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Exploration and mapping of microsatellite markers from subtracted drought stress ESTs in Sorghum bicolor (L.) Moench

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Abstract

Molecular variation within defined genes underlying specific biochemical or physiological functions provide candidate gene-based markers which show very close association with the trait of interest and thus should enable to design superior genotypes. We explored microsatellite loci in a total of 9,892 subtracted drought stress ESTs of sorghum (6,295 after flowering ESTs and 3,597 before flowering ESTs) available in the NCBI dbEST database. Analysis of 9,892 ESTs identified 221 non-redundant ESTs with SSRs, from which 109 functional SSRs were developed. Among them 62 EST-microsatellites (56.8%) exhibited polymorphism for at least one sorghum genotype among the five tested and yielded a total of 161 alleles, with an average of 2.59 alleles per marker. We present a microsatellite linkage map using a RIL population derived from the cross 296B and IS18551. The map contains 128 microsatellite loci distributed over 15 linkage groups, and spanning a genetic distance of 1,074.5 cM. The map includes map positions of 28 drought EST-microsatellites developed and seven new genomic-SSRs, and are distributed throughout the map. The developed EST markers include genes coding for important regulatory proteins and functional proteins that are involved in stress related metabolism. The drought EST-microsatellites will have applications in functional diversity studies, association studies, QTL studies for drought, and other agronomically important traits in sorghum, and comparative genomics studies between sorghum and other members of the Poaceae family.

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Acknowledgments

The authors gratefully acknowledge Pratt et al. (2005) for their contribution to development of subtracted drought stress ESTs and provided them in GeneBank. The first author would like to thank the Council of Scientific and Industrial Research (CSIR), New Delhi, India, for providing financial assistance for his doctoral programme. The work was partly funded by the Department of Biotechnology, Government of India. The authors wish to thank Dr. B. V. S. Reddy, ICRISAT, India for providing the mapping population. We acknowledge Dr. B. Venkatesh Bhat (NRCS), Dr. R. M. Sundaram (DRR) and Dr. C. N. Neeraja (DRR) for critically reading the manuscript and Mr. D. Balakrishna for his help in primer development.

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  1. National Research Center for Sorghum, Rajendranagar, Hyderabad, 500030, India

    G. Srinivas, K. Satish, R. Madhusudhana & N. Seetharama

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  1. G. Srinivas
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  2. K. Satish
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  3. R. Madhusudhana
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  4. N. Seetharama
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Correspondence to R. Madhusudhana.

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Communicated by M. Xu.

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Srinivas, G., Satish, K., Madhusudhana, R. et al. Exploration and mapping of microsatellite markers from subtracted drought stress ESTs in Sorghum bicolor (L.) Moench. Theor Appl Genet 118, 703–717 (2009). https://doi.org/10.1007/s00122-008-0931-z

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