Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats

• Published in: Genome Vol. 47; no. 5; pp. 795 - 804
• Main Authors: Pinto, L.R, Oliveira, K.M, Ulian, E.C, Garcia, A.A.F, Souza, A.P. de
• Format: Journal Article
• Language: English
• Published: Ottawa, Canada NRC Research Press 01.10.2004; Canadian Science Publishing NRC Research Press
• Subjects: Alleles; bioinformatics; cDNA libraries; Databases, Nucleic Acid; DNA Primers - genetics; Expressed Sequence Tags; gene banks; genetic polymorphism; Genomics; microsatellite repeats; Microsatellite Repeats - genetics; Polymorphism, Genetic; Saccharum; Saccharum - genetics; sequence analysis; Sugarcane
• ISSN: 0831-2796; 1480-3321
• DOI: 10.1139/g04-055

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.