151
|
Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation. Proc Natl Acad Sci U S A 2016; 113:12580-12585. [PMID: 27791156 DOI: 10.1073/pnas.1613910113] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology.
Collapse
|
152
|
Yuan XY, Wang RH, Zhao XD, Luo YB, Fu DQ. Role of the Tomato Non-Ripening Mutation in Regulating Fruit Quality Elucidated Using iTRAQ Protein Profile Analysis. PLoS One 2016; 11:e0164335. [PMID: 27732677 PMCID: PMC5061430 DOI: 10.1371/journal.pone.0164335] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/25/2016] [Indexed: 01/08/2023] Open
Abstract
Natural mutants of the Non-ripening (Nor) gene repress the normal ripening of tomato fruit. The molecular mechanism of fruit ripening regulation by the Nor gene is unclear. To elucidate how the Nor gene can affect ripening and fruit quality at the protein level, we used the fruits of Nor mutants and wild-type Ailsa Craig (AC) to perform iTRAQ (isobaric tags for relative and absolute quantitation) analysis. The Nor mutation altered tomato fruit ripening and affected quality in various respects, including ethylene biosynthesis by down-regulating the abundance of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), pigment biosynthesis by repressing phytoene synthase 1 (PSY1), ζ-carotene isomerase (Z-ISO), chalcone synthase 1 (CHS1) and other proteins, enhancing fruit firmness by increasing the abundance of cellulose synthase protein, while reducing those of polygalacturonase 2 (PG2) and pectate lyase (PL), altering biosynthesis of nutrients such as carbohydrates, amino acids, and anthocyanins. Conversely, Nor mutation also enhanced the fruit’s resistance to some pathogens by up-regulating the expression of several genes associated with stress and defense. Therefore, the Nor gene is involved in the regulation of fruit ripening and quality. It is useful in the future as a means to improve fruit quality in tomato.
Collapse
Affiliation(s)
- Xin-Yu Yuan
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing 100083, PR China
| | - Rui-Heng Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing 100083, PR China
| | - Xiao-Dan Zhao
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, People’s Republic of China
| | - Yun-Bo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing 100083, PR China
| | - Da-Qi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing 100083, PR China
- * E-mail:
| |
Collapse
|
153
|
Sun Q, Zhang N, Wang J, Cao Y, Li X, Zhang H, Zhang L, Tan DX, Guo YD. A label-free differential proteomics analysis reveals the effect of melatonin on promoting fruit ripening and anthocyanin accumulation upon postharvest in tomato. J Pineal Res 2016; 61:138-53. [PMID: 26820691 DOI: 10.1111/jpi.12315] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 01/25/2016] [Indexed: 12/11/2022]
Abstract
To better understand the function of melatonin in tomato fruit ripening and quality improvement, a label-free quantitation method was used to investigate the proteins that differ between the control (CK) and 50 μm melatonin treatment (M50) fruits. Proteomics data identified 241 proteins that were significantly influenced by melatonin. These proteins were involved in several ripening-related pathways, including cell wall metabolism, oxidative phosphorylation, carbohydrate, and fatty acid metabolism. Moreover, the application of exogenous melatonin increased eight proteins that are related to anthocyanin accumulation during fruit ripening. Additionally, the affected protein levels correlated with the corresponding gene transcript levels. Further, the total anthocyanin content from M50 increased by 52%, 48%, and 50% at 5, 8, and 13 DAT (day after melatonin treatment), respectively. The melatonin-mediated promotion of fruit ripening and quality might be due to the altered proteins involved in processes associated with ripening. In this work, we indicated that a senescence-related protein was downregulated in the M50 fruit, while a cell apoptosis inhibitor (API5) protein was upregulated. In addition, peroxidases (POD9, POD12, peroxidase p7-like) and catalase (CAT3) significantly increased in the M50 fruits. Based on the previous studies and our data, we inferred that melatonin might be positively related to fruit ripening but negatively related to fruit senescence. This research provides insights into the physiological and molecular mechanisms underlying melatonin-mediated fruit ripening as well as the anthocyanin formation process in tomato fruit at the protein concentration level, and we reveal possible candidates for regulation of anthocyanin formation during fruit ripening.
Collapse
Affiliation(s)
- Qianqian Sun
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Na Zhang
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Jinfang Wang
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Yunyun Cao
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Xingsheng Li
- Shandong Huasheng Agriculture Co. Ltd, Shandong, China
| | - Haijun Zhang
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Lei Zhang
- College of Horticultural Science, China Agricultural University, Beijing, China
| | - Dun-Xian Tan
- Department of Cellular and Structural Biology, The University of Texas Health Science Center, San Antonio, TX, USA
| | - Yang-Dong Guo
- College of Horticultural Science, China Agricultural University, Beijing, China
| |
Collapse
|
154
|
Cheng F, Cheng Z, Meng H, Tang X. The Garlic Allelochemical Diallyl Disulfide Affects Tomato Root Growth by Influencing Cell Division, Phytohormone Balance and Expansin Gene Expression. FRONTIERS IN PLANT SCIENCE 2016; 7:1199. [PMID: 27555862 PMCID: PMC4977361 DOI: 10.3389/fpls.2016.01199] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 07/27/2016] [Indexed: 05/27/2023]
Abstract
Diallyl disulfide (DADS) is a volatile organosulfur compound derived from garlic (Allium sativum L.), and it is known as an allelochemical responsible for the strong allelopathic potential of garlic. The anticancer properties of DADS have been studied in experimental animals and various types of cancer cells, but to date, little is known about its mode of action as an allelochemical at the cytological level. The current research presents further studies on the effects of DADS on tomato (Solanum lycopersicum L.) seed germination, root growth, mitotic index, and cell size in root meristem, as well as the phytohormone levels and expression profile of auxin biosynthesis genes (FZYs), auxin transport genes (SlPINs), and expansin genes (EXPs) in tomato root. The results showed a biphasic, dose-dependent effect on tomato seed germination and root growth under different DADS concentrations. Lower concentrations (0.01-0.62 mM) of DADS significantly promoted root growth, whereas higher levels (6.20-20.67 mM) showed inhibitory effects. Cytological observations showed that the cell length of root meristem was increased and that the mitotic activity of meristematic cells in seedling root tips was enhanced at lower concentrations of DADS. In contrast, DADS at higher concentrations inhibited root growth by affecting both the length and division activity of meristematic cells. However, the cell width of the root meristem was not affected. Additionally, DADS increased the IAA and ZR contents of seedling roots in a dose-dependent manner. The influence on IAA content may be mediated by the up-regulation of FZYs and PINs. Further investigation into the underlying mechanism revealed that the expression levels of tomato EXPs were significantly affected by DADS. The expression levels of EXPB2 and beta-expansin precursor were increased after 3 d, and those of EXP1, EXPB3 and EXLB1 were increased after 5 d of DADS treatment (0.41 mM). This result suggests that tomato root growth may be regulated by multiple expansin genes at different developmental stages. Therefore, we conclude that the effects of DADS on the root growth of tomato seedlings are likely caused by changes associated with cell division, phytohormones, and the expression levels of expansin genes.
Collapse
Affiliation(s)
| | - Zhihui Cheng
- Department of Vegetable Science, College of Horticulture, Northwest A&F UniversityYangling, China
| | | | | |
Collapse
|
155
|
Petit J, Bres C, Mauxion JP, Tai FWJ, Martin LBB, Fich EA, Joubès J, Rose JKC, Domergue F, Rothan C. The Glycerol-3-Phosphate Acyltransferase GPAT6 from Tomato Plays a Central Role in Fruit Cutin Biosynthesis. PLANT PHYSIOLOGY 2016; 171:894-913. [PMID: 27208295 PMCID: PMC4902622 DOI: 10.1104/pp.16.00409] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 04/18/2016] [Indexed: 05/18/2023]
Abstract
The thick cuticle covering and embedding the epidermal cells of tomato (Solanum lycopersicum) fruit acts not only as a protective barrier against pathogens and water loss but also influences quality traits such as brightness and postharvest shelf-life. In a recent study, we screened a mutant collection of the miniature tomato cultivar Micro-Tom and isolated several glossy fruit mutants in which the abundance of cutin, the polyester component of the cuticle, was strongly reduced. We employed a newly developed mapping-by-sequencing strategy to identify the causal mutation underlying the cutin deficiency in a mutant thereafter named gpat6-a (for glycerol-3-phosphate acyltransferase6). To this end, a backcross population (BC1F2) segregating for the glossy trait was phenotyped. Individuals displaying either a wild-type or a glossy fruit trait were then pooled into bulked populations and submitted to whole-genome sequencing prior to mutation frequency analysis. This revealed that the causal point mutation in the gpat6-a mutant introduces a charged amino acid adjacent to the active site of a GPAT6 enzyme. We further showed that this mutation completely abolished the GPAT activity of the recombinant protein. The gpat6-a mutant showed perturbed pollen formation but, unlike a gpat6 mutant of Arabidopsis (Arabidopsis thaliana), was not male sterile. The most striking phenotype was observed in the mutant fruit, where cuticle thickness, composition, and properties were altered. RNA sequencing analysis highlighted the main processes and pathways that were affected by the mutation at the transcriptional level, which included those associated with lipid, secondary metabolite, and cell wall biosynthesis.
Collapse
Affiliation(s)
- Johann Petit
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| | - Cécile Bres
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| | - Jean-Philippe Mauxion
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| | - Fabienne Wong Jun Tai
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| | - Laetitia B B Martin
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| | - Eric A Fich
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| | - Jérôme Joubès
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| | - Jocelyn K C Rose
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| | - Frédéric Domergue
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| | - Christophe Rothan
- Unité Mixte de Recherche 1332 BFP, Institut National de la Recherche Agronomique, Université de Bordeaux, F-33140 Villenave d'Ornon, France (J.P., C.B., J.-P.M., F.W.J.T., C.R.);Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (L.B.B.M., E.A.F., J.K.C.R.);Laboratoire de Biogénèse Membranaire, Université de Bordeaux, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.); andLaboratoire de Biogénèse Membranaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5200, F-33000 Bordeaux, France (J.J., F.D.)
| |
Collapse
|
156
|
Botton A, Rasori A, Ziliotto F, Moing A, Maucourt M, Bernillon S, Deborde C, Petterle A, Varotto S, Bonghi C. The peach HECATE3-like gene FLESHY plays a double role during fruit development. PLANT MOLECULAR BIOLOGY 2016; 91:97-114. [PMID: 26846510 DOI: 10.1007/s11103-016-0445-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/28/2016] [Indexed: 05/10/2023]
Abstract
Tight control of cell/tissue identity is essential for a correct and functional organ patterning, an important component of overall fruit development and eventual maturation and ripening. Despite many investigations regarding the molecular determinants of cell identity in fruits of different species, a useful model able to depict the regulatory networks governing this relevant part of fruit development is still missing. Here we described the peach fruit as a system to link the phenotype of a slow ripening (SR) selection to an altered transcriptional regulation of genes involved in determination of mesocarp cell identity providing insight toward molecular regulation of fruit tissue formation. Morpho-anatomical observations and metabolomics analyses performed during fruit development on the reference cultivar Fantasia, compared to SR, revealed that the mesocarp of SR maintained typical immaturity traits (e.g. small cell size, high amino acid contents and reduced sucrose) throughout development, along with a strong alteration of phenylpropanoid contents, resulting in accumulation of phenylalanine and lignin. These findings suggest that the SR mesocarp is phenotypically similar to a lignifying endocarp. To test this hypothesis, the expression of genes putatively involved in determination of drupe tissues identity was assessed. Among these, the peach HEC3-like gene FLESHY showed a strongly altered expression profile consistent with pit hardening and fruit ripening, generated at a post-transcriptional level. A double function for FLESHY in channelling the phenylpropanoid pathway to either lignin or flavour/aroma is suggested, along with its possible role in triggering auxin-ethylene cross talk at the start of ripening.
