthesis and cell wall modification, which may have potential application in banana molecular breeding.
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Affiliation(s)
- Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest, Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, 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/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - 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/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, 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/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, 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/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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26
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Bhuiyan F, Campos NA, Swennen R, Carpentier S. Characterizing fruit ripening in plantain and Cavendish bananas: A proteomics approach. J Proteomics 2020; 214:103632. [DOI: 10.1016/j.jprot.2019.103632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/10/2019] [Accepted: 12/27/2019] [Indexed: 10/25/2022]
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27
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Garcia-Lozano M, Dutta SK, Natarajan P, Tomason YR, Lopez C, Katam R, Levi A, Nimmakayala P, Reddy UK. Transcriptome changes in reciprocal grafts involving watermelon and bottle gourd reveal molecular mechanisms involved in increase of the fruit size, rind toughness and soluble solids. PLANT MOLECULAR BIOLOGY 2020; 102:213-223. [PMID: 31845303 DOI: 10.1007/s11103-019-00942-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/04/2019] [Indexed: 05/07/2023]
Abstract
Transcriptome landscape reveals the molecular mechanisms involved in the improvement of fruit traits by the grafting of watermelon and bottle gourd. Grafting has been used as a sustainable alternative for watermelon breeding to control soil-borne pathogens and to increase tolerance to various abiotic stresses. However, some reports have shown that grafting can negatively affect the quality of fruits. Despite several field studies on the effects of grafting on fruit quality, the regulation of this process at the molecular level has not been revealed. The aim of this study was to elucidate various molecular mechanisms involved in different tissues of heterografted watermelon and bottle gourd plants. Grafting with bottle gourd rootstock increased the size and rind thickness of watermelon fruits, whereas that with watermelon rootstock produced bottle gourd fruits with higher total soluble solid content and thinner rinds. Correspondingly, genes related to ripening, softening, cell wall strengthening, stress response and disease resistance were differentially expressed in watermelon fruits. Moreover, genes associated mainly with sugar metabolism were differentially expressed in bottle gourd fruits. RNA-seq revealed more than 400 mobile transcripts across the heterografted sets. More than half of these were validated from PlaMoM, a database for plant mobile macromolecules. In addition, some of these mobile transcripts contained a transfer RNA-like structure. Other RNA motifs were also enriched in these transcripts, most with a biological role based on GO analysis. This transcriptome study provided a comprehensive understanding of various molecular mechanisms underlying grafted tissues in watermelon.
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Affiliation(s)
- Marleny Garcia-Lozano
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Sudip Kumar Dutta
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Yan R Tomason
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Carlos Lopez
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Ramesh Katam
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL, 32317, USA
| | - Amnon Levi
- USDA, ARS, U.S. Vegetable Lab, 2700 Savannah Highway, Charleston, SC, USA
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA.
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA.
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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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Dos Santos CP, Batista MC, da Cruz Saraiva KD, Roque ALM, de Souza Miranda R, Alexandre E Silva LM, Moura CFH, Alves Filho EG, Canuto KM, Costa JH. Transcriptome analysis of acerola fruit ripening: insights into ascorbate, ethylene, respiration, and softening metabolisms. PLANT MOLECULAR BIOLOGY 2019; 101:269-296. [PMID: 31338671 DOI: 10.1007/s11103-019-00903-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
The first transcriptome coupled to metabolite analyses reveals major trends during acerola fruit ripening and shed lights on ascorbate, ethylene signalling, cellular respiration, sugar accumulation, and softening key regulatory genes. Acerola is a fast growing and ripening fruit that exhibits high amounts of ascorbate. During ripening, the fruit experience high respiratory rates leading to ascorbate depletion and a quickly fragile and perishable state. Despite its growing economic importance, understanding of its developmental metabolism remains obscure due to the absence of genomic and transcriptomic data. We performed an acerola transcriptome sequencing that generated over 600 million reads, 40,830 contigs, and provided the annotation of 25,298 unique transcripts. Overall, this study revealed the main metabolic changes that occur in the acerola ripening. This transcriptional profile linked to metabolite measurements, allowed us to focus on ascorbate, ethylene, respiration, sugar, and firmness, the major metabolism indicators for acerola quality. Our results suggest a cooperative role of several genes involved in AsA biosynthesis (PMM, GMP1 and 3, GME1 and 2, GGP1 and 2), translocation (NAT3, 4, 6 and 6-like) and recycling (MDHAR2 and DHAR1) pathways for AsA accumulation in unripe fruits. Moreover, the association of metabolites with transcript profiles provided a comprehensive understanding of ethylene signalling, respiration, sugar accumulation and softening of acerola, shedding light on promising key regulatory genes. Overall, this study provides a foundation for further examination of the functional significance of these genes to improve fruit quality traits.
