UC Davis

Given climate change and population growth, it is increasingly important to efficiently grow food crops such as tomato (Solanum lycopersicum) using less irrigation water, a limited resource. Cultivated tomato is susceptible to water stress. In contrast, wild tomato species such as S. habrochaites and S. pennellii are water stress tolerant. The overall goal of this dissertation research was to investigate specific chromosomal regions of S. habrochaites and S. pennellii that are associated with water stress tolerance in the field and their potential use in breeding cultivated tomato. Indirect measures of water stress tolerance were employed, including carbon isotope discrimination (∆13C, an indirect measurement of water use efficiency, WUE), shoot dry weight, and yield to evaluate the various tomato genotypes derived from these two wild species that were grown under field conditions.In chapter one, the goal was to fine map quantitative trait loci (QTL) for maturity, yield, shoot dry weight, and ∆13C on chromosome 9 of S. habrochaites using a set of 21 sub-near-isogenic lines (sub-NILs) in a cultivated tomato background. These sub-NILs and control lines were evaluated in replicated field experiments grown under full and reduced irrigation treatments across two years. Significant QTL were detected for 20 trait-environment combinations. All QTL were partially or completely coincident. The presence of the S. habrochaites allele at QTL was associated with later maturity, lower yields, and greater WUE. Further mapping work is required before these QTL can be implemented in a marker assisted breeding program. In chapter two, cultivated tomato lines containing wild species chromosome introgressions (introgression lines, ILs) on chromosomes 2, 5, and 9 from S. habrochaites and S. pennellii were studied in various combinations in hybrid progeny. The goal was to determine if hybrid combinations of ILs with introgressions from S. habrochaites and S. pennellii improved WUE of genotypes compared to their parent ILs and/or inbred cultivated tomato varieties. A total of 35 genotypes (including two inbred tomato cultivars, homozygous ILs, heterozygous ILs, and hybrids between the two species ILs) were evaluated in the field for maturity, horticultural, yield, and WUE-related (∆13C) traits across two years under full and reduced irrigation treatments. General and specific combining abilities were calculated for the hybrid offspring in a Design II mating design. Hybrids generally had best-parent heterosis for yield, but not ∆13C. Three genotypes had better WUE than both cultivated tomato controls for the genetic background and did not cause significant reductions in yield. Some introgressions that showed positive effects on WUE also exhibited negative effects on other traits, such as fruit weight or maturity. Specific introgressions from both wild species may prove useful for developing hybrid tomato varieties that have acceptable yields yet use less irrigation water in the field. In chapter three, a de novo whole-genome sequence (WGS) of S. habrochaites accession LA1778 was generated using the PacBio RSII system and a Bionano optical map. Twelve pseudomolecules, corresponding to the 12 chromosomes of tomato, were constructed with a total length of approximately 959 Mb. The S. habrochaites WGS had high gene and sequence synteny with the S. lycopersicum reference annotation and sequence, although some inversions were detected. The S. habrochaites chromosome 9 sequence was used to determine the physical locations of previously mapped QTL for tolerance to rapid-onset water stress (stm9), WUE (∆13C), and other horticultural traits. A list of potential genes within each QTL interval was generated using S. lycopersicum genes that mapped to each interval, predicted genes, as well as mapped transcript reads from S. habrochaites acc. LA1777. It is likely that many of these genes can be affected by water stress and some may play a role in the tolerant phenotypes. Further work is required to determine which genes confer the slow-onset and rapid-onset water stress tolerant phenotypes. Some of the wild genomic regions have both negative and positive effects on horticultural traits (i.e., linkage drag). Additional studies need to be conducted to fractionate the QTL that are in repulsion phase linkage. High-resolution QTL mapping can lead to the integration of positive WUE-related loci without negative horticultural effects via marker assisted selection. Collectively, these studies support the conclusion that S. habrochaites and S. pennellii have potential promising uses for breeding cultivated tomato with improved water stress tolerance.