Collapse
Affiliation(s)
- Alessandro Botton
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell'Università, 16, Agripolis, 35020, Legnaro, Italy
| | - Angela Rasori
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell'Università, 16, Agripolis, 35020, Legnaro, Italy
| | - Fiorenza Ziliotto
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell'Università, 16, Agripolis, 35020, Legnaro, Italy
| | - Annick Moing
- UMR1332 Biologie du Fruit et Pathologie, INRA, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
| | - Mickaël Maucourt
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
- UMR1332 Biologie du Fruit et Pathologie, University of Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
| | - Stéphane Bernillon
- UMR1332 Biologie du Fruit et Pathologie, INRA, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
| | - Catherine Deborde
- UMR1332 Biologie du Fruit et Pathologie, INRA, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
| | - Anna Petterle
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell'Università, 16, Agripolis, 35020, Legnaro, Italy
| | - Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell'Università, 16, Agripolis, 35020, Legnaro, Italy
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell'Università, 16, Agripolis, 35020, Legnaro, Italy.
| |
Collapse
|
157
|
Elitzur T, Yakir E, Quansah L, Zhangjun F, Vrebalov J, Khayat E, Giovannoni JJ, Friedman H. Banana MaMADS Transcription Factors Are Necessary for Fruit Ripening and Molecular Tools to Promote Shelf-Life and Food Security. PLANT PHYSIOLOGY 2016; 171:380-91. [PMID: 26956665 PMCID: PMC4854685 DOI: 10.1104/pp.15.01866] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/28/2016] [Indexed: 05/18/2023]
Abstract
Genetic solutions to postharvest crop loss can reduce cost and energy inputs while increasing food security, especially for banana (Musa acuminata), which is a significant component of worldwide food commerce. We have functionally characterized two banana E class (SEPALLATA3 [SEP3]) MADS box genes, MaMADS1 and MaMADS2, homologous to the tomato (Solanum lycopersicum) RIN-MADS ripening gene. Transgenic banana plants repressing either gene (via antisense or RNA interference [RNAi]) were created and exhibited specific ripening delay and extended shelf-life phenotypes, including delayed color development and softening. The delay in fruit ripening is associated with a delay in climacteric respiration and reduced synthesis of the ripening hormone ethylene; in the most severe repressed lines, no ethylene was produced and ripening was most delayed. Unlike tomato rin mutants, banana fruits of all transgenic repression lines responded to exogenous ethylene by ripening normally, likely due to incomplete transgene repression and/or compensation by other MADS box genes. Our results show that, although MADS box ripening gene necessity is conserved across diverse taxa (monocots to dicots), unlike tomato, banana ripening requires at least two necessary members of the SEPALLATA MADS box gene group, and either can serve as a target for ripening control. The utility of such genes as tools for ripening control is especially relevant in important parthenocarpic crops such as the vegetatively propagated and widely consumed Cavendish banana, where breeding options for trait improvement are severely limited.
Collapse
Affiliation(s)
- Tomer Elitzur
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Esther Yakir
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Lydia Quansah
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Fei Zhangjun
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Julia Vrebalov
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Eli Khayat
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - James J Giovannoni
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| | - Haya Friedman
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel 7510001 (T.E., E.Y., L.Q., H.F.);Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center, Cornell University, Ithaca, New York 14853-2901 (F.Z., J.V., J.J.G.); andRahan Meristem, Ltd., Rosh Hanikra, Western Galilee, Israel 22825 (E.K.)
| |
Collapse
|
158
|
Mou W, Li D, Bu J, Jiang Y, Khan ZU, Luo Z, Mao L, Ying T. Comprehensive Analysis of ABA Effects on Ethylene Biosynthesis and Signaling during Tomato Fruit Ripening. PLoS One 2016; 11:e0154072. [PMID: 27100326 PMCID: PMC4839774 DOI: 10.1371/journal.pone.0154072] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/10/2016] [Indexed: 12/16/2022] Open
Abstract
ABA has been widely acknowledged to regulate ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism underlying the interaction between these two hormones are largely unexplored. In the present study, exogenous ABA treatment obviously promoted fruit ripening as well as ethylene emission, whereas NDGA (Nordihydroguaiaretic acid, an inhibitor of ABA biosynthesis) application showed the opposite biological effects. Combined RNA-seq with time-course RT-PCR analysis, our study not only helped to illustrate how ABA regulated itself at the transcription level, but also revealed that ABA can facilitate ethylene production and response probably by regulating some crucial genes such as LeACS4, LeACO1, GR and LeETR6. In addition, investigation on the fruits treated with 1-MCP immediately after ABA exposure revealed that ethylene might be essential for the induction of ABA biosynthesis and signaling at the onset of fruit ripening. Furthermore, some specific transcription factors (TFs) known as regulators of ethylene synthesis and sensibility (e.g. MADS-RIN, TAGL1, CNR and NOR) were also observed to be ABA responsive, which implied that ABA influenced ethylene action possibly through the regulation of these TFs expression. Our comprehensive physiological and molecular-level analysis shed light on the mechanism of cross-talk between ABA and ethylene during the process of tomato fruit ripening.
Collapse
Affiliation(s)
- Wangshu Mou
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang R & D Center for Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Dongdong Li
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang R & D Center for Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Jianwen Bu
- Department of Food Science and Engineering, Shandong Agriculture and Engineering University, Ji’nan 250100, People’s Republic of China
| | - Yuanyuan Jiang
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang R & D Center for Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Zia Ullah Khan
- Department of Agriculture, Abdul Wali Khan University, Mardan 23200, KPK., Pakistan
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang R & D Center for Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang R & D Center for Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Tiejin Ying
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang R & D Center for Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People’s Republic of China
- * E-mail:
| |
Collapse
|
159
|
Meng C, Yang D, Ma X, Zhao W, Liang X, Ma N, Meng Q. Suppression of tomato SlNAC1 transcription factor delays fruit ripening. JOURNAL OF PLANT PHYSIOLOGY 2016; 193:88-96. [PMID: 26962710 DOI: 10.1016/j.jplph.2016.01.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/15/2016] [Accepted: 01/22/2016] [Indexed: 05/02/2023]
Abstract
Fruit ripening is a complex process involving many physiological and biochemical changes, including those for ethylene, carotenoid, and cell wall metabolism. Tomato (Solanum lycopersicum) serves as a research model for fruit development and ripening because it possesses numerous favorable genetic features. In this study, SlNAC1 was cloned. An antisense (AS) vector was constructed and transferred to tomato to further explore the function of SlNAC1. The results showed that AS fruits exhibited delayed ripening and a deeper red appearance when these fruits were fully ripened. Fully ripened AS fruits also produced higher total carotenoid and lycopene contents than those of the wild-type (WT) line. Ethylene production of AS fruits was delayed but occurred to a higher extent than that of WT fruits. The softening of AS fruits was slower than that of WT fruits. Endogenous abscisic acid (ABA) level in AS-4 fruits was lower than that in WT fruits. Exogenous ABA accelerated the softening of AS fruits. Furthermore, AS fruits demonstrated up-regulated expression of genes related to lycopene and ethylene biosynthesis but down-regulated expression of genes related to cell wall metabolism and ABA synthesis. Therefore, SlNAC1 is likely implicated in fruit ripening.
Collapse
Affiliation(s)
- Chen Meng
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, PR China
| | - Dongyue Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street, Tai'an, Shandong 271018, PR China
| | - Xiaocui Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street, Tai'an, Shandong 271018, PR China
| | - Weiyang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street, Tai'an, Shandong 271018, PR China
| | - Xiaoqing Liang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street, Tai'an, Shandong 271018, PR China
| | - Nana Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street, Tai'an, Shandong 271018, PR China.
| | - Qingwei Meng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street, Tai'an, Shandong 271018, PR China
| |
Collapse
|
160
|
Wang X, Ai G, Zhang C, Cui L, Wang J, Li H, Zhang J, Ye Z. Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato. THE NEW PHYTOLOGIST 2016; 209:1442-55. [PMID: 26494192 DOI: 10.1111/nph.13718] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/20/2015] [Indexed: 05/20/2023]
Abstract
Long noncoding RNAs (lncRNAs) regulate gene expression and biological processes. With the development of high-throughput RNA sequencing technology, lncRNAs have been extensively studied in recent years. Nevertheless, the expression and evolution of lncRNAs in plants remain poorly understood. Here, we identified 413 and 709 multi-exon noncoding transcripts from 353 and 595 loci of the cultivar tomato Heinz1706 and its wild relative LA1589, respectively. Systematic comparison of the sequence and expression of lncRNAs showed that they are poorly conserved in Solanaceae, with only < 0.4% lncRNAs present in all sequenced genomes of tomato and potato. Sequence analysis of Lycopersicon-specific lncRNA loci in Solanum lycopersicum and S. pennellii showed that the origins of these molecules are associated with transposable elements (TEs). LncRNA-314, a fruit-specific lncRNA expressed in S. lycopersicum and S. pimpinellifolium, but not in S. pennellii, originated through two evolutionary events: speciation of S. pennellii resulted in insertion of a long terminal repeat (LTR) retrotransposon into chromosome 10 and contributed to most of the transcribed region of lncRNA-314; and a large deletion in Lycopersicon generated the promoter region and part of the transcribed region of lncRNA-314. These results provide novel insights into the evolution of lncRNAs in plants.
Collapse
Affiliation(s)
- Xin Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Guo Ai
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chunli Zhang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Long Cui
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiafa Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| |
Collapse
|
161
|
Kumar V, Irfan M, Ghosh S, Chakraborty N, Chakraborty S, Datta A. Fruit ripening mutants reveal cell metabolism and redox state during ripening. PROTOPLASMA 2016; 253:581-94. [PMID: 26008650 DOI: 10.1007/s00709-015-0836-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 05/17/2015] [Indexed: 05/18/2023]
Abstract
Ripening which leads to fruit senescence is an inimitable process characterized by vivid changes in color, texture, flavor, and aroma of the fleshy fruits. Our understanding of the mechanisms underlying the regulation of fruit ripening and senescence is far from complete. Molecular and biochemical studies on tomato (Solanum lycopersicum) ripening mutants such as ripening inhibitor (rin), nonripening (nor), and never ripe (Nr) have been useful in our understanding of fruit development and ripening. The MADS-box transcription factor RIN, a global regulator of fruit ripening, is vital for the broad aspects of ripening, in both ethylene-dependent and independent manners. Here, we have carried out microarray analysis to study the expression profiles of tomato genes during ripening of wild type and rin mutant fruits. Analysis of the differentially expressed genes revealed the role of RIN in regulation of several molecular and biochemical events during fruit ripening including fruit specialized metabolism and cellular redox state. The role of reactive oxygen species (ROS) during fruit ripening and senescence was further examined by determining the changes in ROS level during ripening of wild type and mutant fruits and by analyzing expression profiles of the genes involved in maintaining cellular redox state. Taken together, our findings suggest an important role of ROS during fruit ripening and senescence, and therefore, modulation of ROS level during ripening could be useful in achieving desired fruit quality.
Collapse
Affiliation(s)
- Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mohammad Irfan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sumit Ghosh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
162
|
Sagawa JM, Stanley LE, LaFountain AM, Frank HA, Liu C, Yuan YW. An R2R3-MYB transcription factor regulates carotenoid pigmentation in Mimulus lewisii flowers. THE NEW PHYTOLOGIST 2016; 209:1049-57. [PMID: 26377817 DOI: 10.1111/nph.13647] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/14/2015] [Indexed: 05/19/2023]
Abstract
Carotenoids are yellow, orange, and red pigments that contribute to the beautiful colors and nutritive value of many flowers and fruits. The structural genes in the highly conserved carotenoid biosynthetic pathway have been well characterized in multiple plant systems, but little is known about the transcription factors that control the expression of these structural genes. By analyzing a chemically induced mutant of Mimulus lewisii through bulk segregant analysis and transgenic experiments, we have identified an R2R3-MYB, Reduced Carotenoid Pigmentation 1 (RCP1), as the first transcription factor that positively regulates carotenoid biosynthesis during flower development. Loss-of-function mutations in RCP1 lead to down-regulation of all carotenoid biosynthetic genes and reduced carotenoid content in M. lewisii flowers, a phenotype recapitulated by RNA interference in the wild-type background. Overexpression of this gene in the rcp1 mutant background restores carotenoid production and, unexpectedly, results in simultaneous decrease of anthocyanin production in some transgenic lines by down-regulating the expression of an activator of anthocyanin biosynthesis. Identification of transcriptional regulators of carotenoid biosynthesis provides the 'toolbox' genes for understanding the molecular basis of flower color diversification in nature and for potential enhancement of carotenoid production in crop plants via genetic engineering.
