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Song B, Li X, Cao B, Zhang M, Korban SS, Yu L, Yang W, Zhao K, Li J, Wu J. An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus. BMC Biol 2022; 20:215. [PMID: 36183077 PMCID: PMC9526952 DOI: 10.1186/s12915-022-01409-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the wild relatives of pear originated in southwest China, this fruit crop was independently domesticated and improved in Asia and Europe, and there are major phenotypic differences (e.g., maturity and fruit firmness) between Asian and European pears. RESULTS: In this study, we examined the genomes of 113 diverse pear accessions using an identity-by-descent (IBD) approach to investigate how historical gene flow has shaped fruit firmness traits in Asian and European pears. We found a 3-Mbp IBD-enriched region (IBD-ER) that has undergone "convergent domestication" in both the Asian and European pear lineages, and a genome-wide association study (GWAS) of fruit firmness phenotypes strongly implicated the TRANSLOCON AT THE INNER CHLOROPLAST ENVELOPE55 (TIC55) locus within this 3-Mbp IBD-ER. Furthermore, we identified a tandem duplication that includes a 12-bp insertion located in the first exon of TIC55 that is uniquely present in Asian pears, and expression analysis showed that the pear TIC55 gene is highly expressed in Asian pear, while it is weakly or not expressed in European pear; this could contribute to the differences in fruit firmness between Asian and European pear fruits. CONCLUSIONS Our findings provide insights into how pear fruit softening has been impacted during domestication, and we identified candidate genes associated with fruit softening that can contribute to the breeding and improvement of pear and other fruit crops.
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Affiliation(s)
- Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaolong Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Present Address: Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Beibei Cao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingyue Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Schuyler S Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Li'ang Yu
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14850, USA
| | - Wenxi Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Zhu F, Jadhav SS, Tohge T, Salem MA, Lee JM, Giovannoni JJ, Cheng Y, Alseekh S, Fernie AR. A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator. PLANT PHYSIOLOGY 2022; 190:250-266. [PMID: 35512210 PMCID: PMC9434188 DOI: 10.1093/plphys/kiac200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/28/2022] [Indexed: 05/31/2023]
Abstract
Although multiple vital genes with strong effects on the tomato (Solanum lycopersicum) ripening process have been identified via the positional cloning of ripening mutants and cloning of ripening-related transcription factors (TFs), recent studies suggest that it is unlikely that we have fully characterized the gene regulatory networks underpinning this process. Here, combining comparative transcriptomics and expression QTLs, we identified 16 candidate genes involved in tomato fruit ripening and validated them through virus-induced gene silencing analysis. To further confirm the accuracy of the approach, one potential ripening regulator, SlWD40 (WD-40 repeats), was chosen for in-depth analysis. Co-expression network analysis indicated that master regulators such as RIN (ripening inhibitor) and NOR (nonripening) as well as vital TFs including FUL1 (FRUITFUL1), SlNAC4 (NAM, ATAF1,2, and CUC2 4), and AP2a (Activating enhancer binding Protein 2 alpha) strongly co-expressed with SlWD40. Furthermore, SlWD40 overexpression and RNAi lines exhibited substantially accelerated and delayed ripening phenotypes compared with the wild type, respectively. Moreover, transcriptome analysis of these transgenics revealed that expression patterns of ethylene biosynthesis genes, phytoene synthase, pectate lyase, and branched chain amino transferase 2, in SlWD40-RNAi lines were similar to those of rin and nor fruits, which further demonstrated that SlWD40 may act as an important ripening regulator in conjunction with RIN and NOR. These results are discussed in the context of current models of ripening and in terms of the use of comparative genomics and transcriptomics as an effective route for isolating causal genes underlying differences in genotypes.
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Affiliation(s)
| | | | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Mohamed A Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Menoufia 32511, Egypt
| | | | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
- US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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53
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Li S, Wu P, Yu X, Cao J, Chen X, Gao L, Chen K, Grierson D. Contrasting Roles of Ethylene Response Factors in Pathogen Response and Ripening in Fleshy Fruit. Cells 2022; 11:cells11162484. [PMID: 36010560 PMCID: PMC9406635 DOI: 10.3390/cells11162484] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Fleshy fruits are generally hard and unpalatable when unripe; however, as they mature, their quality is transformed by the complex and dynamic genetic and biochemical process of ripening, which affects all cell compartments. Ripening fruits are enriched with nutrients such as acids, sugars, vitamins, attractive volatiles and pigments and develop a pleasant taste and texture and become attractive to eat. Ripening also increases sensitivity to pathogens, and this presents a crucial problem for fruit postharvest transport and storage: how to enhance pathogen resistance while maintaining ripening quality. Fruit development and ripening involve many changes in gene expression regulated by transcription factors (TFs), some of which respond to hormones such as auxin, abscisic acid (ABA) and ethylene. Ethylene response factor (ERF) TFs regulate both fruit ripening and resistance to pathogen stresses. Different ERFs regulate fruit ripening and/or pathogen responses in both fleshy climacteric and non-climacteric fruits and function cooperatively or independently of other TFs. In this review, we summarize the current status of studies on ERFs that regulate fruit ripening and responses to infection by several fungal pathogens, including a systematic ERF transcriptome analysis of fungal grey mould infection of tomato caused by Botrytis cinerea. This deepening understanding of the function of ERFs in fruit ripening and pathogen responses may identify novel approaches for engineering transcriptional regulation to improve fruit quality and pathogen resistance.
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Affiliation(s)
- Shan Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Correspondence: (S.L.); (D.G.)
| | - Pan Wu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaofen Yu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jinping Cao
- College of Agriculture and Biotechnology, Zhejiang University, Zijinggang Campus, Hangzhou 310058, China
| | - Xia Chen
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Lei Gao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Kunsong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijinggang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijinggang Campus, Hangzhou 310058, China
| | - Donald Grierson
- College of Agriculture and Biotechnology, Zhejiang University, Zijinggang Campus, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Correspondence: (S.L.); (D.G.)
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54
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Zou J, Li N, Hu N, Tang N, Cao H, Liu Y, Chen J, Jian W, Gao Y, Yang J, Li Z. Co-silencing of ABA receptors (SlRCAR) reveals interactions between ABA and ethylene signaling during tomato fruit ripening. HORTICULTURE RESEARCH 2022; 9:uhac057. [PMID: 35685223 PMCID: PMC9171117 DOI: 10.1093/hr/uhac057] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/20/2022] [Indexed: 06/06/2023]
Abstract
The ripening of fleshy fruits is highly dependent on the regulation of endogenous hormones, including ethylene, abscisic acid (ABA) and other phytohormones. However, the regulatory mechanism of ABA signaling and its interaction with ethylene signaling in fruit ripening are still unclear. In this study, multi-gene interference (RNAi) was applied to silence the ABA receptor genes in tomato for screening the specific receptors that mediate ABA signaling during fruit ripening. The results indicated that the ABA receptors, including SlRCAR9, SlRCAR12, SlRCAR11, and SlRCAR13, participate in the regulation of tomato fruit ripening. Comparative analysis showed that SlRCAR11 and SlRCAR13 play more important roles in mediating ABA signaling during tomato fruit ripening. Co-silencing of the four genes encoding these receptors could weaken the ethylene biosynthesis and signaling pathway at the early stage of tomato fruit ripening, leading to delayed fruit ripening. Meanwhile, co-silencing enhanced fruit firmness, and altered the shelf-life and susceptibility to Botrytis cinerea of the transgenic fruits. Furthermore, blocking ABA signaling did not affect the ability of ethylene to induce fruit ripening, whereas the block may inhibit the effectiveness of ABA in promoting fruit ripening. These results suggested that ABA signaling may be located upstream of ethylene signaling in regulating fruit ripening. Our findings provide a new insight into the complex regulatory network of phytohormones in regulating fruit ripening in tomato.
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Affiliation(s)
- Jian Zou
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), School of Life Science, China West Normal University, Nanchong, Sichuan 637009, China
| | - Ning Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
- School of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, China
| | - Nan Hu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Ning Tang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
- Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing 402160, China
| | - Haohao Cao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yudong Liu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jing Chen
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Wei Jian
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yanqiang Gao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), School of Life Science, China West Normal University, Nanchong, Sichuan 637009, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
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55
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Zhang WW, Zhao SQ, Gu S, Cao XY, Zhang Y, Niu JF, Liu L, Li AR, Jia WS, Qi BX, Xing Y. FvWRKY48 binds to the pectate lyase FvPLA promoter to control fruit softening in Fragaria vesca. PLANT PHYSIOLOGY 2022; 189:1037-1049. [PMID: 35238391 PMCID: PMC9157130 DOI: 10.1093/plphys/kiac091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/29/2022] [Indexed: 05/13/2023]
Abstract
The regulatory mechanisms that link WRKY gene expression to fruit ripening are largely unknown. Using transgenic approaches, we showed that a WRKY gene from wild strawberry (Fragaria vesca), FvWRKY48, may be involved in fruit softening and ripening. We showed that FvWRKY48 is localized to the nucleus and that degradation of the pectin cell wall polymer homogalacturonan, which is present in the middle lamella and tricellular junction zones of the fruit, was greater in FvWRKY48-OE (overexpressing) fruits than in empty vector (EV)-transformed fruits and less substantial in FvWRKY48-RNAi (RNA interference) fruits. Transcriptomic analysis indicated that the expression of pectate lyase A (FvPLA) was significantly downregulated in the FvWRKY48-RNAi receptacle. We determined that FvWRKY48 bound to the FvPLA promoter via a W-box element through yeast one-hybrid, electrophoretic mobility shift, and chromatin immunoprecipitation quantitative polymerase chain reaction experiments, and β-glucosidase activity assays suggested that this binding promotes pectate lyase activity. In addition, softening and pectin degradation were more intense in FvPLA-OE fruit than in EV fruit, and the middle lamella and tricellular junction zones were denser in FvPLA-RNAi fruit than in EV fruit. We speculated that FvWRKY48 maybe increase the expression of FvPLA, resulting in pectin degradation and fruit softening.
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Affiliation(s)
- Wei-Wei Zhang
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Bei Nong Enterprise Management Co. Ltd, Beijing, 102206, China
| | - Shuai-Qi Zhao
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
| | - Si Gu
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
| | - Xiao-Yan Cao
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
| | - Yu Zhang
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
| | - Jun-Fang Niu
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
| | - Lu Liu
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
| | - An-Ran Li
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
| | - Wen-Suo Jia
- College of Horticulture, China Agricultural University, Beijing, China
| | - Bao-Xiu Qi
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
- Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool, UK
- Author for correspondence: (B.X.Q.), (Y.X.)
| | - Yu Xing
- College of Plant Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, China
- Author for correspondence: (B.X.Q.), (Y.X.)