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Affiliation(s)
- Clesivan Pereira Dos Santos
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Mathias Coelho Batista
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Kátia Daniella da Cruz Saraiva
- Federal Institute of Education, Science and Technology of Paraíba, Campus Princesa Isabel, Princesa Isabel, Paraíba, Brazil
| | - André Luiz Maia Roque
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | | | | | | | | | | | - José Hélio Costa
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil.
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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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Wu C, Shan W, Liang S, Zhu L, Guo Y, Chen J, Lu W, Li Q, Su X, Kuang J. MaMPK2 enhances MabZIP93-mediated transcriptional activation of cell wall modifying genes during banana fruit ripening. PLANT MOLECULAR BIOLOGY 2019; 101:113-127. [PMID: 31300998 DOI: 10.1007/s11103-019-00895-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/20/2019] [Indexed: 06/10/2023]
Abstract
Transcriptional regulation is an essential molecular machinery in controlling gene expression in diverse plant developmental processes including fruit ripening. This involves the interaction of transcription factors (TFs) and promoters of target genes. In banana, although a number of fruit ripening-associated TFs have been characterized, their number is relatively small. Here we identified a nuclear-localized basic leucine zipper (bZIP) TF, MabZIP93, associated with banana ripening. MabZIP93 activated cell wall modifying genes MaPL2, MaPE1, MaXTH23 and MaXGT1 by directly binding to their promoters. Transient over-expression of MabZIP93 in banana fruit resulted in the increased expression of MaPL2, MaPE1, MaXTH23 and MaXGT1. Moreover, a mitogen-activated protein kinase MaMPK2 and MabZIP93 were found to interact with MabZIP93. The interaction of MabZIP93 with MaMPK2 enhanced MabZIP93 activation of cell wall modifying genes, which was likely due to the phosphorylation of MabZIP93 mediated by MaMPK2. Overall, this study shows that MaMPK2 interacts with and phosphorylates MabZIP93 to promote MabZIP93-mediated transcriptional activation of cell wall modifying genes, thereby expanding our understanding of gene networks associated with banana fruit ripening.
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Affiliation(s)
- Chaojie Wu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Wei Shan
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Shumin Liang
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Lisha Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yufan Guo
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Jianye Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Wangjin Lu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Qianfeng Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Xinguo Su
- Guangdong Food and Drug Vocational College, Longdongbei Road 321, Tianhe District, Guangzhou, 510520, People's Republic of China.
| | - Jianfei Kuang
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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Dhar YV, Lakhwani D, Pandey A, Singh S, Trivedi PK, Asif MH. Genome-wide identification and interactome analysis of members of two-component system in Banana. BMC Genomics 2019; 20:674. [PMID: 31455217 PMCID: PMC6712864 DOI: 10.1186/s12864-019-6050-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/20/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Ethylene signal transduction in plants is conducted by the two-component system (TCS) which consists of histidine kinase (HK), histidine phosphotransferase (HPT) and response regulators (RRs). This system plays an important role in signal transduction during various cellular processes, including fruit ripening and response to multiple environmental cues. Though members of TCS have been identified in a few plants, no detailed analysis has been carried out in banana. RESULTS Through genome-wide analysis, we identified a total of 80 (25 HK, 10 HPT and 45 RR) and 72 (25 HK, 5 HPT and 42 RR) TCS genes in Musa acuminata and Musa balbisiana respectively. The analysis of identified genes revealed that most of the genes are highly conserved however; there are subtle divergences among various members. Comparative expression analysis revealed an involvement of a set of TCS members during banana fruit ripening. Co-expression network analysis identified a working TCS module with direct interactions of HK-HPT and RR members. The molecular dynamics analysis of TCS module showed a significant change in structural trajectories of TCS proteins in the presence of ethylene. Analysis suggests possible interactions between the HK-HPTs and RRs as well as other members leading to banana fruit ripening. CONCLUSIONS In this study, we identified and compared the members of TCS gene family in two banana species and showed their diversity, within groups on the basis of whole-genome duplication events. Our analysis showed that during banana fruit ripening TCS module plays a crucial role. We also demonstrated a possible interaction mechanism of TCS proteins in the presence and absence of ethylene by molecular dynamics simulations. These findings will help in understanding the functional mechanism of TCS proteins in plants in different conditions.
