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

GOYTIA BERTERO, VALENTINA; CACCHIARELLI, PAOLO; PRATTA, GUILLERMO RAÚL; ARCE, DÉBORA PAMELA

Congreso; Congress A2B2C-SOIBIO-RIABIO Annual Meeting; 2023

A2B2C-RIABIO-SOIBIO

The cultivated tomato (Solanum lycopersicum) is one of the most agriculturallyimportant vegetables. Due to its limited genetic variability, related wild species areoften used in breeding programs to expand the available diversity. From previousexperiments, we were able to obtain the genome and transcriptome of the cv.Caimanta (S. lycopersicum, C) and LA0722 (S. pimpinellifolium, P) progenitors. Asan original contribution of this experiment, we analyzed proteins obtained throughGC-MS and subsequently assigned their respective expression levels, obtained froma 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 wasto develop molecular markers (MMs) from the detected IG, with a particular focus onHeat Shock Proteins (HSPs), a biologically significant superfamily that functions asmolecular chaperones, folding other proteins and preventing their denaturation. Toachieve the proposed objective, protein sequences (https://solgenomics.net/) of 9selected 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 wasperformed 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 sequencescorresponding 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 SingleNucleotide Polymorphisms (SNPs) in the 9 analyzed genes. Developing MMs fromomics data is expected to yield functional markers that can be used to characterizesegregating populations derived from the crossbreeding of C and P.