Genetic diversity analysis of big-bracted dogwood (Cornus florida and C. kousa) cultivars, interspecific hybrids, and wild-collected accessions using RADseq.

Big-bracted dogwoods are popular ornamental trees known for their beautiful spring blooms with showy bracts and four-season appeal. The two most widely grown species are Cornus florida and Cornus kousa, native to Eastern North America and East Asia. Despite their horticultural prominence, there is little information available regarding genetic diversity, population structure, relatedness, and subspecies origins of dogwood cultivars. In this study, 313 cultivars, wild-collected plants, and Rutgers University breeding selections, focusing on C. florida, C. kousa, and interspecific hybrids, were genotyped using restriction-site associated DNA sequencing (RADseq) generating 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 those with white-bracts 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 accessions (ssp. kousa) and cultivars were designated as ssp. chinensis, ssp. kousa, or ssp. hybrid. Using this information, a Kompetitive allele specific PCR (KASP) assay genotyping panel was designed to determine C. kousa trees' subspecies makeup. Results revealed many cases of genetically identical cultivars being sold under different names, especially for pink-bracted cultivars of both species. Additionally, reported parent-progeny relationships were evaluated and either validated or discredited. Finally, the hybrid germplasm analysis validated pedigrees of 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. This diversity study elucidates origins, diversity, and relationships of a large population of big-bracted dogwoods. The results can inform plant breeders, arboreta, and the ornamental plant industry, as most modern cultivars and popular historic cultivars are represented.

Genetic Diversity Analysis of Anisogramma anomala in the Pacific Northwest and New Jersey.

Anisogramma anomala, a biotrophic ascomycete, causes eastern filbert blight (EFB) of hazelnuts (Corylus spp.). EFB is endemic in eastern North America, preventing the commercial production of European hazelnut (C. avellana L.). In contrast, the historic absence of A. anomala in the Pacific Northwest (PNW) supported the development of a robust hazelnut industry. Circa 1960, A. anomala was inadvertently introduced into southwestern Washington, causing orchard devastation. Distribution of the pathogen in the PNW has been hypothesized to be the result of a single-point introduction. This study aimed to investigate the single-point introduction hypothesis of A. anomala by comparing the genetic diversity of A. anomala samples from the PNW and New Jersey (NJ). Specimens from the main PNW production region (n = 60) and an area within the pathogen's native range, NJ (n = 151), were genotyped using 15 simple sequence repeat (SSR) markers. The following were used to assess genetic diversity and population structure: allelic summary statistics, discriminant analysis of principal components, network median-joining tree, analysis of multilocus genotypes, and allelic population diversity analysis. Analyses separated the samples into one cluster containing all the PNW isolates, and five clusters of NJ isolates. The PNW samples were nearly genetically uniform, and the NJ isolates were diverse. These findings support the hypothesis that A. anomala in the PNW was derived from a single-point introduction and corroborate previous studies that have shown A. anomala is very diverse in NJ. This indicates that maintaining restrictions on the movement of Corylus into the PNW is important to prevent the introduction of new populations of A. anomala, thus protecting the PNW hazelnut industry.

Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm.

BACKGROUND: The basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii. In an effort to improve classification of relationships 20 EST-SSR markers with species-level transferability were developed and used to resolve relationships among a diverse panel of 180 Ocimum spp. accessions with varying response to downy mildew. RESULTS: Results obtained from nested Bayesian model-based clustering, analysis of molecular variance and unweighted pair group method using arithmetic average (UPGMA) analyses were synergized to provide an updated phylogeny of the Ocimum genus. Three (major) and seven (sub) population (cluster) models were identified and well-supported (P < 0.001) by PhiPT (ΦPT) values of 0.433 and 0.344, respectively. Allelic frequency among clusters supported previously developed hypotheses of allopolyploid genome structure. Evidence of cryptic population structure was demonstrated for the k1 O. basilicum cluster suggesting prevalence of gene flow. UPGMA analysis provided best resolution for the 36-accession, DM resistant k3 cluster with consistently strong bootstrap support. Although the k3 cluster is a rich source of DM resistance introgression of resistance into the commercially important k1 accessions is impeded by reproductive barriers as demonstrated by multiple sterile F1 hybrids. The k2 cluster located between k1 and k3, represents a source of transferrable tolerance evidenced by fertile backcross progeny. The 90-accession k1 cluster was largely susceptible to downy mildew with accession 'MRI' representing the only source of DM resistance. CONCLUSIONS: High levels of genetic diversity support the observed phenotypic diversity among Ocimum spp. accessions. EST-SSRs provided a robust evaluation of molecular diversity and can be used for additional studies to increase resolution of genetic relationships in the Ocimum genus. Elucidation of population structure and genetic relationships among Ocimum spp. germplasm provide the foundation for improved DM resistance breeding strategies and more rapid response to future disease outbreaks.