Collapse
Affiliation(s)
- Janelle M Sagawa
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Lauren E Stanley
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Amy M LaFountain
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | - Harry A Frank
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | - Chang Liu
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| |
Collapse
|
163
|
Arhondakis S, Bita CE, Perrakis A, Manioudaki ME, Krokida A, Kaloudas D, Kalaitzis P. In silico Transcriptional Regulatory Networks Involved in Tomato Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2016; 7:1234. [PMID: 27625653 PMCID: PMC5003879 DOI: 10.3389/fpls.2016.01234] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 08/03/2016] [Indexed: 05/18/2023]
Abstract
Tomato fruit ripening is a complex developmental programme partly mediated by transcriptional regulatory networks. Several transcription factors (TFs) which are members of gene families such as MADS-box and ERF were shown to play a significant role in ripening through interconnections into an intricate network. The accumulation of large datasets of expression profiles corresponding to different stages of tomato fruit ripening and the availability of bioinformatics tools for their analysis provide an opportunity to identify TFs which might regulate gene clusters with similar co-expression patterns. We identified two TFs, a SlWRKY22-like and a SlER24 transcriptional activator which were shown to regulate modules by using the LeMoNe algorithm for the analysis of our microarray datasets representing four stages of fruit ripening, breaker, turning, pink and red ripe. The WRKY22-like module comprised a subgroup of six various calcium sensing transcripts with similar to the TF expression patterns according to real time PCR validation. A promoter motif search identified a cis acting element, the W-box, recognized by WRKY TFs that was present in the promoter region of all six calcium sensing genes. Moreover, publicly available microarray datasets of similar ripening stages were also analyzed with LeMoNe resulting in TFs such as SlERF.E1, SlERF.C1, SlERF.B2, SLERF.A2, SlWRKY24, SLWRKY37, and MADS-box/TM29 which might also play an important role in regulation of ripening. These results suggest that the SlWRKY22-like might be involved in the coordinated regulation of expression of the six calcium sensing genes. Conclusively the LeMoNe tool might lead to the identification of putative TF targets for further physiological analysis as regulators of tomato fruit ripening.
Collapse
|
164
|
Dougherty L, Zhu Y, Xu K. Assessing the allelotypic effect of two aminocyclopropane carboxylic acid synthase-encoding genes MdACS1 and MdACS3a on fruit ethylene production and softening in Malus. HORTICULTURE RESEARCH 2016; 3:16024. [PMID: 27231553 PMCID: PMC4870385 DOI: 10.1038/hortres.2016.24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/10/2016] [Accepted: 04/11/2016] [Indexed: 05/04/2023]
Abstract
Phytohormone ethylene largely determines apple fruit shelf life and storability. Previous studies demonstrated that MdACS1 and MdACS3a, which encode 1-aminocyclopropane-1-carboxylic acid synthases (ACS), are crucial in apple fruit ethylene production. MdACS1 is well-known to be intimately involved in the climacteric ethylene burst in fruit ripening, while MdACS3a has been regarded a main regulator for ethylene production transition from system 1 (during fruit development) to system 2 (during fruit ripening). However, MdACS3a was also shown to have limited roles in initiating the ripening process lately. To better assess their roles, fruit ethylene production and softening were evaluated at five time points during a 20-day post-harvest period in 97 Malus accessions and in 34 progeny from 2 controlled crosses. Allelotyping was accomplished using an existing marker (ACS1) for MdACS1 and two markers (CAPS866 and CAPS870) developed here to specifically detect the two null alleles (ACS3a-G289V and Mdacs3a) of MdACS3a. In total, 952 Malus accessions were allelotyped with the three markers. The major findings included: The effect of MdACS1 was significant on fruit ethylene production and softening while that of MdACS3a was less detectable; allele MdACS1-2 was significantly associated with low ethylene and slow softening; under the same background of the MdACS1 allelotypes, null allele Mdacs3a (not ACS3a-G289V) could confer a significant delay of ethylene peak; alleles MdACS1-2 and Mdacs3a (excluding ACS3a-G289V) were highly enriched in M. domestica and M. hybrid when compared with those in M. sieversii. These findings are of practical implications in developing apples of low and delayed ethylene profiles by utilizing the beneficial alleles MdACS1-2 and Mdacs3a.
Collapse
Affiliation(s)
- Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
| | - Yuandi Zhu
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
- ()
| |
Collapse
|
165
|
González-Aguilera KL, Saad CF, Chávez Montes RA, Alves-Ferreira M, de Folter S. Selection of Reference Genes for Quantitative Real-Time RT-PCR Studies in Tomato Fruit of the Genotype MT-Rg1. FRONTIERS IN PLANT SCIENCE 2016; 7:1386. [PMID: 27679646 PMCID: PMC5021083 DOI: 10.3389/fpls.2016.01386] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/31/2016] [Indexed: 05/20/2023]
Abstract
Quantitative real-time RT-PCR (qRT-PCR) has become one of the most widely used methods for accurate quantification of gene expression. Since there are no universal reference genes for normalization, the optimal strategy to normalize raw qRT-PCR data is to perform an initial comparison of a set of independent reference genes to assess the most stable ones in each biological model. Normalization of a qRT-PCR experiment helps to ensure that the results are both statistically significant and biologically meaningful. Tomato is the model of choice to study fleshy fruit development. The miniature tomato (Solanum lycopersicum L.) cultivar Micro-Tom (MT) is considered a model system for tomato genetics and functional genomics. A new genotype, containing the Rg1 allele, improves tomato in vitro regeneration. In this work, we evaluated the expression stability of four tomato reference genes, namely CAC, SAND, Expressed, and ACTIN2. We showed that the genes CAC and Exp are the best reference genes of the four we tested during fruit development in the MT-Rg1 genotype. Furthermore, we validated the reference genes by showing that the expression profiles of the transcription factors FRUITFULL1 and APETALA2c during fruit development are comparable to previous reports using other tomato cultivars.
Collapse
Affiliation(s)
- Karla L. González-Aguilera
- Unidad de Genómica Avanzada – Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato, Mexico
| | - Carolina F. Saad
- Laboratório de Genética Molecular Vegetal, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Ricardo A. Chávez Montes
- Unidad de Genómica Avanzada – Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato, Mexico
| | - Marcio Alves-Ferreira
- Laboratório de Genética Molecular Vegetal, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Stefan de Folter
- Unidad de Genómica Avanzada – Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato, Mexico
- *Correspondence: Stefan de Folter,
| |
Collapse
|
166
|
Hao Y, Hu G, Breitel D, Liu M, Mila I, Frasse P, Fu Y, Aharoni A, Bouzayen M, Zouine M. Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato. PLoS Genet 2015; 11:e1005649. [PMID: 26716451 PMCID: PMC4696797 DOI: 10.1371/journal.pgen.1005649] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/14/2015] [Indexed: 11/19/2022] Open
Abstract
Ethylene is the main regulator of climacteric fruit ripening, by contrast the putative role of other phytohormones in this process remains poorly understood. The present study brings auxin signaling components into the mechanism regulating tomato fruit ripening through the functional characterization of Auxin Response Factor2 (SlARF2) which encodes a downstream component of auxin signaling. Two paralogs, SlARF2A and SlARF2B, are found in the tomato genome, both displaying a marked ripening-associated expression but distinct responsiveness to ethylene and auxin. Down-regulation of either SlARF2A or SlARF2B resulted in ripening defects while simultaneous silencing of both genes led to severe ripening inhibition suggesting a functional redundancy among the two ARFs. Tomato fruits under-expressing SlARF2 produced less climacteric ethylene and exhibited a dramatic down-regulation of the key ripening regulators RIN, CNR, NOR and TAGL1. Ethylene treatment failed to reverse the non-ripening phenotype and the expression of ethylene signaling and biosynthesis genes was strongly altered in SlARF2 down-regulated fruits. Although both SlARF proteins are transcriptional repressors the data indicate they work as positive regulators of tomato fruit ripening. Altogether, the study defines SlARF2 as a new component of the regulatory network controlling the ripening process in tomato. The plant hormone ethylene is regarded as the major regulator of fruit ripening but the putative role of other hormones remains elusive. Auxin Response Factors (ARFs) are transcriptional regulators modulating the expression of auxin-response genes shown recently to play a primary role in regulating fruit set in tomato, but the potential role of ARFs in the ripening process is still unknown. We show that among all tomato ARF genes, SlARF2 displays the most remarkable ripening-associated pattern of expression, which prompted its functional characterization. Two paralogs, SlARF2A and SlARF2B are identified in the tomato that are shown to be functionally redundant. The simultaneous down-regulation of SlARF2A/B genes leads to a severe ripening inhibition with a dramatically reduced ethylene production and a strong decrease in the expression of key regulators of fruit ripening such as rin and nor. The study defines SlARF2 as a new component of the regulatory network controlling the ripening process in tomato, suggesting that auxin, in concert with ethylene, might be an essential hormone for fruit ripening. While providing a new insight into the mechanisms underlying the control of fleshy fruit ripening, the study uncovers new avenues towards manipulating the ripening process through means that have not been described so far.
Collapse
Affiliation(s)
- Yanwei Hao
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Guojian Hu
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Dario Breitel
- Weizmann Institute of Science, Department of Plant Sciences, Faculty of Biochemistry, Rehovot, Israel
| | - Mingchun Liu
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Isabelle Mila
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Pierre Frasse
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Yongyao Fu
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Asaph Aharoni
- Weizmann Institute of Science, Department of Plant Sciences, Faculty of Biochemistry, Rehovot, Israel
| | - Mondher Bouzayen
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
- * E-mail: (MB); (MZ)
| | - Mohamed Zouine
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
- * E-mail: (MB); (MZ)
| |
Collapse
|
167
|
McAtee PA, Richardson AC, Nieuwenhuizen NJ, Gunaseelan K, Hoong L, Chen X, Atkinson RG, Burdon JN, David KM, Schaffer RJ. The hybrid non-ethylene and ethylene ripening response in kiwifruit (Actinidia chinensis) is associated with differential regulation of MADS-box transcription factors. BMC PLANT BIOLOGY 2015; 15:304. [PMID: 26714876 PMCID: PMC4696264 DOI: 10.1186/s12870-015-0697-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/21/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ripening in tomato is predominantly controlled by ethylene, whilst in fruit such as grape, it is predominantly controlled by other hormones. The ripening response of many kiwifruit (Actinidia) species is atypical. The majority of ripening-associated fruit starch hydrolysis, colour change and softening occurs in the apparent absence of ethylene production (Phase 1 ripening) whilst Phase 2 ripening requires autocatalytic ethylene production and is associated with further softening and an increase in aroma volatiles. RESULTS To dissect the ripening response in the yellow-fleshed kiwifruit A. chinensis ('Hort16A'), a two dimensional developmental stage X ethylene response time study was undertaken. As fruit progressed through maturation and Phase 1 ripening, fruit were treated with different concentrations of propylene and ethylene. At the start of Phase 1 ripening, treated fruit responded to ethylene, and were capable of producing endogenous ethylene. As the fruit progressed through Phase 1 ripening, the fruit became less responsive to ethylene and endogeneous ethylene production was partially repressed. Towards the end of Phase 1 ripening the fruit were again able to produce high levels of ethylene. Progression through Phase 1 ripening coincided with a developmental increase in the expression of the ethylene-unresponsive MADS-box FRUITFUL-like gene (FUL1). The ability to respond to ethylene however coincided with a change in expression of another MADS-box gene SEPALLATA4/RIPENING INHIBITOR-like (SEP4/RIN). The promoter of SEP4/RIN was shown to be transactivated by EIN3-like transcription factors, but unlike tomato, not by SEP4/RIN itself. Transient over-expression of SEP4/RIN in kiwifruit caused an increase in ethylene production. CONCLUSIONS These results suggest that the non-ethylene/ethylene ripening response observed in kiwifruit is a hybrid of both the tomato and grape ripening progression, with Phase 1 being akin to the RIN/ethylene inhibitory response observed in grape and Phase 2 akin to the RIN-associated autocatalytic ethylene response observed in tomato.
Collapse
Affiliation(s)
- Peter A McAtee
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | | | - Niels J Nieuwenhuizen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Kularajathevan Gunaseelan
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Ling Hoong
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Xiuyin Chen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Ross G Atkinson
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Jeremy N Burdon
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Karine M David
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Robert J Schaffer
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| |
Collapse
|
168
|
Liu M, Pirrello J, Chervin C, Roustan JP, Bouzayen M. Ethylene Control of Fruit Ripening: Revisiting the Complex Network of Transcriptional Regulation. PLANT PHYSIOLOGY 2015; 169:2380-90. [PMID: 26511917 PMCID: PMC4677914 DOI: 10.1104/pp.15.01361] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/21/2015] [Indexed: 05/18/2023]
Abstract
The plant hormone ethylene plays a key role in climacteric fruit ripening. Studies on components of ethylene signaling have revealed a linear transduction pathway leading to the activation of ethylene response factors. However, the means by which ethylene selects the ripening-related genes and interacts with other signaling pathways to regulate the ripening process are still to be elucidated. Using tomato (Solanum lycopersicum) as a reference species, the present review aims to revisit the mechanisms by which ethylene regulates fruit ripening by taking advantage of new tools available to perform in silico studies at the genome-wide scale, leading to a global view on the expression pattern of ethylene biosynthesis and response genes throughout ripening. Overall, it provides new insights on the transcriptional network by which this hormone coordinates the ripening process and emphasizes the interplay between ethylene and ripening-associated developmental factors and the link between epigenetic regulation and ethylene during fruit ripening.
