Automatic identification of GO-Terms related to ripening fruit of tomato based on machine learning

CACCHIARELLI, PAOLO; SPETALE, FLAVIO E.; PRATTA, GUILLERMO R.; TAPIA, ELIZABETH

Santiago de Queretaro

Congreso; ISCB-LA SOIBIO BioNetMX 2022; 2022

Universidad Nacional de Mexico (UNAM) and Bioinformatics Network Mexico (BioNetMX)

Tomato quality is one of the most important factors that help ensure consistentmarketing of tomato fruit. The genome sequencing of tomatoes has provided powerfulinsights into the molecular changes in fruit ripening. Fruit ripening is a part of a complexdevelopmental process that is highly coordinated and includes changes in color,texture, taste and flavor. The automatic identification of biological functionalities ofgenes during the ripening process is important because it detects a list of GO-Termsand genes related to maturation and reveals potential differential attributes to assistwith greater certainty the breeding program in tomato. An analysis of the globalexpression of genes was developed through the technique of massive sequencing ofRNA-seq and phenotypic characterization in parent genotypes. The goal was to identifyGO-Terms of biological processes related to fruit ripening in which genes withdifferential expression are involved and analyze their gene action. The study of geneswas obtained with transcriptional profiles in three mainly ripening stages (Breaker,Mature Green and Red Ripe) and then a new analysis was carried out with the AgriGOtool in order to characterize and identify genes involved in these development stages.In addition, this enrichment analysis allows exploring the biological processes related tofruit ripening in which differential expression transcripts participate. Comparison into thebiological processes domain between these three genotypes generated a list ofconsensus GO-Terms, of which 4 were detected (GO:0044699, GO:0008152,GO:0044710 and GO:0005975). On the other hand, 20 genes were randomly selectedfrom a total of 2,744 genes to estimate the dominant genetic variances. This resultshowed 17 genes with negative overdominance from the parent with the lowest value,and the others showed partial dominance towards lower values. Thus, 60% of thegenes were related to the value of the dominant parent cv. Caimanta and the remaining40% are close to wild accession. This first approach was proposed to identifyGO-Terms related to a development stage in the fruit of tomato and detect potentialgenes of interest to continue with the breeding program and to obtain new varieties oftomatoes