GENETICS AND BREEDING OF EARLY BLIGHT AND BACTERIAL SPOT RESISTANT TOMATOES

Abstract

Chapter I. We employed a rapid and low-cost trait introgression methodology to transfer broad-spectrum genetic resistance to bacterial spot (Xanthamonas spp.) across tomato (Solanum lycopersicum L.) market classes. High-density genotyping of finished lines confirmed resistance introgression and background genome recovery but uncovered cryptic introgressions lurking in the background genome. Near-isogenic fresh market breeding lines were evaluated for horticultural performance and multi-race bacterial spot resistance, demonstrating both race non-specific and race-specific resistance. Digital fruit image analysis revealed subtle changes in tomato fruit quality characteristics and yield trials found differences in maturity that were associated with bacterial spot resistance haplotypes. Chapter II. We investigated the genetic determinants of early blight (Alternaria linariae) resistance in modern tomato breeding lines. Quantitative trait loci (QTL) associated with early blight resistance were detected in cross-market breeding populations and offered substantial protection against stem lesions (collar rot) and moderate protection against defoliation. Subsequent field trials validated the three most promising QTL, EB-1.2, EB-5, and EB-9. Resistance effects for EB-5 and EB-9 were consistent across breeding populations and environments, while EB-1.2’s effect was population-specific. We developed near-isogenic fresh market tomato lines and found their resistance to be largely mediated by EB-5 and EB-9, together capturing 49.0% and 68.7% of the defoliation and stem lesion variance, respectively. Chapter III. Whole-genome resequencing of modern tomato breeding lines paired with efficient local ancestry inference revealed cryptic early blight resistance introgressions that were traced to specific donors. Early blight stem lesion and foliar resistance from EB-9 was traced to the vintage tomato Devon Surprise, which is probably derived from Ailsa Craig. Foliar resistance from EB-5 was traced to Hawaii 7998. Definition of the shared ancestral haplotypes enabled fine mapping of the resistance loci and the identification of candidate variants possibly underlying resistance. Co-analysis with resequencing data for 769 accessions predicted EB-9 resistance in several vintage and cherry tomatoes. Foliar EB-5 resistance was rare among sequenced tomatoes and was not detected with high confidence in any accession. Similarly, we found little evidence of introgression from Solanum habrochaites PI 126445 in modern tomatoes, despite being a commonly cited source of resistance.