Source: TEXAS A&M UNIVERSITY submitted to
COMBATTING ROSE ROSETTE DISEASE: SHORT AND LONG TERM APPROACHES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
1004350
Grant No.
2014-51181-22644
Project No.
TEX09613
Proposal No.
2014-07901
Multistate No.
(N/A)
Program Code
SCRI
Project Start Date
Sep 1, 2014
Project End Date
Aug 31, 2017
Grant Year
2014
Project Director
Byrne, D.
Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001
Performing Department
Horticultural Science
Non Technical Summary
In the past few decades, Rose Rosette Disease (RRD) has spread from its source in the Rockies, through the Mid-West to the East coast. It now threatens to decimate the US rose industry. Garden roses which form the cornerstone of the multi-billion dollar landscape industry, annually generate wholesale US domestic bare root and container production valued at ~ $400 million. There is an urgent need to control RRD. It is caused by a novel plant virus, the Rose rosette virus (RRV), which is transmitted by wind-blown eriophyid mites (Phyllocoptes fructiphilus). Unlike other rose diseases it can kill a rose within two to three years of infection. This long term (5 years) SREP project has four major goals. In the short term, develop Best Management Practices (BMPs), based on host, virus, and vector biology, to minimize the effects of RRD. Key to this effort will be the development of efficient user-friendly diagnostic tools. In the long term, identify additional RRD resistant roses and develop genetic tools to move RRD resistance efficiently into elite rose germplasm by developing high throughput markers (SNPs), consensus maps and identifying marker-trait associations for RRD resistance and consistent flower productivity and quality. Develop an information pipeline, monitoring network and demonstration program to communicate the value of and establish the use of the BMPs through the involvement of the industry in the research and the education process. Improve our understanding of consumer preferences and identify barriers to rose sales. This work is essential to save the rose industry from the devastation of a RRD epidemic and to create new opportunities for rose marketing.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2012110108150%
2110530110120%
2124030113010%
6073120301020%
Goals / Objectives
In the short term, develop a set of Best Management Practices (BMPs) to combat RRD, based on host-virus-vector interaction, to help gardeners, landscapers, producers, and marketers minimize the effect of the disease. Key to this effort will be the development of efficient diagnostic tools to enable rapid, easy-to-use and accurate detection of the virus.In the long term, identify additional sources of resistance and develop genetic tools to move resistance into commercial cultivars by developing high throughput markers (SNPs), constructing diploid and tetraploid consensus maps and identifying marker-trait associations for RRD resistance and consistent flower productivity and quality using a pedigree based analysis approach. Create an information and demonstration pipeline by building on the industry's existing information hub via roserosettedisease.com. to communicate the value of and establish the use of the BMPs through the involvement of the industry in the research process, the rose community in the RRD Monitoring Network, and rose/landscape organizations in the outreach program through their publications, newsletters and web sites (see letters).Improve our understanding of consumer and industry preferences and barriers to rose sales. Disease resistance is the major concern for the rose industry and consumers. We will quantify the weight that consumers and market intermediaries (retailer, wholesaler, landscaper) place on various traits, including RRD and other diseases, assess the market barriers to rose sales, develop a plan to overcome these barriers and evaluate the cost of RRD to the industry and the benefits of this research project.