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Affiliation(s)
- Yogeshwar V Dhar
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Deepika Lakhwani
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067, India
| | - Shikha Singh
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Prabodh K Trivedi
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Mehar H Asif
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Rongkaumpan G, Amsbury S, Andablo-Reyes E, Linford H, Connell S, Knox JP, Sarkar A, Benitez-Alfonso Y, Orfila C. Cell Wall Polymer Composition and Spatial Distribution in Ripe Banana and Mango Fruit: Implications for Cell Adhesion and Texture Perception. FRONTIERS IN PLANT SCIENCE 2019; 10:858. [PMID: 31338100 PMCID: PMC6629905 DOI: 10.3389/fpls.2019.00858] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 06/14/2019] [Indexed: 05/22/2023]
Abstract
Banana (Musa acuminata) and mango (Mangifera indica) are two of the most popular fruits eaten worldwide. They both soften during ripening but their textural attributes are markedly different. This study aimed to elucidate the molecular mechanism underpinning textural differences between banana and mango. We used a novel combination of methods at different scales to analyse the surface properties of fruit cells and the potential contribution of cells and cell wall components to oral processing and texture perception. The results indicated that cell separation occurred easily in both organs under mild mechanical stress. Banana cells showed distinctively elongated shapes with distinct distribution of pectin and hemicellulose epitopes at the cell surface. In contrast, mango had relatively spherical cells that ruptured during cell separation. Atomic force microscopy detected soft surfaces indicative of middle lamella remnants on banana cells, while mango cells had cleaner, smoother surfaces, suggesting absence of middle lamellae and more advanced cell wall disassembly. Comparison of solubilized polymers by cell wall glycome analysis showed abundance of mannan and feruylated xylan in separation exudate from banana but not mango, but comparable levels of pectin and arabinogalactan proteins. Bulk rheology experiments showed that both fruits had similar apparent viscosity and hence might be extrapolated to have similar "oral thickness" perception. On the other hand, oral tribology experiments showed significant differences in their frictional behavior at orally relevant speeds. The instrumental lubrication behavior can be interpreted as "smooth" mouthfeel for mango as compared to "astringent" or "dry" for banana in the later stages of oral processing. The results suggest that cell wall surface properties contribute to lubricating behavior associated with textural perception in the oral phase.
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Affiliation(s)
- Ganittha Rongkaumpan
- Nutritional Sciences and Epidemiology Group, School of Food Science and Nutrition, University of Leeds, Leeds, United Kingdom
| | - Sam Amsbury
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Efren Andablo-Reyes
- Food Colloids and Bioprocessing, School of Food Science and Nutrition, University of Leeds, Leeds, United Kingdom
| | - Holly Linford
- School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
| | - Simon Connell
- School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
| | - J. Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Anwesha Sarkar
- Food Colloids and Bioprocessing, School of Food Science and Nutrition, University of Leeds, Leeds, United Kingdom
| | - Yoselin Benitez-Alfonso
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Caroline Orfila
- Nutritional Sciences and Epidemiology Group, School of Food Science and Nutrition, University of Leeds, Leeds, United Kingdom
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Gamez RM, Rodríguez F, Vidal NM, Ramirez S, Vera Alvarez R, Landsman D, Mariño-Ramírez L. Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006. BMC Genomics 2019; 20:378. [PMID: 31088352 PMCID: PMC6518610 DOI: 10.1186/s12864-019-5763-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/02/2019] [Indexed: 12/19/2022] Open
Abstract
Background Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate into high farming costs and are hazardous to the environment when used excessively. Beneficial free-living soil bacteria that colonize the rhizosphere are known as plant growth-promoting rhizobacteria (PGPR). PGPR affect plant growth in direct or indirect ways and hold great promise for sustainable agriculture. Results PGPR of the genera Bacillus and Pseudomonas in banana cv. Williams were evaluated. These plants were produced through in vitro culture and inoculated individually with two rhizobacteria, Bacillus amyloliquefaciens strain Bs006 and Pseudomonas fluorescens strain Ps006. Control plants without microbial inoculum were also evaluated. These plants were kept in a controlled climate growth room with conditions required to favor plant-microorganism interactions. These interactions were evaluated at 1-, 48- and 96-h using transcriptome sequencing after inoculation to establish differentially expressed genes (DEGs) in