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Deng CH, Naithani S, Kumari S, Cobo-Simón I, Quezada-Rodríguez EH, Skrabisova M, Gladman N, Correll MJ, Sikiru AB, Afuwape OO, Marrano A, Rebollo I, Zhang W, Jung S. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database (Oxford) 2023; 2023:baad088. [PMID: 38079567 PMCID: PMC10712715 DOI: 10.1093/database/baad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.
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Affiliation(s)
- Cecilia H Deng
- Molecular and Digital Breeding, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
| | - Irene Cobo-Simón
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute of Forest Science (ICIFOR-INIA, CSIC), Madrid, Spain
| | - Elsa H Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria Skrabisova
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Nick Gladman
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - Melanie J Correll
- Agricultural and Biological Engineering Department, University of Florida, 1741 Museum Rd, Gainesville, FL 32611, USA
| | | | | | - Annarita Marrano
- Phoenix Bioinformatics, 39899 Balentine Drive, Suite 200, Newark, CA 94560, USA
| | | | - Wentao Zhang
- National Research Council Canada, 110 Gymnasium Pl, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sook Jung
- Department of Horticulture, Washington State University, 303c Plant Sciences Building, Pullman, WA 99164-6414, USA
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Tomatoes: An Extensive Review of the Associated Health Impacts of Tomatoes and Factors That Can Affect Their Cultivation. BIOLOGY 2022; 11:biology11020239. [PMID: 35205105 PMCID: PMC8869745 DOI: 10.3390/biology11020239] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023]
Abstract
Simple Summary The research outlined in this review paper discusses potential health benefits associated with a diet enriched with tomatoes and tomato products. This includes details of previous studies investigating the anticancer properties of tomatoes, protection against cardiovascular and neurodegenerative diseases and diabetes, maintenance of a healthy gut microbiome, and improved skin health, fertility, immune response, and exercise recovery. The specific parts of a tomato fruit that contribute these health benefits are also outlined. The potential disadvantages to a tomato-rich diet are detailed, especially the consumption of supplements that contain compounds found in tomatoes, such as lycopene. This review also discusses how the cultivation of tomato plants can affect the nutritional value of the fruit harvested. Different environmental growing conditions such as light intensity, growing media, and temperature are explained in terms of the impact they have on the quality of fruit, its nutrient content, and hence the potential health benefits acquired from eating the fruit. Abstract This review outlines the health benefits associated with the regular consumption of tomatoes and tomato products. The first section provides a detailed account of the horticultural techniques that can impact the quality of the fruit and its nutritional properties, including water availability, light intensity, temperature, and growing media. The next section provides information on the components of tomato that are likely to contribute to its health effects. The review then details some of the health benefits associated with tomato consumption, including anticancer properties, cardiovascular and neurodegenerative diseases and skin health. This review also discusses the impact tomatoes can have on the gut microbiome and associated health benefits, including reducing the risk of inflammatory bowel diseases. Other health benefits of eating tomatoes are also discussed in relation to effects on diabetes, the immune response, exercise recovery, and fertility. Finally, this review also addresses the negative effects that can occur as a result of overconsumption of tomato products and lycopene supplements.
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Zhang Q, Xu M, Xia X, Komatsuda T, Varshney RK, Shi K. Crop genetics research in Asia: improving food security and nutrition. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1339-1344. [PMID: 32306095 DOI: 10.1007/s00122-020-03597-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Mingliang Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
| | - Kai Shi
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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Li Q, Sapkota M, van der Knaap E. Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement. HORTICULTURE RESEARCH 2020; 7:36. [PMID: 32194972 PMCID: PMC7072075 DOI: 10.1038/s41438-020-0258-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/09/2020] [Accepted: 02/11/2020] [Indexed: 05/14/2023]
Abstract
Directed breeding of horticultural crops is essential for increasing yield, nutritional content, and consumer-valued characteristics such as shape and color of the produce. However, limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches. Natural genetic changes in cis-regulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression. Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner. The advent of CRISPR/Cas-mediated cis-regulatory region engineering (cis-engineering) provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement. Here, we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops. We describe strategies and limitations for its use in crop improvement, including de novo cis-regulatory element (CRE) discovery, precise genome editing, and transgene-free genome editing. In addition, we discuss the challenges and prospects regarding current technologies and achievements. CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.
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Affiliation(s)
- Qiang Li
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA USA
| | - Manoj Sapkota
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA USA
- Department of Horticulture, University of Georgia, Athens, GA USA
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