Project Methods
Best Management Practices. Rapid and sensitive diagnostic protocols. Both Field Detection System using a lateral flow device (antibody and nucleotide based detection) and Laboratory Detection System using LAMP (Reverse transcription-Loop mediated isothermal amplification of DNA) and self-quenched primer (SqP) technology will be developed. The most consistent assay will be tested and validated by two diagnostic labs (TAMU, OSU) and then moved via outreach to other plant diagnostic labs. Epidemiology. The temperature effects (25C to 40 C) on Phyllocoptes fructiphilus populations and its ability to transmit Rose rosette virus by using potted plants and infesting them with infected mites and following the mite reproduction, virus transmission and symptom development. The relationship between virus movement within a plant and symptomology will be assessed by inoculating rose plants with RRV and then following them for symptoms and virus in canes, roots and meristems. RRV movement in the commercial rose planting will be followed with rogueing of symptomatic plants and without rogueing in 4 locations (TX and TN) via symptomology and by testing plants for RRV. Pattern and rate of spread will be determined.Chemical control in the field. We will test 2 Syngenta antiviral compounds and 4 commercial use only labeled miticide treatments (Forbid, Kontos, Avid, and Akari at company recommended rates) in a randomized complete block design with 8 replications. Data will be collected for RRD symptoms, RRV and the P. fructiphilus population. Biological control of P. fructiphilus. Infested plants will be placed in cages with 'water moats' to prevent movement of predatory mites (Syngenta proprietary product). Into half of the cages, predatory mites will be introduced to evaluate their efficacy to reduce populations of eriophyid mites.EvaluationDevelop better RRV diagnostic tests (1-2 years), validate these (years 2-3) and have them available for routine use (year 5). Assessed by surveying commercial/public diagnostic laboratories and publications/presentations.Improved BMPs with better understanding of mite/virus biology and efficacy of chemical/biological/antiviral control agents. Assessed by RRD frequency/distribution data from RRD Monitoring program and sale figures for rose.Identify sources of resistance and develop tools to transfer it to elite germplasm. Roses will be planted (3-4 replications) at two evaluation sites (TN and DE) with augmented RRD pressure and will be rated for symptoms for 3 years. Plants that remain symptomless at the end of each year will be assayed for RRV and checked for mite infestation and further tested for resistance via graft inoculation to distinguish among tolerance to the virus (asymptomatic plants with virus) and resistance to the viral infection or to the mite vector. Optimize Digital Genotyping. Digital Genotyping (DG) as developed for sorghum in Dr. Klein's laboratory will be optimized for use with rose. We propose to use digital genotyping to discover at least 1000 SNPs across the 560Mbp rose genome. DNA will be sequenced on the Illumina HiSeq2000. The sequences will be aligned and the SNPs/INDELs identified using the bioinformatics pipeline will be combined with 40 SSRs to create the consensus genetic maps (diploid ~400 plants, 3 crosses and tetraploid ~800 plants, 5 crosses) with JoinMap V4 and/or the TetraploidMap program. Discover markers associated with RRD resistance. Five rose breeders will create hybrid populations (~500 seedlings from 5-10 inter related populations) among RRD resistant and susceptible parents. These seedlings will be propagated and at the end of the 2nd year will be planted in RRD free site (TX) and in RRD evaluation plots (TN and DE). These populations will be phenotyped for RRD resistance and genotyped via DG. FlexQTL, a Pedigree Based Analysis approach for QTL discovery will be used to identify markers associated with RRD resistance.EvaluationOptimize DG technology for rose to create consensus maps for the diploid/tetraploid rose and to genotype marker discovery population.Identify additional sources of tolerance or resistance to RRV or Phyllocoptes fructiphilus.With FlexQTL identify ~10 SNP markers associated with RRD resistance and highly abundant and consistent flower production and quality. Screen parents/progenies of collaborating breeders to verify their usefulness. Increase the number of rose breeders using MAB.Document with refereed publications, presentations, and breeder surveys.Consumer preferences and market barriers. Assess U.S. consumer preferences for rose attributes using Discrete Choice Experiments (DCE) in different market segments and investigate the heterogeneity in rose preferences. The questionnaire (developed via focus groups) will be administered through an in person discrete choice experiment using high quality pictures combined with eye tracking technology and electromyographic (EMG) data to assess respondent's cognitive response. Identify market barriers inhibiting rose sales. We will survey intermediary (wholesaler, retailer, and landscaper) preferences for and willingness