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United States Department of Agriculture

Agricultural Research Service

Timothy Rinehart
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Research Interests


My overall objective is to develop strategies for breeding new and improved woody ornamental germplasm adapted to the southeastern United States. I focus on understanding the genetic basis of host-plant resistance to diseases and insects and integrating that knowledge

viamolecular-based breeding programs. Primarily, I develop SSR markers for woody ornamental crops and establish breeding collaborations. Because relatively little genetic research is dedicated to improving ornamental crops, my work encompasses everything from classical genetics, genome sizing, mutation breeding, ploidy and ploidy manipulation, to molecular genetics, marker-assisted breeding, map-based cloning, and bioinformatics. I also serve as a biotechnology resource for the Southern Horticultural Laboratory and I have active collaborations on Rhizoctonia web blights, flea beetle and rootworm pests on woody ornamentals, and the genetic structure of bacterial and fungal populations in alternative “whole tree” potting substrates.


I have several ongoing molecular marker projects using microsatellites (SSR markers) including hydrangea, crapemyrtle, dogwood, redbud, and fringe tree.

Recent accomplishements include technology transfer of molecular tools for H. macrophylla in collaboration with commercial nursery owners and professionals in the U.S., Belgium, and New Zealand. Application of this biotechnology included the detection mislabeled plants (during production and in the marketplace), confirmation of parentage including hybrids resulting from open-pollination, verification of interspecific and intergeneric hybrids, resolving true-to-name disputes, and supporting evidence for plant patent protection of select cultivars. Morphology-based assessments of pedigree or relatedness are prone to error and once mislabeled or lost from trade, it has been difficult to reestablish a cultivar identity based solely on botanical descriptions. The tools I developed can be used to test hypotheses about pedigrees, accurately report parentage, and enforce plant patent and true-to-name warranties. The SSR loci, primer design, DNA sequences, and datasets are available for public use.

Initially Dr. Sandy Reed and I characterized the genetic diversity within and between Hydrangea species and over 250 Hydrangea macrophylla cultivars during the initial establishment of a marker-assisted breeding program. Interspecific hybrids between H. macrophylla and other hydrangea species are an untapped source of genetic potential and diversity estimates are the cornerstone of a roadmap for future hydrangea breeding. I am currently working on specific markers for marker assisted selection, with an emphasis on powdery mildew resistance, which segregates in the H. macrophylla mapping populations. We also continue to use these SSR markers to explore genetic diversity in related species including H. paniculata, H. indochinensis, and Dichroa febrifuga, with an emphasis on accelerating interspecific and intergeneric hybridization to broaden the genetic base for developing new H. macrophylla cultivars. 

The first genetic linkage map for H. macrophylla is in preparation and I have inititated a small scale Targeting Induced Local Lesions In Genomes project, or TILLING, to uncover economically important genes in hydrangea. The forward genetic screen using EMS mutagenesis produced an array of dominant mutant phenotypes including variegation, varying degrees of dwarfism, and aberrant leaf morphologies. If stabilized, some of these traits may be useful in breeding new hydrangea cultivars. The reverse genetic screen will target genes involved in flowering, stress/drought tolerance, and pest resistance.  PCR primers for gene targets will be designed from my hydrangea transcriptome sequencing project using next generation DNA sequencing (Roche 454).

Crapemyrtles are the one of the most popular and profitable flowering trees in the Southeast US nursery trade due to their drought tolerance and 100+ days of flowering.  SSR markers for Lagerstroemia (crapemeyrtle) were developed and used to characterized the genetic diversity within and between Lagerstroemia species and over 100 crapemyrtle cultivars. They've been used to verify new hybrids between existing L. indica and L. subcostata, L. limii, and L. speciosa, which represent an untapped source of genetic potential. Much like hydrangea, SSR markers have the ability to detect mislabeled plants, confirm parentage of hybrids from open-pollinated selections, verify hybrids, resolve true-to-name disputes, and support plant patent protection of select cultivars.  In order to encourage use of the SSR loci I developed, the SSR loci, primer design, DNA sequences, and datasets are available for public use. Future work is focused on marker assisted selection for flea beetle resistance, which segregates in mapping populations, and a linkage map.



Last Modified: 8/15/2016
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