Validated SSR marker kit for diversity analysis of sorghum 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 Sorghum 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 prebreeding crosses. The associated SSR marker kits are 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 germpalsm. The sorghum SSR kit has been elaborated in the frame of a large genotyping project (3384 sorghum accessions x 48 SSR loci) supported by the Generation Challenge Program.  It is composed of the allelic sizes of 3 controls for each of the 48 SSR locus. The 3 controls are composed of 10 DNA samples mixed in 2 pools of 3 and 1 pool of 4 individuals.  The 10 individuals were chosen from 48 Sorghum samples presenting a fair picture of the overall genetic diversity, in order to represent a large range of allelic diversity, both in term of allele number and allele sizes. Each control is amplified for each marker, and allelic sizes are used as control sizes.


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

Also refer to the following for complete marker and background information: 

CLAIRE BILLOT, RONAN RIVALLAN, MBAYE NDOYE SALL, DANIEL FONCEKA, MONIQUE DEU, JEAN-CHRISTOPHE GLASZMANN, JEAN-LOUIS NOYER, JEAN-FRANÇOIS RAMI, ANGE-MARIE RISTERUCCI, PATRICK WINCKER, PUNA RAMU and CHARLES T. HASH. A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae).  American Journal of Botany: e245–e250. 2012. 

Markers cited above are freely available for use.  This information can be taken to any qualified laboratory for generation of markers and subsequent genotyping of germplasm materials.  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.

If you need assistance in the use of these markers refer to  IBP Breeding Services or for more information contact Mark Sawkins or Chunlin He.

Supplementary Resources


KONG , L. , J. DONG , AND G. E. HART . 2000 . Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs). Theoretical and Applied Genetics 101 : 438 – 448.

MUTEGI , E. , F. SAGNARD , K. SEMAGN , M. DEU , M. MURAYA , B. KANYENJI , S. DE VILLIERS , ET AL . 2011 . Genetic structure and relationships within and between cultivated and wild sorghum ( Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers. Theoretical and Applied Genetics 122 : 989 – 1004 .

Poster: Sarah McGrath, Jean-Francois Rami, Christophe Glaszmann. 2010. Genotyping validation of GCP reference sets

Associated germplasm:

A reference set of 375 accessions.  The average gene diversity among the reference set is 0.713 with an average PIC value 0.679, which is equal to global composite collection. For an expanded description click  For a detailed list click

For ordering and more information contact:

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

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