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Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane

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Abstract

A large sugarcane EST (expressed sequence tag) project recently gave us access to 261,609 EST sequences from sugarcane, assembled into 81,223 clusters. Among these, we identified 88 resistance gene analogs (RGAs) based on their homology to typical pathogen resistance genes, using a stringent BLAST search with a threshold e-value of e−50. They included representatives of the three major groups of resistance genes with NBS/LRR, LRR or S/T KINASE domains. Fifty RGAs showed a total of 148 single-dose polymorphic RFLP markers, which could be located on the sugarcane reference genetic map (constructed in cultivar R570, 2n=~115). Fifty-five SSR loci corresponding to 134 markers in R570 were also mapped to enable the classification of the various haplotypes into homology groups. Several RGA clusters were found. One cluster of two LRR-like loci mapped close to the only disease resistance gene known so far in sugarcane, which confers resistance to common rust. Detailed sequence comparison between two NBS/LRR RGA clusters in relation to their orthologs in rice and maize suggests their polyphyletic origins, and indicates that the degree of divergence between paralogous RGAs in sugarcane can be larger than that from an ortholog in a distant species.

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Acknowledgements

M. Rossi, P. G. Araujo and V. M. Dias were recipients of FAPESP fellowships. This work was partially supported by grants from FAPESP and CNPq (Brazil). We thank J. C. Glaszmann, L. Grivet, G. Piperidis, J. B. Morel and Cristina Juarez for helpful contributions

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Authors and Affiliations

  1. Departamento de Botanica, Instituto de Biociencias, Universidade de São Paulo, Rua do Matão 277, 055080-090 SP, São Paulo, Brazil

    M. Rossi, P. G. Araujo, V. M. Dias & M.-A. Van Sluys

  2. UMR1096, CIRAD, TA 40/03, Avenue Agropolis, 34398 Cedex 5, Montpellier, France

    F. Paulet, O. Garsmeur & A. D'Hont

  3. Yunnan Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Eastern Lingquan Road 363, 661600 , Kaiyuan, Yunnan, P.R. China

    H. Chen

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  1. M. Rossi
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  2. P. G. Araujo
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  3. F. Paulet
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  4. O. Garsmeur
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  5. V. M. Dias
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  6. H. Chen
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  7. M.-A. Van Sluys
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  8. A. D'Hont
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Correspondence to A. D'Hont.

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Communicated by M.-A. Grandbastien

The first two authors contributed equally to this paper

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Rossi, M., Araujo, P.G., Paulet, F. et al. Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane. Mol Gen Genomics 269, 406–419 (2003). https://doi.org/10.1007/s00438-003-0849-8

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  • DOI: https://doi.org/10.1007/s00438-003-0849-8

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