Chromosome 9 in tomato: Identification, characterization, and transcriptomics of QTL associated with water stress tolerance trait

Cultivated tomato (Solanum lycopersicum L.) is susceptible to abiotic stresses, including water and temperature stress. In contrast, wild tomato (Solanum habrochaites) exhibits tolerance to several abiotic stresses, including drought and chilling. Root chilling (to 6°C) induces rapid-onset water stress by impeding water movement from roots to shoots. S. habrochaites responds to root chilling by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) fails to close stomata and wilts. Root-to-shoot signaling is involved in this response. It was determined previously that this trait (shoot turgor maintenance under root chilling) is controlled by a 2.7 cM major QTL (designated stm9) on chromosome 9 from S. habrochaites..;In chapter one, recombinant sub-near-isogenic lines (sub-NILs) for chromosome 9 were marker-selected, and 18 sub-NILs that contained unique introgressions were phenotyped for shoot turgor maintenance under root chilling in two sets of replicated experiments (Fall and Spring). The trait data was used to localize stm9 to a 0.32 cM region. A single QTL was detected that was coincident for both the Spring and Fall datasets, suggesting that the gene or genes contributing to shoot turgor maintenance under root chilling reside within the marker interval H9 - T1673. In the S. lycopersicum reference genome sequence, this chromosome 9 region is gene-rich and contains representatives of gene families that have been associated with abiotic stress tolerance.;In chapter two, deficit irrigation was used in the field to impose slow-onset water stress to the same set of 18 sub-NILs in experiments conducted for two years. Trait data were analyzed with principle component analysis and multiple analysis of variance to investigate the underlying relationships among proxy traits for water-use efficiency (WUE) including carbon isotope discrimination (Delta13C) and specific leaf area (SLA) with horticultural traits including maturity and yield. While many trait QTL were coincident or overlapping, our results suggested that the genes controlling QTL for Delta 13C and SLA in this chromosome 9 region are distinct from each other and from genes controlling maturity and yield. The majority of phenotypic variation among the sub-NILs was accounted for by Delta13C and SLA, with minor contributions from the horticultural traits. This region of chromosome 9 contains potentially valuable wild alleles for breeding cultivated tomatoes with improved WUE while selecting for yield maintenance.;In chapter three, the effect of the S. habrochaites introgressed chromosome 9 region on transcriptional regulation in response to root chilling was investigated. RNA from roots of a set of paired near-isogenic-lines (NILs) differing only for the presence or absence of a S. habrochaites introgression containing stm9 in an otherwise S. lycopersicum background was obtained at five time points during exposure to root chilling. The samples were subjected to mRNA-Seq analysis, and differential expression analysis and hierarchical clustering of transcript levels were used to determine changes in and patterns of mRNA levels. Transcriptional regulation in response to root chilling was more specific in chilling-tolerant NIL175, yet more complex in susceptible NIL163. De novo transcription of stress-response genes was not involved in transcriptional regulation in either NIL. Gene ontology analysis indicated that serine/threonine kinase activity likely has an important role in root chilling response in tolerant NIL175.