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56
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Zheng X, Yuan Y, Huang B, Hu X, Tang Y, Xu X, Wu M, Gong Z, Luo Y, Gong M, Gao X, Wu G, Zhang Q, Zhang L, Chan H, Zhu B, Li Z, Ferguson L, Deng W. Control of fruit softening and Ascorbic acid accumulation by manipulation of SlIMP3 in tomato. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1213-1225. [PMID: 35258157 PMCID: PMC9129080 DOI: 10.1111/pbi.13804] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/25/2022] [Indexed: 05/29/2023]
Abstract
Postharvest deterioration is among the major challenges for the fruit industry. Regulation of the fruit softening rate is an effective strategy for extending shelf-life and reducing the economic losses due postharvest deterioration. The tomato myoinositol monophosphatase 3 gene SlIMP3, which showed highest expression level in fruit, was expressed and purified. SlIMP3 demonstrated high affinity with the L-Gal 1-P and D-Ins 3-P, and acted as a bifunctional enzyme in the biosynthesis of AsA and myoinositol. Overexpression of SlIMP3 not only improved AsA and myoinositol content, but also increased cell wall thickness, improved fruit firmness, delayed fruit softening, decreased water loss, and extended shelf-life. Overexpression of SlIMP3 also increased uronic acid, rhamnose, xylose, mannose, and galactose content in cell wall of fruit. Treating fruit with myoinositol obtained similar fruit phenotypes of SlIMP3-overexpressed fruit, with increased cell wall thickness and delayed fruit softening. Meanwhile, overexpression of SlIMP3 conferred tomato fruit tolerance to Botrytis cinerea. The function of SlIMP3 in cell wall biogenesis and fruit softening were also verified using another tomato species, Ailsa Craig (AC). Overexpression of SlDHAR in fruit increased AsA content, but did not affect the cell wall thickness or fruit firmness and softening. The results support a critical role for SlIMP3 in AsA biosynthesis and cell wall biogenesis, and provide a new method of delaying tomato fruit softening, and insight into the link between AsA and cell wall metabolism.
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Affiliation(s)
- Xianzhe Zheng
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Yujin Yuan
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Xiaowei Hu
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Yuwei Tang
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Xin Xu
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Mengbo Wu
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Zehao Gong
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Yingqing Luo
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Min Gong
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Xueli Gao
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Guanle Wu
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Qiongdan Zhang
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Lu Zhang
- Department of Horticulture and Landscape ArchitectureOklahoma State UniversityStillwaterOKUSA
| | - Helen Chan
- Department of Plant SciencesUniversity of California Davis, One Shields AvenueDavisCAUSA
| | - Benzhong Zhu
- Laboratory of Fruit BiologyCollege of Food Science & Nutritional EngineeringChina Agricultural UniversityBeijingChina
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
| | - Louise Ferguson
- Department of Plant SciencesUniversity of California Davis, One Shields AvenueDavisCAUSA
| | - Wei Deng
- Key Laboratory of Plant Hormones and Development Regulation of ChongqingSchool of Life SciencesChongqing UniversityChongqingChina
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Nie H, Shi Y, Geng X, Xing G. CRISRP/Cas9-Mediated Targeted Mutagenesis of Tomato Polygalacturonase Gene ( SlPG) Delays Fruit Softening. FRONTIERS IN PLANT SCIENCE 2022; 13:729128. [PMID: 35665160 PMCID: PMC9162796 DOI: 10.3389/fpls.2022.729128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 04/21/2022] [Indexed: 06/12/2023]
Abstract
Polygalacturonase (PG) gene has been documented as a key candidate for the improvement of fruit firmness, which is a target trait for tomato production because it facilitates transportation and storage. To reduce the expression of the PG gene, most of the elite commercial tomato varieties were obtained by RNA interference technology. However, this approach of producing commercialized tomatoes by integration of the exogenous gene is controversial. In this work, CRISPR/Cas9 technology was used to induce the targeted mutagenesis of the SlPG gene to delay the softening of tomato fruit. Results showed that the SlPG gene was frameshift mutated by 4 bp deletion, 10 bp deletion, and 1 bp insertion, which generated premature translation termination codons. Compared with wild-type (WT), homozygous T1-generation tomato plants exhibited late fruit softening under natural conditions. Consistent with this phenomenon, the firmness value of WT fruit was lower in slpg mutant fruit, and the physiological loss of water was higher. Collectively, these data demonstrate that the mutation of the SlPG gene delays tomato fruit softening. More importantly, 8 out of 20 transgene-free tomato plants, which were homozygous for null alleles of SlPG, were separated in the T3-generation of line slpgT2-#2. This transgene-free slpg may provide materials for more in-depth research of SlPG functions and the molecular mechanism of fruit softening in tomatoes.
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Affiliation(s)
- Hongmei Nie
- College of Horticulture/Collaborative Innovation Center of Improving Quality and Increasing Profits for Protected Vegetables in Shanxi, Shanxi Agricultural University, Taigu, China
| | - Yu Shi
- College of Horticulture/Collaborative Innovation Center of Improving Quality and Increasing Profits for Protected Vegetables in Shanxi, Shanxi Agricultural University, Taigu, China
| | - Xueqing Geng
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guoming Xing
- College of Horticulture/Collaborative Innovation Center of Improving Quality and Increasing Profits for Protected Vegetables in Shanxi, Shanxi Agricultural University, Taigu, China
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58
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Mir TUG, Wani AK, Akhtar N, Shukla S. CRISPR/Cas9: Regulations and challenges for law enforcement to combat its dual-use. Forensic Sci Int 2022; 334:111274. [DOI: 10.1016/j.forsciint.2022.111274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/15/2022]
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59
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Germano TA, de Oliveira MFR, Aziz S, Oliveira AER, da Cruz Saraiva KD, Dos Santos CP, Moura CFH, Costa JH. Transcriptome profiling of cashew apples (Anacardium occidentale) genotypes reveals specific genes linked to firmness and color during pseudofruit development. PLANT MOLECULAR BIOLOGY 2022; 109:83-100. [PMID: 35332428 DOI: 10.1007/s11103-022-01257-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
We found 34 and 71 key genes potentially involved in flavonoid biosynthesis and cell wall disassembly, respectively, which could be associated with specific peel coloration and softening of each genotype. Cashew apple (Anacardium occidentale) has a great economic importance worldwide due to its high nutritional value, peculiar flavor and aroma. During ripening, the peduncle develops different peel color and becomes quickly fragile due to its oversoftening, impacting its consumers' acceptance. In view of this, the understanding about its transcriptional dynamics throughout ripening is imperative. In this study, we performed a transcriptome sequencing of two cashew apple genotypes (CCP 76 and BRS 265), presenting different firmness and color peel, in the immature and ripe stages. Comparative transcriptome analysis between immature and ripe cashew apple revealed 4374 and 3266 differentially expressed genes (DEGs) to CCP 76 and BRS 265 genotypes, respectively. These genes included 71 and 34 GDEs involved in the cell wall disassembly and flavonoid biosynthesis, respectively, which could be associated with firmness loss and anthocyanin accumulation during cashew apple development. Then, softer peduncle of CCP 76 could be justified by down-regulated EXP and up-regulation of genes involved in pectin degradation (PG, PL and PAE) and in cell wall biosynthesis. Moreover, genes related to flavonoid biosynthesis (PAL, C4H and CHS) could be associated with early high accumulation of anthocyanin in red-peel peduncle of BRS 265. Finally, expression patterns of the selected genes were tested by real-time quantitative PCR (qRT-PCR), and the qRT-PCR results were consistent with transcriptome data. The information generated in this work will provide insights into transcriptome responses to cashew apple ripening and hence, it will be helpful for cashew breeding programs aimed at developing genotypes with improved quality traits.
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Affiliation(s)
- Thais Andrade Germano
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil
| | - Matheus Finger Ramos de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil
| | - Shahid Aziz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil
| | - Antonio Edson Rocha Oliveira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, CEP 05508-900, Brazil
| | - Kátia Daniella da Cruz Saraiva
- Ciência e Tecnologia da Paraíba, Instituto Federal de Educação, Campus Princesa Isabel, Princesa Isabel, PB, CEP 58755-000, Brazil
| | - Clesivan Pereira Dos Santos
- Departamento de Química, Universidade Estadual de Ponta Grossa, Campus Uvaranas, Ponta Grossa, PR, CEP 84030-900, Brazil
| | | | - José Hélio Costa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil.
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Kumari C, Sharma M, Kumar V, Sharma R, Kumar V, Sharma P, Kumar P, Irfan M. Genome Editing Technology for Genetic Amelioration of Fruits and Vegetables for Alleviating Post-Harvest Loss. Bioengineering (Basel) 2022; 9:bioengineering9040176. [PMID: 35447736 PMCID: PMC9028506 DOI: 10.3390/bioengineering9040176] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/02/2022] [Accepted: 04/15/2022] [Indexed: 01/13/2023] Open
Abstract
Food security and crop production are challenged worldwide due to overpopulation, changing environmental conditions, crop establishment failure, and various kinds of post-harvest losses. The demand for high-quality foods with improved nutritional quality is also growing day by day. Therefore, production of high-quality produce and reducing post-harvest losses of produce, particularly of perishable fruits and vegetables, are vital. For many decades, attempts have been made to improve the post-harvest quality traits of horticultural crops. Recently, modern genetic tools such as genome editing emerged as a new approach to manage and overcome post-harvest effectively and efficiently. The different genome editing tools including ZFNs, TALENs, and CRISPR/Cas9 system effectively introduce mutations (In Dels) in many horticultural crops to address and resolve the issues associated with post-harvest storage quality. Henceforth, we provide a broad review of genome editing applications in horticulture crops to improve post-harvest stability traits such as shelf life, texture, and resistance to pathogens without compromising nutritional value. Moreover, major roadblocks, challenges, and their possible solutions for employing genome editing tools are also discussed.
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Affiliation(s)
- Chanchal Kumari
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Megha Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Vinay Kumar
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Vinay Kumar
- Department of Physiology and Cell Biology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA;
| | - Parul Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
- Correspondence: (P.S.); (M.I.)
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
- Correspondence: (P.S.); (M.I.)
