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García-Gómez BE, Salazar JA, Nicolás-Almansa M, Razi M, Rubio M, Ruiz D, Martínez-Gómez P. Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective. Int J Mol Sci 2020; 22:E333. [PMID: 33396946 PMCID: PMC7794732 DOI: 10.3390/ijms22010333] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/21/2020] [Accepted: 12/26/2020] [Indexed: 02/07/2023] Open
Abstract
In plants, fruit ripening is a coordinated developmental process that requires the change in expression of hundreds to thousands of genes to modify many biochemical and physiological signal cascades such as carbohydrate and organic acid metabolism, cell wall restructuring, ethylene production, stress response, and organoleptic compound formation. In Prunus species (including peaches, apricots, plums, and cherries), fruit ripening leads to the breakdown of complex carbohydrates into sugars, fruit firmness reductions (softening by cell wall degradation and cuticle properties alteration), color changes (loss of green color by chlorophylls degradation and increase in non-photosynthetic pigments like anthocyanins and carotenoids), acidity decreases, and aroma increases (the production and release of organic volatile compounds). Actually, the level of information of molecular events at the transcriptional, biochemical, hormonal, and metabolite levels underlying ripening in Prunus fruits has increased considerably. However, we still poorly understand the molecular switch that occurs during the transition from unripe to ripe fruits. The objective of this review was to analyze of the molecular bases of fruit quality in Prunus species through an integrated metabolic, genomic, transcriptomic, and epigenetic approach to better understand the molecular switch involved in the ripening process with important consequences from a breeding point of view.
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Affiliation(s)
- Beatriz E. García-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - Juan A. Salazar
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - María Nicolás-Almansa
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - Mitra Razi
- Department of Horticulture, Faculty of Agriculture, University of Zajan, Zanjan 45371-38791, Iran;
| | - Manuel Rubio
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - David Ruiz
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
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Sahebi M, Hanafi MM, Azizi P, Hakim A, Ashkani S, Abiri R. Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives. Mol Biotechnol 2016; 57:880-903. [PMID: 26271955 DOI: 10.1007/s12033-015-9884-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia,
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Shiratake K, Suzuki M. Omics studies of citrus, grape and rosaceae fruit trees. BREEDING SCIENCE 2016; 66:122-38. [PMID: 27069397 PMCID: PMC4780796 DOI: 10.1270/jsbbs.66.122] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/01/2015] [Indexed: 05/06/2023]
Abstract
Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.
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Affiliation(s)
- Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
- Corresponding author (e-mail: )
| | - Mami Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
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Abstract
The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.
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Affiliation(s)
- Manoj K Rai
- a Department of Botany , Biotechnology Centre, Jai Narain Vyas University , Jodhpur , Rajasthan , India
| | - N S Shekhawat
- a Department of Botany , Biotechnology Centre, Jai Narain Vyas University , Jodhpur , Rajasthan , India
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Klie S, Osorio S, Tohge T, Drincovich MF, Fait A, Giovannoni JJ, Fernie AR, Nikoloski Z. Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species. PLANT PHYSIOLOGY 2014; 164:55-68. [PMID: 24243932 PMCID: PMC3875825 DOI: 10.1104/pp.113.226142] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 11/13/2013] [Indexed: 05/18/2023]
Abstract
Computational analyses of molecular phenotypes traditionally aim at identifying biochemical components that exhibit differential expression under various scenarios (e.g. environmental and internal perturbations) in a single species. High-throughput metabolomics technologies allow the quantification of (relative) metabolite levels across developmental stages in different tissues, organs, and species. Novel methods for analyzing the resulting multiple data tables could reveal preserved dynamics of metabolic processes across species. The problem we address in this study is 2-fold. (1) We derive a single data table, referred to as a compromise, which captures information common to the investigated set of multiple tables containing data on different fruit development and ripening stages in three climacteric (i.e. peach [Prunus persica] and two tomato [Solanum lycopersicum] cultivars, Ailsa Craig and M82) and two nonclimacteric (i.e. strawberry [Fragaria × ananassa] and pepper [Capsicum chilense]) fruits; in addition, we demonstrate the power of the method to discern similarities and differences between multiple tables by analyzing publicly available metabolomics data from three tomato ripening mutants together with two tomato cultivars. (2) We identify the conserved dynamics of metabolic processes, reflected in the data profiles of the corresponding metabolites that contribute most to the determined compromise. Our analysis is based on an extension to principal component analysis, called STATIS, in combination with pathway overenrichment analysis. Based on publicly available metabolic profiles for the investigated species, we demonstrate that STATIS can be used to identify the metabolic processes whose behavior is similarly affected during fruit development and ripening. These findings ultimately provide insights into the pathways that are essential during fruit development and ripening across species.
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Affiliation(s)
- Sebastian Klie
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | | | - Takayuki Tohge
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - María F. Drincovich
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - Aaron Fait
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - James J. Giovannoni
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - Alisdair R. Fernie
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - Zoran Nikoloski
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
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