plants elicited by the interaction with the two rhizobacteria. Additionally, droplet digital PCR was performed at 1, 48, 96 h, and also at 15 and 30 days to validate the expression patterns of selected DEGs. The banana cv. Williams transcriptome reported differential expression in a large number of genes of which 22 were experimentally validated. Genes validated experimentally correspond to growth promotion and regulation of specific functions (flowering, photosynthesis, glucose catabolism and root growth) as well as plant defense genes. This study focused on the analysis of 18 genes involved in growth promotion, defense and response to biotic or abiotic stress. Conclusions Differences in banana gene expression profiles in response to the rhizobacteria evaluated here (Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006) are influenced by separate bacterial colonization processes and levels that stimulate distinct groups of genes at various points in time. Electronic supplementary material The online version of this article (10.1186/s12864-019-5763-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rocío M Gamez
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 14 Vía Mosquera, Bogotá, Colombia.,Universidad de la Sabana, Chía, Colombia
| | - Fernando Rodríguez
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 14 Vía Mosquera, Bogotá, Colombia
| | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894-6075, USA
| | - Sandra Ramirez
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 14 Vía Mosquera, Bogotá, Colombia
| | - Roberto Vera Alvarez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894-6075, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894-6075, USA
| | - Leonardo Mariño-Ramírez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894-6075, USA.
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R Parijadi AA, Ridwani S, Dwivany FM, Putri SP, Fukusaki E. A metabolomics-based approach for the evaluation of off-tree ripening conditions and different postharvest treatments in mangosteen (Garcinia mangostana). Metabolomics 2019; 15:73. [PMID: 31054000 DOI: 10.1007/s11306-019-1526-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/10/2019] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Metabolomics is an important tool to support postharvest fruit development and ripening studies. Mangosteen (Garcinia mangostana L.) is a tropical fruit with high market value but has short shelf-life during postharvest handling. Several postharvest technologies have been applied to maintain mangosteen fruit quality during storage. However, there is no study to evaluate the metabolite changes that occur in different harvesting and ripening condition. Additionally, the effect of postharvest treatment using a metabolomics approach has never been studied in mangosteen. OBJECTIVES The aims of this study were to evaluate the metabolic changes between different harvesting and ripening condition and to evaluate the effect of postharvest treatment in mangosteen. METHODS Mangosteen ripening stage were collected with several different conditions ("natural on-tree", "random on-tree" and "off-tree"). The metabolite changes were investigated for each ripening condition. Additionally, mangosteen fruit was harvested in stage 2 and was treated with several different treatments (storage at low temperature (LT; 12.3 ± 1.4 °C) and stress inducer treatment (methyl jasmonate and salicylic acid) in comparison with control treatment (normal temperature storage) and the metabolite changes were monitored over the course of 10 days after treatment. The metabolome data obtained from gas chromatography coupled with mass spectrometry were analyzed by multivariate analysis, including hierarchical clustering analysis, principal component analysis, and partial to latent squares analysis. RESULTS "On-tree" ripening condition showed the progression of ripening process in accordance with the accumulation of some aroma precursor metabolites in the flesh part and pectin breakdown in the peel part. Interestingly, similar trend was found in the "off-tree" ripening condition although the progression of ripening process observed through color changes occurred much faster compared to "on-tree" ripening. Additionally, low-temperature treatment is shown as the most effective treatment to prolong mangosteen shelf-life among all postharvest treatments tested in this study compared to control treatment. After postharvest treatment, a total of 71 and 65 metabolites were annotated in peel and flesh part of mangosteen, respectively. Several contributed metabolites (xylose, galactose, galacturonic acid, glucuronate, glycine, and rhamnose) were decreased after treatment in the peel part. However, low-temperature treatment did not show any significant differences compared to a room temperature treatment in the flesh part. CONCLUSIONS Our findings clearly indicate that there is a similar trend of metabolic changes between on-tree and off-tree ripening conditions. Additionally, postharvest treatment directly or indirectly influences many metabolic processes (cell-wall degrading process, sweet-acidic taste quality) during postharvest treatment.