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Xu Z, Dai J, Kang T, Shah K, Li Q, Liu K, Xing L, Ma J, Zhang D, Zhao C. PpePL1 and PpePL15 Are the Core Members of the Pectate Lyase Gene Family Involved in Peach Fruit Ripening and Softening. FRONTIERS IN PLANT SCIENCE 2022; 13:844055. [PMID: 35401624 PMCID: PMC8990770 DOI: 10.3389/fpls.2022.844055] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/07/2022] [Indexed: 06/12/2023]
Abstract
Pectin is the major component in the primary cell wall and middle lamella, maintaining the physical stability and mechanical strength of the cell wall. Pectate lyase (PL), a cell wall modification enzyme, has a major influence on the structure of pectin. However, little information and no comprehensive analysis is available on the PL gene family in peach (Prunus persica L. Batsch). In this study, 20 PpePL genes were identified in peach. We characterized their physicochemical characteristics, sequence alignments, chromosomal locations, and gene structures. The PpePL family members were classified into five groups based on their phylogenetic relationships. Among those, PpePL1, 9, 10, 15, and 18 had the higher expression abundance in ripe fruit, and PpePL1, 15, and 18 were upregulated during storage. Detailed RT-qPCR analysis revealed that PpePL1 and PpePL15 were responsive to ETH treatment (1 g L-1 ethephon) with an abundant transcript accumulation, which suggested these genes were involved in peach ripening and softening. In addition, virus-induced gene silencing (VIGS) technology was used to identify the roles of PpePL1 and PpePL15. Compared to controls, the RNAi fruit maintained greater firmness in the early storage stage, increased acid-soluble pectin (ASP), and reduced water-soluble pectin (WSP). Moreover, transmission electron microscopy (TEM) showed that cell wall degradation was reduced in the fruit of RNAi-1 and RNAi-15, which indicated that softening of the RNAi fruit has been delayed. Our results indicated that PpePL1 and PpePL15 play an important role in peach softening by depolymerizing pectin and degrading cell wall.
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Xu X, Chen Y, Li B, Zhang Z, Qin G, Chen T, Tian S. Molecular mechanisms underlying multi-level defense responses of horticultural crops to fungal pathogens. HORTICULTURE RESEARCH 2022; 9:uhac066. [PMID: 35591926 PMCID: PMC9113409 DOI: 10.1093/hr/uhac066] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/07/2022] [Indexed: 05/21/2023]
Abstract
The horticultural industry helps to enrich and improve the human diet while contributing to growth of the agricultural economy. However, fungal diseases of horticultural crops frequently occur during pre- and postharvest periods, reducing yields and crop quality and causing huge economic losses and wasted food. Outcomes of fungal diseases depend on both horticultural plant defense responses and fungal pathogenicity. Plant defense responses are highly sophisticated and are generally divided into preformed and induced defense responses. Preformed defense responses include both physical barriers and phytochemicals, which are the first line of protection. Induced defense responses, which include innate immunity (pattern-triggered immunity and effector-triggered immunity), local defense responses, and systemic defense signaling, are triggered to counterstrike fungal pathogens. Therefore, to develop regulatory strategies for horticultural plant resistance, a comprehensive understanding of defense responses and their underlying mechanisms is critical. Recently, integrated multi-omics analyses, CRISPR-Cas9-based gene editing, high-throughput sequencing, and data mining have greatly contributed to identification and functional determination of novel phytochemicals, regulatory factors, and signaling molecules and their signaling pathways in plant resistance. In this review, research progress on defense responses of horticultural crops to fungal pathogens and novel regulatory strategies to regulate induction of plant resistance are summarized, and then the problems, challenges, and future research directions are examined.
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Affiliation(s)
- Xiaodi Xu
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Shi L, Liu Q, Qiao Q, Zhu Y, Huang W, Wang X, Ren Z. Exploring the effects of pectate and pectate lyase on the fruit softening and transcription profiling of Solanum lycopersicum. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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64
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Wang D, Seymour GB. Molecular and biochemical basis of softening in tomato. MOLECULAR HORTICULTURE 2022; 2:5. [PMID: 37789493 PMCID: PMC10515243 DOI: 10.1186/s43897-022-00026-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/20/2022] [Indexed: 10/05/2023]
Abstract
We review the latest information related to the control of fruit softening in tomato and where relevant compare the events with texture changes in other fleshy fruits. Development of an acceptable texture is essential for consumer acceptance, but also determines the postharvest life of fruits. The complex modern supply chain demands effective control of shelf life in tomato without compromising colour and flavour.The control of softening and ripening in tomato (Solanum lycopersicum) are discussed with respect to hormonal cues, epigenetic regulation and transcriptional modulation of cell wall structure-related genes. In the last section we focus on the biochemical changes closely linked with softening in tomato including key aspects of cell wall disassembly. Some important elements of the softening process have been identified, but our understanding of the mechanistic basis of the process in tomato and other fruits remains incomplete, especially the precise relationship between changes in cell wall structure and alterations in fruit texture.
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Affiliation(s)
- Duoduo Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Graham B Seymour
- Divison of Plant and Crop Sciences, University of Nottingham, Sutton Bonington, Loughborough, Leics, LE12 5RD, UK.
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Zhang H, Zhang Y, Wang P, Zhang J. Transcriptome profiling of genes associated with fruit firmness in the melon variety 'Baogua' ( Cucumis melo ssp. agrestis Jeffrey). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:301-313. [PMID: 35400878 PMCID: PMC8943068 DOI: 10.1007/s12298-022-01131-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED Fruit firmness is an important trait of melons due to its effect on fresh fruit consumption, storage, and transport. However, information on the expression of genes influencing the fruit firmness of 'Baogua' (BG) melon (Cucumis melo ssp. agrestis Jeffrey) remains rare. This study aimed to identify the key genes associated with the firmness of BG fruit sampled at 14 and 28 days after pollination (dap) via transcriptome sequencing. A total of 1113 up-regulated and 2224 down-regulated differentially expressed genes (DEGs) were identified. The main Gene Ontology terms assigned to the DEGs were phosphotransferase activity, alcohol group as acceptor, protein phosphorylation, and protein kinase activity. The enriched KEGG pathways involving the DEGs were starch and sucrose metabolism, diterpenoid biosynthesis, plant hormone signal transduction, and MAPK signaling pathway-plant. In addition, qRT-PCR verified that four GAL genes, namely, CmGAL1-4, were differentially expressed at 0, 7, 14, 21, and 28 dap. Our data revealed that CmGAL1 expression was highest at 21 dap. However, the expression levels of CmGAL2-4 were highest at 14 dap. The sequence of CmGAL1 was similar to the sequences of homologs from melon and cucumber. Subcellular localization analysis revealed CmGAL1 was located in the cell membrane and cytoplasm. Our findings implied that fruit development at 14 dap, which is a key time-point, varies considerably from fruit development at 28 dap. Our present study provides new information on the genes associated with BG fruit firmness and help improve the storage and transport of BG fruit prior to processing. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01131-5.
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Affiliation(s)
- Huijun Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, 235000 Anhui Province China
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, Anhui Jianghuai Horticulture Seeds Co., Ltd, Huaibei, 235000 Anhui Province China
| | - Yan Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, 235000 Anhui Province China
| | - Pengcheng Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031 Anhui Province China
- Key Laboratory of Intelligent Seedling Breeding in Vegetable Factory, Ma-an-shan, 238200 Anhui Province China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031 Anhui Province China
| | - Jian Zhang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031 Anhui Province China
- Key Laboratory of Intelligent Seedling Breeding in Vegetable Factory, Ma-an-shan, 238200 Anhui Province China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031 Anhui Province China
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Zhu F, Wen W, Cheng Y, Fernie AR. The metabolic changes that effect fruit quality during tomato fruit ripening. MOLECULAR HORTICULTURE 2022; 2:2. [PMID: 37789428 PMCID: PMC10515270 DOI: 10.1186/s43897-022-00024-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/12/2022] [Indexed: 10/05/2023]
Abstract
As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Weiwei Wen
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany.
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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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Xie L, Wu Y, Duan X, Li T, Jiang Y. Proteomic and physiological analysis provides an elucidation of Fusarium proliferatum infection causing crown rot on banana fruit. Microbiol Res 2021; 256:126952. [PMID: 34968824 DOI: 10.1016/j.micres.2021.126952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/10/2021] [Accepted: 12/19/2021] [Indexed: 11/30/2022]
Abstract
Fusarium proliferatum causes the crown rot of harvested banana fruit but the underling infection mechanism remains unclear. Here, proteomic changes of the banana peel with and without inoculation of F. proliferatum were evaluated. In addition, we investigated the effects of F. proliferatum infection on cell structure, hormone content, primary metabolites and defense-related enzyme activities in the banana peel. Our results showed that F. proliferatum infection mainly affects cell wall components and inhibits the activities of polyphenoloxidase, peroxidase, and chitinase. Gel free quantitative proteomic analysis showed 92 down-regulated and 29 up-regulated proteins of banana peel after F. proliferatum infection. These proteins were mainly related to defense response to biotic stress, chloroplast structure and function, JA signaling pathway, and primary metabolism. Although jasmonic acid (JA) content and JA signaling component coronatine-insensitive (COI) protein were induced by F. proliferatum infection, JA-responsible defense genes/proteins were downregulated. In contrast, expression of senescence-related genes was induced by F. proliferatum, indicating that F. proliferatum modulated the JA signaling to accelerate the senescence of banana fruit. Additionally, salicylic acid (SA) content and SA signaling for resistance acquisition were inhibited by F. proliferatum. Taken together, these results suggest that F. proliferatum depolymerizes the cell wall barrier, impairs the defense system in banana fruit, and activates non-defensive JA-signaling pathway accelerated the senescence of banana fruit. This study provided the elucidation of the prominent pathways disturbed by F. proliferatum in banana fruit, which will facilitate the development of a new strategy to control crown rot of banana fruit and improvement of banana cultivars.
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Affiliation(s)
- Lihong Xie
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yanfei Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xuewu Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Taotao Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Yueming Jiang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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Zhang QY, Ge J, Liu XC, Wang WQ, Liu XF, Yin XR. Consensus co-expression network analysis identifies AdZAT5 regulating pectin degradation in ripening kiwifruit. J Adv Res 2021; 40:59-68. [PMID: 36100334 PMCID: PMC9481940 DOI: 10.1016/j.jare.2021.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
CCNA was advanced by introducing physiological traits. Six cell wall genes and four transcription factors were identified for pectin degradation. A series of experiments validated the regulations of AdZAT5 on AdPL5 and Adβ-Gal5. CCNA would be powerful for phishing the unknown regulators with higher efficiency and accuracy.