to supply roses that are disease-resistant and consistently produce high flower number and quality to identify the possible marketing barriers to supplying disease resistant rose cultivars. An online survey (500 randomly chosen participants and self selected participants) will be used to gather data across several states to get a representative sample of the US industry. We will use a mixed logit with two sets of variables (roses product and tested individual attributes). Socioeconomic impacts of RRD research. The potential economic and social impacts of the project will be estimated by calculating the current economic impacts of damages due to RRD and the total economic impacts with economic multipliers generated by the IMPLAN Pro social accounting software. The rate of resistance and adoption will be estimated to calculate the socioeconomic impacts of the project to the rose industry. A benefit-cost analysis of the amount of funding and the results driven benefits of the proposal will be estimated, including the education and outreach component.EvaluationAssessment of consumer expectations and preferences for attributes of garden roses.Determine the trade barriers in the rose industry supply chain and develop a plan to overcome them.End consumer and industry knowledge of RRD resistant garden roses is increased.Estimate the socioeconomic impacts of the adoption of varieties to the rose and green industries.Measured by on-site and online registration lists and journal publication, and socioeconomic analysis of the impact of RRD.Efforts. We will develop the training programs and educational materials to support the Monitoring Network and the national RRD BMP training programs. We will set up a series of demonstration and validation trials with public gardens, research/extension services, and partner with various public/private horticultural organizations to disseminate the information via roserosettedisease.com and extension web sites, newsletters, popular press articles, social media and presentations. These materials will be put online as documents but also as a series of interactive courses, each focused towards the various segments of the industry: consumers, public display gardens, garden centers and producers. Further communication is also done via collaborative work with rose breeders etc. and the participants of the RRD Monitoring Network.EvaluationIncreased awareness of RRD.Adoption of the improved BMPs developed by the project.Fewer problems with RRD and consequently greater use of roses in the garden.Measured by consumer/industry surveys, the number of articles highlighting the issue and ornamental industry sales figures.

Progress 09/01/15 to 08/31/16

Outputs
Target Audience:During the second year of the project we have communicated progress to our scientific colleagues (6 journal articles, 3 conference proceedings, APS Special Session, ASHS Workshop, 31 presentations at professional meetings), to extension professionals, green industry professionals and Master Gardeners through training workshops, to a wide audience in the green industry including producers, landscapers, garden centers, marketers, horticulturists, plant breeders/evaluators, plant protection specialists, and consumers via 87 extension/public presentations (8600 contacts), interviews (industry publications), social media (Combating RRD Facebook page with 470 likes, 5,000 engaged users, reach of ~40,000,Twitter), Youtube (https://www.youtube.com/watch?v=gEU8vyUaNf4&feature=youtu.be) articles in the American Rose Magazine, by demonstration gardens (TX, OK, TN), teaching classes at the Universities, hiring students as summer interns and diagnostic work (OSU/TAMU) and to rose breeders directly through their involvement in the creation of the hybrid rose populations for the project. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training was provided to multiple groups of Extension professionals and Master Gardeners, and 4 college students in various aspects of the research (cloning and sequencing the RRV NP, cytogenetics, genetics, horticultural evaluation). Project participants and graduate students participated in the annual meetings of the American Phytopathogy Society (RRD Special Session), the American Society of Horticultural Sciences (RRD Workshop), the Plant and Animal Genome (invited talk at Ornamental Genomics session) conference as well as other professional meetings. In addition, the PI and graduate students attended the FlexQTL Training Workshop held in conjunction with the RoseBREED II Annual meeting. How have the results been disseminated to communities of interest?During the second year of the project we have communicated progress to our scientific colleagues (6 journal articles, 3 conference proceedings, APS Special Session, ASHS Workshop, 31 presentations at professional meetings), to extension professionals, green industry professionals and Master Gardeners through training workshops, to a wide audience in the green industry including producers, landscapers, garden centers, marketers, horticulturists, plant breeders/evaluators, plant protection specialists, and consumers via 87 extension/public presentations (8600 contacts), interviews (industry publications), social media (Combating RRD Facebook page with 470 likes, 5,000 engaged users, reach of ~40,000,Twitter), Youtube (https://www.youtube.com/watch?v=gEU8vyUaNf4&feature=youtu.be), articles in the American Rose Magazine, by demonstration gardens (TX, OK, TN), teaching classes at the Universities, hiring students as summer interns and diagnostic work (OSU/TAMU) and to rose breeders directly through their involvement in the creation of the hybrid rose populations for the project. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 1. In the short term, develop a set of Best Management Practices (BMPs) to combat RRD Objective 1a. Develop rapid/robust diagnostic test for Rose rosette virus Verified the robustness and consistency of Loop Mediated Isothermal Amplification of DNA (LAMP) and Helicase Depedent Amplification with Self-quenched Primers (HAD-SqP) assays for RRV detection in several laboratories. EMARA F&R7/8 primer set was designed from the conserved domains of the RNA conserved dependent RNA polymerase of the six species of Emaravirus to broadly detect viruses in the genus Emaravirus. Primers were designed to distinguish among 3 species of the Phyllocoptes mites and detect the presence of RRV simultaneously. Developed a suitable gel based-isothermal RT-RPA assay for the sensitive (1 fg), rapid (less than 30 minutes) detection of RRV for point-of care testing of field samples. The RT-exoRPA (isothermal reverse transcription-recombinase polymerase amplification) assay for the rapid and sensitive (1 fg virus) detection of RRV combined with the rapid technique viral RNA extraction procedure (< 5 min) reduces the time of analysis to less than 15 min, with simple equipment and can be used efficiently in field assays for rapid indexing of the RRV. RRV NP-specific rabbit polyclonal antibody was developed. Detectable at ~10ng/mL in ACP ELISA. Five of the RRV NP-specific monoclonal antibodies (McAbs) reacted strongly to ACP (antigen coated plate) and of these three reacted to both the ACP and the TAS (triple antibody sandwich) ELISA assay. Validation in diagnostic lab was completed for the real-time PCR published by Dr. Ochoa-Corona. The method is reliable and provides results in as little as 3 hours reducing the time for analysis by 50%. Lab validation of other above described methods are ongoing. Objective 1b. Epidemiology P. fructiphilus was observed overwintering within the protection of spent flower buds indicating that flower bud removal in the fall may reduce of mite vector population. Floral/vegetative structure differences among roses presented unique niches that may influence the population density of the mite vector, other mites and their predators by influencing their survival. Rapid rogueing of symptomatic plants was a more effective control strategy than was the pruning of symptomatic canes to base of the graft union. Non host Miscanthus sinensis barriers reduced symptom development by more than 50%. Objective 1c. Chemical/biological field control options Weekly application of miticides (bifenthrin, fenpyroximate, spiromesifen and spirotetramat) was found to be effective (one-week spray intervals) in preventing rose rosette symptom development. Further studies to determine the optimal spray interval and the effectiveness of additional miticides (abamectin and bifenazate) on mite populations and symptoms development are under way. In the long term, identify additional sources of resistance and develop genetic tools to move resistance into commercial cultivars. Objective 2a. Identify additional sources of host plant resistance to RRD Observational studies have identified about 430 roses susceptible to RRD. Potentially resistant roses are in RRD field evaluation trials in Tennessee, Delaware, Texas and Oklahoma. 317 rose genotypes are being evaluated for resistance to RRD in field plots in Delaware and Tennessee. Symptoms are expected to develop this fall and in the spring of 2017. 300 rose accessions have been evaluated for resistance to black spot and cercospora, tolerance to heat, and landscape suitability in two trials in Texas. Of the roses being evaluated, 19% show good field resistance to black spot, 69% show good field resistance to cercospora and 9% show good resistance to both diseases. Unfortunately, most of those with little disease are species or species hybrids and not easily used in breeding. Objective 2b. Optimize Digital Genotyping Digital genotyping protocol has been optimized and used to sequence/identify SNPs on ~ 600 rose genotypes using the strawberry genome sequence as the reference genome. Objective 2c. Create diploid and tetraploid consensus maps Constructed individual genetic maps for three diploid mapping populations and created a consensus map with 3,500 SNPs (~0.25 cM/marker). Objective 2d. Discover markers associated with RRD resistance Preliminary work on using the MapQTL and FlexQTL software to analyze large numbers of SNP markers is being done on black spot resistance and various flower/architectural traits. Germination on