Development of model web-server for crop variety identification using throughput SNP genotyping data

Nishu Raghav,U B Angadi,Sonia Sheoran,C N Mishra,Arun Gupta,Sarika Jaiswal,Neeraj Kumar,G P Singh,Ratan Tiwari,Vinod Tiwari,Rajender Singh,Pradeep Sharma,Anil Rai,Deepender Kumar,Dinesh Kumar,M A Iquebal,Surinder Paul

doi:10.1038/s41598-019-41204-2

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.

Highlights

Out of 250–300 thousands edible plant species, only 5% are relevant to agriculture
If variety identification system (VIS) tool is available to breeders, growers and the general industry, it would be instrumental in rapid identification, germplasm registration and traceability of the produce of concerned crop variety
The majority of the crop diversity is present in developing countries and global use of germplasm is often encountered with sovereignty and access benefit sharing (ABS) issues[4]

Summary

Introduction

Out of 250–300 thousands edible plant species, only 5% are relevant to agriculture. Among these, three species, namely maize, rice and wheat fulfills 60% of the caloric needs of humans[1]. To protect intellectual property (IP) of variety by granting statutory Plant Breeders Rights (PBR), it requires testing of distinctness, uniformity and stability (DUS) called DUS testing It has limitations like growth stage specificity, environmental influence, phenotypic plasticity, ineffectiveness over large collections, lack of rapidity besides statistical compromise in the values of descriptors. If VIS tool is available to breeders, growers and the general industry, it would be instrumental in rapid identification, germplasm registration and traceability of the produce of concerned crop variety The majority of the crop diversity is present in developing countries and global use of germplasm is often encountered with sovereignty and access benefit sharing (ABS) issues[4] This is a great challenge for taxonomy, law, ethical consideration and technology to establish varietal status.

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Results

Conclusion