Introduction Cell wall degradation and remodeling is the key factor causing fruit softening during ripening. Objectives To explore the mechanism underlying postharvest cell wall metabolism, a transcriptome analysis method for more precious prediction on functional genes was needed. Methods Kiwifruits treated by ethylene (a conventional and effective phytohormone to accelerate climacteric fruit ripening and softening as kiwifruits) or air were taken as materials. Here, Consensus Coexpression Network Analysis (CCNA), a procedure evolved from Weighted Gene Co-expression Network Analysis (WGCNA) package in R, was applied and generated 85 consensus clusters from twelve transcriptome libraries. Advanced and comprehensive modifications were achieved by combination of CCNA and WGCNA with introduction of physiological traits, including firmness, cell wall materials, cellulose, hemicellulose, water soluble pectin, covalent binding pectin and ionic soluble pectin. Results As a result, six cell wall metabolisms related structural genes AdGAL1, AdMAN1, AdPL1, AdPL5, Adβ-Gal5, AdPME1 and four transcription factors AdZAT5, AdDOF3, AdNAC083, AdMYBR4 were identified as hub candidate genes for pectin degradation. Dual-luciferase system and electrophoretic mobility shift assays validated that promoters of AdPL5 and Adβ-Gal5 were recognized and trans-activated by transcription factor AdZAT5. The relatively higher enzyme activities of PL and β-Gal were observed in ethylene treated kiwifruit, further emphasized the critical roles of these two pectin related genes for fruit softening. Moreover, stable transient overexpression AdZAT5 in kiwifruit significantly enhanced AdPL5 and Adβ-Gal5 expression, which confirmed the in vivo regulations between transcription factor and pectin related genes. Conclusion Thus, modification and application of CCNA would be powerful for the precious phishing the unknown regulators. It revealed that AdZAT5 is a key factor for pectin degradation by binding and regulating effector genes AdPL5 and Adβ-Gal5.
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Kang J, Gong J, Zhang L, Gao Z, Xie Q, Hu Z, Chen G. A novel E6-like gene, E6-2, affects fruit ripening in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111066. [PMID: 34763858 DOI: 10.1016/j.plantsci.2021.111066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Tomato fruit ripening is a complicated and well-coordinated process with numerous metabolic changes resulted from endogenous hormone and genetic regulators. Although the regulation of MADS-box transcription factor (MADS-RIN) controlling fruit ripening has been widely reported, its mechanisms underlying need to be further improved. Here, we characterized a novel tomato E6-like gene, E6-2, whose transcripts showed a high accumulation in fruit ripening stages (Breaker, Breaker+4 and Breaker+7), but a low level was observed in Never ripe (Nr) and ripening inhibitor (rin) mutants. MADS-RIN directly activates the expression of E6-2 in vivo. Additionally, a remarkable reduction of E6-2 was observed in wild-type (WT) tomato fruits at the MG stage treated with 1-MCP. RNAi-mediated silencing of E6-2 resulted in delayed fruit ripening, reduced accumulation of the total carotenoid and lycopene, reduced content of ethylene production, and increased contents of the total pectin, cellulose, starch and soluble sugar. Moreover, the expression of carotenoid biosynthesis genes (PSY1, PDS and ZDS), ripening-related genes (CNR, PG and ERF4), ethylene biosynthesis genes (ACS2, ACO1 and ACO3), ethylene-responsive genes (E4 and E8) and cell wall metabolism genes (TBG4, PL, EXP1 and XTH5) were inhibited in E6-2 -RNAi lines. These results indicate that E6-2 plays an important role in regulating tomato fruit ripening targeted by RIN.
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Affiliation(s)
- Jing Kang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Jun Gong
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Lincheng Zhang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Zihan Gao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
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Wang X, Pan L, Wang Y, Meng J, Deng L, Niu L, Liu H, Ding Y, Yao JL, Nieuwenhuizen NJ, Ampomah-Dwamena C, Lu Z, Cui G, Wang Z, Zeng W. PpIAA1 and PpERF4 form a positive feedback loop to regulate peach fruit ripening by integrating auxin and ethylene signals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111084. [PMID: 34763869 DOI: 10.1016/j.plantsci.2021.111084] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 05/24/2023]
Abstract
The signaling pathways of both auxin and ethylene regulate peach fruit ripening via the Aux/IAA and ERF transcription factors, respectively. However, the molecular mechanisms that coordinate both auxin and ethylene signals during peach fruit ripening remain unclear. In this study, we show that PpIAA1 and PpERF4 act as key players in a positive feedback loop, and promote peach fruit ripening by directly binding to and enhancing the activity of target gene promoters. PpIAA1 increased the expression of the ethylene biosynthesis gene PpACS1. Furthermore, PpERF4 enhanced the transcription of PpACO1 and PpIAA1 genes by binding to their promoters. Additionally, PpIAA1 and PpERF4 bound to each other to form a complex, which then enhanced the transcription of abscisic acid biosynthesis genes (PpNCED2 and PpNCED3) and the fruit softening gene (PpPG1) to levels higher than those achieved by each transcription factor individually. Moreover, overexpression of PpIAA1 in tomato accelerated fruit ripening and shortened the fruit shelf-life by increasing the production of ethylene and the expression levels of ripening regulator genes. Collectively, these results advance our understanding of the molecular mechanisms underlying peach fruit ripening and softening via auxin and ethylene signaling pathways.
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Affiliation(s)
- Xiaobei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Lei Pan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Yan Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Junren Meng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Li Deng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Liang Niu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Hui Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Yifeng Ding
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Jia-Long Yao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China; The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | | | | | - Zhenhua Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Guochao Cui
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Zhiqiang Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China.
| | - Wenfang Zeng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China.
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Gao Y, Hu Y, Shen J, Meng X, Suo J, Zhang Z, Song L, Wu J. Acceleration of Aril Cracking by Ethylene in Torreya grandis During Nut Maturation. FRONTIERS IN PLANT SCIENCE 2021; 12:761139. [PMID: 34745193 PMCID: PMC8565854 DOI: 10.3389/fpls.2021.761139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Torreya grandis 'Merrillii' is a famous nut with great nutritional value and high medicinal value. Aril cracking is an important process for seed dispersal, which is also an indicator of seed maturation. However, the cracking mechanism of T. grandis aril during the maturation stage remains largely unknown. Here, we provided a comprehensive view of the physiological and molecular levels of aril cracking in T. grandis by systematically analyzing its anatomical structure, physiological parameters, and transcriptomic response during the cracking process. These results showed that the length of both epidermal and parenchymatous cell layers significantly increased from 133 to 144 days after seed protrusion (DASP), followed by a clear separation between parenchymatous cell layers and kernel, which was accompanied by a breakage between epidermal and parenchymatous cell layers. Moreover, analyses of cell wall composition showed that a significant degradation of cellular wall polysaccharides occurred during aril cracking. To examine the global gene expression changes in arils during the cracking process, the transcriptomes (96 and 141 DASP) were analyzed. KEGG pathway analysis of DEGs revealed that 4 of the top 10 enriched pathways were involved in cell wall modification and 2 pathways were related to ethylene biosynthesis and ethylene signal transduction. Furthermore, combining the analysis results of co-expression networks between different transcription factors, cell wall modification genes, and exogenous ethylene treatments suggested that the ethylene signal transcription factors (ERF11 and ERF1A) were involved in aril cracking of T. grandis by regulation of EXP and PME. Our findings provided new insights into the aril cracking trait in T. grandis.
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Affiliation(s)
- Yadi Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an City, China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an City, China
| | - Yuanyuan Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an City, China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an City, China
| | - Jiayi Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an City, China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an City, China
| | - Xuecheng Meng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an City, China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an City, China
| | - Jinwei Suo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an City, China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an City, China
| | - Zuying Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an City, China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an City, China
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an City, China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an City, China
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an City, China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an City, China
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Zheng H, Jin R, Liu Z, Sun C, Shi Y, Grierson D, Zhu C, Li S, Ferguson I, Chen K. Role of the tomato fruit ripening regulator MADS-RIN in resistance to Botrytis cinerea infection. FOOD QUALITY AND SAFETY 2021. [DOI: 10.1093/fqsafe/fyab028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Tomato MADS-RIN (RIN) transcription factor has been shown to be a master activator regulating fruit ripening. Recent studies have revealed that in addition to activating many other cell wall genes, it also represses expression of XTH5, XTH8, and MAN4a, which are positively related to excess flesh softening and cell wall degradation, which might indicate it has a potential role in pathogen resistance of ripening fruit. In this study, both wild-type (WT) and RIN-knockout (RIN-KO) mutant tomato fruit were infected with Botrytis cinerea to investigate the function of RIN in defense against pathogen infection during ripening. The results showed that RIN-KO fruit were much more sensitive to B. cinerea infection with larger lesion sizes. Transcriptome data and qRT-PCR assay indicate genes of phenylalanine ammonialyase (PAL) and chitinase (CHI) in RIN-KO fruit were reduced and their corresponding enzyme activities were decreased. Transcripts of genes encoding pathogenesis-related proteins (PRs), including PR1a, PRSTH2, and APETALA2/Ethylene Response Factor (AP2/ERF) including ERF.A1, Pti5, Pti6, ERF.A4, were reduced in RIN-KO fruit compared to WT fruit. Moreover, in the absence of RIN the expression of genes encoding cell wall-modifying enzymes XTH5, XTH8, MAN4a has been reported to be elevated, which is potentially correlated with cell wall properties. When present, RIN represses transcription of XTH5 by activating ERF.F4, a class II (repressor class) ERF gene family member, and ERF.F5. These results support the conclusion that RIN enhances ripening-related resistance to gray mold infection by upregulating pathogen-resistance genes and defense enzyme activities as well as reducing accumulation of transcripts encoding some cell wall enzymes.
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Affiliation(s)
| | | | | | | | | | - Donald Grierson
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou,China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Loughborough,UK
| | | | | | - Ian Ferguson
- Zhejiang University (Visiting Scientist), Hangzhou, China
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Rajput M, Choudhary K, Kumar M, Vivekanand V, Chawade A, Ortiz R, Pareek N. RNA Interference and CRISPR/Cas Gene Editing for Crop Improvement: Paradigm Shift towards Sustainable Agriculture. PLANTS 2021; 10:plants10091914. [PMID: 34579446 PMCID: PMC8467553 DOI: 10.3390/plants10091914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 01/09/2023]
Abstract
With the rapid population growth, there is an urgent need for innovative crop improvement approaches to meet the increasing demand for food. Classical crop improvement approaches involve, however, a backbreaking process that cannot equipoise with increasing crop demand. RNA-based approaches i.e., RNAi-mediated gene regulation and the site-specific nuclease-based CRISPR/Cas9 system for gene editing has made advances in the efficient targeted modification in many crops for the higher yield and resistance to diseases and different stresses. In functional genomics, RNA interference (RNAi) is a propitious gene regulatory approach that plays a significant role in crop improvement by permitting the downregulation of gene expression by small molecules of interfering RNA without affecting the expression of other genes. Gene editing technologies viz. the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) have appeared prominently as a powerful tool for precise targeted modification of nearly all crops' genome sequences to generate variation and accelerate breeding efforts. In this regard, the review highlights the diverse roles and applications of RNAi and CRISPR/Cas9 system as powerful technologies to improve agronomically important plants to enhance crop yields and increase tolerance to environmental stress (biotic or abiotic). Ultimately, these technologies can prove to be important in view of global food security and sustainable agriculture.
