EXPLORING CIEST: FROM MICROSATELLITES TO IN SILICO DIFFERENTIAL DISPLAY

¹ Biotechnology Lab., Centro APTA Citros Sylvio Moreira, Cordeiropolis, SP- Brasil 13490-970

² Embrapa Milho e Sorgo

³ Embrapa Recursos Genéticos e Biotecnologia

With the purpose of integrating all the knowledge accumulated so far on genetic mapping with new data on functional and comparative genomics of Citrus species, a large EST sequencing project has been initiated focusing on the response of citrus to different biotic and abiotic stress factors. Data mining is focusing on the discovery and evaluation of microsatellite and SNP markers and the identification of differentially expressed genes among the different conditions tested. Scanning through 32.2 Mb of non-redundant citrus EST data yielded a total of 14,237 SSR motifs. Abundance, length distribution, frequency, and informative quality as markers were evaluated for all SSRs found in this data set. In order to compare cDNA libaries obtained from flavedo of fruits of different ages, a database containing non-redundant sequences from all cDNA libraries was constructed and used to evaluate in silico gene expression levels. Gene expression data was used to construct gene clusters with similar responses using Self Organizing Maps. Eight distinct clusters containing genes with similar expression profiles were identified. In a similar approach, differentially expressed genes between healthy sweet orange plants and plants infected with Xylella fastidiosa were identified. A Chi-square test and contingency tables were used to statistically identify differentially expressed genes.