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Front. Plant Sci. | doi: 10.3389/fpls.2017.02009

Putative microsatellite DNA marker-based wheat genomic resource for varietal improvement and management

 Sarika Jaiswal1, Sonia Sheoran2,  Vasu Arora1, U B. Angadi1,  Mir A. Iquebal1, Nishu Raghav2, Bharti Aneja2, Deepender Kumar2,  Rajender Singh2,  Pradeep Sharma2, G P. Singh2,  ANIL RAI1, Ratan Tiwari2 and  Dinesh Kumar1*
  • 1Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR), India
  • 2Indian Institute of Wheat and Barley Research, Indian Council of Agricultural Research, India

Wheat fulfils 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/ physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. TaSSRDb (Triticum aestivum SSR database) is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476169) from complex, hexaploid wheat genome (~17 GB) along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb) and lowest (74.57 SSRs /Mb) SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT) lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL(Quantitative trait locus) discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness,Uniformity and Stability) testing, EDV(Essentially Derived Variety)/IV(Initial Variety) disputes, seed purity and hybrid wheat testing. All these are required in germplasm management as well as also in the endeavour of wheat productivity.

Keywords: EDV, e-PCR, Seed purity, Triticum aestivum, molecular marker, SSR, DUs

Received: 25 Jul 2017; Accepted: 10 Nov 2017.

Edited by:

Nicolas Rispail, Consejo Superior de Investigaciones Científicas (CSIC), Spain

Reviewed by:

Mikhail P. Ponomarenko, Institute of Cytology and Genetics (RAS), Russia
Enrique Medina-Acosta, State University of Norte Fluminense, Brazil
Valeria Terzi, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Italy
Jingyin Yu, Oil Crops Research institute, China
Jose M. Soriano, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Spain  

Copyright: © 2017 Jaiswal, Sheoran, Arora, Angadi, Iquebal, Raghav, Aneja, Kumar, Singh, Sharma, Singh, RAI, Tiwari and Kumar. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Dinesh Kumar, Indian Agricultural Statistics Research Institute (ICAR), Centre for Agricultural Bioinformatics, Library Avenue, PUSA, New Delhi, 110012, Delhi, India,