Detection and use of SNP in sugarcane

The Brazilian Sugarcane EST Project (SUCEST) recently produced about 250,000 ESTs derived from the sequencing of the 5' end or both ends of approximately 230,000 randomly cloned cDNAs from 27 libraries. These ESTs have been clustered and Single Nucleotide Polymorphism (SNP) has systematically been searched inside alignments. A total of about 43,000 SNPs were detected. Among these, we further searched sites that overlapped with the recognition sequence of the four restriction enzymes EcoRV, EcoRI, HindIII and Barn HI. A total of 416 were identified. For a sample of these we defined primers in order to amplify the gene region containing the SNP. For these site genotyping should be permitted through a simple and cheap technique involving PCR amplification, restriction of the PCR product and migration in an agarose gel. We used this technique to genotype 55 individuals chosen among representative of ancestral species S. officinarum and S. spontaneum, modem commercial cultivars and samples of two controlled crosses. The results arc discussed and the domain of use of this new technology is delimited in the particular context of sugarcane. (Texte intégral