Collapse
Affiliation(s)
- Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China (M.L.);Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 32607, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.); andInstitut National de la Recherche Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 52627, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.)
| | - Julien Pirrello
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China (M.L.);Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 32607, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.); andInstitut National de la Recherche Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 52627, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.)
| | - Christian Chervin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China (M.L.);Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 32607, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.); andInstitut National de la Recherche Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 52627, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.)
| | - Jean-Paul Roustan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China (M.L.);Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 32607, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.); andInstitut National de la Recherche Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 52627, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.)
| | - Mondher Bouzayen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China (M.L.);Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 32607, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.); andInstitut National de la Recherche Agronomique, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, CS 52627, F-31326, France (M.L., J.P., C.C., J.-P.R., M.B.)
| |
Collapse
|
169
|
Hao Y, Hu G, Breitel D, Liu M, Mila I, Frasse P, Fu Y, Aharoni A, Bouzayen M, Zouine M. Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato. PLoS Genet 2015. [PMID: 26716451 DOI: 10.1371/journal.pgen.10.05649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
Ethylene is the main regulator of climacteric fruit ripening, by contrast the putative role of other phytohormones in this process remains poorly understood. The present study brings auxin signaling components into the mechanism regulating tomato fruit ripening through the functional characterization of Auxin Response Factor2 (SlARF2) which encodes a downstream component of auxin signaling. Two paralogs, SlARF2A and SlARF2B, are found in the tomato genome, both displaying a marked ripening-associated expression but distinct responsiveness to ethylene and auxin. Down-regulation of either SlARF2A or SlARF2B resulted in ripening defects while simultaneous silencing of both genes led to severe ripening inhibition suggesting a functional redundancy among the two ARFs. Tomato fruits under-expressing SlARF2 produced less climacteric ethylene and exhibited a dramatic down-regulation of the key ripening regulators RIN, CNR, NOR and TAGL1. Ethylene treatment failed to reverse the non-ripening phenotype and the expression of ethylene signaling and biosynthesis genes was strongly altered in SlARF2 down-regulated fruits. Although both SlARF proteins are transcriptional repressors the data indicate they work as positive regulators of tomato fruit ripening. Altogether, the study defines SlARF2 as a new component of the regulatory network controlling the ripening process in tomato.
Collapse
Affiliation(s)
- Yanwei Hao
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Guojian Hu
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Dario Breitel
- Weizmann Institute of Science, Department of Plant Sciences, Faculty of Biochemistry, Rehovot, Israel
| | - Mingchun Liu
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Isabelle Mila
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Pierre Frasse
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Yongyao Fu
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Asaph Aharoni
- Weizmann Institute of Science, Department of Plant Sciences, Faculty of Biochemistry, Rehovot, Israel
| | - Mondher Bouzayen
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Mohamed Zouine
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Castanet-Tolosan, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, France
| |
Collapse
|
170
|
Giménez E, Dominguez E, Pineda B, Heredia A, Moreno V, Lozano R, Angosto T. Transcriptional Activity of the MADS Box ARLEQUIN/TOMATO AGAMOUS-LIKE1 Gene Is Required for Cuticle Development of Tomato Fruit. PLANT PHYSIOLOGY 2015; 168:1036-48. [PMID: 26019301 PMCID: PMC4741332 DOI: 10.1104/pp.15.00469] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/27/2015] [Indexed: 05/21/2023]
Abstract
Fruit development and ripening entail key biological and agronomic events, which ensure the appropriate formation and dispersal of seeds and determine productivity and yield quality traits. The MADS box gene Arlequin/tomato Agamous-like1 (hereafter referred to as TAGL1) was reported as a key regulator of tomato (Solanum lycopersicum) reproductive development, mainly involved in flower development, early fruit development, and ripening. It is shown here that silencing of the TAGL1 gene (RNA interference lines) promotes significant changes affecting cuticle development, mainly a reduction of thickness and stiffness, as well as a significant decrease in the content of cuticle components (cutin, waxes, polysaccharides, and phenolic compounds). Accordingly, overexpression of TAGL1 significantly increased the amount of cuticle and most of its components while rendering a mechanically weak cuticle. Expression of the genes involved in cuticle biosynthesis agreed with the biochemical and biomechanical features of cuticles isolated from transgenic fruits; it also indicated that TAGL1 participates in the transcriptional control of cuticle development mediating the biosynthesis of cuticle components. Furthermore, cell morphology and the arrangement of epidermal cell layers, on whose activity cuticle formation depends, were altered when TAGL1 was either silenced or constitutively expressed, indicating that this transcription factor regulates cuticle development, probably through the biosynthetic activity of epidermal cells. Our results also support cuticle development as an integrated event in the fruit expansion and ripening processes that characterize fleshy-fruited species such as tomato.
Collapse
Affiliation(s)
- Estela Giménez
- Centro de Investigación en Biotecnología Agroalimentaria, Universidad de Almería, 04120 Almeria, Spain (E.G., R.L., T.A.);Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Malaga, Spain (E.D., A.H.); andInstituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain (B.P., V.M.)
| | - Eva Dominguez
- Centro de Investigación en Biotecnología Agroalimentaria, Universidad de Almería, 04120 Almeria, Spain (E.G., R.L., T.A.);Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Malaga, Spain (E.D., A.H.); andInstituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain (B.P., V.M.)
| | - Benito Pineda
- Centro de Investigación en Biotecnología Agroalimentaria, Universidad de Almería, 04120 Almeria, Spain (E.G., R.L., T.A.);Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Malaga, Spain (E.D., A.H.); andInstituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain (B.P., V.M.)
| | - Antonio Heredia
- Centro de Investigación en Biotecnología Agroalimentaria, Universidad de Almería, 04120 Almeria, Spain (E.G., R.L., T.A.);Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Malaga, Spain (E.D., A.H.); andInstituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain (B.P., V.M.)
| | - Vicente Moreno
- Centro de Investigación en Biotecnología Agroalimentaria, Universidad de Almería, 04120 Almeria, Spain (E.G., R.L., T.A.);Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Malaga, Spain (E.D., A.H.); andInstituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain (B.P., V.M.)
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria, Universidad de Almería, 04120 Almeria, Spain (E.G., R.L., T.A.);Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Malaga, Spain (E.D., A.H.); andInstituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain (B.P., V.M.)
| | - Trinidad Angosto
- Centro de Investigación en Biotecnología Agroalimentaria, Universidad de Almería, 04120 Almeria, Spain (E.G., R.L., T.A.);Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Malaga, Spain (E.D., A.H.); andInstituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain (B.P., V.M.)
| |
Collapse
|
171
|
Saladié M, Cañizares J, Phillips MA, Rodriguez-Concepcion M, Larrigaudière C, Gibon Y, Stitt M, Lunn JE, Garcia-Mas J. Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties. BMC Genomics 2015; 16:440. [PMID: 26054931 PMCID: PMC4460886 DOI: 10.1186/s12864-015-1649-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 05/20/2015] [Indexed: 11/14/2022] Open
Abstract
Background In climacteric fruit-bearing species, the onset of fruit ripening is marked by a transient rise in respiration rate and autocatalytic ethylene production, followed by rapid deterioration in fruit quality. In non-climacteric species, there is no increase in respiration or ethylene production at the beginning or during fruit ripening. Melon is unusual in having climacteric and non-climacteric varieties, providing an interesting model system to compare both ripening types. Transcriptomic analysis of developing melon fruits from Védrantais and Dulce (climacteric) and Piel de sapo and PI 161375 (non-climacteric) varieties was performed to understand the molecular mechanisms that differentiate the two fruit ripening types. Results Fruits were harvested at 15, 25, 35 days after pollination and at fruit maturity. Transcript profiling was performed using an oligo-based microarray with 75 K probes. Genes linked to characteristic traits of fruit ripening were differentially expressed between climacteric and non-climacteric types, as well as several transcription factor genes and genes encoding enzymes involved in sucrose catabolism. The expression patterns of some genes in PI 161375 fruits were either intermediate between. Piel de sapo and the climacteric varieties, or more similar to the latter. PI 161375 fruits also accumulated some carotenoids, a characteristic trait of climacteric varieties. Conclusions Simultaneous changes in transcript abundance indicate that there is coordinated reprogramming of gene expression during fruit development and at the onset of ripening in both climacteric and non-climacteric fruits. The expression patterns of genes related to ethylene metabolism, carotenoid accumulation, cell wall integrity and transcriptional regulation varied between genotypes and was consistent with the differences in their fruit ripening characteristics. There were differences between climacteric and non-climacteric varieties in the expression of genes related to sugar metabolism suggesting that they may be potential determinants of sucrose content and post-harvest stability of sucrose levels in fruit. Several transcription factor genes were also identified that were differentially expressed in both types, implicating them in regulation of ripening behaviour. The intermediate nature of PI 161375 suggested that classification of melon fruit ripening behaviour into just two distinct types is an over-simplification, and that in reality there is a continuous spectrum of fruit ripening behaviour. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1649-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Montserrat Saladié
- IRTA, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain. .,Present address: School of Chemistry and Biochemistry, Biochemistry and Molecular Biology, The University of Western Australia, Crawley, WA, 6009, Australia.
| | - Joaquin Cañizares
- COMAV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València (UPV), Camino de Vera s/n, Valencia, 46022, Spain.
| | - Michael A Phillips
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Manuel Rodriguez-Concepcion
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Christian Larrigaudière
- IRTA, Parc Científic i Tecnològic Agroalimentari, Parc de Gardeny, Edifici Fruitcentre, Lleida, 25003, Spain.
| | - Yves Gibon
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany. .,Present address: INRA Bordeaux, University of Bordeaux, UMR1332 Fruit Biology and Pathology, Villenave d'Ornon, F-33883, France.
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany.
| | - John Edward Lunn
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany.
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| |
Collapse
|
172
|
Ferraro G, D'Angelo M, Sulpice R, Stitt M, Valle EM. Reduced levels of NADH-dependent glutamate dehydrogenase decrease the glutamate content of ripe tomato fruit but have no effect on green fruit or leaves. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3381-9. [PMID: 25878356 DOI: 10.1093/jxb/erv150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Glutamate (Glu) is a taste enhancer that contributes to the characteristic flavour of foods. In fruit of tomato (Solanum lycopersicum L.), the Glu content increases dramatically during the ripening process, becoming the most abundant free amino acid when the fruit become red. There is also a concomitant increase in NADH-dependent glutamate dehydrogenase (GDH) activity during the ripening transition. This enzyme is located in the mitochondria and catalyses the reversible amination of 2-oxoglutarate to Glu. To investigate the potential effect of GDH on Glu metabolism, the abundance of GDH was altered by artificial microRNA technology. Efficient silencing of all the endogenous SlGDH genes was achieved, leading to a dramatic decrease in total GDH activity. This decrease in GDH activity did not lead to any clear morphological or metabolic phenotype in leaves or green fruit. However, red fruit on the transgenic plants showed markedly reduced levels of Glu and a large increase in aspartate, glucose and fructose content in comparison to wild-type fruit. These results suggest that GDH is involved in the synthesis of Glu in tomato fruit during the ripening processes. This contrasts with the biological role ascribed to GDH in many other tissues and species. Overall, these findings suggest that GDH has a major effect on the control of metabolic composition during tomato fruit ripening, but not at other stages of development.
