The pursuit of useful quantitative resistance to Phytophthora infestans in tomato resulting from genomic introgressions from S olanum habrochaites

In chapters 1 and 2, I describe the mapping of QTL controlling 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits, within these two chromosomal regions at higher resolution by evaluating chromosome 5 and chromosome 11 sub-NILs in replicated field experiments over two years. By determining the genetic architecture and environmental stability of QTL controlling horticultural traits and their linkage relationships to each other and to P. infestans resistance QTL, I was able to assess the implications of these factors on use of wild QTL alleles for the improvement of cultivated tomato via breeding. Each previously detected single horticultural trait QTL fractionated into two or more QTL. For the chromosome 5 QTL region, a total of 41 QTL were detected across all traits, with ~30% exhibiting significant QTL x environment interactions. For the chromosome 11 QTL region, a total of 34 QTL were detected across all traits, with 14% exhibiting significant QTL x environment interactions (QTL x E). Co-location of QTL for multiple traits within each chromosomal region suggests either pleiotropy or tightly-linked genes control these traits. I conclude each of the first two chapters by discussing the challenges and opportunities presented by the complex genetic architecture of horticultural and P. infestans resistance trait QTL within these two regions introgressed from S. habrochaites on tomato chromosomes 5 and 11. Sub-NILs for each chromosome region with the highest levels of resistance to P. infestans and acceptable horticultural trait phenotypes were identified.;In chapter 3, I describe the combining ability study I conducted with selected sub-NILs to evaluate the potential utility of the wild species resistance QTL alleles for breeding F1 hybrid cultivars and to identify sub-NILs with the highest combining ability for late blight disease resistance. The sub-NILs were mated with inbred testers in factorial mating designs (Design II). F1 hybrid progeny from these two sets of sub-NILs, in which each hybrid was heterozygous for one or more QTL resistance alleles on chromosome 5 or 11, were evaluated for P. infestans resistance in replicated field and growth chamber experiments. Differences in combining ability were found in growth chamber but not field experiments, suggesting that sub-NILs contributed similar levels of resistance to their F1 hybrid progeny in the field, but different levels in the growth chamber. Significant QTL x environment interactions were detected across field and growth chamber experiments. Sub-NILs were identified that expressed P. infestans resistance in F1 hybrid combinations, suggesting that these sub-NILs could be useful for breeding F1 hybrid varieties with enhanced resistance. The expression of quantitative resistance to P. infestans in F1 hybrids derived from each sub-NIL parent was provided by multiple QTL alleles from S. habrochaites. In chapter 4, I conducted a set of quantitative PCR (qPCR) experiments in order to investigate the potential effects of each of these two chromosomal regions containing resistance QTL on the in planta growth of P. infestans. Two tomato near-isogenic lines (NILs), NIL5 and NIL11, containing S. habrochaites QTL introgressions on chromosomes 5 and 11, respectively, and the susceptible control cultivar E6203 were each inoculated with single droplets of a P. infestans spore suspension in randomized and replicated growth chamber experiments. At 48, 72, 84, 96, 108, 120, and 144 hours post-inoculation, leaf disc samples were obtained from the inoculation sites and DNA was extracted. Duplex qPCRs were performed on each DNA sample, using two probes: a single-copy tomato genomic sequence, Solyc09g008610, and the P. infestans O8 DNA family with thousands of copies per genome. This duplex assay design allowed detection and quantification of P. infestans biomass in the three host genotypes over time. The in planta growth of P. infestans in NIL5 was significantly delayed, relative to NIL11 and the susceptible control E6203. The qPCR results corresponded with the rate of lesion symptom development in each host genotype, suggesting that the quantitative resistance to P. infestans conferred by the S. habrochaites chromosome 5 QTL has a physiological and/or biochemical basis that results in a delay in the latent period. Furthermore, these results suggest that resistance conferred by the chromosome 11 QTL may be due to an avoidance mechanism that was overcome by the inoculation technique. By understanding the mechanisms underlying the quantitative resistance conferred by these QTL, plant breeders can make better decisions about their deployment in tomato cultivars for improved quantitative resistance to P. infestans .