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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

2021 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
This is the third report for Project 8020-21000-072-00D, which began on 4/14/2018. Significant progress was made on both objectives, which fall under NP301. Under Objective 1.A., we completed a genome wide association study and built a genetic linkage map showing the locations of important traits. Whole genome sequencing has been completed using genomic deoxyribonucleic acid (DNA) derived from Hydrangea macrophylla cv Veitchii through PacBio continuous long-read (CLR). Illumina and HiC sequencing were implemented for genome polishing and scaffolding. Ribonucleic acid (RNA) was extracted for cDNA library preparation and sequencing for genome annotation. Genome assembly, polishing and scaffolding has been completed while genome annotation is ongoing. We continued phenotyping a large F2 mapping population of Hydrangea macrophylla for reblooming through the second 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 verified single nucleotide polymorphisms (SNPs) in wild-collected populations of oakleaf hydrangea and used these molecular markers to examine population structure of the species. We maintained a large field trial of oakleaf hydrangea from across its native range and phenotyped plants through the second year of growth. Under Objective 1.C., we performed quantitative trait loci (QTL) analysis to identify three genomic regions associated with reblooming. We are currently testing markers within this region to develop marker-assisted breeding for reblooming. Under Objective 2.A., we advanced efforts to introduce genetic variation through ploidy manipulation. We tested polyploid plants for photosynthesis and water use and developed new triploid seedlings through controlled crosses. Under Objective 2.B., progeny from crosses between Dichroa and Hydrangea were evaluated with the goal of identifying powdery mildew resistant hybrids with phenotypes closer to the hydrangea parent. Powdery mildew and leaf spot screening was initiated for these progenies and is ongoing. Under Objective 2.C., the Callicarpa germplasm trial was completed. Collections of Osmanthus and Hydrangea were phenotyped in multi-year field trials. Seedlings representing novel Osmanthus hybrids were evaluated from germination through second year’s growth.

1. Completion of a high-density genetic map of hydrangea. Inflorescence timing and type are two of the most valuable traits in bigleaf hydrangea (Hydrangea macrophylla). Molecular marker-assisted selection can greatly reduce the time necessary to breed cultivars with the desired inflorescence characteristics. ARS scientists in McMinnville, Tennessee, developed a molecular map of hydrangea and verified the location of a marker that was tightly associated with inflorescence type. The map also led to the discovery of three regions that are associated with the reblooming trait. This map and associated information will lead to efficient development of additional markers for high-throughput screening, as well as the discovery of candidate genes to enable genome-editing for precision breeding in hydrangea.

Review Publications
Bika, R., Palmer, C., Alexander, L.W., Baysal-Gurel, F. 2020. Comparative performance of reduced-risk fungicides and biorational products in management of post-harvest Botrytis cinerea on hydrangea cut flowers. HortTechnology.
Pandey, M., Addesso, K.M., Alexander, L.W., Youssef, N.N., Oliver, J.B. 2021. Relationship of imported fire ant (Hymenoptera: Formicidae) integument coloration to cuticular hydrocarbon and venom alkaloid indice. Environmental Entomology. 1-7.
Wu, X., Hulse-Kemp, A.M., Wadl, P.A., Smith, Z., Mockaitis, K., Staton, M.E., Rinehart, T.A., Alexander, L.W. 2021. Genomic resource development for hydrangea (Hydrangea macrophylla (Thunb.) Ser.) – A transcriptome assembly and a high-density genetic linkage map. Horticulturae.