Detection of SNP from EST data in sugarcane
Discovering Single Nucleotide Polymorphism (SNP) thanks to Expressed Sequence Tags (ESTs) has proven to be valuable for the human genes, however this approach is not yet documented in plants. A large collection of more than 250 000 ESTs has been constituted for sugarcane by a network of Brazilian laboratories (SUCEST project; http://sucest.lad.ic.unicamp.br/en/). As sugarcane is highly polyploid and heterozygous, several alleles are expected to be present among the redundant sequence tags of each given gene, making this EST database a potential source for SNP discovery. A detailed study of sequence polymorphism is presented here for several genes in order to test the relevance of this approach. Perspectives for more automated large-scale detection methods, as well as perspective for using this information are discussed in the particular context of polyploid sugarcane.
| Main Authors: | , , |
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| Format: | conference_item biblioteca |
| Language: | eng |
| Published: |
Scherago International
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| Subjects: | F30 - Génétique et amélioration des plantes, Saccharum, polymorphisme génétique, gène, http://aims.fao.org/aos/agrovoc/c_6725, http://aims.fao.org/aos/agrovoc/c_24031, http://aims.fao.org/aos/agrovoc/c_3214, |
| Online Access: | http://agritrop.cirad.fr/487406/ |
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| Summary: | Discovering Single Nucleotide Polymorphism (SNP) thanks to Expressed Sequence Tags (ESTs) has proven to be valuable for the human genes, however this approach is not yet documented in plants. A large collection of more than 250 000 ESTs has been constituted for sugarcane by a network of Brazilian laboratories (SUCEST project; http://sucest.lad.ic.unicamp.br/en/). As sugarcane is highly polyploid and heterozygous, several alleles are expected to be present among the redundant sequence tags of each given gene, making this EST database a potential source for SNP discovery. A detailed study of sequence polymorphism is presented here for several genes in order to test the relevance of this approach. Perspectives for more automated large-scale detection methods, as well as perspective for using this information are discussed in the particular context of polyploid sugarcane. |
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