Pinto Luciana Rossini, Oliveira Karine Miranda, Ulian Eugênio César, Garcia Antonio Augusto Franco, de Souza Anete Pereira
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.
Genome. 2004 Oct;47(5):795-804. 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.
通过挖掘EST数据库，以经济实用的方式开发了甘蔗微卫星或简单序列重复序列（SSR）。对SUCEST（甘蔗EST）数据库的一项调查显示，在43141个序列簇中共有2005个含有SSR。其中，8.2%为二核苷酸重复，30.5%为三核苷酸重复，61.3%为四核苷酸重复。除二核苷酸外，富含CG的基序类型最为常见。观察到EST-SSR与从甘蔗基因组文库中分离的SSR在三核苷酸基序类型的丰度上存在差异。在用于EST测序的不同cDNA文库中，来自卷叶（LR）的文库中SSR更为常见。在30个测试的SSR中，有23个在18个甘蔗商业品种中产生了可评分的多态性。这些EST-SSR表现出中等水平的多态性，一些SSR产生了独特的指纹图谱。在评估的18个品种中观察到的等位基因数量从2到15不等，平均每个位点有6.04个等位基因。多态性信息含量（PIC）值范围为0.28至0.90，平均值为0.66。在两个亲本（SP 80-180；SP 80-4966）和6个F1个体中筛选的EST-SSR产生了52个分离标记，这些标记有可能用于甘蔗作图。发现EST-SSR存在于与参与重要代谢途径（如糖类生物合成）的蛋白质具有显著同源性的序列簇中，证明EST-SSR是构建功能性甘蔗图谱的宝贵工具。
