TWO ITALIAN TOMATO LANDRACES SHOW DISTINCTIVE GENE NETWORK PROFILES IN RESPONSE TO WATER DEFICIT

Considered as one of the most important horticultural crops worldwide, tomato (Solanum lycopersicum L.) has had a huge agronomical success in the Mediterranean area, where numerous local landraces which show great phenotypic diversity were selected. Among the several landraces grown in Southern Italy and analyzed by our research group, two of these, Lucariello (LUC) and Crovarese (CRO) showed interesting phenotypes in field trials repeated over several years. LUC and CRO displayed a high tolerance to drought stress, and produced fruits of high quality and long shelf life despite the low water input regimes, making them very attractive economically and scientifically. To identify the components involved in drought stress responses, we pursued a transcriptome study on CRO and LUC plants subjected to drought stress by water withholding for 13 days. Our trascriptome sequencing was done in conjunction with a whole-genome resequencing project of CRO and LUC, which allowed us first to use the specific genomes of CRO and LUC as reference for the bioinformatic pipeline, and to merge the genomic data with drought stress-induced gene expression variations. Using RNA sequencing on leaf samples, we identified 2954 and 2015 genes up-regulated upon stress in CRO and LUC, respectively. By contrast, 3912 genes were down- regulated in CRO and 2671 in LUC. Gene Onthology (GO) enrichment analysis on up-regulated and down-regulated genes shared between CRO and LUC revealed that several of the enriched categories were stress-related. Comparison of the RNA-seq results with polymorphic genes identified within the resequencing project revealed 300 drought-responsive genes common to CRO and LUC which carried sequence polymorphisms with a potentially disruptive impact on their function. Among these, 101 were up- and 199 down-regulated genes in drought stress conditions. The polymorphisms identified included nonsense mutations generating premature stop codons in a number of expressed genes. The pectinase family involved in cell wall organization showed a striking number of members, 42 whose expression was repressed by water deprivation. Among these, 3 genes were selected (Solyc01g079180, Solyc05g014000, Solyc09g075460) for expression analysis in CRO, LUC and in a commercial genotype (Red Setter, RS) during two cycles of stress and a recovery phase. Results highlighted an opposite behavior of these genes between the traditional landraces and RS during the second cycle of stress, where an expression inhibition was observed in CRO and LUC compared to an upregulation in RS. The observed downregulation of the pectinase genes could be part of a genotype-specific response to drought, leading to reduced degradation of pectin structure in the cell wall to respond to water scarcity. Altogether, the gene expression data presented here contribute to an understanding of the drought tolerance displayed in ? the field by CRO and LUC and to the identification of genes putatively involved in the stress adaptation features of these traditional landraces.