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Affiliation(s)
- Meenakshi Rajput
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer 305801, Rajasthan, India; (M.R.); (K.C.); (M.K.)
| | - Khushboo Choudhary
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer 305801, Rajasthan, India; (M.R.); (K.C.); (M.K.)
| | - Manish Kumar
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer 305801, Rajasthan, India; (M.R.); (K.C.); (M.K.)
| | - V. Vivekanand
- Centre for Energy and Environment, Malaviya National Institute of Technology, Jaipur 302017, Rajasthan, India;
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden;
- Correspondence: (A.C.); (N.P.)
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden;
| | - Nidhi Pareek
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer 305801, Rajasthan, India; (M.R.); (K.C.); (M.K.)
- Correspondence: (A.C.); (N.P.)
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75
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Al Hinai TZS, Vreeburg RAM, Mackay CL, Murray L, Sadler IH, Fry SC. Fruit softening: evidence for pectate lyase action in vivo in date (Phoenix dactylifera) and rosaceous fruit cell walls. ANNALS OF BOTANY 2021; 128:511-525. [PMID: 34111288 PMCID: PMC8422893 DOI: 10.1093/aob/mcab072] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/08/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The programmed softening occurring during fruit development requires scission of cell wall polysaccharides, especially pectin. Proposed mechanisms include the action of wall enzymes or hydroxyl radicals. Enzyme activities found in fruit extracts include pectate lyase (PL) and endo-polygalacturonase (EPG), which, in vitro, cleave de-esterified homogalacturonan in mid-chain by β-elimination and hydrolysis, respectively. However, the important biological question of whether PL exhibits action in vivo had not been tested. METHODS We developed a method for specifically and sensitively detecting in-vivo PL products, based on Driselase digestion of cell wall polysaccharides and detection of the characteristic unsaturated product of PL action. KEY RESULTS In model in-vitro experiments, pectic homogalacturonan that had been partially cleaved by commercial PL was digested to completion with Driselase, releasing an unsaturated disaccharide ('ΔUA-GalA'), taken as diagnostic of PL action. ΔUA-GalA was separated from saturated oligogalacturonides (EPG products) by electrophoresis, then subjected to thin-layer chromatography (TLC), resolving ΔUA-GalA from higher homologues. The ΔUA-GalA was confirmed as 4-deoxy-β-l-threo-hex-4-enopyranuronosyl-(1→4)-d-galacturonic acid by NMR spectroscopy. Driselase digestion of cell walls from ripe fruits of date (Phoenix dactylifera), pear (Pyrus communis), rowan (Sorbus aucuparia) and apple (Malus pumila) yielded ΔUA-GalA, demonstrating that PL had been acting in vivo in these fruits prior to harvest. Date-derived ΔUA-GalA was verified by negative-mode mass spectrometry, including collision-induced dissociation (CID) fragmentation. The ΔUA-GalA:GalA ratio from ripe dates was roughly 1:20 (mol mol-1), indicating that approx. 5 % of the bonds in endogenous homogalacturonan had been cleaved by in-vivo PL action. CONCLUSIONS The results provide the first demonstration that PL, previously known from studies of fruit gene expression, proteomic studies and in-vitro enzyme activity, exhibits enzyme action in the walls of soft fruits and may thus be proposed to contribute to fruit softening.
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Affiliation(s)
- Thurayya Z S Al Hinai
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King’s Buildings, Max Born Crescent, Edinburgh, UK
| | - Robert A M Vreeburg
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King’s Buildings, Max Born Crescent, Edinburgh, UK
| | - C Logan Mackay
- EastCHEM School of Chemistry, The University of Edinburgh, The King’s Buildings, Edinburgh, UK
| | - Lorna Murray
- EastCHEM School of Chemistry, The University of Edinburgh, The King’s Buildings, Edinburgh, UK
| | - Ian H Sadler
- EastCHEM School of Chemistry, The University of Edinburgh, The King’s Buildings, Edinburgh, UK
| | - Stephen C Fry
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King’s Buildings, Max Born Crescent, Edinburgh, UK
- For correspondence. E-mail
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Advances in Vacuum Ultraviolet Photolysis in the Postharvest Management of Fruit and Vegetables Along the Value Chains: a Review. FOOD BIOPROCESS TECH 2021. [DOI: 10.1007/s11947-021-02703-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Xia X, Cheng X, Li R, Yao J, Li Z, Cheng Y. Advances in application of genome editing in tomato and recent development of genome editing technology. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2727-2747. [PMID: 34076729 PMCID: PMC8170064 DOI: 10.1007/s00122-021-03874-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 05/07/2023]
Abstract
Genome editing, a revolutionary technology in molecular biology and represented by the CRISPR/Cas9 system, has become widely used in plants for characterizing gene function and crop improvement. Tomato, serving as an excellent model plant for fruit biology research and making a substantial nutritional contribution to the human diet, is one of the most important applied plants for genome editing. Using CRISPR/Cas9-mediated targeted mutagenesis, the re-evaluation of tomato genes essential for fruit ripening highlights that several aspects of fruit ripening should be reconsidered. Genome editing has also been applied in tomato breeding for improving fruit yield and quality, increasing stress resistance, accelerating the domestication of wild tomato, and recently customizing tomato cultivars for urban agriculture. In addition, genome editing is continuously innovating, and several new genome editing systems such as the recent prime editing, a breakthrough in precise genome editing, have recently been applied in plants. In this review, these advances in application of genome editing in tomato and recent development of genome editing technology are summarized, and their leaving important enlightenment to plant research and precision plant breeding is also discussed.
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Affiliation(s)
- Xuehan Xia
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xinhua Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Rui Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Juanni Yao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yulin Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
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Pan H, Lyu S, Chen Y, Xu S, Ye J, Chen G, Wu S, Li X, Chen J, Pan D. MicroRNAs and Transcripts Associated with an Early Ripening Mutant of Pomelo ( Citrus grandis Osbeck). Int J Mol Sci 2021; 22:9348. [PMID: 34502256 PMCID: PMC8431688 DOI: 10.3390/ijms22179348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
'Liuyuezaoyou' is an early-ripening cultivar selected from a bud mutation of Citrus grandis Osbeck 'Guanximiyou'. They were designated here as MT and WT, respectively. The fruit of MT matures about 45 days earlier than WT, which was accompanied by significant changes in key phytohormones, sugar compounds and organic acids. Recent studies have showed that microRNAs (miRNAs) play an important role in regulation of fruit ripening process. The aim of this study was to compare MT fruits with WT ones to uncover if miRNAs were implicated in the ripening of C. grandis. Fruits of both WT and MT at four developmental stages were analyzed using high-throughput sequencing and RT-PCR. Several independent miRNA libraries were constructed and sequenced. A total of 747 known miRNAs were identified and 99 novel miRNAs were predicted across all libraries. The novel miRNAs were found to have hairpin structures and possess star sequences. These results showed that transcriptome and miRNAs are substantially involved in a complex and comprehensive network in regulation of fruit ripening of this species. Further analysis of the network model revealed intricate interactions of miRNAs with mRNAs during the fleshy fruit ripening process. Several identified miRNAs have potential targets. These include auxin-responsive protein IAA9, sucrose synthase 3, V-type proton ATPase, NCED1 (ABA biosynthesis) and PL1/5 (pectate lyase genes), as well as NAC100 putative coordinated regulation networks, whose interactions with respective miRNAs may contribute significantly to fruit ripening of C. grandis.
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Affiliation(s)
- Heli Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Shiheng Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL 32703, USA
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural and Forestry University, Hangzhou 311300, China
| | - Yanqiong Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Shirong Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Jianwen Ye
- Agricultural and Rural Bureau of Pinghe County, Zhangzhou 363700, China;
| | - Guixin Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Shaohua Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Xiaoting Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Jianjun Chen
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL 32703, USA
| | - Dongming Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
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Hunter DA, Napier NJ, Erridge ZA, Saei A, Chen RKY, McKenzie MJ, O’Donoghue EM, Hunt M, Favre L, Lill RE, Brummell DA. Transcriptome Responses of Ripe Cherry Tomato Fruit Exposed to Chilling and Rewarming Identify Reversible and Irreversible Gene Expression Changes. FRONTIERS IN PLANT SCIENCE 2021; 12:685416. [PMID: 34335654 PMCID: PMC8322768 DOI: 10.3389/fpls.2021.685416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Tomato fruit stored below 12°C lose quality and can develop chilling injury upon subsequent transfer to a shelf temperature of 20°C. The more severe symptoms of altered fruit softening, uneven ripening and susceptibility to rots can cause postharvest losses. We compared the effects of exposure to mild (10°C) and severe chilling (4°C) on the fruit quality and transcriptome of 'Angelle', a cherry-type tomato, harvested at the red ripe stage. Storage at 4°C (but not at 10°C) for 27 days plus an additional 6 days at 20°C caused accelerated softening and the development of mealiness, both of which are commonly related to cell wall metabolism. Transcriptome analysis using RNA-Seq identified a range of transcripts encoding enzymes putatively involved in cell wall disassembly whose expression was strongly down-regulated at both 10 and 4°C, suggesting that accelerated softening at 4°C was due to factors unrelated to cell wall disassembly, such as reductions in turgor. In fruit exposed to severe chilling, the reduced transcript abundances of genes related to cell wall modification were predominantly irreversible and only partially restored upon rewarming of the fruit. Within 1 day of exposure to 4°C, large increases occurred in the expression of alternative oxidase, superoxide dismutase and several glutathione S-transferases, enzymes that protect cell contents from oxidative damage. Numerous heat shock proteins and chaperonins also showed large increases in expression, with genes showing peak transcript accumulation after different times of chilling exposure. These changes in transcript abundance were not induced at 10°C, and were reversible upon transfer of the fruit from 4 to 20°C. The data show that genes involved in cell wall modification and cellular protection have differential sensitivity to chilling temperatures, and exhibit different capacities for recovery upon rewarming of the fruit.
