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Mansueto L, Kretzschmar T, Mauleon R, King GJ. Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research. GIGABYTE 2024; 2024:gigabyte137. [PMID: 39469541 PMCID: PMC11515022 DOI: 10.46471/gigabyte.137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 10/06/2024] [Indexed: 10/30/2024] Open
Abstract
Global changes in cannabis legislation after decades of stringent regulation and heightened demand for its industrial and medicinal applications have spurred recent genetic and genomics research. An international research community emerged and identified the need for a web portal to host cannabis-specific datasets that seamlessly integrates multiple data sources and serves omics-type analyses, fostering information sharing. The Tripal platform was used to host public genome assemblies, gene annotations, quantitative trait loci and genetic maps, gene and protein expression data, metabolic profiles and their sample attributes. Single nucleotide polymorphisms were called using public resequencing datasets on three genomes. Additional applications, such as SNP-Seek and MapManJS, were embedded into Tripal. A multi-omics data integration web-service Application Programming Interface (API), developed on top of existing Tripal modules, returns generic tables of samples, properties and values. Use cases demonstrate the API's utility for various omics analyses, enabling researchers to perform multi-omics analyses efficiently. Availability and implementation The web portal can be accessed at www.icgrc.info.
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Affiliation(s)
- Locedie Mansueto
- Southern Cross University, Military Road, Lismore New South Wales, 2480, Australia
| | - Tobias Kretzschmar
- Southern Cross University, Military Road, Lismore New South Wales, 2480, Australia
| | - Ramil Mauleon
- Southern Cross University, Military Road, Lismore New South Wales, 2480, Australia
- International Rice Research Institute, Pili Drive, Los Baños Laguna, 4031, Philippines
| | - Graham J. King
- Southern Cross University, Military Road, Lismore New South Wales, 2480, Australia
- Recombics, Alstonville, New South Wales, 2480, Australia
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Rolling WR, Senalik D, Iorizzo M, Ellison S, Van Deynze A, Simon PW. CarrotOmics: a genetics and comparative genomics database for carrot ( Daucus carota). Database (Oxford) 2022; 2022:6693759. [PMID: 36069936 PMCID: PMC9450951 DOI: 10.1093/database/baac079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 08/19/2022] [Accepted: 09/01/2022] [Indexed: 11/15/2022]
Abstract
Abstract
CarrotOmics (https://carrotomics.org/) is a comprehensive database for carrot (Daucus carota L.) breeding and research. CarrotOmics was developed using resources available at the MainLab Bioinformatics core (https://www.bioinfo.wsu.edu/) and is implemented using Tripal with Drupal modules. The database delivers access to download or visualize the carrot reference genome with gene predictions, gene annotations and sequence assembly. Other genomic resources include information for 11 224 genetic markers from 73 linkage maps or genotyping-by-sequencing and descriptions of 371 mapped loci. There are records for 1601 Apiales species (or subspecies) and descriptions of 9408 accessions from 11 germplasm collections representing more than 600 of these species. Additionally, 204 Apiales species have phenotypic information, totaling 28 517 observations from 10 041 biological samples. Resources on CarrotOmics are freely available, search functions are provided to find data of interest and video tutorials are available to describe the search functions and genomic tools. CarrotOmics is a timely resource for the Apiaceae research community and for carrot geneticists developing improved cultivars with novel traits addressing challenges including an expanding acreage in tropical climates, an evolving consumer interested in sustainably grown vegetables and a dynamic environment due to climate change. Data from CarrotOmics can be applied in genomic-assisted selection and genetic research to improve basic research and carrot breeding efficiency.
Database URL
https://carrotomics.org/
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Affiliation(s)
- William R Rolling
- Vegetable Crop Research Unit, USDA-ARS , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
- Department of Horticulture, University of Wisconsin-Madison , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
| | - Douglas Senalik
- Vegetable Crop Research Unit, USDA-ARS , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
- Department of Horticulture, University of Wisconsin-Madison , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
| | - Massimo Iorizzo
- Department of Horticultural Science and Plants for Human Health Institute, North Carolina State University , NC Research Campus, 600 Laureate Way, Kannapolis, NC 28081, USA
| | - Shelby Ellison
- Department of Horticulture, University of Wisconsin-Madison , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
| | - Allen Van Deynze
- College of Agricultural & Environmental Sciences, Seed Biotechnology Center, University of California-Davis , 150 Mrak Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Philipp W Simon
- Vegetable Crop Research Unit, USDA-ARS , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
- Department of Horticulture, University of Wisconsin-Madison , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
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Yu J, Jung S, Cheng CH, Lee T, Zheng P, Buble K, Crabb J, Humann J, Hough H, Jones D, Campbell JT, Udall J, Main D. CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122805. [PMID: 34961276 PMCID: PMC8705096 DOI: 10.3390/plants10122805] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/11/2021] [Accepted: 12/12/2021] [Indexed: 05/12/2023]
Abstract
Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.
