title: Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats.
abstract: Sugarcane microsatellites or simple sequence repeats (SSR) were developed in an economical and practical way by mining EST databases. A survey in the SUCEST (sugarcane EST) database revealed a total of 2005 clusters out of 43,141 containing SSRs. Of these, 8.2% were dinucleotide, 30.5% were trinucleotide, and 61.3% were tetranucleotide repeats. Except for dinucleotides, the CG-rich motif types were the most common. Differences in abundance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic libraries. Among the different cDNA libraries used for EST sequencing, SSRs were more frequent in the ones derived from leaf roll (LR). Twenty-three out of 30 tested SSRs produced scorable polymorphisms in 18 sugarcane commercial clones. These EST-SSRs showed a moderate level of polymorphism with some SSRs producing unique fingerprints. The number of alleles observed among the 18 clones evaluated varied from 2 to 15, with an average of 6.04 alleles/locus. The polymorphism information content (PIC) values ranged from 0.28 to 0.90 with a mean of 0.66. The EST-SSRs screened over both parents (SP 80-180; SP 80-4966) and 6 F1 individuals produced 52 segregating markers that could potentially be used for sugarcane mapping. The EST-SSRs were found in clusters that had significant homology to proteins involved in important metabolic pathways such as sugar biosynthesis, proving that EST-SSRs are a valuable tool for the construction of a functional sugarcane map.
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG) - Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-970, Campinas-SP, Brasil.
authors.forename: Luciana Rossini
authors.initials: LR
authors.lastname: Pinto
authors.forename: Karine Miranda
authors.initials: KM
authors.lastname: Oliveira
authors.forename: Eugênio César
authors.initials: EC
authors.lastname: Ulian
authors.forename: Antonio Augusto Franco
authors.initials: AA
authors.lastname: Garcia
authors.forename: Anete Pereira
authors.initials: AP
authors.lastname: de Souza
mesh_terms: D000483:Alleles; D017931:DNA Primers / Q000235:genetics; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D018895:Microsatellite Repeats / Q000235:genetics*; D011110:Polymorphism, Genetic; D031786:Saccharum / Q000235:genetics*
chemical_list: D017931:DNA Primers