GIS Applications as a Significant Tool in Genetic Studies (original) (raw)
Related papers
2008
The overall goal of the project “Global Information on Germplasm Accessions” is to improve access by breeders and other users to the germplasm they need in gene banks around the world. The project covers all major food crops, with a focus on 22 crops: banana, barley, beans, breadfruit, cassava, chickpea, coconut, cowpea, faba bean, finger millet, grass pea, maize, major aroids, lentil, pearl millet, pigeon pea, potato, rice, sorghum, sweet potato, wheat, and yam, and a limited number of other crops of interest to the project collaborators.
Geographic information systems (GIS) and the conservation and use of plant genetic resources
Managing plant genetic diversity. Proceedings of an international conference, Kuala Lumpur, Malaysia, 12-16 June 2000, 2002
This paper describes how spatial analysis of the geo-referenced data generated by the process of conservation and use of genetic resources, using GIS, can feedback to enhance and facilitate the process, and add value to the germplasm collections.
Computer tools for spatial analysis of plant genetic resources data: 1. DIVA-GIS
Bulletin de Ressources Phytogénétiques, 2001
Computer tools for spatial analysis of plant genetic resources data: 1. DIVA-GIS The DIVA-GIS software allows analysis of genebank and herbarium databases to elucidate genetic, ecological and geographic patterns in the distribution of crops and wild species. It useful for scientists who cannot afford generic commercial GIS software, or do not have the time to learn how to use it, and for others who require a GIS that is specifically designed for genetic resources work. Coordinate data are often absent from genebank databases, or if present are sometimes inaccurate. DIVA-GIS helps improve data quality by assigning coordinates, using a large digital gazetteer. DIVA-GIS can also be used to check existing coordinates using overlays of the collection-site and administrative boundary databases. Maps can then be made of the collection sites. Analytical functions implemented in DIVA include mapping of richness and diversity, distribution of useful traits and location of areas with complementary diversity. DIVA can also extract climate data for all terrestrial locations, which can be used to describe the environment of collection sites.
Genetic Resources and Crop Evolution An International Journal
Ex situ conservation in genebanks is the most important way of conserving plant genetic resources for food and agriculture (PGRFA) (FAO 2010). The use of germplasm conserved in genebanks depends to a large extent on the quality and quantity of data available about each accession. Initial selection of accessions for use in research or breeding is often made based on the available passport information, which describes the source of the material. Availability of collecting site description or geographic coordinates is considered a quality indicator in particular for accessions of wild species and landraces (Van Hintum et al. in Plant Genet Resour Charact Util 9(3):478–485, 2011). However lack or unavailability of accession specific data, including passport and location data, continues to represent a constraint to enhanced utilization of accessions (FAO 2010; Khoury et al. in Genet Resour Crop Evol 57(4):625–639, 2010). Collecting mission reports and collecting forms provide original data, including location data, about materials collected and distributed to genebanks. The International Board for Plant Genetic Resources and its successor, the International Plant Genetic Resources Institute (now Bioversity International) have supported the collection of over 225,000 samples of PGRFA during the last quarter of the past century. The documentation gathered at the time of their collection has recently been digitized, passport data extracted, and made available through the web (http://www.central-repository.cgiar.org/; http://singer. cgiar.org/index.jsp?page=biomissions), where it can be consulted to integrate and improve the quality of passport data. Collected samples can be linked to accessions in genebanks. The original collecting mission reports often include eco-geographic, environmental, biotic and climate data that can be used to improve knowledge about the accessions and facilitate their utilization.
