Related Experiment Videos
Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats.
Luciana Rossini Pinto1, Karine Miranda Oliveira, Eugênio César Ulian
1Centro 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
|October 23, 2004
Summary
Economical sugarcane simple sequence repeat (SSR) markers were developed by mining EST databases. These EST-SSRs revealed moderate polymorphism, yielding 52 segregating markers for sugarcane genetic mapping.
Area of Science:
- Plant genetics and genomics
- Molecular biology
- Bioinformatics
Background:
- Microsatellites, or simple sequence repeats (SSRs), are valuable genetic markers.
- Developing SSRs from expressed sequence tag (EST) databases offers an economical approach.
- Sugarcane (Saccharum officinarum) genetic mapping requires efficient marker systems.
Purpose of the Study:
- To develop and characterize SSR markers from sugarcane EST databases.
- To assess the polymorphism and utility of these EST-derived SSRs for genetic analysis and mapping in sugarcane.
- To identify SSRs associated with important metabolic pathways.
Main Methods:
- Mining the SUCEST EST database for microsatellite sequences.
- Bioinformatic analysis to identify SSR types (di-, tri-, tetranucleotide) and motif frequencies.
- Testing selected EST-SSRs for polymorphism in commercial sugarcane clones and mapping populations.
- Analyzing allele numbers and polymorphism information content (PIC).
Main Results:
- A total of 2005 clusters containing SSRs were identified in the SUCEST database.
- Tetranucleotide repeats were the most abundant type (61.3%), followed by trinucleotide (30.5%) and dinucleotide (8.2%).
- Twenty-three out of 30 tested EST-SSRs produced scorable polymorphisms in 18 sugarcane clones, with an average of 6.04 alleles/locus and a mean PIC of 0.66.
- 52 segregating markers were identified in an F1 population, indicating potential for sugarcane mapping.
- Identified EST-SSRs showed homology to proteins involved in sugar biosynthesis.
Conclusions:
- EST databases provide an efficient resource for developing sugarcane SSR markers.
- The developed EST-SSRs exhibit moderate polymorphism and are suitable for genetic analysis and mapping.
- These markers are valuable for constructing a functional sugarcane genetic map and understanding gene function.