Exploiting rice–sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map

Abstract

The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag (EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50 homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using parental pairs of two existing sorghum mapping populations. About 28% of these new markers detected polymorphism in this 4-entry panel. A subset of 55 polymorphic EST-derived SSR markers were mapped onto the existing skeleton map of a recombinant inbred population derived from cross N13 × E 36-1, which is segregating for Striga resistance and the stay-green component of terminal drought tolerance. These new EST-derived SSR markers mapped across all 10 sorghum linkage groups, mostly to regions expected based on prior knowledge of rice–sorghum synteny. The ESTs from which these markers were derived were then mapped in silico onto the aligned sorghum genome sequence, and 88% of the best hits corresponded to linkage-based positions. This study demonstrates the utility of comparative genomic information in targeted development of markers to fill gaps in linkage maps of related crop species for which sufficient genomic tools are not available.

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Acknowledgments

The research fellowship provided to PR by the Council of Scientific and Industrial Research (CSIR), New Delhi, India is greatly acknowledged. KB acknowledges the financial support provided by the Ethiopian Government and ICRISAT. Work reported here was partially funded by the CGIAR Generation Challenge Program (GCP).

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Correspondence to C. T. Hash.

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P. Ramu and B. Kassahun contributed equally to this work.

Communicated by T. Sasaki.

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Ramu, P., Kassahun, B., Senthilvel, S. et al. Exploiting rice–sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map. Theor Appl Genet 119, 1193–1204 (2009). https://doi.org/10.1007/s00122-009-1120-4

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Keywords

  • Sorghum
  • Amplify Fragment Length Polymorphism
  • Simple Sequence Repeat Marker
  • Rice Chromosome
  • Simple Sequence Repeat Motif