Acta Horticulturae, 2010
The mission of the GRIN-Global Project is to create a new, scalable version of the Germplasm Resource Information System (GRIN) to provide the world's crop genebanks with a powerful, flexible, easy-to-use plant genetic resource (PGR) information management system. The system will help safeguard PGR and information vital to global food security, and encourage PGR use. Developed jointly by the USDA Agricultural Research Service, Bioversity International and the Global Crop Diversity Trust, GRIN-Global will be deployed in selected plant genebanks worldwide in 2010. The .NET Framework and Visual Studio development environment were chosen for the project. A core set of web services, enterprise services or other technologies will update data stored locally or on networks, distribute centralized data to off-site systems, and enable third party data sharing. The database and interface(s) will accommodate commercial and open-source programming tools, be database-flexible (PostgreSQL, MySQL, MS SQL Server, Oracle) and require no licensing fees. The database will be deployable on standalone computers or networked systems. Iterative programming strategies will support continuous product evaluation and refinement; advanced prototypes will be extensively beta-tested. GRIN-Global supports uploading and downloading passport, phenotype and molecular marker data in a spreadsheet format. Bioversity International will deploy GRIN-Global internationally, working cooperatively to document the new system in Arabic, English, French, Russian and Spanish, translate its interface, and implement it in developing countries. Implementation will be monitored and barriers to adoption identified. Users will evaluate GRIN-Global's impact and suggest improvements following implementation. GRIN AND THE NEED FOR GRIN-GLOBAL Many of the world's national genebanks, responsible for the safeguarding and availability of their country's plant genetic resource (PGR) collections, have lacked
An overview of biodiversity informatics with special reference to plant genetic resources
2012
The ever-increasing significance of biodiversity conservation and advancements in computer technology for digitization and management of data have catapulted biodiversity informatics into limelight. Biodiversity informatics enhances the efficiency of biodiversity management by researchers, policy makers, and funding agencies. Plant genetic resources (PGR) are a key component of biodiversity as they have a direct bearing on food and nutritional security. As a result, PGR informatics that specifically deals with agro-biodiversity needs greater patronage. This overview describes the state of biodiversity informatics with special reference to PGR informatics. The aim of this review is to generate awareness about the existing biodiversity information systems and to stimulate initiatives from all the concerned to frame a comprehensive action plan for developing biodiversity informatics in gene-rich countries with a special reference to India.
A Gateway to Plant Genetic Resources Utilization
Acta Horticulturae, 2013
The world is faced with the need to increase crop productivity, develop varieties that are better adapted to face environmental and biological constraints, and meet the needs of local communities. To meet these challenges farmers and breeders must have access to a wide range of plant genetic resources together with the essential information about the traits they possess that facilitates their utilization. Accurate characterization and evaluation data promote utilization, especially if it is available in an easily usable or standard format. Bioversity International (Bioversity) aims to stimulate the characterization and evaluation of germplasm collections by providing uniform standards for the description and exchange of information on plants. The CGIAR (Consultative Group on International Agricultural Research) centres along with crop research institutes and networks have collaborated with Bioversity in the production of standards or 'descriptors'. Crop standards are an important tool that permits the international community to find and exchange information in a 'common' language. These standards have been adopted by the GCP (Generation Challenge Programme) Ontology Consortium, FAO WIEWS, EURISCO (the European Plant Genetic Resources Catalogue), CGIAR centres and are also being promoted by the Crop Genebank Knowledge Base and GRIN. These data standards constitute the backbone of the GENESYS global portal for access to information on plant genetic resources. GENESYS heralds a new paradigm for access to and use of these resources. GENESYS 1.0 was released in May 2011 following nearly three years of development by Bioversity on behalf of the CGIAR System-wide Genetic Resources Programme (SGRP) and in partnership with the International Treaty on Plant Genetic Resources for Food and Agriculture and the Global Crop Diversity Trust. It brings together the passport data from three of the major genebank information networks-SINGER (the CGIAR System-wide Information Network for Genetic Resources), EURISCO and GRIN, the USDA system which added further value through the inclusion of characterization and evaluation data.
2017
Sharing and reusing data in research is a welcome and encouraged practice since it maximises the scientific outcomes given limited financial, material and human resources. Interdisciplinary research is considered to benefit from this practice, uniting researchers and data from two or more disciplines to advance fundamental understanding or tackle problems whose solution is beyond the limit of an individual body of knowledge. Here we discuss the challenges of combining data across disciplines, focusing in particular on associating geographic location data with genetic data in the context of a project involving Crop Science and Geospatial Information Science disciplines. This project aims to improve understanding of how geographical, environmental and anthropogenic factors affect the genetic variation in a neglected and underutilised crop called Bambara groundnut.
Using GIS to check co-ordinates of genebank accessions
1999
The geographic coordinates of the locations where germplasm accessions have been collected are usually documented in genebank databases. However, the coordinate data are often incomplete and may contain errors. This paper describes procedures to check for errors, to determine the cause of these errors and to assign new coordinates , using Geographical Information Systems (GIS). These procedures can assist in improving the quality of genebank databases, and with that, increase the capability for analysis and use of crop genetic diversity.