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ARS Home » Northeast Area » Washington, D.C. » National Arboretum » Floral and Nursery Plants Research » Research » Research Project #434613

Research Project: Genetic Improvement of Nursery Crops through Functional Genomics and Breeding

Location: Floral and Nursery Plants Research

2022 Annual Report

Objective 1: Establish long-term experimental hydrangea populations, and develop information management systems and standards for hydrangea phenotyping and genetic mapping to accelerate the development of disease and stress resistant hydrangea cultivars with superior product quality. [NP301, C1, PS1A; NP301, C4, PS4A] Sub-objective 1.A. Establish and phenotype Hydrangea macrophylla experimental populations for identification of disease resistance and ornamental traits. Sub-objective 1.B. Establish, genotype, and phenotype a range-wide Hydrangea quercifolia collection for natural genetic variation for disease resistance and ornamental traits. Sub-objective 1.C. Develop new phenotyping methods for important traits and create associated data management systems for genomic and phenotypic data. Objective 2: Develop, evaluate, and release improved germplasm of hydrangea and other high-value, native, and underrepresented nursery crop species to expand market opportunities for producers, stimulate consumer interest, and mitigate the environmental footprint of nursery production. [NP301, C1, PS1B] Sub-objective 2.A. Accelerate the development of superior Hydrangea germplasm using ploidy manipulations, and wide hybridization. Sub-objective 2.B. Evaluate germplasm including Hydrangea, Osmanthus, and Hamamelis for nursery production and breeding improvement potential. Sub-objective 2.C - Improve resource use efficiency and/or reduce nutrient runoff in container nursery production through data-driven research on substrates, fertilizer, and irrigation.

During the next five years, Hydrangea and Osmanthus selections from previous breeding cycles will be progagated and distributed to cooperators. Germplasm evalutations of new species and cultivars will ensure a broad base for future cultivar development. We will confirm the three major powdery-mildew resistance SNPs in the two most resistant and two most susceptible cultivars using real-time PCR with TaqMan probes. Controlled crosses between the most powdery mildew-resistant and most susceptible cultivar are underway. This F1 mapping population will be genotyped via RT-PCR in the same manner as the mapping parents. This population will be planted in the field for a minimum three-year observation period. During this time, natural powdery mildew incidence and/or induced powdery mildew infection will be recorded. Digital images of each plant will be obtained in regular intervals throughout the growing season. Image analysis will be used to monitor the progression of disease infection and the number and size of new inflorescences. Together, the genotype and phenotype data will be used to refine the genome-wide association analysis, determine the efficacy of marker-assisted selection for powdery mildew resistance at the seedling stage in Hydrangea, and identify plants for further gene expression analysis. For genetic and horticultural analysis of oakleaf hydrangea, we will sample up to 20 populations within each state on a longitudinal/latitudinal cline, as well as representing the full diversity of environments in which the species occurs. Within each of these populations we will sample up to 20 plants. Three to five recently expanded leaves will be collected from selected plants, stored flat in Ziploc bags and stored in coolers with unique identifiers linked with each bag. Plant morphology, location, and other notes will be recorded using the EpiCollect5 web application. Leaves will be shipped overnight via UPS to the USDA-ARS in McMinnville, TN for processing, DNA isolation, and storage. Genotyping-by-sequencing will be performed by the University of Minnesota Genomics core facility. Bioinformatic support will be provided by the ARS NEA Statistics Group. Ten populations per state on a longitudinal/latitudinal cline, as well as representing the full diversity of environments in which the species occurs, will be evaluated for current generation estimates of genetic diversity and levels of inbreeding and for common garden horticultural characterizations in Minnesota, Mississippi, and Tennessee. Each location will evaluate 25-50 individuals of each population (60 populations total) for growth, form, floral, and disease resistance traits. Over 1500 F2 seedlings derived from hybridizations between 'Snow Queen' and the compact cultivars Pee Wee and Sikes Dwarf were evaluated for compact plant habit, quality and quantity of inflorescences, disease resistance and fall foliage color. Seven plants from this population have been selected for compact form and superior floral display. Seed and seedlings from these selected plants will be used for development of disease-screening methods.

Progress Report
Significant progress was made on both Objectives, which fall under NP301. Under Objective 1.A., we annotated the genome of bigleaf hydrangea and confirmed gene locations for inflorescence type and double-flowering. We continued phenotyping a large F2 mapping population of bigleaf hydrangea for reblooming through the third year of growth. This well-characterized population will be used for genetic mapping of powdery mildew resistance and reblooming and for determining gene-trait associations. Under Objective 1.B. We maintained a large field trial of oakleaf hydrangea from across its native range and phenotyped plants through the third year of growth. We used genetic data collected last year to determine population structure of oakleaf hydrangea across its native range and identify populations with unique DNA sequences. Under Objective 1.C., we genotyped the bigleaf hydrangea F2 mapping populations at three genomic regions associated with reblooming. This data will be integrated with functional analysis to verify reblooming genes in hydrangea. Under Objective 2.A., we completed genome sizing of 74 individual plants resulting from unreduced gamete breeding or mutation and continued phenotyping them for floral and disease resistance traits. Under Objective 2.B., we continued evaluating powdery mildew resistance and flowering in progeny from crosses between Dichroa febrifuga and bigleaf hydrangea. Six powdery mildew resistant offspring (based on two-year data) were selected for stock increase. Under Objective 2.C., collections of Osmanthus were phenotyped in multi-year field trials. Seedlings representing novel Osmanthus hybrids were evaluated from germination through third year’s growth in preparation for field trials next year. We initiated a trial to identify reblooming bigleaf hydrangea cultivars for full sun container production and a trial to investigate the effect of substrate on phosphorus leaching in container production. We collected seed of incense cedar throughout its native range in California to evaluate production merit in the southeast.


Review Publications
Sun, Y., Dou, H., Perez, C., Niu, G., Alexander, L.W. 2022. Growth, Gas Exchange, and Mineral Nutrients of Hydrangea Hybrids to Saline Water Irrigation. HortScience. 57(2):319-329.
Neupane, K., Alexander, L.W., Baysal-Gurel, F. 2022. Management of Phytophthora cinnamomi using fungicides and host plant defense inducers under drought conditions: A case-study of flowering dogwoods. Plant Disease. 106:475-485.
Sherwood, A., Alexander, L.W., Mcnamara, S., Clark, M., Hokanson, S. 2021. Horticultural characterization of wild Hydrangea quercifolia seedlings collected throughout the species native range. Journal of the American Society for Horticultural Science. 56(9):1-11.
Landaverde, A.C., Shreckhise, J.H., Altland, J.E. 2020. Storage procedures affect pH, electrical conductivity, and nutrient concentrations of pour-through leachate from pine bark and peat-based substrates. HortScience. 55(10):1597-1604.