Transcriptome analysis of two tomato genotypes and their hybrids

FORTUNY, AGUSTINA; MENGARELLI, DIEGO A.; PEREIRA DA COSTA, JAVIER H; RODRÍGUEZ, GUSTAVO RUBÉN; ZANOR, MARIA INES

Congreso; Reunión Argentina de Fisiología vegetal; 2021

RNA sequencing (RNA-Seq) is an accurate tool used toanalyse gene expression across transcriptomes and enables detection of novelgenes related to interesting features. Previously, 20 hybrids obtained bycrossing five tomato (Solanum lycopersicum L.) cultivars following afull diallel mating design were evaluated to estimate heterosis and reciprocaleffect on agronomic traits and metabolites. In this work, the transcriptomeprofiles of red ripe fruits of four genotypes selected from those previousresults were analysed by RNA-Seq. The aim was to detect differentiallyexpressed genes (DEGs) among the genotypes. Three biological replicates of thecultivars Querubín FCA (Q) and Gema FCA (G) used as parental lines, as well astheir hybrids Q x G and G x Q were evaluated. Illumina Novaseq 6000 platformwas used to conduct paired-end-sequencing (2 x 150 bp) for each sample.Next-generation sequencing generated ~560 million reads. After removinglow-quality reads and trimming adapter sequences, only high-quality reads(99.43%) were retained. Read alignment against S. lycopersicum referencegenome ITAG 4.0 achieved an average-mapping rate of 93.01%. For each sample,17,887 genes were used for differential expression analysis. Six comparisonswere made between the four genotypes. Using a FDR < 0.001 and log2FC|2|, 200 DEGs were detected when all comparisons were considered. Enriched GOterms were: stimulus-response, either endogenous or exogenous, biotic orabiotic (biological processes), transcription factors (molecular function), andnucleus (cellular component). Transcriptome profile analysis enabled to findDEGs among the genotypes with the highest number when hybrids were compared.