Collapse
Affiliation(s)
- Gisela Ferraro
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Ocampo y Esmeralda, Predio CCT, Rosario 2000, Argentina
| | - Matilde D'Angelo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Ocampo y Esmeralda, Predio CCT, Rosario 2000, Argentina
| | - Ronan Sulpice
- NUI Galway, Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre, Botany and Plant Science, Galway, Ireland
| | - Mark Stitt
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Estela M Valle
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Ocampo y Esmeralda, Predio CCT, Rosario 2000, Argentina
| |
Collapse
|
173
|
Gao C, Ju Z, Cao D, Zhai B, Qin G, Zhu H, Fu D, Luo Y, Zhu B. MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:370-82. [PMID: 25516062 DOI: 10.1111/pbi.12297] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/04/2014] [Accepted: 10/20/2014] [Indexed: 05/18/2023]
Abstract
The development and ripening of tomato fruit are complex processes involving many gene regulatory pathways at the transcriptional and post-transcriptional level. Ripening inhibitor (RIN) is a vital transcription factor, which targets numerous ripening-related genes at the transcriptional level during tomato fruit ripening. MicroRNAs (miRNAs) are a class of short noncoding RNAs that play important roles in post-transcriptional gene regulation. To elucidate the potential regulatory relationship between rin and miRNAs during fruit development and ripening, we identified known miRNAs and profiled their expression in wild-type tomato and rin mutant using a deep sequencing approach combined with quantitative RT-PCR. A total of 33 known miRNA families were identified, of which 14 miRNA families were differently accumulated. Subsequent promoter analysis showed that possible RIN-binding motifs (CArG-box) tended to occur frequently in the promoter regions of partial differently expressed miRNAs. In addition, ethylene may participate in the regulation of miRNAs accumulation during tomato fruit ripening. Chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assay confirmed the direct binding of RIN to the promoter of MIR172a. Collectively, these results showed a close correlation between miRNA expression and RIN as well as ethylene, which further elucidated the regulatory roles of miRNAs during fruit development and ripening and enriched the regulatory network of RIN in tomato fruit.
Collapse
Affiliation(s)
- Chao Gao
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | | | | | | | | | | | | | | | | |
Collapse
|
174
|
Pons Puig C, Dagar A, Marti Ibanez C, Singh V, Crisosto CH, Friedman H, Lurie S, Granell A. Pre-symptomatic transcriptome changes during cold storage of chilling sensitive and resistant peach cultivars to elucidate chilling injury mechanisms. BMC Genomics 2015; 16:245. [PMID: 25887353 PMCID: PMC4391166 DOI: 10.1186/s12864-015-1395-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cold storage induces chilling injury (CI) disorders in peach fruit (woolliness/mealiness, flesh browning and reddening/bleeding) manifested when ripened at shelf life. To gain insight into the mechanisms underlying CI, we analyzed the transcriptome of 'Oded' (high tolerant) and 'Hermoza' (relatively tolerant to woolliness, but sensitive to browning and bleeding) peach cultivars at pre-symptomatic stages. The expression profiles were compared and validated with two previously analyzed pools (high and low sensitive to woolliness) from the Pop-DG population. The four fruit types cover a wide range of sensitivity to CI. The four fruit types were also investigated with the ROSMETER that provides information on the specificity of the transcriptomic response to oxidative stress. RESULTS We identified quantitative differences in a subset of core cold responsive genes that correlated with sensitivity or tolerance to CI at harvest and during cold storage, and also subsets of genes correlating specifically with high sensitivity to woolliness and browning. Functional analysis indicated that elevated levels, at harvest and during cold storage, of genes related to antioxidant systems and the biosynthesis of metabolites with antioxidant activity correlates with tolerance. Consistent with these results, ROSMETER analysis revealed oxidative stress in 'Hermoza' and the progeny pools, but not in the cold resistant 'Oded'. By contrast, cold storage induced, in sensitivity to woolliness dependant manner, a gene expression program involving the biosynthesis of secondary cell wall and pectins. Furthermore, our results indicated that while ethylene is related to CI tolerance, differential auxin subcellular accumulation and signaling may play a role in determining chilling sensitivity/tolerance. In addition, sugar partitioning and demand during cold storage may also play a role in the tolerance/sensitive mechanism. The analysis also indicates that vesicle trafficking, membrane dynamics and cytoskeleton organization could have a role in the tolerance/sensitive mechanism. In the case of browning, our results suggest that elevated acetaldehyde related genes together with the core cold responses may increase sensitivity to browning in shelf life. CONCLUSIONS Our data suggest that in sensitive fruit a cold response program is activated and regulated by auxin distribution and ethylene and these hormones have a role in sensitivity to CI even before fruit are cold stored.
Collapse
Affiliation(s)
- Clara Pons Puig
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politecnica de Valencia, E-48022, Valencia, Spain.
| | - Anurag Dagar
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, P.O. Box 6, Bet Dagan, 50250, Israel.
| | - Cristina Marti Ibanez
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politecnica de Valencia, E-48022, Valencia, Spain.
| | - Vikram Singh
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, P.O. Box 6, Bet Dagan, 50250, Israel.
| | - Carlos H Crisosto
- Plant Sciences Department, University of California Davis, 1 Shields Ave, Davis, CA, 95616, USA.
| | - Haya Friedman
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, P.O. Box 6, Bet Dagan, 50250, Israel.
| | - Susan Lurie
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, P.O. Box 6, Bet Dagan, 50250, Israel.
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politecnica de Valencia, E-48022, Valencia, Spain.
| |
Collapse
|
175
|
Weng L, Zhao F, Li R, Xu C, Chen K, Xiao H. The zinc finger transcription factor SlZFP2 negatively regulates abscisic acid biosynthesis and fruit ripening in tomato. PLANT PHYSIOLOGY 2015; 167:931-49. [PMID: 25637453 PMCID: PMC4348780 DOI: 10.1104/pp.114.255174] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/26/2015] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) regulates plant development and adaptation to environmental conditions. Although the ABA biosynthesis pathway in plants has been thoroughly elucidated, how ABA biosynthetic genes are regulated at the molecular level during plant development is less well understood. Here, we show that the tomato (Solanum lycopersicum) zinc finger transcription factor SlZFP2 is involved in the regulation of ABA biosynthesis during fruit development. Overexpression of SlZFP2 resulted in multiple phenotypic changes, including more branches, early flowering, delayed fruit ripening, lighter seeds, and faster seed germination, whereas down-regulation of its expression caused problematic fruit set, accelerated ripening, and inhibited seed germination. SlZFP2 represses ABA biosynthesis during fruit development through direct suppression of the ABA biosynthetic genes NOTABILIS, SITIENS, and FLACCA and the aldehyde oxidase SlAO1. We also show that SlZFP2 regulates fruit ripening through transcriptional suppression of the ripening regulator COLORLESS NON-RIPENING. Using bacterial one-hybrid screening and a selected amplification and binding assay, we identified the (A/T)(G/C)TT motif as the core binding sequence of SlZFP2. Furthermore, by RNA sequencing profiling, we found that 193 genes containing the SlZFP2-binding motifs in their promoters were differentially expressed in 2 d post anthesis fruits between the SlZFP2 RNA interference line and its nontransgenic sibling. We propose that SlZFP2 functions as a repressor to fine-tune ABA biosynthesis during fruit development and provides a potentially valuable tool for dissecting the role of ABA in fruit ripening.
Collapse
Affiliation(s)
- Lin Weng
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (L.W., F.Z., R.L., H.X.); andFruit Science Institute, Zhejiang University, Hangzhou 310058, China (C.X., K.C.)
| | - Fangfang Zhao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (L.W., F.Z., R.L., H.X.); andFruit Science Institute, Zhejiang University, Hangzhou 310058, China (C.X., K.C.)
| | - Rong Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (L.W., F.Z., R.L., H.X.); andFruit Science Institute, Zhejiang University, Hangzhou 310058, China (C.X., K.C.)
| | - Changjie Xu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (L.W., F.Z., R.L., H.X.); andFruit Science Institute, Zhejiang University, Hangzhou 310058, China (C.X., K.C.)
| | - Kunsong Chen
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (L.W., F.Z., R.L., H.X.); andFruit Science Institute, Zhejiang University, Hangzhou 310058, China (C.X., K.C.)
| | - Han Xiao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (L.W., F.Z., R.L., H.X.); andFruit Science Institute, Zhejiang University, Hangzhou 310058, China (C.X., K.C.)
| |
Collapse
|
176
|
Dong Y, Wang YZ. Seed shattering: from models to crops. FRONTIERS IN PLANT SCIENCE 2015; 6:476. [PMID: 26157453 PMCID: PMC4478375 DOI: 10.3389/fpls.2015.00476] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/15/2015] [Indexed: 05/19/2023]
Abstract
Seed shattering (or pod dehiscence, or fruit shedding) is essential for the propagation of their offspring in wild plants but is a major cause of yield loss in crops. In the dicot model species, Arabidopsis thaliana, pod dehiscence necessitates a development of the abscission zones along the pod valve margins. In monocots, such as cereals, an abscission layer in the pedicle is required for the seed shattering process. In the past decade, great advances have been made in characterizing the genetic contributors that are involved in the complex regulatory network in the establishment of abscission cell identity. We summarize the recent burgeoning progress in the field of genetic regulation of pod dehiscence and fruit shedding, focusing mainly on the model species A. thaliana with its close relatives and the fleshy fruit species tomato, as well as the genetic basis responsible for the parallel loss of seed shattering in domesticated crops. This review shows how these individual genes are co-opted in the developmental process of the tissues that guarantee seed shattering. Research into the genetic mechanism underlying seed shattering provides a premier prerequisite for the future breeding program for harvest in crops.
Collapse
Affiliation(s)
| | - Yin-Zheng Wang
- *Correspondence: Yin-Zheng Wang, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China,
| |
Collapse
|
177
|
Jia Z, Jiang B, Gao X, Yue Y, Fei Z, Sun H, Wu C, Sun S, Hou W, Han T. GmFULa, a FRUITFULL homolog, functions in the flowering and maturation of soybean. PLANT CELL REPORTS 2015; 34:121-32. [PMID: 25326369 DOI: 10.1007/s00299-014-1693-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 09/17/2014] [Accepted: 10/07/2014] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE A FRUITFULL homolog GmFULa was cloned and found to play roles in the flowering and maturation of soybean. Soybean varieties exhibit great diversity in terms of flowering and maturation due to differences in their photoperiodic responses. The underlying mechanism remains unclear despite the fact that some upstream flowering genes have been studied. FRUITFULL (FUL) genes are one group of downstream flowering genes known to have major roles in reproductive transition, floral meristem identity, and floral organ identity. However, FUL homologs and their functions are poorly understood in soybean. Here, a soybean FUL homolog was cloned from the late-maturing photoperiod-sensitive soybean variety Zigongdongdou (ZGDD) and designated GmFULa. In ZGDD, GmFULa exhibited a terminal-preferential expression pattern, with higher expression in the root and shoot apices than in the middle parts. Diurnal rhythm analysis revealed that photoperiod regulates the GmFULa expression level but does not alter its diurnal rhythm. ZGDD was maintained under different photoperiod conditions (long day, LD; short day, SD; LD after 13 short days, SD13-LD) to assess GmFULa expression in newly expanded leaves and in the shoot apex. From this analysis, GmFULa expression was detected in the floral meristem, floral organs and their primordia; trifoliate leaves; and the inflorescence meristem, with the expression levels induced by SD and inhibited by LD. GmFULa expression was also associated with maturity in seven soybean varieties with different photoperiod sensitivities. Therefore, photoperiod conditions affect the expression level of GmFULa but not its diurnal rhythm. The gene plays pleiotropic roles in reproductive transition, flowering, and leaf development and is associated with maturity in soybean.
Collapse
Affiliation(s)
- Zhen Jia
- The National Key Facility for Crop Gene Resources and Genetic Improvement and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, The Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
178
|
Liu L, Shao Z, Zhang M, Wang Q. Regulation of carotenoid metabolism in tomato. MOLECULAR PLANT 2015; 8:28-39. [PMID: 25578270 DOI: 10.1016/j.molp.2014.11.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 10/14/2014] [Indexed: 05/20/2023]
Abstract
Carotenoids serve diverse functions in vastly different organisms that both produce and consume them. Enhanced carotenoid accumulation is of great importance in the visual and functional properties of fruits and vegetables. Significant progress has been achieved in recent years in our understanding of carotenoid biosynthesis in tomato (Solanum lycopersicum) using biochemical and genetics approaches. The carotenoid metabolic network is temporally and spatially controlled, and plants have evolved strategic tactics to regulate carotenoid metabolism in response to various developmental and environmental factors. In this review, we summarize the current status of studies on transcription factors and phytohormones that regulate carotenoid biosynthesis, catabolism, and storage capacity in plastids, as well as the responses of carotenoid metabolism to environmental cues in tomato fruits. Transcription factors function either in cooperation with or independently of phytohormone signaling to regulate carotenoid metabolism, providing novel approaches for metabolic engineering of carotenoid composition and content in tomato.
