Development of EST-SSR annotated database in olive (Olea europaea)

Abstract

Olive tree (Olea europaea L.) is one of the most important oil producing crops in the world and the genetic identification of several genotypes by using molecular markers is the first step in its breeding programs. A set of 1,801 well-informative EST-SSR primers targeting specific Olive genes included in different biological processes and pathways were generated using 11,215 Olive EST sequences acquired from the NCBI database. Our bioinformatics analytical procedure showed that 8295 SSR motifs were detected which belonged to different motif types with occurrences of 77.6%, 11.84%, 8.62%, 0.84%, 0.77% and 0.29% for Mononucleotide, trinucleotide, dinucleotide, hexanucleotide, pentanucleotide and tetranucleotide respectively. The appearance of the AAG/CTT repeat was highly represented in trinucleotide and the representation of AG/CT was high in dinucleotide repeats. Results obtained from functional annotation of olives EST sequences targeted with our primers set indicated that 78.5% of these sequences having homology with known proteins, while 4.2% was homologous to hypothetical, predicted, unnamed or uncharacterized proteins and the 17.3% sequences did not possess homology with any known proteins. Our EST-SSR primer set cover a total of 92 biological pathways such as carbohydrate metabolism pathway, energy metabolism & carbon fixation in photosynthetic organism pathway including 11 pathways associated with lipid metabolism .A twenty five randomly selected primers were applied to 9 Egyptian cultivated olive accessions to test its amplification and polymorphism detection efficacy. All tested primers were successfully amplified and only 10 exhibited detectable polymorphism.