Bioinformatic identification of sequence variants by integrating omic data to design functional DNA markers in tomato

GOYTIA BERTERO, VALENTINA; CACCHIARELLI, P.; GUILLERMO RAUL PRATTA; ARCE, D.P.

Rosario, Santa Fe

Congreso; XIII Congreso Argentino de Bioinformática y Biología Computacional, XIII Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (XIII SoIBio) y III Reunión Anual de la Red Iberoamericana de Inteligencia Artificial para Big BioData (III; 2023

SoIBio, RIABio, A2B2C

The cultivated tomato (Solanum lycopersicum) is one of the most agriculturally important vegetables. Due to its limited genetic variability, related wild species are often used in breeding programs to expand the available diversity. From previous experiments, we were able to obtain the genome and transcriptome of the cv. Caimanta (S. lycopersicum, C) and LA0722 (S. pimpinellifolium, P) progenitors. As an original contribution of this experiment, we analyzed proteins obtained through GC-MS and subsequently assigned their respective expression levels, obtained from a previous RNAseq experiment, allowing us to identify induced genes (IG) during thefruit maturation process in both genotypes (C and P). The objective of this study was to develop molecular markers (MMs) from the detected IG, with a particular focus on Heat Shock Proteins (HSPs), a biologically significant superfamily that functions as molecular chaperones, folding other proteins and preventing their denaturation. To achieve the proposed objective, protein sequences (https://solgenomics.net/) of 9 selected chaperones (SOLYC03G113930, HSP20 - SOLYC04G082720, HSP20 - SOLYC05G014280, HSP20 - SOLYC06G076570, HSP20 - SOLYC07G006180, RIPENING REGULATED PROTEIN - SOLYC07G042250, CHAPERONINE21 -SOLYC09G011030, HSP70 - SOLYC09G075950, HSP70 - SOLYC12G056780, CHAPERONE PROTEIN P-23) were obtained. Subsequently, a BLASTn was performed on both progenitors to detect the start and end positions of the genes. 1000 bases were added to each start coordinate to extract the DNA sequences corresponding to the chaperones from the genomes of C and P. Comparing theseregions through sequence alignment using the Needle program (https://www.ebi.ac.uk/Tools/psa/emboss_needle/) revealed numerous Single Nucleotide Polymorphisms (SNPs) in the 9 analyzed genes. Developing MMs from omics data is expected to yield functional markers that can be used to characterize segregating populations derived from the crossbreeding of C and P.