Collapse
Affiliation(s)
- Lihong Liu
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Zhiyong Shao
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Min Zhang
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
179
|
Ma N, Feng H, Meng X, Li D, Yang D, Wu C, Meng Q. Overexpression of tomato SlNAC1 transcription factor alters fruit pigmentation and softening. BMC PLANT BIOLOGY 2014; 14:351. [PMID: 25491370 PMCID: PMC4272553 DOI: 10.1186/s12870-014-0351-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/25/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Fruit maturation and ripening are genetically regulated processes that involve a complex interplay of plant hormones, growth regulators and multiple biological and environmental factors. Tomato (Solanum lycopersicum) has been used as a model of biological and genetic studies on the regulation of specific ripening pathways, including ethylene, carotenoid and cell wall metabolism. This model has also been used to investigate the functions of upstream signalling and transcriptional regulators. Thus far, many ripening-associated transcription factors that influence fruit development and ripening have been reported. NAC transcription factors are plant specific and play important roles in many stages of plant growth and development, such as lateral root formation, secondary cell wall synthesis, and embryo, floral organ, vegetative organ and fruit development. RESULTS Tissue-specific analysis by quantitative real-time PCR showed that SlNAC1 was highly accumulated in immature green fruits; the expression of SlNAC1 increased with fruit ripening till to the highest level at 7 d after the breaker stage. The overexpression of SlNAC1 resulted in reduced carotenoids by altering carotenoid pathway flux and decreasing ethylene synthesis mediated mainly by the reduced expression of ethylene biosynthetic genes of system-2, thus led to yellow or orange mature fruits. The results of yeast one-hybrid experiment demonstrated that SlNAC1 can interact with the regulatory regions of genes related lycopene and ethylene synthesis. These results also indicated that SlNAC1 inhibited fruit ripening by affecting ethylene synthesis and carotenoid accumulation in SlNAC1 overexpression lines. In addition, the overexpression of SlNAC1 reduced the firmness of the fruits and the thickness of the pericarp and produced more abscisic acid, resulting in the early softening of fruits. Hence, in SlNAC1 overexpression lines, both ethylene-dependent and abscisic acid-dependent pathways are regulated by SlNAC1 in fruit ripening regulatory network. CONCLUSIONS SlNAC1 had a broad influence on tomato fruit ripening and regulated SlNAC1 overexpression tomato fruit ripening through both ethylene-dependent and abscisic acid-dependent pathways. Thus, this study provided new insights into the current model of tomato fruit ripening regulatory network.
Collapse
Affiliation(s)
- Nana Ma
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Hailong Feng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Xia Meng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Dong Li
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Dongyue Yang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Qingwei Meng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| |
Collapse
|
180
|
Palumbo MC, Zenoni S, Fasoli M, Massonnet M, Farina L, Castiglione F, Pezzotti M, Paci P. Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine development. THE PLANT CELL 2014; 26:4617-35. [PMID: 25490918 PMCID: PMC4311215 DOI: 10.1105/tpc.114.133710] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named "fight-club hubs" characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named "switch genes" was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops.
Collapse
Affiliation(s)
- Maria Concetta Palumbo
- Institute for Computing Applications "Mauro Picone," National Research Council, 00185 Rome, Italy
| | - Sara Zenoni
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Marianna Fasoli
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Mélanie Massonnet
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Lorenzo Farina
- Department of Computer, Control, and Management Engineering, "Sapienza" University of Rome, 00185 Rome, Italy
| | - Filippo Castiglione
- Institute for Computing Applications "Mauro Picone," National Research Council, 00185 Rome, Italy
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti," National Research Council, 00185 Rome, Italy SysBio Centre for Systems Biology, 00185 Rome, Italy
| |
Collapse
|
181
|
España L, Heredia-Guerrero JA, Reina-Pinto JJ, Fernández-Muñoz R, Heredia A, Domínguez E. Transient silencing of CHALCONE SYNTHASE during fruit ripening modifies tomato epidermal cells and cuticle properties. PLANT PHYSIOLOGY 2014; 166:1371-86. [PMID: 25277718 PMCID: PMC4226350 DOI: 10.1104/pp.114.246405] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 09/29/2014] [Indexed: 05/20/2023]
Abstract
Tomato (Solanum lycopersicum) fruit ripening is accompanied by an increase in CHALCONE SYNTHASE (CHS) activity and flavonoid biosynthesis. Flavonoids accumulate in the cuticle, giving its characteristic orange color that contributes to the eventual red color of the ripe fruit. Using virus-induced gene silencing in fruits, we have down-regulated the expression of SlCHS during ripening and compared the cuticles derived from silenced and nonsilenced regions. Silenced regions showed a pink color due to the lack of flavonoids incorporated to the cuticle. This change in color was accompanied by several other changes in the cuticle and epidermis. The epidermal cells displayed a decreased tangential cell width; a decrease in the amount of cuticle and its main components, cutin and polysaccharides, was also observed. Flavonoids dramatically altered the cuticle biomechanical properties by stiffening the elastic and viscoelastic phase and by reducing the ability of the cuticle to deform. There seemed to be a negative relation between SlCHS expression and wax accumulation during ripening that could be related to the decreased cuticle permeability to water observed in the regions silencing SlCHS. A reduction in the overall number of ester linkages present in the cutin matrix was also dependent on the presence of flavonoids.
Collapse
Affiliation(s)
- Laura España
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (L.E., J.J.R.-P., R.F.-M., A.H., E.D.), and Departamento de Biología Molecular y Bioquímica (L.E., A.H.), Universidad de Málaga, E-29071 Malaga, Spain;Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750 Malaga, Spain (J.J.R.-P., R.F.-M., E.D.); andNanophysics, Istituto Italiano di Tecnologia, 16163 Genoa, Italy (J.A.H.-G.)
| | - José A Heredia-Guerrero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (L.E., J.J.R.-P., R.F.-M., A.H., E.D.), and Departamento de Biología Molecular y Bioquímica (L.E., A.H.), Universidad de Málaga, E-29071 Malaga, Spain;Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750 Malaga, Spain (J.J.R.-P., R.F.-M., E.D.); andNanophysics, Istituto Italiano di Tecnologia, 16163 Genoa, Italy (J.A.H.-G.)
| | - José J Reina-Pinto
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (L.E., J.J.R.-P., R.F.-M., A.H., E.D.), and Departamento de Biología Molecular y Bioquímica (L.E., A.H.), Universidad de Málaga, E-29071 Malaga, Spain;Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750 Malaga, Spain (J.J.R.-P., R.F.-M., E.D.); andNanophysics, Istituto Italiano di Tecnologia, 16163 Genoa, Italy (J.A.H.-G.)
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (L.E., J.J.R.-P., R.F.-M., A.H., E.D.), and Departamento de Biología Molecular y Bioquímica (L.E., A.H.), Universidad de Málaga, E-29071 Malaga, Spain;Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750 Malaga, Spain (J.J.R.-P., R.F.-M., E.D.); andNanophysics, Istituto Italiano di Tecnologia, 16163 Genoa, Italy (J.A.H.-G.)
| | - Antonio Heredia
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (L.E., J.J.R.-P., R.F.-M., A.H., E.D.), and Departamento de Biología Molecular y Bioquímica (L.E., A.H.), Universidad de Málaga, E-29071 Malaga, Spain;Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750 Malaga, Spain (J.J.R.-P., R.F.-M., E.D.); andNanophysics, Istituto Italiano di Tecnologia, 16163 Genoa, Italy (J.A.H.-G.)
| | - Eva Domínguez
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (L.E., J.J.R.-P., R.F.-M., A.H., E.D.), and Departamento de Biología Molecular y Bioquímica (L.E., A.H.), Universidad de Málaga, E-29071 Malaga, Spain;Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750 Malaga, Spain (J.J.R.-P., R.F.-M., E.D.); andNanophysics, Istituto Italiano di Tecnologia, 16163 Genoa, Italy (J.A.H.-G.)
| |
Collapse
|
182
|
Beisken S, Earll M, Baxter C, Portwood D, Ament Z, Kende A, Hodgman C, Seymour G, Smith R, Fraser P, Seymour M, Salek RM, Steinbeck C. Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants. Sci Data 2014; 1:140029. [PMID: 25977786 PMCID: PMC4322568 DOI: 10.1038/sdata.2014.29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/06/2014] [Indexed: 12/02/2022] Open
Abstract
Application of mass spectrometry enables the detection of metabolic differences between groups of related organisms. Differences in the metabolic fingerprints of wild-type Solanum lycopersicum and three monogenic mutants, ripening inhibitor (rin), non-ripening (nor) and Colourless non-ripening (Cnr), of tomato are captured with regard to ripening behaviour. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a time series of the ripening behaviour at discrete intervals with a focus on changes post-anthesis. Internal standards and quality controls were used to ensure system stability. The raw data of the samples and reference compounds including study protocols have been deposited in the open metabolomics database MetaboLights via the metadata annotation tool Isatab to enable efficient re-use of the datasets, such as in metabolomics cross-study comparisons or data fusion exercises.
Collapse
Affiliation(s)
- Stephan Beisken
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 2HA, UK
| | - Mark Earll
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Charles Baxter
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - David Portwood
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Zsuzsanna Ament
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Aniko Kende
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Charlie Hodgman
- Centre for Plant Integrative Biology, University of Nottingham , Loughborough, Leicestershire LE12 5RD, UK
| | - Graham Seymour
- Centre for Plant Integrative Biology, University of Nottingham , Loughborough, Leicestershire LE12 5RD, UK
| | - Rebecca Smith
- Centre for Plant Integrative Biology, University of Nottingham , Loughborough, Leicestershire LE12 5RD, UK
| | - Paul Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill , Egham, Surrey TW20 0EX, UK
| | - Mark Seymour
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Reza M Salek
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 2HA, UK
| | - Christoph Steinbeck
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 2HA, UK
| |
Collapse
|
183
|
Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RCHJ, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JKC, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 2014. [PMID: 25064008 DOI: 10.1038/ng3046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
Collapse
Affiliation(s)
- Anthony Bolger
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany
| | - Federico Scossa
- 1] Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per l'Orticoltura, Pontecagnano, Italy
| | - Marie E Bolger
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Florian Maumus
- French National Institute for Agricultural Research (INRA), UR1164 Research Unit in Genomics Info (URGI), INRA de Versailles-Grignon, Versailles, France
| | - Takayuki Tohge
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Hadi Quesneville
- French National Institute for Agricultural Research (INRA), UR1164 Research Unit in Genomics Info (URGI), INRA de Versailles-Grignon, Versailles, France
| | - Saleh Alseekh
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Iben Sørensen
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Gabriel Lichtenstein
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - Eric A Fich
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Mariana Conte
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - Heike Keller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Korbinian Schneeberger
- 1] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. [2] Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rainer Schwacke
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Itai Ofner
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Julia Vrebalov
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Yimin Xu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Sonia Osorio
- 1] Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain
| | - Saulo Alves Aflitos
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Elio Schijlen
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - José M Jiménez-Goméz
- 1] Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany. [2] INRA, UMR 1318, Institut Jean-Pierre Bourgin, Versailles, France
| | - Malgorzata Ryngajllo
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Seisuke Kimura
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Ravi Kumar
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Daniel Koenig
- 1] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. [2] Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Lauren R Headland
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Roeland C H J van Ham
- 1] Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands. [2]
| | - René Klein Lankhorst
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Linyong Mao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Alexander Vogel
- Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany
| | - Borjana Arsova
- Entwicklungs und Molekularbiologie der Pflanzen, Heinrich Heine Universität, Düsseldorf, Germany
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen, Germany
| | - Zhangjun Fei
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA. [3] US Department of Agriculture Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA
| | - Jocelyn K C Rose
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Dani Zamir
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Fernando Carrari
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - James J Giovannoni
- 1] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA. [2] US Department of Agriculture Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Björn Usadel
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany. [3] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| |
Collapse
|
184
|
Cao D, Ju Z, Gao C, Mei X, Fu D, Zhu H, Luo Y, Zhu B. Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum. Gene 2014; 550:230-7. [PMID: 25149677 DOI: 10.1016/j.gene.2014.08.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/15/2014] [Accepted: 08/19/2014] [Indexed: 12/29/2022]
Abstract
Recent studies have reported that decreased level of DNA cytosine methylation in the global genome was closely related to the initiation of tomato (Solanum lycopersicum) fruit ripening. However, genome-scale analysis of cytosine-5 DNA methyltransferases (C5-MTases) and demethylases in tomato has not been engaged. In this study, 7 C5-MTases and 3 demethylases were identified in tomato genome, which probably contributed to DNA cytosine methylation level in tomato. The 7 C5-MTases were categorized into 4 subgroups, and the 3 demethylases were classified into 2 subgroups based on phylogenetic analyses. Comprehensive analysis of their structure and genomic localization was also performed in this paper. According to online RNA-seq data, 4 S. lycopersicum C5-MTase (SlC5-MTase) genes (SlMET, SlDRM1L1, SlDRM5, SlMET3L) were expressed higher than others, and one DNA demethylase gene (SlDML) was significantly changed during tomato fruit development and ripening. Furthermore, all these five gene expressions at breaker (BK) stage changed with 1-methylcyclopropene (1-MCP) treatment, indicating that they were regulated by ethylene directly or indirectly in tomato fruit. In addition, subcellular localization analysis indicated that SlDRM1L1 and SlDRM5 located in the nucleus might have responsibility for RNA-directed DNA methylation (RdDM). Collectively, this paper provided a framework for gene discovery and functional characterization of C5-MTases and DNA demethylases in other Solanaceae species.
