Functional Microsatellite Marker Development from the Sugarcane Sequence Tag Database (SUCEST) using Bioinformatic Tools

Simple sequence repeat are also known as microsatellites which produces high degree of polymorphism in plant and animal genome. For the study of functional genomics of sugarcane simple sequence repeat were mined form the different expressed sequence tags deposited in the publically assessed sugarcane SUCEST database through in silicotechnique, WebSat and Blast2GO bioinformatics software. A total 2335 EST-SSRs were identified, accounting for approximately 5.5% of the total 37 libraries cluster searched and subjected to websat for detection di, tri, tetra, penta and hexa nucleotide motifs with minimum 3 repeats and primers were designed as per Primer3 program. From the obtained results, variations in simple sequence repeats were contributed to 20.2, 17.6, 53.3, 7.4, 1.0 and 0.5% for mono to hexa motifs respectively. In this survey, the GC content in the tri nucleotide repeats was found to be most abundant.

BLAST, Gene Ontology mapping and annotation of selected sequences were performed with the Blast2GO software. Top blastx hits of NCBI showed higher similarity with poaceae family members.  Mapping retrieved the gene ontology extracted from UniProtKB, GR_protein, TAIR database resources. Annotations and descriptive analysis was performed through combined graph for biological processes, molecular functions and cellular component distributions. Obtained results highlighted the involvement of potential ESTs useful in carbohydrate transportation, response to stress and stimulus, metabolic processes, cellular organization and signaling. Hence this analyzed bioinformatics data would directly help to perform functional SSR based molecular marker study towards better understanding of sucrose accumulation and yield traits in selected sugarcane genotypes.

Key words:  Sugarcane, simple sequence repeat, SUCEST database, Websat and Blast2GO software.