Genomic Insights into the Origin of a Thermotolerant Tomato Line and Identification of Candidate Genes for Heat Stress

Abstract

Climate change represents the main problem for agricultural crops, and the constitution of heat-tolerant genotypes is an important breeder’s strategy to reduce yield losses. The aim of the present study was to investigate the whole genome of a heat-tolerant tomato genotype (E42), in order to identify candidate genes involved in its response to high temperature. E42 presented a high variability for chromosomes 1, 4, 7 and 12, and phylogenetic analysis highlighted its relationship with the wild S. pimpinellifolium species. Variants with high (18) and moderate (139) impact on protein function were retrieved from two lists of genes related to heat tolerance and reproduction. This analysis permitted us to prioritize a subset of 35 candidate gene mapping in polymorphic regions, some colocalizing in QTLs controlling flowering in tomato. Among these genes, we identified 23 HSPs, one HSF, six involved in flowering and five in pollen activity. Interestingly, one gene coded for a flowering locus T1 and mapping on chromosome 11 resides in a QTL region controlling flowering and also showed 100% identity with an S. pimpinellifolium allele. This study provides useful information on both the E42 genetic background and heat stress response, and further studies will be conducted to validate these genes.

Exploring the gene expression network involved in the heat stress response of a thermotolerant tomato genotype

“…In order to reduce the number of genes to be further investigated in the future, we focused on those showing variants highlighted by Graci et al [ 17 ] with HIGH and/or MODERATE impact in the gene coding regions and mapping in the most polymorphic regions in the genome of E42, which derive from the wild species S. pimpinellifolium . This analysis allowed to narrow the number of genes to 13 (Table 2 ), all showing at least one polymorphism determining a MODERATE impact on the protein, whereas only in one case a polymorphism with a predicted HIGH impact was observed.…”

“…Resequencing data of the E42 genotype already available at the Department of Agricultural Sciences of University of Naples Federico II [ 17 ] were used to investigate the presence and the distribution of binding motif sequences in the promoter regions of the genotype for the tomato response to HS. Moreover, in order to investigate how tomato genes interact with each other, publicly transcriptomic data of RNA-sequencing (RNA-seq) experiments obtained from different tomato tissues were retrieved from NCBI database.…”

“…Raw FASTQ files of the E42 genotype were processed as reported by Graci et al [ 17 ]. The resulted filtered Variant Calling Format file (VCF) was converted into a consensus FASTA file by using the consensus command of bcftools [ 20 ].…”

“…Moreover, to investigate the gene interactions among tomato genes, public transcriptomic data of RNA-seq experiments were retrieved from the NCBI database, and a GCN analysis was performed. The combination of the results obtained from both the genomic and transcriptomic analyses, and the integration with the findings of Graci et al [ 17 ], allowed us to narrow to 13 the number of HS-related candidate genes mapping in E42 polymorphic regions introgressed from the thermotolerant wild species S. pimpinellifolium . As a whole, the selected genes exhibit HSE binding motifs in the promoter and interact with transcriptional factors (TFs) involved in the response to high temperatures, as evidenced from the GCN analysis.…”

“…This purpose was pursued by investigating genomic and transcriptomic resources available in our laboratory or retrieved from public data. In particular, the genomic analyses conducted in our laboratory by Graci et al [ 17 ] evidenced a high number of polymorphic regions compared to Heinz tomato reference genome, regions putatively introgressed from the heat-tolerant wild ancestor S. pimpinellifolium. In addition, a subset of candidate genes was selected in these polymorphic regions, in some cases also colocalizing in QTLs for high temperature responses.…”