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Affiliation(s)
- Donald A. Hunter
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Nathanael J. Napier
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Zoe A. Erridge
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Ali Saei
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Ronan K. Y. Chen
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Marian J. McKenzie
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Erin M. O’Donoghue
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Martin Hunt
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Laurie Favre
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
- Centre for Postharvest and Refrigeration Research, Massey University, Palmerston North, New Zealand
| | - Ross E. Lill
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - David A. Brummell
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
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Anees M, Gao L, Umer MJ, Yuan P, Zhu H, Lu X, He N, Gong C, Kaseb MO, Zhao S, Liu W. Identification of Key Gene Networks Associated With Cell Wall Components Leading to Flesh Firmness in Watermelon. FRONTIERS IN PLANT SCIENCE 2021; 12:630243. [PMID: 34239519 PMCID: PMC8259604 DOI: 10.3389/fpls.2021.630243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/20/2021] [Indexed: 05/15/2023]
Abstract
Flesh firmness of watermelon is an important quality trait for commercial fruit values, including fruit storability, transportability, and shelf life. To date, knowledge of the gene networks underlying this trait is still limited. Herein, we used weighted genes co-expression network analysis (WGCNA) based on correlation and the association of phenotypic data (cell wall contents) with significantly differentially expressed genes between two materials, a near isogeneic line "HWF" (with high average flesh firmness) and inbred line "203Z" (with low average flesh firmness), to identify the gene networks responsible for changes in fruit flesh firmness. We identified three gene modules harboring 354 genes; these gene modules demonstrated significant correlation with water-soluble pectin, cellulose, hemicellulose, and protopectin. Based on intramodular significance, eight genes involved in cell wall biosynthesis and ethylene pathway are identified as hub genes within these modules. Among these genes, two genes, Cla012351 (Cellulose synthase) and Cla004251 (Pectinesterase), were significantly correlated with cellulose (r 2 = 0.83) and protopectin (r 2 = 0.81); three genes, Cla004120 (ERF1), Cla009966 (Cellulose synthase), and Cla006648 (Galactosyltransferase), had a significant correlation with water-soluble pectin (r 2 = 0.91), cellulose (r 2 = 0.9), and protopectin (r 2 = 0.92); and three genes, Cla007092 (ERF2a), Cla004119 (probable glycosyltransferase), and Cla018816 (Xyloglucan endotransglucosylase/hydrolase), were correlated with hemicellulose (r 2 = 0.85), cellulose (r 2 = 0.8), and protopectin (r 2 = 0.8). This study generated important insights of biosynthesis of a cell wall structure and ethylene signaling transduction pathway, the mechanism controlling the flesh firmness changes in watermelon, which provide a significant source to accelerate future functional analysis in watermelon to facilitate crop improvement.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shengjie Zhao
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenge Liu
- Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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81
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Yadav A, Fennec A, Guan C, Yang Y, Kochanek B, Israel D, Izhaki A, Zilkah S, Friedman H. Phenotypic Characterization of Postharvest Fruit Qualities in Astringent and Non-astringent Persimmon ( Diospyros kaki) Cultivars. Front Genet 2021; 12:670929. [PMID: 34163526 PMCID: PMC8215578 DOI: 10.3389/fgene.2021.670929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
Phenotypic characterization of postharvest traits is essential for the breeding of high-quality fruits. To compare postharvest traits of different genetic lines, it is essential to use a reference point during fruit development that will be common to all the lines. In this study, we employed a non-destructive parameter of chlorophyll levels to establish a similar physiological age and compared several postharvest traits of ten astringent and seven non-astringent persimmon cultivars. The fruit's traits examined were astringency, weight, total soluble solids (TSS), titratable acidity (TA), chlorophyll levels (I AD ), color (hue), firmness, color development and firmness loss during storage, crack development, and susceptibility to Alternaria infection. Although the chlorophyll (I AD ) index and color (hue) showed a high correlation among mature fruits of all cultivars, the chlorophyll parameter could detect higher variability in each cultivar, suggesting that I AD is a more rigorous parameter for detecting the developmental stage. The average weight, TSS, and TA were similar between astringent and non-astringent cultivars. Cracks appeared only on a few cultivars at harvest. Resistance to Alternaria infection and firmness were lower in astringent than in non-astringent cultivars. Only the astringent cultivar "32" was resistant to infection possibly due to the existence of an efficient peel barrier. It was concluded that a high correlation existed between astringency, susceptibility to Alternaria infection, and firmness. Cracks did not correlate with astringency or firmness. The phenotypic traits evaluated in this work can be used in future breeding programs for elite persimmon fruits.
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Affiliation(s)
- Akhilesh Yadav
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| | - Anton Fennec
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| | - Changfei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Yong Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Bettina Kochanek
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| | - David Israel
- Department of Fruit Tree Sciences, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| | - Anat Izhaki
- Department of Fruit Tree Sciences, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| | - Shmuel Zilkah
- Department of Fruit Tree Sciences, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| | - Haya Friedman
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
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82
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Ito Y, Nakamura N, Kotake-Nara E. Semi-dominant effects of a novel ripening inhibitor (rin) locus allele on tomato fruit ripening. PLoS One 2021; 16:e0249575. [PMID: 33886595 PMCID: PMC8061929 DOI: 10.1371/journal.pone.0249575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/21/2021] [Indexed: 11/17/2022] Open
Abstract
The tomato (Solanum lycopersicum) ripening inhibitor (rin) mutation completely represses fruit ripening, as rin fruits fail to express ripening-associated genes and remain green and firm. Moreover, heterozygous rin fruits (rin/+) ripen normally but have extended shelf life, an important consideration for this perishable fruit crop; therefore, heterozygous rin has been widely used to breed varieties that produce red tomatoes with improved shelf life. We previously used CRISPR/Cas9 to produce novel alleles at the rin locus. The wild-type allele RIN encodes a MADS-box transcription factor and the novel allele, named as rinG2, generates an early stop codon, resulting in C-terminal truncation of the transcription factor. Like rin fruits, rinG2 fruits exhibit extended shelf life, but unlike rin fruits, which remain yellow-green even after long-term storage, rinG2 fruits turn orange due to ripening-associated carotenoid production. Here, to explore the potential of the rinG2 mutation for breeding, we characterized the effects of rinG2 in the heterozygous state (rinG2/+) compared to the effects of rin/+. The softening of rinG2/+ fruits was delayed compared to the wild type but to a lesser degree than rin/+ fruits. Lycopene and β-carotene levels in rinG2/+ fruits were similar to those of the wild type, whereas rin/+ fruits accumulated half the amount of β-carotene compared to the wild type. The rinG2/+ fruits produced lower levels of ethylene than wild-type and rin/+ fruits. Expression analysis revealed that in rinG2/+ fruits, the rinG2 mutation (like rin) partially inhibited the expression of ripening-associated genes. The small differences in the inhibitory effects of rinG2 vs. rin coincided with small differences in phenotypes, such as ethylene production, softening, and carotenoid accumulation. Therefore, rinG2 represents a promising genetic resource for developing tomato cultivars with extended shelf life.
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Affiliation(s)
- Yasuhiro Ito
- Food Research Institute, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Nobutaka Nakamura
- Food Research Institute, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Eiichi Kotake-Nara
- Food Research Institute, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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83
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Liu Q, Yang F, Zhang J, Liu H, Rahman S, Islam S, Ma W, She M. Application of CRISPR/Cas9 in Crop Quality Improvement. Int J Mol Sci 2021; 22:4206. [PMID: 33921600 PMCID: PMC8073294 DOI: 10.3390/ijms22084206] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
The various crop species are major agricultural products and play an indispensable role in sustaining human life. Over a long period, breeders strove to increase crop yield and improve quality through traditional breeding strategies. Today, many breeders have achieved remarkable results using modern molecular technologies. Recently, a new gene-editing system, named the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, has also succeeded in improving crop quality. It has become the most popular tool for crop improvement due to its versatility. It has accelerated crop breeding progress by virtue of its precision in specific gene editing. This review summarizes the current application of CRISPR/Cas9 technology in crop quality improvement. It includes the modulation in appearance, palatability, nutritional components and other preferred traits of various crops. In addition, the challenge in its future application is also discussed.
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Affiliation(s)
- Qier Liu
- Institute of Agricultural Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Fan Yang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Jingjuan Zhang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Hang Liu
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shanjida Rahman
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shahidul Islam
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Wujun Ma
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Maoyun She
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
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84
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Silva CJ, van den Abeele C, Ortega-Salazar I, Papin V, Adaskaveg JA, Wang D, Casteel CL, Seymour GB, Blanco-Ulate B. Host susceptibility factors render ripe tomato fruit vulnerable to fungal disease despite active immune responses. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2696-2709. [PMID: 33462583 PMCID: PMC8006553 DOI: 10.1093/jxb/eraa601] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/19/2020] [Indexed: 05/03/2023]
Abstract
The increased susceptibility of ripe fruit to fungal pathogens poses a substantial threat to crop production and marketability. Here, we coupled transcriptomic analyses with mutant studies to uncover critical processes associated with defense and susceptibility in tomato (Solanum lycopersicum) fruit. Using unripe and ripe fruit inoculated with three fungal pathogens, we identified common pathogen responses reliant on chitinases, WRKY transcription factors, and reactive oxygen species detoxification. We established that the magnitude and diversity of defense responses do not significantly impact the interaction outcome, as susceptible ripe fruit mounted a strong immune response to pathogen infection. Then, to distinguish features of ripening that may be responsible for susceptibility, we utilized non-ripening tomato mutants that displayed different susceptibility patterns to fungal infection. Based on transcriptional and hormone profiling, susceptible tomato genotypes had losses in the maintenance of cellular redox homeostasis, while jasmonic acid accumulation and signaling coincided with defense activation in resistant fruit. We identified and validated a susceptibility factor, pectate lyase (PL). CRISPR-based knockouts of PL, but not polygalacturonase (PG2a), reduced susceptibility of ripe fruit by >50%. This study suggests that targeting specific genes that promote susceptibility is a viable strategy to improve the resistance of tomato fruit against fungal disease.
