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Alsamir M, Mahmood T, Trethowan R, Ahmad N. An overview of heat stress in tomato ( Solanum lycopersicum L.). Saudi J Biol Sci 2021; 28:1654-1663. [PMID: 33732051 PMCID: PMC7938145 DOI: 10.1016/j.sjbs.2020.11.088] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/23/2022] Open
Abstract
Heat stress has been defined as the rise of temperature for a period of time higher than a threshold level, thereby permanently affecting the plant growth and development. Day or night temperature is considered as the major limiting factor for plant growth. Earlier studies reported that night temperature is an important factor in the heat reaction of the plants. Tomato cultivars capable of setting viable fruits under night temperatures above 21 °C are considered as heat-tolerant cultivars. The development of breeding objectives is generally summarized in four points: (a) cultivars with higher yield, (b) disease resistant varieties in the 1970s, (c) long shelf-life in 1980s, and (d) nutritive and taste quality during 1990s. Some unique varieties like the dwarf "Micro-Tom", and the first transgenic tomato (FlavrSavr) were developed through breeding; they were distributed late in the 1980s. High temperature significantly affects seed, pollen viability and root expansion. Researchers have employed different parameters to evaluate the tolerance to heat stress, including membrane thermo stability, floral characteristics (Stigma exertion and antheridia cone splitting), flower number, and fruit yield per plant. Reports on pollen viability and fruit set/plant under heat stress by comparing the pollen growth and tube development in heat-treated and non-heat-stressed conditions are available in literature. The electrical conductivity (EC) have been used to evaluate the tolerance of some tomato cultivars in vitro under heat stress conditions as an indication of cell damage due to electrolyte leakage; they classified the cultivars into three groups: (a) heat tolerant, (b) moderately heat tolerant, and (c) heat sensitive. It is important to determine the range in genetic diversity for heat tolerance in tomatoes. Heat stress experiments under field conditions offer breeders information to identify the potentially heat tolerant germplasm.
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Affiliation(s)
- Muhammed Alsamir
- Plant Breeding Institute, Faculty of Agriculture and Environment, University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia
| | - Tariq Mahmood
- Plant Breeding Institute, Faculty of Agriculture and Environment, University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia
| | - Richard Trethowan
- Plant Breeding Institute, Faculty of Agriculture and Environment, University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia
| | - Nabil Ahmad
- Plant Breeding Institute, Faculty of Agriculture and Environment, University of Sydney, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia
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Salhi A, Negrão S, Essack M, Morton MJL, Bougouffa S, Razali R, Radovanovic A, Marchand B, Kulmanov M, Hoehndorf R, Tester M, Bajic VB. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. Sci Rep 2017; 7:5968. [PMID: 28729549 PMCID: PMC5519719 DOI: 10.1038/s41598-017-05448-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/25/2017] [Indexed: 12/29/2022] Open
Abstract
Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published literature. We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms. To illustrate the utility of DES-TOMATO, we provide several examples how one can efficiently use this KB to retrieve known or potentially novel information. DES-TOMATO is free for academic and nonprofit users and can be accessed at http://cbrc.kaust.edu.sa/des_tomato/, using any of the mainstream web browsers, including Firefox, Safari and Chrome.
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Affiliation(s)
- Adil Salhi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Sónia Negrão
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Mitchell J L Morton
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Salim Bougouffa
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Rozaimi Razali
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Aleksandar Radovanovic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | | | - Maxat Kulmanov
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Robert Hoehndorf
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, 23955-6900, Saudi Arabia
| | - Mark Tester
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia.
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, 23955-6900, Saudi Arabia.
