Applied Genomics
Capacity Building
Genotyping Services
Public Domain
CFA - Molecular Breeding
Genome Sequences
Workshops / Conferences
5th NGGIBCI - 2015
4th NGGIBCI - 2014
VI ICLGG - 2012
3rd NGS Workshop - 2012
2nd NGS Workshop - 2010
1st NGS Workshop- 2009
2nd MAS Workshop- 2010
AAGB - 2008
 High-throughput molecular marker genotyping services

With an objective to enhance adoption of molecular breeding by NARS partners, marker genotyping services are being offered on cost-to-cost basis. Please contact Mahendar Thudi for availing these genotyping services.

Molecular markers have been realized powerful tools for genetic dissections and manipulation of many traits of importance in agriculture. However, their full potential, especially in breeding, is yet to be demonstrated. This is due to a number of limitations, with cost and throughput as major issues. Hence providing marker services to the breeders and researchers for NARS and SMES in developing countries has been one of the major goals of CEG. In this context, Genotyping Service Laboratory (GSL) as a part of the CEG is offering following genotyping services.

SSR genotyping

Among molecular markers, SSR markers were considered the markers of choice. As a result, during last three years, the CEG has been offering SSR genotyping services to a number of partners in India and other countries. During 2011, a total of 1.5 million SSR data points were generated for different projects like diversity, mapping, marker-assisted selection etc., for wide range of species like tomato, potato, maize, rice, chickpea, pigeonpea, common bean, banana, mango and litchi.

For availing SSR genotyping services, markers are already available for sorghum, pearl millet, chickpea, groundnut and pigeonpea, sweet potato, rice, tomato. SSR genotyping service can be extended to any crop provided the users either provide or ask GSL to buy the primer pairs for their crop of interest.

DArT genotyping

DArT is a cost effective and whole-genome genotyping tool. The technology is not dependent on having DNA sequence information, is expandable based on the user's needs, and is high-throughput and low cost. DArT arrays have been developed now for groundnut, pearl millet, pigeonpea and sorghum, and are being routinely used.

DArT genotyping service can also be extended to any crop species provided user will bear the array development costs.

SNP genotyping

Until recently, SSR markers were used as the markers of choice in breeding applications; however over the past few years, considerable progress has been made in high-throughput single nucleotide polymorphism (SNP) genotyping technologies. At present, after validating and identification of the most informative SNPs in elite lines, 96-plex GoldenGate VeraCode oligo pool assay (OPA) for chickpea and 48-plex GoldenGate VeraCode OPA for pigeonpea have been established.

OPAs can be developed for any crop upto 384-SNP plex for availing the SNP genotyping services.


As reference genome sequences are becoming available/undergoing for several crops, genotyping by sequencing (GBS) seems to be an option. Efforts are underway to offer GBS for Chickpea, Pigeonpea and Sorghum by using MiSeq. These efforts will be extended to other crops also.

For availing above mentioned genotyping services, please send your project details to:

Ms. Anu Chitikineni
Senior Manager (Sequencing, Informatics and Services Unit)
Research Program - Genetic Gains
Center of Excellence in Genomics (CEG)
Bldg 300, ICRISAT
Patancheru- 502324, Greater Hyderabad
Tel: 040 3071 3345
Fax: 040 3071 3074/75
Email: a.chitikineni@cgiar.org

Please contact : Dr Rajeev Varshney, Director-Center of Excellence in Genomics, ICRISAT, Patancheru, 502 324, India;
Office: +91 40 3071 3305; Email : r.k.varshney@cgiar.org
© Center of Excellence in Genomics. 2008