Obtention and characterization of the genomes of mitochondria and chloroplast from two tomato genotypes

DEFARGE, NICOLAS; CAMBIASO, VLADIMIR; RODRÍGUEZ, GUSTAVO RUBÉN

Rosario

Workshop; vo Congreso Argentino de Bioinformática y Biología Computacional, la 13va Conferencia Iberoamericana de Bioinformática y la 3ra reunión anual de la red RiaBio; 2023

In tomato (Solanum lycopersicum L.), two types of crossings are used to improve the quality and quantity of production. Intervarietal crossings are made between different cultivars to obtain hybrid plants with higher performance than their parents, while crossings with wild species are used to transfer beneficial genes into the crop. Reciprocal effects (ER) refer to changes in the hybrid’s phenotype when the sexual role of the parents is reversed. Our research showed that reciprocal effects exist for fruit attributes in tomatoes, and the maternally inherited mitochondrial and chloroplastic genes could be the cause. In order to develop molecular markers that allow us to track the inheritance of mitochondria and chloroplasts, we reconstructed the cytoplasmic genomes aligning reads obtained from whole genome sequences of the S. lycopersicum cultivar Caimanta (C) and the S. pimpinifolium accession LA0722.Illumina reads were aligned to the available mitochondrial (MF034193, accession LA1479) and chloroplast (NC_007898.2, accession LA3023) reference genomes using Bowtie2. This resulted in an alignment rate of 5.23% and 12.11% for C and 5.39% and 17.61% for LA0722, respectively. Cytoplasmic genomes were entirely covered with a mean mapping quality of 34.53 and 29.73 for C (mitochondria and chloroplast, respectively), and 34.49 and 29.74 for LA0722. Four insertion/deletions (INDELs) and nine single nucleotide polymorphisms (SNPs) were found to discriminate the mitochondrial genomes of the two tomato genotypes, while we found 18 INDELs and 57 SNPs at the chloroplast genomes comparations.We aligned Illumina reads from two parental genotypes used in our tomato breeding program to the available mitochondrial and chloroplast reference genomes. This allowed us to assemble usable cytoplasmatic reference genomes for C and LA0722, and identify and map INDELs and SNPs that discriminate between both accessions. These results will serve as a basis for developing molecular markers that allow us to track the inheritance of mitochondria and chloroplasts  hybrids and segregating populations derived of their cross. This will help us verify if cases of paternal/maternal inheritance in tomatoes. Furthermore, this work may reveal that QTLs for agronomic traits of interest are linked to chloroplasts and mitochondrial genomes.