Collapse
Affiliation(s)
- Dongyan Cao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zheng Ju
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Chao Gao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaohong Mei
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Daqi Fu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| |
Collapse
|
185
|
Ferrándiz C, Fourquin C. Role of the FUL-SHP network in the evolution of fruit morphology and function. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4505-13. [PMID: 24482369 DOI: 10.1093/jxb/ert479] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Arabidopsis research in the last decade has started to unravel the genetic networks directing gynoecium and fruit patterning in this model species. Only recently, the work from several groups has also started to address the conservation of these networks in a wide number of species with very different fruit morphologies, and we are now beginning to understand how they might have evolved. This review summarizes recent advances in this field, focusing mainly on MADS-box genes with a well-known role in dehiscence zone development, while also discussing how these studies may contribute to expand our views on fruit evolution.
Collapse
Affiliation(s)
- Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), UPV-CSIC, Av. de los Naranjos s/n 46022 Valencia, Spain
| | - Chloé Fourquin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), UPV-CSIC, Av. de los Naranjos s/n 46022 Valencia, Spain
| |
Collapse
|
186
|
Kumar R, Khurana A, Sharma AK. Role of plant hormones and their interplay in development and ripening of fleshy fruits. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4561-75. [PMID: 25028558 DOI: 10.1093/jxb/eru277] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant hormones have been extensively studied for their roles in the regulation of various aspects of plant development. However, in the last decade important new insights have been made into their action during development and ripening, in both dry and fleshy fruits. Emerging evidence suggests that relative functions of plant hormones are not restricted to a particular stage, and a complex network of more than one plant hormone is involved in controlling various aspects of fruit development. Though some areas are extensively covered, considerable gaps in our knowledge and understanding still exist in the control of hormonal networks and crosstalk between different hormones during fruit expansion, maturation, and various other aspects of ripening. Here, we evaluate the new knowledge on their relative roles during tomato fruit development with a view to understand their mechanism of action in fleshy fruits. For a better understanding, pertinent evidences available on hormonal crosstalk during fruit development in other species are also discussed. We envisage that such detailed knowledge will help design new strategies for effective manipulation of fruit ripening.
Collapse
Affiliation(s)
- Rahul Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India. Current address: Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Ashima Khurana
- Zakir Husain Delhi College, University of Delhi, New Delhi 110002, India
| | - Arun K Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| |
Collapse
|
187
|
Kourmpetli S, Drea S. The fruit, the whole fruit, and everything about the fruit. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4491-503. [PMID: 24723396 DOI: 10.1093/jxb/eru144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fruits come in an impressive array of shapes, sizes, and consistencies, and also display a huge diversity in biochemical/metabolite profiles, wherein lies their value as rich sources of food, nutrition, and pharmaceuticals. This is in addition to their fundamental function in supporting and dispersing the developing and mature seeds for the next generation. Understanding developmental processes such as fruit development and ripening, particularly at the genetic level, was once largely restricted to model and crop systems for practical and commercial reasons, but with the expansion of developmental genetic and evo-devo tools/analyses we can now investigate and compare aspects of fruit development in species spanning the angiosperms. We can superimpose recent genetic discoveries onto the detailed characterization of fruit development and ripening conducted with primary considerations such as yield and harvesting efficiency in mind, as well as on the detailed description of taxonomically relevant characters. Based on our own experience we focus on two very morphologically distinct and evolutionary distant fruits: the capsule of opium poppy, and the grain or caryopsis of cereals. Both are of massive economic value, but because of very different constituents; alkaloids of varied pharmaceutical value derived from secondary metabolism in opium poppy capsules, and calorific energy fuel derived from primary metabolism in cereal grains. Through comparative analyses in these and other fruit types, interesting patterns of regulatory gene function diversification and conservation are beginning to emerge.
Collapse
Affiliation(s)
- Sofia Kourmpetli
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Sinéad Drea
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| |
Collapse
|
188
|
Karlova R, Chapman N, David K, Angenent GC, Seymour GB, de Maagd RA. Transcriptional control of fleshy fruit development and ripening. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4527-41. [PMID: 25080453 DOI: 10.1093/jxb/eru316] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fleshy fruits have evolved to be attractive to frugivores in order to enhance seed dispersal, and have become an indispensable part of the human diet. Here we review the recent advances in the understanding of transcriptional regulation of fleshy fruit development and ripening with a focus on tomato. While aspects of fruit development are probably conserved throughout the angiosperms, including the model plant Arabidopsis thaliana, it is shown that the likely orthologues of Arabidopsis genes have distinct functions in fleshy fruits. The model for the study of fleshy fruit development is tomato, because of the availability of single gene mutants and transgenic knock-down lines. In other species, our knowledge is often incomplete or absent. Tomato fruit size and shape are co-determined by transcription factors acting during formation of the ovary. Other transcription factors play a role in fruit chloroplast formation, and upon ripening impact quality aspects such as secondary metabolite content. In tomato, the transcription factors NON-RIPENING (NOR), COLORLESS NON-RIPENING (CNR), and RIPENING INHIBITOR (MADS-RIN) in concert with ethylene signalling regulate ripening, possibly in response to a developmental switch. Additional components include TOMATO AGAMOUS-LIKE1 (TAGL1), APETALA2a (AP2a), and FRUITFULL (FUL1 and FUL2). The links between this highly connected regulatory network and downstream effectors modulating colour, texture, and flavour are still relatively poorly understood. Intertwined with this network is post-transcriptional regulation by fruit-expressed microRNAs targeting several of these transcription factors. This important developmental process is also governed by changes in DNA methylation levels and possibly chromatin remodelling.
Collapse
Affiliation(s)
- Rumyana Karlova
- Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands Laboratory of Molecular Biology, Wageningen University, 6700 ET Wageningen, The Netherlands
| | - Natalie Chapman
- Plant and Crop Science Division, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Karine David
- University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University, 6700 ET Wageningen, The Netherlands Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
| | - Graham B Seymour
- Plant and Crop Science Division, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Ruud A de Maagd
- Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands Chair group Bioinformatics, Wageningen University, 6700 ET Wageningen, The Netherlands
| |
Collapse
|
189
|
Hen-Avivi S, Lashbrooke J, Costa F, Aharoni A. Scratching the surface: genetic regulation of cuticle assembly in fleshy fruit. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4653-64. [PMID: 24916070 DOI: 10.1093/jxb/eru225] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The hydrophobic cuticular membrane of land plants performs a number of important roles during fruit development, including protection from a range of abiotic and biotic stresses. The components of the fleshy fruit cuticle are synthesized and secreted from the epidermal cells. While the biosynthetic and transport pathways of the cuticle have been thoroughly investigated for a number of decades, the regulatory mechanisms allowing fine tuning of cuticle deposition are only now beginning to be elucidated. Transcription factors belonging to the APETALA2, homeodomain-leucine zipper IV, and MYB families have been shown to be important regulators of both cuticle biosynthesis and epidermal cell differentiation, highlighting the connection between these processes. The involvement of MADS-box transcription factors demonstrates the link between fruit ripening and cuticle deposition. Epigenetic and post-transcriptional regulatory mechanisms also play a role in the control of cuticle biosynthesis, in addition to phytohormones, such as abscisic acid, that have been shown to stimulate cuticle deposition. These various levels of genetic regulation allow the plant constantly to maintain and adjust the cuticle in response to environmental and developmental cues.
Collapse
Affiliation(s)
- Shelly Hen-Avivi
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Justin Lashbrooke
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, San Michele all'Adige, 38010, TN, Italy Institute for Wine Biotechnology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Fabrizio Costa
- Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, San Michele all'Adige, 38010, TN, Italy
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
190
|
The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 2014; 46:1034-8. [PMID: 25064008 PMCID: PMC7036041 DOI: 10.1038/ng.3046] [Citation(s) in RCA: 310] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/30/2014] [Indexed: 11/12/2022]
Abstract
Björn Usadel and colleagues report the genome sequence of the wild tomato species Solanum pennellii. The authors identify genes important for stress tolerance, metabolism and fruit maturation and suggest that transposable elements have had an important role in the evolution of the S. penellii stress response. Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum1. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance2. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
Collapse
|
191
|
Wang S, Lu G, Hou Z, Luo Z, Wang T, Li H, Zhang J, Ye Z. Members of the tomato FRUITFULL MADS-box family regulate style abscission and fruit ripening. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3005-14. [PMID: 24723399 PMCID: PMC4071821 DOI: 10.1093/jxb/eru137] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The tomato (Solanum lycopersicum) protein MADS-RIN plays important roles in fruit ripening. In this study, the functions of two homologous tomato proteins, FUL1 and FUL2, which contain conserved MIKC domains that typify plant MADS-box proteins, and which interact with MADS-RIN, were analysed. Transgenic functional analysis showed that FUL1 and FUL2 function redundantly in fruit ripening regulation, but exhibit distinct roles in the regulation of cellular differentiation and expansion. Over-expression of FUL2 in tomato resulted in a pointed tip at the blossom end of the fruit, together with a thinner pericarp, reduced stem diameter, and smaller leaves, but no obvious phenotypes resulted from FUL1 over-expression. Dual suppression of FUL1 and FUL2 substantially inhibited fruit ripening by blocking ethylene biosynthesis and decreasing carotenoid accumulation. In addition, the levels of transcript corresponding to ACC SYNTHASE2 (ACS2), which plays a key role in ethylene biosynthesis, were significantly decreased in the FUL1/FUL2 knock-down tomato fruits. Overall, our results suggest that FUL proteins can regulate tomato fruit ripening through fine-tuning ethylene biosynthesis and the expression of ripening-related genes.
Collapse
Affiliation(s)
- Shufen Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Gang Lu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng Hou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhidan Luo
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
192
|
Sotelo-Silveira M, Marsch-Martínez N, de Folter S. Unraveling the signal scenario of fruit set. PLANTA 2014; 239:1147-58. [PMID: 24659051 DOI: 10.1007/s00425-014-2057-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/05/2014] [Indexed: 05/22/2023]
Abstract
Long-term goals to impact or modify fruit quality and yield have been the target of researchers for many years. Different approaches such as traditional breeding,mutation breeding, and transgenic approaches have revealed a regulatory network where several hormones concur in a complex way to regulate fruit set and development,and these networks are shared in some way among species with different kinds of fruits. Understanding the molecular and biochemical networks of fruit set and development could be very useful for breeders to meet the current and future challenges of agricultural problems.