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Affiliation(s)
- Jing Yu
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Taein Lee
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Katheryn Buble
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - James Crabb
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Jodi Humann
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Heidi Hough
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Don Jones
- Cotton Incorporated, Cary, NC 27513, USA;
| | - J. Todd Campbell
- The Agricultural Research Service of U.S. Department of Agriculture, Florence, SC 29501, USA;
| | - Josh Udall
- The Agricultural Research Service of U.S. Department of Agriculture, College Station, TX 77845, USA;
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
- Correspondence: ; Tel.: +1-509-335-2774
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Ren H, He Y, Qi X, Zheng X, Zhang S, Yu Z, Hu F. The bayberry database: a multiomic database for Myrica rubra, an important fruit tree with medicinal value. BMC PLANT BIOLOGY 2021; 21:452. [PMID: 34615485 PMCID: PMC8493685 DOI: 10.1186/s12870-021-03232-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/28/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important fruit tree in China, and has high medicinal value. At present, the genome, transcriptome and germplasm resources of bayberry have been reported. In order to make more convenient use of these data, the Bayberry Database was established. RESULTS The Bayberry Database is a comprehensive and intuitive data platform for examining the diverse annotated genome and germplasm resources of this species. This database contains nine central functional domains to interact with multiomic data: home, genome, germplasm, markers, tools, map, expression, reference, and contact. All domains provide pathways to a variety of data types composed of a reference genome sequence, transcriptomic data, gene patterns, phenotypic data, fruit images of Myrica rubra varieties, gSSR data, gene maps with annotation and evolutionary analyses. The tools module includes BLAST search, keyword search, sequence fetch and enrichment analysis functions. CONCLUSIONS The web address of the database is as follows http://www.bayberrybase.cn/ . The Myrica rubra database is an intelligent, interactive, and user-friendly system that enables researchers, breeders and horticultural personnel to browse, search and retrieve relevant and useful information and thus facilitate genomic research and breeding efforts concerning Myrica rubra. This database will be of great help to bayberry research and breeding in the future.
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Affiliation(s)
- Haiying Ren
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Yuanhao He
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037 China
| | - Xingjiang Qi
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Xiliang Zheng
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Shuwen Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Zheping Yu
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Fengrong Hu
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
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Jung S, Lee T, Gasic K, Campbell BT, Yu J, Humann J, Ru S, Edge-Garza D, Hough H, Main D. The Breeding Information Management System (BIMS): an online resource for crop breeding. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6355633. [PMID: 34415997 PMCID: PMC8378516 DOI: 10.1093/database/baab054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/14/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022]
Abstract
In this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System (BIMS), a free, secure and online breeding management system that allows breeders to store, manage, archive and analyze their private breeding data. BIMS is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. BIMS incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. BIMS comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium. Database URLs: (https://www.rosaceae.org/), (https://www.cottongen.org/), (https://www.citrusgenomedb.org/), (https://www.pulsedb.org/) and (https://www.vaccinium.org/)
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Taein Lee
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Ksenija Gasic
- Plant and Environmental Sciences Department, 171 Poole Agricultural Center, Clemson University, Clemson, SC 29634, USA
| | - B Todd Campbell
- Coastal Plains Soil, Water, and Plant Research Center, USDA-ARS, 2611 West Lucas St., Florence, SC 29501-1242, USA
| | - Jing Yu
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Jodi Humann
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Sushan Ru
- Department of Horticulture, University of Auburn, 287 CASIC Building/120 Funchess, Auburn, AL 36849, USA
| | - Daniel Edge-Garza
- Centre for Horticultural Science, The University of Queensland, Brisbane St Lucia, Brisbane, QLD 4072, Australia
| | - Heidi Hough
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
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Iezzoni AF, McFerson J, Luby J, Gasic K, Whitaker V, Bassil N, Yue C, Gallardo K, McCracken V, Coe M, Hardner C, Zurn JD, Hokanson S, van de Weg E, Jung S, Main D, da Silva Linge C, Vanderzande S, Davis TM, Mahoney LL, Finn C, Peace C. RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops. HORTICULTURE RESEARCH 2020; 7:177. [PMID: 33328430 PMCID: PMC7603521 DOI: 10.1038/s41438-020-00398-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 08/30/2020] [Indexed: 05/05/2023]
Abstract
The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding-a "chasm" existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project ("Ros" signifying a Rosaceae genomics, genetics, and breeding community initiative, and "BREED", indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.
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Affiliation(s)
- Amy F Iezzoni
- Michigan State University, East Lansing, MI, 48824, USA.
| | - Jim McFerson
- Washington State University, Wenatchee, WA, 98801, USA
| | - James Luby
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | | | - Chengyan Yue
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | - Michael Coe
- Cedar Lake Research Group, Portland, OR, 97215, USA
| | | | | | | | - Eric van de Weg
- Wageningen University and Research, 6700 AA, Wageningen, The Netherlands
| | - Sook Jung
- Washington State University, Pullman, WA, 99164, USA
| | - Dorrie Main
- Washington State University, Pullman, WA, 99164, USA
| | | | | | | | | | | | - Cameron Peace
- Washington State University, Pullman, WA, 99164, USA
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