ArticleScientific reports2019
Development of model web-server for crop variety identification using throughput SNP genotyping data.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Genome-wide association mapping of distinctness, uniformity and stability traits and varietal identification in rice (Oryza sativa L.).Journal of the science of food and agriculture · 2026Article
- DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis.International journal of molecular sciences · 2023Article
- Article
- Genome-wide analysis-based single nucleotide polymorphism marker sets to identify diverse genotypes in cabbage cultivars (Brassica oleracea var. capitata).Scientific reports · 2022Article
- Potato Cultivar Identification in South Africa Using a Custom SNP Panel.Plants (Basel, Switzerland) · 2022Article
- Effective identification of varieties by nucleotide polymorphisms and its application for essentially derived variety identification in rice.BMC bioinformatics · 2022Article
- RNA-Seq Analysis of Developing Grains of Wheat to Intrigue Into the Complex Molecular Mechanism of the Heat Stress Response.Frontiers in plant science · 2022Article
- Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review.Foods (Basel, Switzerland) · 2021Review
- The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation.The plant genome · 2021Article
- A Fast, Naked-Eye Assay for Varietal Traceability in the Durum Wheat Production Chain.Foods (Basel, Switzerland) · 2020Article
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Crop varieties or genotypes of a given species are pivotal for agricultural production and ownership, management and improvement of their germplasm is a great challenge. Its morphological identification requires time, cost and descriptors are often compromised statistically due to phenotypic plasticity. Development of DNA based signature of varieties can overcome these limitations. There is a global need to implement world trade organization (WTO) and intellectual property rights (IPR) guidelines of Plant Breeders Rights (PBR) where DUS (distinctness, uniformity and stability) testing can be supplemented by DNA profile. Universalization and minimization of SNP number without compromising identification accuracy is the major challenge in development of varietal profile by rapid genotype assay. Besides this, there is no server-based approach reducing computational skill with global accessibility of referral phenotypic and genotypic data. We report world's first model web server for crop variety identification using >350 Indian wheat varieties and Axiom 35 K SNP chip data. Standard filtering and linkage disequilibrium approach were used to develop varietal signature in Linux using HTML, Java, PHP and MySQL with provision of QR code generator to facilitate bar-coding. Phylogenetic tree constructed by selected SNPs confirms six major trait based clusters of varieties and their pedigree. Our user friendly server based tool, VISTa (Variety Identification System of Triticum aestivum) ( http://webtom.cabgrid.res.in/vista ) can be used in DUS testing having dispute resolution of sovereignty and access benefit sharing (ABS) issues. This model approach can be used in other crops with pan-global level management of crop germplasm in endeavour of crop productivity.
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