Collapse
|
193
|
Ferreira e Silva GF, Silva EM, Azevedo MDS, Guivin MAC, Ramiro DA, Figueiredo CR, Carrer H, Peres LEP, Nogueira FTS. microRNA156-targeted SPL/SBP box transcription factors regulate tomato ovary and fruit development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:604-18. [PMID: 24580734 DOI: 10.1111/tpj.12493] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 01/18/2014] [Accepted: 02/19/2014] [Indexed: 05/18/2023]
Abstract
Fruit ripening in tomato (Solanum lycopersicum L.) is well understood at the molecular level. However, information regarding genetic pathways associated with tomato ovary and early fruit development is still lacking. Here, we investigate the possible role(s) of the microRNA156/SQUAMOSA promoter-binding protein-like (SPL or SBP box) module (miR156 node) in tomato ovary development. miR156-targeted S. lycopersicum SBP genes were dynamically expressed in developing flowers and ovaries, and miR156 was mainly expressed in meristematic tissues of the ovary, including placenta and ovules. Transgenic tomato cv. Micro-Tom plants over-expressing the AtMIR156b precursor exhibited abnormal flower and fruit morphology, with fruits characterized by growth of extra carpels and ectopic structures. Scanning electron microscopy and histological analyses showed the presence of meristem-like structures inside the ovaries, which are probably responsible for the ectopic organs. Interestingly, expression of genes associated with meristem maintenance and formation of new organs, such as LeT6/TKN2 (a KNOX-like class I gene) and GOBLET (a NAM/CUC-like gene), was induced in developing ovaries of transgenic plants as well as in the ovaries of the natural mutant Mouse ear (Me), which also displays fruits with extra carpels. Conversely, expression of the MADS box genes MACROCALYX (MC) and FUL1/TDR4, and the LEAFY ortholog FALSIFLORA, was repressed in the developing ovaries of miR156 over-expressors, suggesting similarities with Arabidopsis at this point of the miR156/SPL pathway but with distinct functional consequences in reproductive development. Altogether, these observations suggest that the miR156 node is involved in maintenance of the meristematic state of ovary tissues, thereby controlling initial steps of fleshy fruit development and determinacy.
Collapse
Affiliation(s)
- Geraldo Felipe Ferreira e Silva
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, State University of Sao Paulo, Botucatu, Sao Paulo, 18618-970, Brazil; Centro de Biotecnologia Agricola, Escola Superior de Agricultura 'Luiz de Queiroz', University of Sao Paulo, 13418-900, Piracicaba, Sao Paulo, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
194
|
Dong T, Chen G, Tian S, Xie Q, Yin W, Zhang Y, Hu Z. A non-climacteric fruit gene CaMADS-RIN regulates fruit ripening and ethylene biosynthesis in climacteric fruit. PLoS One 2014; 9:e95559. [PMID: 24751940 PMCID: PMC3994064 DOI: 10.1371/journal.pone.0095559] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 03/28/2014] [Indexed: 11/19/2022] Open
Abstract
MADS-box genes have been reported to play a major role in the molecular circuit of developmental regulation. Especially, SEPALLATA (SEP) group genes play a central role in the developmental regulation of ripening in both climacteric and non-climacteric fruits. However, the mechanisms underlying the regulation of SEP genes to non-climacteric fruits ripening are still unclear. Here a SEP gene of pepper, CaMADS-RIN, has been cloned and exhibited elevated expression at the onset of ripening of pepper. To further explore the function of CaMADS-RIN, an overexpressed construct was created and transformed into ripening inhibitor (rin) mutant tomato plants. Broad ripening phenotypes were observed in CaMADS-RIN overexpressed rin fruits. The accumulation of carotenoid and expression of PDS and ZDS were enhanced in overexpressed fruits compared with rin mutant. The transcripts of cell wall metabolism genes (PG, EXP1 and TBG4) and lipoxygenase genes (TomloxB and TomloxC) accumulated more abundant compared to rin mutant. Besides, both ethylene-dependent genes including ACS2, ACO1, E4 and E8 and ethylene-independent genes such as HDC and Nor were also up-regulated in transgenic fruits at different levels. Moreover, transgenic fruits showed approximately 1–3 times increase in ethylene production compared with rin mutant fruits. Yeast two-hybrid screen results indicated that CaMADS-RIN could interact with TAGL1, FUL1 and itself respectively as SlMADS-RIN did in vitro. These results suggest that CaMADS-RIN affects fruit ripening of tomato both in ethylene-dependent and ethylene-independent aspects, which will provide a set of significant data to explore the role of SEP genes in ripening of non-climacteric fruits.
Collapse
Affiliation(s)
- Tingting Dong
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Guoping Chen
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Shibing Tian
- The Institute of Vegetable Research, Chongqing Academy of Agricultural Sciences, Chongqing, People’s Republic of China
| | - Qiaoli Xie
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Wencheng Yin
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Yanjie Zhang
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Zongli Hu
- Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
- * E-mail:
| |
Collapse
|
195
|
Zhang Y, Hu Z, Chu G, Huang C, Tian S, Zhao Z, Chen G. Anthocyanin accumulation and molecular analysis of anthocyanin biosynthesis-associated genes in eggplant (Solanum melongena L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:2906-12. [PMID: 24654563 DOI: 10.1021/jf404574c] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Eggplant (Solanum melongena L.) is an edible fruit vegetable cultivated and consumed worldwide. The purple eggplant is more eye-catching and popular for the health-promoting anthocyanins contained in the fruit skin. Two kinds of anthocyanin were separated and identified from purple cultivar (Zi Chang) by high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. To investigate the molecular mechanisms of anthocyanin accumulation in eggplant, the transcripts of anthocyanin biosynthetic and regulatory genes were analyzed in the fruit skin and the flesh of the purple cultivar and the white cultivar (Bai Xue). Compared with the other tissues, SmMYB1 and all anthocyanin biosynthetic genes except PAL were dramatically upregulated in the fruit skin of the purple cultivar. Overexpression of SmMYB1 activated abundant anthocyanin accumulation in the regenerating shoots of eggplant. These results prove that transcriptional activation of SmMYB1 accounts for constitutive upregulation of most anthocyanin biosynthetic genes and the onset of anthocyanin biosynthesis in the purple cultivar.
Collapse
Affiliation(s)
- Yanjie Zhang
- Bioengineering College, Chongqing University , Campus A, 174 Shapingba Main Street, Chongqing 400044, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
196
|
Overexpression of a novel MADS-box gene SlFYFL delays senescence, fruit ripening and abscission in tomato. Sci Rep 2014; 4:4367. [PMID: 24621662 PMCID: PMC3952145 DOI: 10.1038/srep04367] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/20/2014] [Indexed: 01/05/2023] Open
Abstract
MADS-domain proteins are important transcription factors involved in many biological processes of plants. In our study, a tomato MADS-box gene, SlFYFL, was isolated. SlFYFL is expressed in all tissues of tomato and significantly higher in mature leave, fruit of different stages, AZ (abscission zone) and sepal. Delayed leaf senescence and fruit ripening, increased storability and longer sepals were observed in 35S:FYFL tomato. The accumulation of carotenoid was reduced, and ethylene content, ethylene biosynthetic and responsive genes were down-regulated in 35S:FYFL fruits. Abscission zone (AZ) did not form normally and abscission zone development related genes were declined in AZs of 35S:FYFL plants. Yeast two-hybrid assay revealed that SlFYFL protein could interact with SlMADS-RIN, SlMADS1 and SlJOINTLESS, respectively. These results suggest that overexpression of SlFYFL regulate fruit ripening and development of AZ via interactions with the ripening and abscission zone-related MADS box proteins.
Collapse
|
197
|
Nguyen CV, Vrebalov JT, Gapper NE, Zheng Y, Zhong S, Fei Z, Giovannoni JJ. Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening. THE PLANT CELL 2014; 26:585-601. [PMID: 24510723 PMCID: PMC3967027 DOI: 10.1105/tpc.113.118794] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/20/2013] [Accepted: 01/15/2014] [Indexed: 05/18/2023]
Abstract
Fruit ripening is the summation of changes rendering fleshy fruit tissues attractive and palatable to seed dispersing organisms. For example, sugar content is influenced by plastid numbers and photosynthetic activity in unripe fruit and later by starch and sugar catabolism during ripening. Tomato fruit are sinks of photosynthate, yet unripe green fruit contribute significantly to the sugars that ultimately accumulate in the ripe fruit. Plastid numbers and chlorophyll content are influenced by numerous environmental and genetic factors and are positively correlated with photosynthesis and photosynthate accumulation. GOLDEN2-LIKE (GLK) transcription factors regulate plastid and chlorophyll levels. Tomato (Solanum lycopersicum), like most plants, contains two GLKs (i.e., GLK1 and GLK2/UNIFORM). Mutant and transgene analysis demonstrated that these genes encode functionally similar peptides, though differential expression renders GLK1 more important in leaves, while GLK2 is predominant in fruit. A latitudinal gradient of GLK2 expression influences the typical uneven coloration of green and ripe wild-type fruit. Transcriptome profiling revealed a broader fruit gene expression gradient throughout development. The gradient influenced general ripening activities beyond plastid development and was consistent with the easily observed yet poorly studied ripening gradient present in tomato and many fleshy fruits.
Collapse
Affiliation(s)
- Cuong V. Nguyen
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | | | - Nigel E. Gapper
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Silin Zhong
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
- School of Life Sciences, Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
- U.S. Department of Agriculture/Agriculture Research Service, Robert W. Holley Centre for Agriculture and Health, Ithaca, New York 14853
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
- U.S. Department of Agriculture/Agriculture Research Service, Robert W. Holley Centre for Agriculture and Health, Ithaca, New York 14853
- Address correspondence to
| |
Collapse
|
198
|
Shima Y, Fujisawa M, Kitagawa M, Nakano T, Kimbara J, Nakamura N, Shiina T, Sugiyama J, Nakamura T, Kasumi T, Ito Y. Tomato FRUITFULL homologs regulate fruit ripening via ethylene biosynthesis. Biosci Biotechnol Biochem 2014; 78:231-7. [DOI: 10.1080/09168451.2014.878221] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Certain MADS-box transcription factors play central roles in regulating fruit ripening. RIPENING INHIBITOR (RIN), a tomato MADS-domain protein, acts as a global regulator of ripening, affecting the climacteric rise of ethylene, pigmentation changes, and fruit softening. Previously, we showed that two MADS-domain proteins, the FRUITFULL homologs FUL1 and FUL2, form complexes with RIN. Here, we characterized the FUL1/FUL2 loss-of-function phenotype in co-suppressed plants. The transgenic plants produced ripening-defective fruits accumulating little or no lycopene. Unlike a previous study on FUL1/FUL2 suppressed tomatoes, our transgenic fruits showed very low levels of ethylene production, and this was associated with suppression of the genes for 1-aminocyclopropane-1-carboxylic acid synthase, a rate-limiting enzyme in ethylene synthesis. FUL1/FUL2 suppression also caused the fruit to soften in a manner independent of ripening, possibly due to reduced cuticle thickness in the peel of the suppressed tomatoes.
Collapse
Affiliation(s)
- Yoko Shima
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Masaki Fujisawa
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | | | - Toshitsugu Nakano
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Junji Kimbara
- Research Institute, Kagome Co., Ltd., Nasushiobara, Japan
| | - Nobutaka Nakamura
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takeo Shiina
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Junichi Sugiyama
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Toshihide Nakamura
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takafumi Kasumi
- Department of Chemistry and Life Science, Nihon University, Fujisawa, Japan
| | - Yasuhiro Ito
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| |
Collapse
|
199
|
Wang Y, Wang W, Cai J, Zhang Y, Qin G, Tian S. Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening. Genome Biol 2014; 15:548. [PMID: 25464976 DOI: 10.1186/preaccept-3895766441330481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits. RESULTS Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. We show that the proteins whose abundances change during ripening stages are involved in various cellular processes. We additionally evaluate changes in the nuclear proteome in the ripening-deficient mutant, ripening-inhibitor (rin), carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assays, we provide evidence that RIN directly binds to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affects protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and a genome-wide survey of the E2 gene family in tomatoes identified five more E2s as direct targets of RIN. Virus-induced gene silencing assays show that two E2s are involved in the regulation of fruit ripening. CONCLUSIONS Our results uncover a novel function of protein ubiquitination, identifying specific E2s as regulators of fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.
Collapse
|
200
|
Wang Y, Wang W, Cai J, Zhang Y, Qin G, Tian S. Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening. Genome Biol 2014; 15:548. [PMID: 25464976 PMCID: PMC4269173 DOI: 10.1186/s13059-014-0548-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 11/18/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits. RESULTS Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. We show that the proteins whose abundances change during ripening stages are involved in various cellular processes. We additionally evaluate changes in the nuclear proteome in the ripening-deficient mutant, ripening-inhibitor (rin), carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assays, we provide evidence that RIN directly binds to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affects protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and a genome-wide survey of the E2 gene family in tomatoes identified five more E2s as direct targets of RIN. Virus-induced gene silencing assays show that two E2s are involved in the regulation of fruit ripening. CONCLUSIONS Our results uncover a novel function of protein ubiquitination, identifying specific E2s as regulators of fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.
Collapse
Affiliation(s)
- Yuying Wang
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
| | - Weihao Wang
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| | - Jianghua Cai
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| | - Yanrui Zhang
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| | - Guozheng Qin
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
| | - Shiping Tian
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| |
Collapse
|