Introgression of genetic resistance to downy mildew (peronospora belbahrii) in a non-model plant species, sweet basil (ocimum basilicum)

Abstract

Sweet basil (Ocimum basilicum) is among the most widely cultivated culinary herbs in the United States, Western Europe and Israel. Despite relative economic importance, breeding and genetic study of this plant species has been largely neglected, rendering its >3 Gbp genome largely unexplored. The deficit in available O. basilicum genetic and genomic resources has been highlighted by a worldwide downy mildew epidemic caused by obligate oomycete Peronospora belbahrii, which has yet to be mediated by disease resistant varieties. The goal of this dissertation research was to narrow the information gap preventing an effective disease resistance breeding response. Specific objectives were to: 1) determine population structure and estimate genetic diversity among a panel of downy mildew resistant and susceptible Ocimum spp. accessions, 2) identify mode of inheritance for resistance to downy mildew in a full-sibling family and 3) construct a linkage map for detection of quantitative trait loci (QTL) associated with DM resistance. A nested, model-based cluster analysis demonstrated three major delineations within the Ocimum genus with additional evidence for cryptic structure, especially within the economically important k1 O. basilicum cluster. Distribution of DM resistance was concentrated outside the k1 O. basilicum cluster with the exception of a single k1 genotype, ‘MRI’. Analysis of downy mildew response across F2 and backcross populations over two years and two locations demonstrated major gene control of downy mildew resistance conferred by MRI. Finally, a restriction site associated DNA sequencing (RADseq) approach facilitated the discovery and mapping of >1,800 single nucleotide polymorphism (SNP) and expressed sequence tag simple sequence repeat (EST-SSR) markers. The resulting genetic map was validated by the detection of a major QTL, dm11.1, which explained 38-55% of the phenotypic variance observed for the MRI x SB22 F2 mapping population. Disomic inheritance of SNP and SSR markers support previous cytological evidence that basil has evolved an allopolyploid genome. Results of this dissertation provide the most robust phylogenetic examination of the Ocimum genus to date, characterization of DM heritability across multiple environments and the first report of genetic/QTL mapping for O. basilicum. A current case study is provided for the feasibility of breeding a non-model plant species using classical genetic theory in combination with modern genomic technologies.