Please use this identifier to cite or link to this item: http://repositorio.unicamp.br/jspui/handle/REPOSIP/73923
Type: Artigo de periódico
Title: Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats
Author: Pinto, LR
Oliveira, KM
Ulian, EC
Garcia, AAF
de Souza, AP
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 F-1 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.
Subject: sugarcane
polyploid
expressed sequence tags (ESTs)
microsatellites (SSRs)
genetic mapping
Country: Canadá
Editor: Natl Research Council Canada
Rights: fechado
Identifier DOI: 10.1139/G04-055
Date Issue: 2004
Appears in Collections:Artigos e Materiais de Revistas Científicas - Unicamp

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