Theoretical and Applied Genetics

, Volume 126, Issue 8, pp 2051–2064 | Cite as

Assessment of genetic diversity in the sorghum reference set using EST-SSR markers

  • P. RamuEmail author
  • C. Billot
  • J-F. Rami
  • S. Senthilvel
  • H. D. Upadhyaya
  • L. Ananda Reddy
  • C. T. HashEmail author
Original Paper


Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379–0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping.


Sorghum Polymorphic Information Content Wild Accession Wild Genotype Average Polymorphic Information Content 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank the two anonymous reviewers for their helpful suggestions and comments. This work is a part of the Ph.D. thesis of PR. The research fellowship provided to PR by the Council of Scientific and Industrial Research (CSIR), New Delhi, India is greatly acknowledged. Work reported here was supported by the grant from the Generation Challenge Programme (GCP) of the CGIAR.

Supplementary material

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Supplementary material 1 (XLS 97 kb)
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Supplementary material 3 (PPT 302 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • P. Ramu
    • 1
    • 2
    Email author
  • C. Billot
    • 3
  • J-F. Rami
    • 3
  • S. Senthilvel
    • 1
  • H. D. Upadhyaya
    • 1
  • L. Ananda Reddy
    • 2
  • C. T. Hash
    • 1
    • 4
    Email author
  1. 1.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)HyderabadIndia
  2. 2.Department of GeneticsOsmania UniversityHyderabadIndia
  3. 3.Cirad, UMR AGAPMontpellierFrance
  4. 4.ICRISAT Sahelian CenterNiameyNiger

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