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Affiliation(s)
- Christian J Silva
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Casper van den Abeele
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | | | - Victor Papin
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
- Ecole Nationale Supérieure Agronomique de Toulouse, Toulouse, France
| | - Jaclyn A Adaskaveg
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Duoduo Wang
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- School of Biosciences, Plant and Crop Science Division, University of Nottingham, Sutton Bonington, Loughborough, UK
| | - Clare L Casteel
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Graham B Seymour
- School of Biosciences, Plant and Crop Science Division, University of Nottingham, Sutton Bonington, Loughborough, UK
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85
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Cui Y, Zhai Y, Flaishman M, Li J, Chen S, Zheng C, Ma H. Ethephon induces coordinated ripening acceleration and divergent coloration responses in fig (Ficus carica L.) flowers and receptacles. PLANT MOLECULAR BIOLOGY 2021; 105:347-364. [PMID: 33185823 DOI: 10.1007/s11103-020-01092-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/04/2020] [Indexed: 05/15/2023]
Abstract
The regulatory landscape of ethephon-accelerated fig ripening is revealed; flowers and receptacles exhibit opposite responses in anthocyanin accumulation; PG, PL and EXP are suggested key genes in fig softening. Ethephon is used to accelerate fig-fruit ripening for improvement of harvesting efficiency, but the underlying molecular mechanism is still unclear. To elucidate the detailed biological mechanism of ethylene-accelerated fig ripening, fruit in phase II (the lag phase on the double sigmoid growth curve) were treated with ethephon, and reached commercial ripeness 6 days earlier than the nontreated controls. Transcriptomes of flowers and the surrounding receptacles-which together make up the pseudocarp in fig fruit-were analyzed. There were 5189, 5818 and 2563 differentially expressed genes (DEGs) 2, 4 and 6 days after treatment (DAT) in treated compared to control fruit, screened by p-adjust < 0.05 and |log2(fold change) |≥ 2. The DEGs were significantly enriched in plant hormone metabolism and signal transduction, cell-wall modification, sugar accumulation and anthocyanin accumulation pathways. DEGs in the first three pathway categories demonstrated an overall similar expression change in flowers and receptacles, whereas DEGs in anthocyanin pigmentation revealed divergent transcript abundance. Specifically, in both flowers and receptacles, ethephon significantly upregulated 1-aminocyclopropane-1-carboxylate oxidase and downregulated most of the ethylene-response factor genes; polygalacturonase, pectate lyase and expansin were mainly upregulated; two acid beta-fructofuranosidases were upregulated. However, structural genes in the anthocyanin-synthesis pathway were mainly downregulated in female flowers 2 and 4 DAT, whereas they were upregulated in the receptacles. Our study reveals the regulatory landscape of the two tissues of fig fruit in ethylene-induced ripening; the differentially expressed pathways and genes provide valuable resources for the mining of target genes for crucial biological and commercial trait improvement.
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Affiliation(s)
- Yuanyuan Cui
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yanlei Zhai
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Moshe Flaishman
- Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Jinping Li
- Fig Research Institute of Weiyuan County, Neijiang, 642450, Sichuan, China
| | - Shangwu Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Chuanlin Zheng
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Huiqin Ma
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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86
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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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87
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Salava H, Thula S, Mohan V, Kumar R, Maghuly F. Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects. Int J Mol Sci 2021; 22:E682. [PMID: 33445555 PMCID: PMC7827871 DOI: 10.3390/ijms22020682] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.
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Affiliation(s)
- Hymavathi Salava
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Sravankumar Thula
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic;
| | - Vijee Mohan
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA;
| | - Rahul Kumar
- Plant Translational Research Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Fatemeh Maghuly
- Plant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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88
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Changwal C, Shukla T, Hussain Z, Singh N, Kar A, Singh VP, Abdin MZ, Arora A. Regulation of Postharvest Tomato Fruit Ripening by Endogenous Salicylic Acid. FRONTIERS IN PLANT SCIENCE 2021; 12:663943. [PMID: 34163503 PMCID: PMC8216237 DOI: 10.3389/fpls.2021.663943] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/06/2021] [Indexed: 05/22/2023]
Abstract
Exogenous application of salicylic acid (SA) has been known for delaying ripening in many fruit and vegetables. But the function of endogenous SA in relation to postharvest fruit performance is still unexplored. To understand the role of endogenous SA in postharvest fruit ripening of tomato, 33 tomato lines were examined for their endogenous SA content, membrane stability index (MSI), and shelf life (SL) at turning and red stages of tomato fruit ripening. Six tomato lines having contrasting shelf lives from these categories were subjected further for ethylene (ET) evolution, 1-aminocyclopropane-1-carboxylic acid synthase (ACS), 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), polygalacturonase (PG), pectin methyl esterase (PME), antioxidant assays and lipid peroxidation. It was found that high endogenous SA has a direct association with low ET evolution, which leads to the high SL of fruit. High lycopene content was also found to be correlated with high SA. Total antioxidants, PG, and PME decreased and lipid peroxidation increased from turning to red stage of tomato fruit development. Furthermore, these lines were subjected to expression analysis for SA biosynthesis enzymes viz. Solanum lycopersicum Isochorismate Synthase (SlICS) and SlPAL. Real-time PCR data revealed that high SL lines have high SlPAL4 expression and low SL lines have high SlPAL6 expression. Based on the results obtained in this study, it was concluded that endogenous SA regulates ET evolution and SL with the aid of the antioxidative defense system, and SlPAL4 and SlPAL6 genes play significant but opposite roles during fruit ripening.
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Affiliation(s)
- Chunoti Changwal
- Division of Plant Physiology, ICAR - Indian Agricultural Research Institute, New Delhi, India
- Department of Biotechnology, Faculty of Science, Center for Transgenic Plant Development, Jamia Hamdard, New Delhi, India
| | - Tushita Shukla
- Division of Plant Physiology, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Zakir Hussain
- Division of Vegetable Sciences, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Neera Singh
- Division of Agricultural Chemicals, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Abhijit Kar
- Division of Post-harvest Technology, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Virendra P. Singh
- Division of Plant Physiology, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - M. Z. Abdin
- Department of Biotechnology, Faculty of Science, Center for Transgenic Plant Development, Jamia Hamdard, New Delhi, India
| | - Ajay Arora
- Division of Plant Physiology, ICAR - Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Ajay Arora
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89
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Liu M, Zhang Z, Xu Z, Wang L, Chen C, Ren Z. Overexpression of SlMYB75 enhances resistance to Botrytis cinerea and prolongs fruit storage life in tomato. PLANT CELL REPORTS 2021; 40:43-58. [PMID: 32990799 DOI: 10.1007/s00299-020-02609-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
SlMYB75 increased the accumulation of JA and improved the scavenging of excess H2O2 to resist B. cinerea. Overexpression of SlMYB75 greatly prolongs tomato fruit storage life. Botrytis cinerea (B. cinerea) is a major threat to the production and storage life of tomato (Solanum lycopersicum) fruit around the world. SlMYB75 is an R2R3MYB transcription factor associated with the biosynthesis of anthocyanidin, but little is known about its function in the resistance of tomato to B. cinerea. In this study, we found that the overexpression of SlMYB75 regulated the accumulation of jasmonic acid (JA) and promoted the JA-mediated signaling pathway to resist B. cinerea infection. Moreover, the activities of peroxidase and superoxide dismutase, which were activated to scavenge hydrogen peroxide produced as a result of the B. cinerea infection, were enhanced in the transgenic tomato plants. Scanning electron microscopy images showed that the wax on the fruit skin surface was significantly decreased in the transgenic tomatoes compared with the wild type. However, SlMYB75 prolonged fruit storage life by both enhancing resistance to B. cinerea and directly downregulating the fruit shelf life-related gene SlFSR. Collectively, this study provides a good candidate gene for breeding high-quality tomatoes with a long storage life and high disease resistance.
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Affiliation(s)
- Mengyu Liu
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhen Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhixuan Xu
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Lina Wang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Chunhua Chen
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhonghai Ren
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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90
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Qiu D, Xu S, Wang Y, Zhou M, Hong L. Primary Cell Wall Modifying Proteins Regulate Wall Mechanics to Steer Plant Morphogenesis. FRONTIERS IN PLANT SCIENCE 2021; 12:751372. [PMID: 34868136 PMCID: PMC8635508 DOI: 10.3389/fpls.2021.751372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/27/2021] [Indexed: 05/14/2023]
Abstract
Plant morphogenesis involves multiple biochemical and physical processes inside the cell wall. With the continuous progress in biomechanics field, extensive studies have elucidated that mechanical forces may be the most direct physical signals that control the morphology of cells and organs. The extensibility of the cell wall is the main restrictive parameter of cell expansion. The control of cell wall mechanical properties largely determines plant cell morphogenesis. Here, we summarize how cell wall modifying proteins modulate the mechanical properties of cell walls and consequently influence plant morphogenesis.
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Affiliation(s)
- Dengying Qiu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Shouling Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ming Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lilan Hong
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Lilan Hong,
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91
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Shipman EN, Yu J, Zhou J, Albornoz K, Beckles DM. Can gene editing reduce postharvest waste and loss of fruit, vegetables, and ornamentals? HORTICULTURE RESEARCH 2021; 8:1. [PMID: 33384412 PMCID: PMC7775472 DOI: 10.1038/s41438-020-00428-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 05/22/2023]
Abstract
Postharvest waste and loss of horticultural crops exacerbates the agricultural problems facing humankind and will continue to do so in the next decade. Fruits and vegetables provide us with a vast spectrum of healthful nutrients, and along with ornamentals, enrich our lives with a wide array of pleasant sensory experiences. These commodities are, however, highly perishable. Approximately 33% of the produce that is harvested is never consumed since these products naturally have a short shelf-life, which leads to postharvest loss and waste. This loss, however, could be reduced by breeding new crops that retain desirable traits and accrue less damage over the course of long supply chains. New gene-editing tools promise the rapid and inexpensive production of new varieties of crops with enhanced traits more easily than was previously possible. Our aim in this review is to critically evaluate gene editing as a tool to modify the biological pathways that determine fruit, vegetable, and ornamental quality, especially after storage. We provide brief and accessible overviews of both the CRISPR-Cas9 method and the produce supply chain. Next, we survey the literature of the last 30 years, to catalog genes that control or regulate quality or senescence traits that are "ripe" for gene editing. Finally, we discuss barriers to implementing gene editing for postharvest, from the limitations of experimental methods to international policy. We conclude that in spite of the hurdles that remain, gene editing of produce and ornamentals will likely have a measurable impact on reducing postharvest loss and waste in the next 5-10 years.
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Affiliation(s)
- Emma N Shipman
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA.
| | - Jingwei Yu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Jiaqi Zhou
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Karin Albornoz
- Departamento de Produccion Vegetal, Universidad de Concepcion, Region del BioBio, Concepcion, Chile.
| | - Diane M Beckles
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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Abstract
This article comments on:
Paniagua C, Ric-Varas P, Garcia-Gago JA, López-Casado G, Blanco-Portales R, Muñoz-Blanco J, Schückel J, Knox JP, Matas AJ, Quesada MA, Posé S, Mercado JA. 2020. Elucidating the role of polygalacturonase genes in strawberry fruit softening. Journal of Experimental Botany 71, 7103–7117.
