Integrating omic data to detect association between sHSP transcripts and phenotypic variability in tomato fruits

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

Rosario

Congreso; XIII Argentine Congress of Bioinformatics and Computational Biology (XIII CAB2C); 2023

A2B2C - SOIBIO - RIABIO

Background: Fruit ripening is a complex developmental process highly coordinated by different genefamilies such as small Heat Shock Proteins (sHSP), which maintain cell homeostasis and are a superfamilyof chaperones that have been characterized in other organisms. In plants, sHSP promotes protein foldingand disaggregation during stress or developmental changes. Previously, we obtained the transcriptomeof cv. Caimanta (C, S. lycopersicum), the exotic LA0722 (P, S. pimpinellifolium), and their interspecific hybrid(CxP) in 3 main stages of ripening. Also, agronomic characterization of fruit attributes was achieved inthe three genotypes.Results: The objective of this communication was to evaluate the association between both datasets. AGeneralized Procrustean Analysis (GPA) was applied to gene expression levels of two clusters of sHSPlocated on chromosomes 6 and 9, respectively, as transcriptomic data, and 11 quantitative fruit traits asphenomic data. Also, an estimation of the degrees of dominance (d/a) was carried out for the levels ofgene expression and the fruit traits. Principal Components 1 (PC1) and 2 (PC2) from the GPA explained77.4% and 22.6% of the total variability, respectively. In the biplot, the consensus positions of P and CxPwere close at positive values of PC1, while C was located at negative values. Contrarily, P and CxP werediscriminated against by PC2 because the exotic parent was on its negative values and the hybrid on thepositive ones. C was located at 0 value. Nevertheless, for each genotype positions according totranscriptomic and phenomic characterizations were similar, indicating a high association among bothdatasets. Also, d/a for all traits evidenced a high dominance of the wild genome, which agreed to theproximity of P and CxP in the biplot.Conclusions: The integration of transcriptomic and phenomic data by PGA and d/a estimation allows theidentification of a high degree of association among expression levels of both sHSP genes andquantitative traits. This information can be applied in breeding programs to get optimal use of exoticgenes obtaining new varieties with adequate fruit quality traits