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Affiliation(s)
- Anjaritha A R Parijadi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sobir Ridwani
- Center of Tropical Horticultural Studies, Institut Pertanian Bogor, Jl. Raya Pajajaran, Bogor, 16144, Indonesia
| | - Fenny M Dwivany
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, Jawa Barat, 40132, Indonesia
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, Jawa Barat, 40132, Indonesia.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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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: 27] [Impact Index Per Article: 5.4] [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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Bubici G, Kaushal M, Prigigallo MI, Gómez-Lama Cabanás C, Mercado-Blanco J. Biological Control Agents Against Fusarium Wilt of Banana. Front Microbiol 2019; 10:616. [PMID: 31024469 PMCID: PMC6459961 DOI: 10.3389/fmicb.2019.00616] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/11/2019] [Indexed: 11/13/2022] Open
Abstract
In the last century, the banana crop and industry experienced dramatic losses due to an epidemic of Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f.sp. cubense (Foc) race 1. An even more dramatic menace is now feared due to the spread of Foc tropical race 4. Plant genetic resistance is generally considered as the most plausible strategy for controlling effectively such a devastating disease, as occurred for the first round of FWB epidemic. Nevertheless, with at least 182 articles published since 1970, biological control represents a large body of knowledge on FWB. Remarkably, many studies deal with biological control agents (BCAs) that reached the field-testing stage and even refer to high effectiveness. Some selected BCAs have been repeatedly assayed in independent trials, suggesting their promising value. Overall under field conditions, FWB has been controlled up to 79% by using Pseudomonas spp. strains, and up to 70% by several endophytes and Trichoderma spp. strains. Lower biocontrol efficacy (42-55%) has been obtained with arbuscular mycorrhizal fungi, Bacillus spp., and non-pathogenic Fusarium strains. Studies on Streptomyces spp. have been mostly limited to in vitro conditions so far, with very few pot-experiments, and none conducted in the field. The BCAs have been applied with diverse procedures (e.g., spore suspension, organic amendments, bioformulations, etc.) and at different stages of plant development (i.e., in vitro, nursery, at transplanting, post-transplanting), but there has been no evidence for a protocol better than another. Nonetheless, new bioformulation technologies (e.g., nanotechnology, formulation of microbial consortia and/or their metabolites, etc.) and tailor-made consortia of microbial strains should be encouraged. In conclusion, the literature offers many examples of promising BCAs, suggesting that biocontrol can greatly contribute to limit the damage caused by FWB. More efforts should be done to further validate the currently available outcomes, to deepen the knowledge on the most valuable BCAs, and to improve their efficacy by setting up effective formulations, application protocols, and integrated strategies.
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Affiliation(s)
- Giovanni Bubici
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Protezione Sostenibile delle Piante (IPSP), Bari, Italy
| | - Manoj Kaushal
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania
| | - Maria Isabella Prigigallo
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Protezione Sostenibile delle Piante (IPSP), Bari, Italy
| | | | - Jesús Mercado-Blanco
- Department of Crop Protection, Institute for Sustainable Agriculture (CSIC), Córdoba, Spain
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Song QA, Catlin NS, Brad Barbazuk W, Li S. Computational analysis of alternative splicing in plant genomes. Gene 2019; 685:186-195. [PMID: 30321657 DOI: 10.1016/j.gene.2018.10.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 09/16/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022]
Abstract
Computational analyses play crucial roles in characterizing splicing isoforms in plant genomes. In this review, we provide a survey of computational tools used in recently published, genome-scale splicing analyses in plants. We summarize the commonly used software and pipelines for read mapping, isoform reconstruction, isoform quantification, and differential expression analysis. We also discuss methods for analyzing long reads and the strategies to combine long and short reads in identifying splicing isoforms. We review several tools for characterizing local splicing events, splicing graphs, coding potential, and visualizing splicing isoforms. We further discuss the procedures for identifying conserved splicing isoforms across plant species. Finally, we discuss the outlook of integrating other genomic data with splicing analyses to identify regulatory mechanisms of AS on genome-wide scale.
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Affiliation(s)
- Qi A Song
- Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America
| | - Nathan S Catlin
- Department of Biology, University of Florida, Gainesville, FL 32611, United States of America
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL 32611, United States of America; Genetics Institute, University of Florida, Gainesville, FL 32611, United States of America
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America.
