Big-bracted dogwood genetic diversity and powdery mildew disease resistance investigation using genomic tools
Creators: name: Moreau, Erin Lynn Pfarr
Publisher: name: No Publisher Supplied
Year: 2022

description: Big-bracted dogwoods are popular ornamental trees prized for their beautiful spring blooms with showy bracts, striking red fruits, attractive fall color, and graceful form. The two most widely grown species are Cornus florida and Cornus kousa, native to Eastern North America and East Asia, respectively. Despite their horticultural prominence, there is little information about the genetic diversity, population structure, relatedness, and subspecies origins of dogwood cultivars. Therefore, an extensive genetic diversity study was conducted with over 310 cultivars, wild-collected plants, and breeding selections, focusing on C. florida, C. kousa, interspecific hybrids, and Rutgers breeding selections. The double digest restriction-site associated DNA sequencing (ddRadseq) technique was used to genotype the plants for thousands of single nucleotide polymorphism (SNP) and insertion deletion (Indel) markers. The research results showed high genetic diversity among C. florida and C. kousa wild-collected plants and cultivars. For C. florida, pink-bracted plants formed a distinct clade from white-bracted with the Mexican C. florida ssp. urbiniana forming an outgroup. For C. kousa, Chinese-collected plants (ssp. chinensis) were a distinct subspecies with clear separation from Japanese and Korean plants (ssp. kousa) and cultivars were designated as ssp. chinensis, ssp. kousa, or ssp. hybrid. A Kompetitive allele specific PCR (KASP) assay genotyping panel was designed to easily determine C. kousa trees’ subspecies makeup. Results revealed many cases of genetically identical cultivars being sold under different names, especially for desirable pink-bracted cultivars of both species. Additionally, possible parent-progeny relationships were evaluated and either validated or discredited. The research validated interspecific F1 hybrids and found many of the recent Rutgers breeding selections contain small regions of pacific dogwood (C. nuttallii) DNA introgressed into C. kousa backgrounds. The results of this diversity study are useful to plant breeders, arboreta, and the industry, as most modern cultivars and popular historic cultivars are represented. For breeders and the industry, one of C. florida’s most problematic diseases is powdery mildew (PM) caused by Erysiphe pulchra, which disfigures leaves, decreases growth, and negatively affects flowering. PM resistance breeding efforts have been hindered by the rarity of PM resistance in available germplasm and knowledge of its genetic control. The second chapter details a quantitative trait loci (QTL) mapping study for PM resistance/tolerance in two full sibling populations segregating for PM response. High-density genetic linkage maps were constructed for the two mapping populations using ddRadseq-derived markers. These linkage maps are the densest to date for C. florida and are being used to improve the draft reference genome. One major QTL (LOD = 11.36 and R² = 58.9%) was identified in the second population. Furthermore, a minor QTL (LOD = 3.30 and R² = 7.8%) was detected in the first population. Due to their proximity on LG3, these QTL may be designating the same locus or tightly linked loci. This is the first report of QTL associated with PM response on LG3 in C. florida and lays the groundwork for the development of marker-assisted selection for PM resistance in C. florida breeding programs. In the third section of this research, susceptibility (S) genes were explored as a possible target for gene editing to increase PM resistance in C. florida. PM S genes in the Mildew locus o (MLO) family are conserved in higher plants and have been knocked out or down to increase PM resistance in barley, Arabidopsis, rose, and many other species. Nineteen putative C. florida MLO genes were found, manually curated, and assigned to MLO clades I-VII. Five C. florida MLO genes belonged to Clade V and of these, three were significantly upregulated at one time point after infection with PM, designating them as possible PM S genes. CRISPR vectors were constructed to knock out the three putative PM S genes singly and in combination and were used to transiently infect dogwood leaves. However, CRISPR-edited DNA was not recovered from the leaves and significant differences were not observed in PM levels compared to controls, underlying the need for further development of CRISPR transformation and somatic embryogenesis protocols. With further validation, the three putative PM S MLO genes could potentially be used as targets of genome editing to produce PM resistant dogwoods.