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Prem Krishnan BV, Arunachalam V. Database of predicted SCAR markers in five fruit and three vegetable crops. J Genet 2016; 95:171-5. [PMID: 27019446 DOI: 10.1007/s12041-016-0620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Rodriguez-Esteban R. Biocuration with insufficient resources and fixed timelines. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav116. [PMID: 26708987 PMCID: PMC4691339 DOI: 10.1093/database/bav116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/17/2015] [Indexed: 11/14/2022]
Abstract
Biological curation, or biocuration, is often studied from the perspective of creating and maintaining databases that have the goal of mapping and tracking certain areas of biology. However, much biocuration is, in fact, dedicated to finite and time-limited projects in which insufficient resources demand trade-offs. This typically more ephemeral type of curation is nonetheless of importance in biomedical research. Here, I propose a framework to understand such restricted curation projects from the point of view of return on curation (ROC), value, efficiency and productivity. Moreover, I suggest general strategies to optimize these curation efforts, such as the ‘multiple strategies’ approach, as well as a metric called overhead that can be used in the context of managing curation resources.
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Affiliation(s)
- Raul Rodriguez-Esteban
- Roche Pharmaceutical Research and Early Development, pRED Informatics, Roche Innovation Center Basel, Basel 4070, Switzerland
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Fernandez-Pozo N, Menda N, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA. The Sol Genomics Network (SGN)--from genotype to phenotype to breeding. Nucleic Acids Res 2014; 43:D1036-41. [PMID: 25428362 PMCID: PMC4383978 DOI: 10.1093/nar/gku1195] [Citation(s) in RCA: 382] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Sol Genomics Network (SGN, http://solgenomics.net) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives. SGN hosts whole genome data for an increasing number of Solanaceae family members including tomato, potato, pepper, eggplant, tobacco and Nicotiana benthamiana. The database also stores loci and phenotype data, which researchers can upload and edit with user-friendly web interfaces. Tools such as BLAST, GBrowse and JBrowse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools are available. A new tool was recently implemented to improve Virus-Induced Gene Silencing (VIGS) constructs called the SGN VIGS tool. With the growing genomic and phenotypic data in the database, SGN is now advancing to develop new web-based breeding tools and implement the code and database structure for other species or clade-specific databases.
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Affiliation(s)
| | - Naama Menda
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Jeremy D Edwards
- Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
| | - Surya Saha
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Isaak Y Tecle
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | | | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0002, USA
| | | | - Anuradha Pujar
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Hartmut Foerster
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Aimin Yan
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA
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Lall R, Thomas G, Singh S, Singh A, Wadhwa G. Comparative genome analysis of Solanum lycopersicum and Solanum tuberosum. Bioinformation 2013; 9:923-8. [PMID: 24307771 PMCID: PMC3842579 DOI: 10.6026/97320630009923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 10/30/2013] [Indexed: 11/23/2022] Open
Abstract
Solanum lycopersicum and Solanum tuberosum are agriculturally important crop species as they are rich sources of starch, protein, antioxidants, lycopene, beta-carotene, vitamin C, and fiber. The genomes of S. lycopersicum and S. tuberosum are currently available. However the linear strings of nucleotides that together comprise a genome sequence are of limited significance by themselves. Computational and bioinformatics approaches can be used to exploit the genomes for fundamental research for improving their varieties. The comparative genome analysis, Pfam analysis of predicted reviewed paralogous proteins was performed. It was found that S. lycopersicum proteins belong to more families, domains and clans in comparison with S. tuberosum. It was also found that mostly intergenic regions are conserved in two genomes followed by exons, intron and UTR. This can be exploited to predict regions between genomes that are similar to each other and to study the evolutionary relationship between two genomes, leading towards the development of disease resistance, stress tolerance and improved varieties of tomato.
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Affiliation(s)
- Rohit Lall
- Department of Molecular and Cellular Engineering, SHIATS, Allahabad-211007
| | - George Thomas
- Department of Molecular and Cellular Engineering, SHIATS, Allahabad-211007
| | - Satendra Singh
- Department of Computational Biology & Bioinformatics, SHIATS, Allahabad-211007
| | - Archana Singh
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi-110012
| | - Gulshan Wadhwa
- Department of Biotechnology, Ministry of Science and Technology, New Delhi – 110003
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