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Molecular and Genetic Bases of Fruit Firmness Variation in Blueberry—A Review. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8090174] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Blueberry (Vaccinium spp.) has been recognized worldwide as a valuable source of health-promoting compounds, becoming a crop with some of the fastest rising consumer demand trends. Fruit firmness is a key target for blueberry breeding as it directly affects fruit quality, consumer preference, transportability, shelf life, and the ability of cultivars to be machine harvested. Fruit softening naturally occurs during berry development, maturation, and postharvest ripening. However, some genotypes are better at retaining firmness than others, and some are crispy, which is a putatively extra-firmness phenotype that provides a distinct eating experience. In this review, we summarized important studies addressing the firmness trait in blueberry, focusing on physiological and molecular changes affecting this trait at the onset of ripening and also the genetic basis of firmness variation across individuals. New insights into these topics were also achieved by using previously available data and historical records from the blueberry breeding program at the University of Florida. The complex quantitative nature of firmness in an autopolyploid species such as blueberry imposes additional challenges for the implementation of molecular techniques in breeding. However, we highlighted some recent genomics-based studies and the potential of a QTL (Quantitative Trait Locus) mapping analysis and genome editing protocols such as CRISPR/Cas9 to further assist and accelerate the breeding process for this important trait.
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Nascimento TP, Castro-Alves VC, Castelan FP, Calhau MFNS, Saraiva LA, Agopian RG, Cordenunsi-Lysenko BR. Metabolomic profiling reveals that natural biodiversity surrounding a banana crop may positively influence the nutritional/sensorial profile of ripe fruits. Food Res Int 2018; 124:165-174. [PMID: 31466636 DOI: 10.1016/j.foodres.2018.07.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/12/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022]
Abstract
This study is part of an extensive project that evaluated the effects of a natural ecosystem on a healthy banana crop and the quality of its fruit. In particular, the study examined the influence of the maintenance of natural biodiversity (Atlantic forest) near a conventional banana crop on the metabolic profiling of ripe banana fruits. Results revealed differences between ripe fruits harvested from plants near the natural forest (Near-NF) and fruits harvested in areas distant from the natural forest (Distant-NF). A total of 76 metabolites were identified in ripe banana fruits. Bananas harvested from Near-NF plot showed increased levels of γ-aminobutyric acid and reduced levels of putrescine compared with fruits from Distant-NF plot. Furthermore, fatty acids profile suggests that ripe fruits harvested from Near-NF plot had increased nutritional quality compared with fruits from Distant-NF plot. Multivariate statistical analysis revealed that these metabolites, which potentially influence the nutritional/sensorial quality of ripe fruits, also contributed to distinguishing fruits harvested from Near-NF and Distant-NF plots. Collectively, the results suggest that the natural biodiversity surrounding a crop area could benefit ripe banana nutritional/sensorial quality. The maintenance of natural forest fragments thus appears to be a promising tool for increasing the quality of fruit crops.
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Affiliation(s)
- Talita P Nascimento
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Victor C Castro-Alves
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil; Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, SP, Brazil
| | - Florence P Castelan
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil; Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, SP, Brazil
| | - Maria Fernanda N S Calhau
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lorenzo A Saraiva
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Roberta G Agopian
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil; Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, SP, Brazil
| | - Beatriz Rosana Cordenunsi-Lysenko
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil; Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, SP, Brazil; Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo, SP, Brazil.
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Guo YF, Zhang YL, Shan W, Cai YJ, Liang SM, Chen JY, Lu WJ, Kuang JF. Identification of Two Transcriptional Activators MabZIP4/5 in Controlling Aroma Biosynthetic Genes during Banana Ripening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6142-6150. [PMID: 29809003 DOI: 10.1021/acs.jafc.8b01435] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The transcriptional regulation of aroma formation genes remains poorly understood in the banana. In this work, we found that the expressions of a subset of aroma biosynthetic genes including MaOMT1, MaMT1, MaGT1, MaBCAT1, MaACY1, MaAGT1, and BanAAT, as well as two bZIP genes, MabZIP4 and MabZIP5, were down-regulated when prestored at 7 °C compared to those prestored at 22 °C during the ripening process of banana. Furthermore, MabZIP4 and MabZIP5 were shown to be able to activate the transcription of these aroma biosynthetic genes. Importantly, MabZIP4 directly binds to BanAAT promoter, while MabZIP5 binds to the promoters of MaMT1, MaACY1, MaAGT1, and BanAAT via the G-box motif, implicating the diverse functional significances of MabZIPs in controlling aroma biosynthesis in banana. Overall, this work sheds new insights on the understanding of transcriptional regulatory mechanisms associated with aroma formation during banana ripening.
