Validated SSR marker kit for diversity analysis of chickpea germplasm collections


GCP Project G4007.01 Genotyping validation of the GCP reference sets. PI: Jean-Francois Rami, CIRAD, Montpellier, France


Jean-Francois Rami, CIRAD, Montpellier, France


Hari Upadhyaya, ICRISAT, Patancheru, India

Product Description/Background

The Chickpea Reference Set is composed of a core set of accessions representing the genetic diversity of the entirety of the ICRISAT germplasm bank collection. The reference set represents a critical resource for plant scientists to study new adaptative traits, discover new favorable alleles and also new parental lines for pre-breeding crosses. The associated SSR marker kit is a set of markers based upon the reference set that can be used to characterize local collections. Using this same set of markers, any scientist will be able to compare the diversity of his/her own diversity panel with the reference set, and request appropriate accessions from the reference set to introduce new diversity in his/her germplasm. The reference kit  is composed of 35 SSRs with a sequence list and protocol, germplasm checks, and allele sizes of markers for those checks  In the frame of the Generation Challenge Program, an assessment of the overall genetic diversity of 3000 chickpea accessions was conducted through the use of SSR markers, distributed throughout the genome. This task was shared between two institutes: ICRISAT and ICARDA, Aleppo, Syria. The originating genetic diversity study provided an overview on population structure as well as the allelic diversity that can be associated with the phenotypic trait. In addition, based on genotyping data obtained with 35 SSR markers, an effort has been made to provide the international community with a genotyping kit that could be used as a reference kit to compare with other genetic diversity studies in the future.


Access the following site for marker characteristics, composition of controls, and allelic patterns of control samples of the set:

Markers descrubed in above site are freely available for use.  This information can be taken to any qualified laboratory for generation of markers and subsequent genotyping of germplasm materials. Conveniently,  ICRISAT which maintains the chickpea germplasm reference set will provide this service. In addition, the Integrated Breeding Platform Genotyping Service provides a set of options for users to access different marker service laboratories in the public and private sector with clear contractual conditions. The service identifies laboratories able to provide services for genetic diversity analysis and plant breeding applications and negotiates favourable terms for IBP clients. Laboratories are selected on the basis of competitive cost, fit with quality control requirements and expeditious delivery. Click here for a list and description of laboratories and services. Click on  Service request for details of how to access genotyping services through the platform. For additional information and help on using the IBP Marker Service, contact Chunlin He.

Supplementary Resources


Hari D. Upadhyaya, , Mahendar Thudi, Naresh Dronavalli, Neha Gujaria,  Sube Singh, Shivali Sharma and Rajeev K. Varshney. Genomic tools and germplasm diversity for chickpea improvement. Plant Genetic Resources: Characterization and Utilization (2011) 9(1); 45–58.  doi:10.1017/S1479262110000468

Hari D Upadhyaya, Sangam L Dwivedi, Michael Baum, Rajeev K Varshney, Sripada M Udupa, Cholenahalli LL Gowda, David Hoisington and Sube Singh. Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biology 2008, 8:106 doi:10.1186/1471-2229-8-106

Associated germplasm:

A reference set consisting of 300 genetically most diverse accessions have been formed. This reference set captured 1315 (78%) of the 1683 composite collection alleles, representing diversity from the entire spectrum of composite collection.  For a detailed list click

For more information contact: 

Dr H D Upadhyaya
Assistant Research Program Director-Grain Legumes 
and Principal Scientist and Head Gene Bank
Andhra Pradesh, India 

Back to top