ESTs as a source for sequence polymorphism discovery in sugarcarne : example of the Adh genes

Grivet Laurent, Glaszmann Jean-Christophe, Vincentz Michel, Da Silva F., Arruda Paulo. 2003. ESTs as a source for sequence polymorphism discovery in sugarcarne : example of the Adh genes. Theoretical and Applied Genetics, 106 : 190-197.

Résumé : Expressed sequence tags (ESTs) have proven to be a valuable tool to discover single nucleotide polymorphism (SNP) in human genes but their use for this purpose is still limited in higher plants. Using a database of approximately 250,000 sugarcane ESTs we have recovered 219 sequences encoding alcohol dehydrogenases (Adh), which tagged 178 distinct cDNAs from 27 libraries, constructed from at least four different cultivars. The partitioning of these ESTs into paralogous genes revealed three Adh genes expressed in sugarcane, one Adh2 and two Adh1. The soundness of the partition was carefully checked by comparison to external data, especially from the closely related sorghum. Analysis of polymorphism in the alignments of EST sequences revealed a total of 37 highly reliable SNPs in the coding and untranslated regions of the three Adh genes. In the coding regions, the mean occurrence of SNPs was one for every 122 base pair. A total of eight insertiondeletions was observed, their occurrence being limited to untranslated regions. These results show that EST data constitute an invaluable source of sequence polymorphism for sugarcane that is worth carefully collecting for the future development of new marker tools.

Mots-clés Agrovoc : Saccharum, gène, polymorphisme génétique

Classification Agris : F30 - Génétique et amélioration des plantes

Auteurs et affiliations

• Grivet Laurent, CIRAD-CA-Canne à sucre (BRA)
• Glaszmann Jean-Christophe, CIRAD-AMIS-BIOTROP (FRA) ORCID: 0000-0001-9918-875X
• Vincentz Michel, UNICAMP (BRA)
• Da Silva F., CBMEG (BRA)
• Arruda Paulo, CBMEG (BRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/513727/)

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