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Affiliation(s)
- Yu-Fan Guo
- 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-Liang Zhang
- 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
| | - Wei Shan
- 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
| | - Yong-Jian Cai
- 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
| | - Shu-Min Liang
- 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
| | - 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
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42
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Liu J, Zhang J, Miao H, Jia C, Wang J, Xu B, Jin Z. Elucidating the Mechanisms of the Tomato ovate Mutation in Regulating Fruit Quality Using Proteomics Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:10048-10057. [PMID: 29120173 DOI: 10.1021/acs.jafc.7b03656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The ovate mutation has frequently been used to study changes in fruit shape but not fruit quality. A deterioration in fruit quality associated with the ovate mutation was discovered in this study. To elucidate how ovate influences the quality of fruit, we performed a proteomics analysis of the fruits of the ovate mutant (LA3543) and wild-type ("Ailsa Craig", LA2838A) using tandem mass tag analysis. The results indicated that the ovate mutation significantly influences fruit quality in a number of ways, including by reducing the expression of 1-aminocyclopropane-1-carboxylic acid oxidase 3 (ACO3) in ethylene biosynthesis, improving firmness by reducing the amount of pectinesterase and polygalacturonase, reducing sugar accumulation by downregulating the abundance of mannan endo-1,4-β-mannosidase 4, β-galactosidase, and β-amylase, and reducing the malic acid content by downregulating the accumulation of malic enzymes and malate synthase. These findings could inform future improvements in fruit quality.
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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 , 4 Xueyuan Road, Haikou 571101, China
| | - Jing Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, 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 , 4 Xueyuan Road, Haikou 571101, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, 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 , 4 Xueyuan Road, 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 , 4 Xueyuan Road, Haikou 571101, China
- Key Laboratory of Genetic Improvement of Bananas, Chinese Academy of Tropical Agricultural Sciences , Haikou Experimental Station, Haikou, Hainan Province 570102, China
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43
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The draft genome of tropical fruit durian (Durio zibethinus). Nat Genet 2017; 49:1633-1641. [DOI: 10.1038/ng.3972] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/18/2017] [Indexed: 01/22/2023]
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44
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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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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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46
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47
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Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size. Sci Rep 2016; 6:36304. [PMID: 27824099 PMCID: PMC5099886 DOI: 10.1038/srep36304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/13/2016] [Indexed: 11/21/2022] Open
Abstract
Litchi chinensis is a subtropical fruit crop, popular for its nutritional value and taste. Fruits with small seed size and thick aril are desirable in litchi. To gain molecular insight into gene expression that leads to the reduction in the size of seed in Litchi chinensis, transcriptomes of two genetically closely related genotypes, with contrasting seed size were compared in developing ovules. The cDNA library constructed from early developmental stages of ovules (0, 6, and 14 days after anthesis) of bold- and small-seeded litchi genotypes yielded 303,778,968 high quality paired-end reads. These were de-novo assembled into 1,19,939 transcripts with an average length of 865 bp. A total of 10,186 transcripts with contrast in expression were identified in developing ovules between the small- and large- seeded genotypes. A majority of these differences were present in ovules before anthesis, thus suggesting the role of maternal factors in seed development. A number of transcripts indicative of metabolic stress, expressed at higher level in the small seeded genotype. Several differentially expressed transcripts identified in such ovules showed homology with Arabidopsis genes associated with different stages of ovule development and embryogenesis.
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48
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Wyatt LE, Strickler SR, Mueller LA, Mazourek M. Comparative analysis of Cucurbita pepo metabolism throughout fruit development in acorn squash and oilseed pumpkin. HORTICULTURE RESEARCH 2016; 3:16045. [PMID: 27688889 PMCID: PMC5030761 DOI: 10.1038/hortres.2016.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 05/23/2023]
Abstract
Both the fruit mesocarp and the seeds of winter squash can be used for consumption, although the focus of breeding efforts varies by cultivar. Cultivars bred for fruit consumption are selected for fruit mesocarp quality traits such as carotenoid content, percent dry matter, and percent soluble solids, while these traits are essentially ignored in oilseed pumpkins. To compare fruit development in these two types of squash, we sequenced the fruit transcriptome of two cultivars bred for different purposes: an acorn squash, 'Sweet REBA', and an oilseed pumpkin, 'Lady Godiva'. Putative metabolic pathways were developed for carotenoid, starch, and sucrose synthesis in winter squash fruit and squash homologs were identified for each of the structural genes in the pathways. Gene expression, especially of known rate-limiting and branch point genes, corresponded with metabolite accumulation both across development and between the two cultivars. Thus, developmental regulation of metabolite genes is an important factor in winter squash fruit quality.