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Affiliation(s)
- David A Brummell
- The New Zealand Institute for Plant and Food Research Limited, Private Bag, Palmerston North, New Zealand
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93
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Yan F, Gao Y, Pang X, Xu X, Zhu N, Chan H, Hu G, Wu M, Yuan Y, Li H, Zhong S, Hada W, Deng W, Li Z. BEL1-LIKE HOMEODOMAIN4 regulates chlorophyll accumulation, chloroplast development, and cell wall metabolism in tomato fruit. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5549-5561. [PMID: 32492701 DOI: 10.1093/jxb/eraa272] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 05/29/2020] [Indexed: 05/21/2023]
Abstract
Tomato (Solanum lycopersicum) is a model plant for studying fruit development and ripening. In this study, we found that down-regulation of a tomato bell-like homeodomain 4 (SlBL4) resulted in a slightly darker-green fruit phenotype and increased accumulation of starch, fructose, and glucose. Analysis of chlorophyll content and TEM observations was consistent with these phenotypes, indicating that SlBL4 was involved in chlorophyll accumulation and chloroplast formation. Ripened fruit of SlBL4-RNAi plants had noticeably decreased firmness, larger intercellular spaces, and thinner cell walls than the wild-type. RNA-seq identified differentially expressed genes involved in chlorophyll metabolism, chloroplast development, cell wall metabolism, and carotenoid metabolism. ChIP-seq identified (G/A) GCCCA (A/T/C) and (C/A/T) (C/A/T) AAAAA (G/A/T) (G/A) motifs. SlBL4 directly inhibited the expression of protoporphyrinogen oxidase (SlPPO), magnesium chelatase H subunit (SlCHLD), pectinesterase (SlPE), protochlorophyllide reductase (SlPOR), chlorophyll a/b binding protein 3B (SlCAB-3B), and homeobox protein knotted 2 (TKN2). In contrast, it positively regulated the expression of squamosa promoter binding protein-like colorless non-ripening (LeSPL-CNR). Our results indicate that SlBL4 is involved in chlorophyll accumulation, chloroplast development, cell wall metabolism, and the accumulation of carotenoids during tomato fruit ripening, and provide new insights for the transcriptional regulation mechanism of BELL-mediated fruit growth and ripening.
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Affiliation(s)
- Fang Yan
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, School of Life Science, Inner Mongolia University, Hohhot, China
| | - Yushuo Gao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaoqin Pang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Xin Xu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Ning Zhu
- The State Key Laboratory of Agrobiotechnology, The School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Helen Chan
- University of California, Davis, CA, USA
| | - Guojian Hu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Mengbo Wu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Yujin Yuan
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Honghai Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Silin Zhong
- The State Key Laboratory of Agrobiotechnology, The School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wuriyanghan Hada
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, School of Life Science, Inner Mongolia University, Hohhot, China
| | - Wei Deng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
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94
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Zhang WW, Zhao SQ, Zhang LC, Xing Y, Jia WS. Changes in the cell wall during fruit development and ripening in Fragaria vesca. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:54-65. [PMID: 32526611 DOI: 10.1016/j.plaphy.2020.05.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 05/27/2023]
Abstract
Although fruit expansion during ripening has been extensively studied, the structural and metabolic mechanisms remain largely unknown. Here, we report the critical roles of cell separation and cell wall metabolism in the coordinated regulation of fruit expansion in Fragaria vesca. Anatomical observations indicated that a syndrome of cell separation occurred from the very earliest stage of fruit set. Cell separation led to an increase in apoplastic space, and the time course of this increase coincided with the period of fruit development and ripening. Moreover, massive cellulose disassembly occurred when cells were fully separated, which coincided with the expansion of cell and fruit volume. Consistent with the anatomical observations, both histochemistry and composition analysis indicated correlations between cell separation and the cell wall metabolism. These observations suggest that cell separation, cell elongation and cell wall disassembly occur simultaneously during fruit ripening in Fragaria vesca.
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Affiliation(s)
- Wei-Wei Zhang
- College of Horticulture, China Agricultural University, Beijing, China; Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, College of Plant Science and Technology, Beijing University of Agriculture, China
| | - Shuai-Qi Zhao
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, College of Plant Science and Technology, Beijing University of Agriculture, China
| | - Ling-Chao Zhang
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, College of Plant Science and Technology, Beijing University of Agriculture, China
| | - Yu Xing
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, College of Plant Science and Technology, Beijing University of Agriculture, China.
| | - Wen-Suo Jia
- College of Horticulture, China Agricultural University, Beijing, China.
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Niu J, Shi Y, Huang K, Zhong Y, Chen J, Sun Z, Luan M, Chen J. Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:149. [PMID: 32843898 PMCID: PMC7441727 DOI: 10.1186/s13068-020-01789-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 08/16/2020] [Indexed: 06/07/2023]
Abstract
BACKGROUND Akebia trifoliata (Thunb.) Koidz may have applications as a new potential source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. RESULTS In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. CONCLUSIONS Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.
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Affiliation(s)
- Juan Niu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Yaliang Shi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Kunyong Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Yicheng Zhong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Jing Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Zhimin Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Jianhua Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
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97
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Yang X, Guo X, Chen G, Dong D, Liu F, Yang Y, Yang Y, Li G. Comparison of defense responses of transgenic potato lines expressing three different Rpi genes to specific Phytophthora infestans races based on transcriptome profiling. PeerJ 2020; 8:e9096. [PMID: 32411536 PMCID: PMC7207217 DOI: 10.7717/peerj.9096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Potato late blight, one of the most devastating diseases in potato, is caused by the oomycete Phytophthora infestans. Over 20 resistance genes have been cloned including R1, R3a, and R3b. The distinctions between defense response mechanisms mediated by different resistance genes are still unclear. Here we performed transcriptome profiling in three transgenic lines, R1, R3a, and R3b, and wild-type Desiree under inoculation with two P. infestans isolates, 89148 (race 0) and CN152 (super race), using RNA-seq. Compared with wild type, specific differentially expressed genes (DEGs) were identified in the three transgenic lines. The highest number of DEGs occurred in transgenic R3b, with 779 DEGs in response to isolate 89148 and 864 DEGs in response to infection by CN152, followed by transgenic R1 lines with 408 DEGs for isolate 89148 and 267 DEGs for CN152. Based on gene ontology, the most common GO terms (15 for 89148 and 20 for CN152) were enriched in transgenic R3a and R3b lines. This indicates that the defense pathways mediated by R3a and R3b are more similar than those mediated by R1. Further separate GO analysis of up- or down-regulated DEGs showed that the down-regulated DEGs mainly functioned in mediating the resistance of potato to P. infestans 89148 by response to stress biological process and to CN152 by oxidation reduction biological process. KEGG pathways of DNA replication, plant-pathogen interaction and pentose and glucuronate interconversions are unique for transgenic R1, R3a, and R3b lines in incompatible interactions. Quantitative real-time PCR experimental validation confirmed the induced expression of DEGs in the late blight resistance signaling pathway. Our results will lay a solid foundation for further understanding the mechanisms of plant-pathogen interactions, and provide a theoretical reference for durable resistance in potato.
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Affiliation(s)
- Xiaohui Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Xiao Guo
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Guangxia Chen
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Daofeng Dong
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Fang Liu
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yuanjun Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yu Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing, China
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98
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Sun H, Hao P, Gu L, Cheng S, Wang H, Wu A, Ma L, Wei H, Yu S. Pectate lyase-like Gene GhPEL76 regulates organ elongation in Arabidopsis and fiber elongation in cotton. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110395. [PMID: 32081256 DOI: 10.1016/j.plantsci.2019.110395] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/02/2019] [Accepted: 12/27/2019] [Indexed: 05/08/2023]
Abstract
Pectate lyases (PELs) play important roles in plant growth and development, mainly by degrading the pectin in primary cell walls. However, the role of PELs in cotton fiber elongation, which also involves changes in cellular structure and components, is poorly understood. Therefore, we aimed to isolate and characterize GhPEL76, as we suspected it to contribute to the regulation of fiber elongation. Expression analysis (qRT-PCR) revealed that GhPEL76 is predominately expressed in cotton fiber, with significantly different expression levels in long- and short-fiber cultivars, and that GhPEL76 expression is responsive to gibberellic acid and indoleacetic acid treatment. Furthermore, GhPEL76 promoter-driven β-glucuronidase activity was detected in the roots, hypocotyls, and leaves of transgenic Arabidopsis plants, and the overexpression of GhPEL76 in transgenic Arabidopsis promoted the elongation of several organs, including petioles, hypocotyls, primary roots, and trichomes. Additionally, the virus-induced silencing of GhPEL76 in cotton reduced fiber length, and both yeast one-hybrid and transient dual-luciferase assays suggested that GhbHLH13, a bHLH transcription factor that is up-regulated during fiber elongation, activates GhPEL76 expression by binding to the G-box of the GhPEL76 promoter region. Therefore, these results suggest GhPEL76 positively regulates fiber elongation and provide a basis for future studies of cotton fiber development.
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Affiliation(s)
- Huiru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Life Science, Yan'an University, Yan'an, 716000, China; College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Life Science, Yan'an University, Yan'an, 716000, China.
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Zhang H, Li X, Yu H, Zhang Y, Li M, Wang H, Wang D, Wang H, Fu Q, Liu M, Ji C, Ma L, Tang J, Li S, Miao J, Zheng H, Yi H. A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement. iScience 2019; 22:16-27. [PMID: 31739171 PMCID: PMC6864349 DOI: 10.1016/j.isci.2019.10.049] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/23/2019] [Accepted: 10/24/2019] [Indexed: 01/28/2023] Open
Abstract
Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding. Provides a high-quality assembly for melon genome Explains a considerable proportion of epidermis thickness Melons in China are introduced from different routes Haplotypes of alleles associated with agronomic traits enable efficient breeding
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Affiliation(s)
- Hong Zhang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Yongbing Zhang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Meihua Li
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Haojie Wang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Dengming Wang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Huaisong Wang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiushi Fu
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Changmian Ji
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Liming Ma
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Juan Tang
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Song Li
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Jianshun Miao
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101200, China.
| | - Hongping Yi
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China.
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Pontiggia D, Spinelli F, Fabbri C, Licursi V, Negri R, De Lorenzo G, Mattei B. Changes in the microsomal proteome of tomato fruit during ripening. Sci Rep 2019; 9:14350. [PMID: 31586085 PMCID: PMC6778153 DOI: 10.1038/s41598-019-50575-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/23/2019] [Indexed: 11/09/2022] Open
Abstract
The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress.
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Affiliation(s)
- Daniela Pontiggia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Spinelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Claudia Fabbri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy
| | - Giulia De Lorenzo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy. .,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy.
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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