Genetic and Genomic Dissection of Water Stress Tolerance in Near-Isogenic Lines Derived from Wild Tomato (SOLANUM HABROCHAITES).

Global climate change and limited fresh-water resources pose challenges to agricultural production worldwide. Breeding crops for tolerance to limited water and increased water use efficiency (WUE) would improve production sustainability by requiring less water for a given level of yield. A wild tomato (S. habrochaites) that originates from the Peruvian Andes exhibits tolerance to abiotic stresses, including limited water and chilling temperatures. When exposed to rapid-onset water stress induced by root chilling (6°C), S. habrochaites responds by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) fails to close stomata and wilts. This trait is controlled by a major QTL (stm9), which was mapped to a 0.32 cM region on chromosome 9 using sub-near-isogenic lines (sub-NILs). To determine if other traits associated with water stress tolerance in the field map to this region, we evaluated this same set of sub-NILs in replicated field experiments in 2012 and 2013 under severely restricted drip irrigation (i.e., slow-onset water stress) and normal irrigation. Traits measured included total fruit yield, shoot dry weight, maturity, specific leaf area, leaf phenolic content, and delta-13C (indicative of WUE). Significant QTL for all traits except phenolic content were detected in this introgressed region, and the QTL were closely linked to (but not coincidental with) stm9. In the S. lycopersicum reference genome, this region is gene-rich. We are currently sequencing S. habrochaites genomic BACs for chromosome 9 and conducting mRNA-seq transcriptome analyses of sub-NILs to facilitate identification of QTL candidate genes for subsequent functional testing. Our results to date indicate that chromosome 9 in S. habrochaites contains multiple genes controlling tolerance to water stress and chilling temperatures. Our research will help identify target genes suitable for marker-assisted breeding of tomato for enhanced abiotic stress tolerance and productivity with limited water.