Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats. Pinto, L., R., Oliveira, K., M., Ulian, E., C., Garcia, A., A., F., & Souza, A., P. Genome, 47(5):795-804, 2004. ![Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats [pdf]](https://bibbase.org/img/filetypes/pdf.svg "pdf")
Paper abstract bibtex 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 abun- dance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic librar- ies. 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/lo- cus. 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.
@article{
title = {Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats},
type = {article},
year = {2004},
identifiers = {[object Object]},
keywords = {expressed sequence tags (ESTs),genetic mapping,microsatellites (SSRs),polyploid,sugarcane},
pages = {795-804},
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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 abun- dance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic librar- ies. 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/lo- cus. 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.},
bibtype = {article},
author = {Pinto, L R and Oliveira, K M and Ulian, E C and Garcia, A A F and Souza, A P},
journal = {Genome},
number = {5}
}
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