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Affiliation(s)
- Lindsay E Wyatt
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA
| | | | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Michael Mazourek
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA
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49
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Pandey A, Alok A, Lakhwani D, Singh J, Asif MH, Trivedi PK. Genome-wide Expression Analysis and Metabolite Profiling Elucidate Transcriptional Regulation of Flavonoid Biosynthesis and Modulation under Abiotic Stresses in Banana. Sci Rep 2016; 6:31361. [PMID: 27539368 PMCID: PMC4990921 DOI: 10.1038/srep31361] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/18/2016] [Indexed: 12/17/2022] Open
Abstract
Flavonoid biosynthesis is largely regulated at the transcriptional level due to the modulated expression of genes related to the phenylpropanoid pathway in plants. Although accumulation of different flavonoids has been reported in banana, a staple fruit crop, no detailed information is available on regulation of the biosynthesis in this important plant. We carried out genome-wide analysis of banana (Musa acuminata, AAA genome) and identified 28 genes belonging to 9 gene families associated with flavonoid biosynthesis. Expression analysis suggested spatial and temporal regulation of the identified genes in different tissues of banana. Analysis revealed enhanced expression of genes related to flavonol and proanthocyanidin (PA) biosynthesis in peel and pulp at the early developmental stages of fruit. Genes involved in anthocyanin biosynthesis were highly expressed during banana fruit ripening. In general, higher accumulation of metabolites was observed in the peel as compared to pulp tissue. A correlation between expression of genes and metabolite content was observed at the early stage of fruit development. Furthermore, this study also suggests regulation of flavonoid biosynthesis, at transcriptional level, under light and dark exposures as well as methyl jasmonate (MJ) treatment in banana.
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Affiliation(s)
- Ashutosh Pandey
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, INDIA.,National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Government of India, C-127, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali 160071, India
| | - Anshu Alok
- National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Government of India, C-127, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali 160071, India
| | - Deepika Lakhwani
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, INDIA
| | - Jagdeep Singh
- National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Government of India, C-127, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali 160071, India
| | - Mehar H Asif
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, INDIA
| | - Prabodh K Trivedi
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, INDIA
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Han YC, Kuang JF, Chen JY, Liu XC, Xiao YY, Fu CC, Wang JN, Wu KQ, Lu WJ. Banana Transcription Factor MaERF11 Recruits Histone Deacetylase MaHDA1 and Represses the Expression of MaACO1 and Expansins during Fruit Ripening. PLANT PHYSIOLOGY 2016; 171:1070-84. [PMID: 27208241 PMCID: PMC4902611 DOI: 10.1104/pp.16.00301] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/02/2016] [Indexed: 05/18/2023]
Abstract
Phytohormone ethylene controls diverse developmental and physiological processes such as fruit ripening via modulation of ethylene signaling pathway. Our previous study identified that ETHYLENE RESPONSE FACTOR11 (MaERF11), a transcription factor in the ethylene signaling pathway, negatively regulates the ripening of banana, but the mechanism for the MaERF11-mediated transcriptional regulation remains largely unknown. Here we showed that MaERF11 has intrinsic transcriptional repression activity in planta. Electrophoretic mobility shift assay and chromatin immunoprecipitation analyses demonstrated that MaERF11 binds to promoters of three ripening-related Expansin genes, MaEXP2, MaEXP7 and MaEXP8, as well as an ethylene biosynthetic gene MaACO1, via the GCC-box motif. Furthermore, expression patterns of MaACO1, MaEXP2, MaEXP7, and MaEXP8 genes are correlated with the changes of histone H3 and H4 acetylation level during fruit ripening. Moreover, we found that MaERF11 physically interacts with a histone deacetylase, MaHDA1, which has histone deacetylase activity, and the interaction significantly strengthens the MaERF11-mediated transcriptional repression of MaACO1 and Expansins Taken together, these findings suggest that MaERF11 may recruit MaHDA1 to its target genes and repress their expression via histone deacetylation.
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Affiliation(s)
- 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 (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - 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 (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - 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 (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Xun-Cheng Liu
- 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 (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - 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 (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Chang-Chun Fu
- 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 (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Jun-Ning Wang
- 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 (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Ke-Qiang Wu
- 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 (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - 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 (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
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