Integrating marker-assisted backcross breeding and genomic analysis to obtain thermotolerant tomato genotypes for the fresh market

Abstract Current climate change significantly impacts on agriculture, negatively affecting plant growth and development of many agricultural crops including tomato. To adapt to current increase in temperatures, it is essential to develop novel heat tolerant cultivars. The present study describes a backcross breeding program developed to produce new genotypes suitable for the fresh tomato market that exhibit the favorable characteristics of the previously selected thermotolerant genotype E42. This was achieved by converting the determinate plant habitus of E42 to indeterminate. The SP_CAPS marker designed to target a SNP in the self-pruning gene, which is responsible for the plant habitus, enabled us to accelerate the selection of indeterminate plants, thus obtaining nine BC 4 S 1 lines. The evaluation of ten phenotypic traits in two different growth conditions (open field and under plastic tunnel) evidenced the good performances of the BC 4 S 1 lines and the phenotypic recovery of the recurrent parent in all of them. Interestingly, one genotype exceeded the mean yield values of the group when grown in open field. In addition, the analysis of the ddRAD sequencing data revealed a high level of genomic recovery, with only a few variants retained from the donor parents. Clear linkage drag was assessed in almost all the BC 4 S 1 lines around the self-pruning gene that was targeted using Marker Assisted Selection. Altogether, this work provided improved thermotolerant genotypes with high fruit quality that may find place in the tomato fresh market.