crosses done in 2015 was poor (~2%). The populations with Rosa palustris are small (<10 seedlings). The largest diploid population is cross with Papa Hemeray (~50). Three small populations with Rosa setigera x polyantha were made available by David Zlesak. Several populations with 'Homerun' as a parent are available for analysis as are a few F2 populations derived from these. Potential parents were assessed for their chromosome number and pollen fertility. More than 6,000 pollinations were done in 2016. This includes 1,328 tetraploid and 5,288 diploid pollinations. The average hip set for the diploid and tetraploid crosses was 24% and 54% respectively. Create an information and demonstration pipeline. Objective 3a. Develop a RRD Monitoring Network The RRD reporting APP along with training materials are in the final stages of development Objective 3b. Develop national RRD BMP training materials This fall, Olson will release the national version of the rose rosette disease fact sheet as well as scripted powerpoint slides and recorded powerpoint presentations. Added another 140 images of rose rosette symptoms on the Bugwood.org database which serves as a national source of images of this disease. Objective 3c. Develop an information pipeline In the process of creating a Combating Rose Rosette website to serve as the central location to find accurate information on RRD management and training materals. Established a "Combating Rose Rosette Disease" Facebook page. It currently has about 467 (up from 200 in 2015) followers. Over 450 individuals have followed, 5,000 have interacted and it has reached over 40,000 individuals During the second year of the project we have communicated our progress to our scientific colleagues (31 professional presentations), a wide audience in the green industry including producers, landscapers, garden centers, plant protection specialists, marketers, plant breeders/evaluators,and consumers (87 presentations),articles in American Rose Magazine, via social media (Combating Rose Rosette Facebook page and twitter account) and to rose breeders directly through their involvement in the creation of the hybrid rose populations for the project. Improve our understanding of consumer and industry preferences and barriers to rose sales. Objective 4a. Assess U.S. consumer preferences A preliminary assessment of the rose attributes that drive demand have been established. We are developing pilot tests for the consumer experiments using eye tracking and other behavioral response equipment to analyze the external validity of responses. Objective 4b Identify market barriers inhibiting sales of new roses The chronological value chain for nursery growers who produce roses and other important ornamental shrubs was analyzed. Thus far, the key data collection points were identified and data management protocols established to ensure that the appropriate data are captured during the project. An economic engineering approach was developed to estimate the initial capital investment, production costs, and product prices for the baseline and alternative nursery disease management models. Objective 4c. Socioeconomic impacts of RRD research Work on objective 4b is preparing the groundwork and developing the database to do the socioeconomic analysis of the RRD research.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Shefali Dobhal; Jennifer D Olson; Mohammad Arif, Ph.D; Johnny A Garcia Suarez; Francisco M Ochoa-Corona. 2016. A simplified strategy for sensitive detection of Rose rosette virus compatible with three RT-PCR Chemistries. Journal of Virological Methods 232:47-56
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Binoy Babu, Brian K. Washburn, Kristina Poduch, Gary Knox and Mathews Paret. 2016. Identification and characterization of two novel genomic RNA segments RNA5 and RNA6 in Rose rosette virus infecting roses Acta Virologica 60(2):41-50.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Babu, B., J. Avyamperumal, D. Jones, T. S. Schubert, C. Baker, B. Washburn, S. Miller, K. Poduch, G. Knox, F. Ochoa-Corona, and M. Paret. 2016. Development of a rapid, sensitive TaqMan real-time RT-PCR assay for the detection of Rose rosette virus using multiple gene targets. Journal of Virological Methods. September 2016 235:41-50
  • Type: Other Status: Published Year Published: 2015 Citation: Windham, M 2015. Unravelling rose rosette Acta Horticulturae, 1085:409-413
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Palma, Marco A., Bridget K. Behe, Charles R. Hall, Patricia T. Huddleston, and Tom Fernandez. 2016. Tracking position premiums in discrete choice experiments. Applied Economics Letters. Published online DOI:10.1080/13504851.2016.1150941.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Perez, Maria, Marco Palma, Bridget Behe, and Charles Hall. 2016. Structural Breaks and Future Growth of the Green Industry. J. Environ. Hort. 34(1):5255.
  • Type: Other Status: Published Year Published: 2015 Citation: Byrne D. H.,E. Roundey,P. Klein, and M. Yan. 2015. Combating Rose Rosette Disease: Are there resistant roses? American Rose Magazine 43(5):78-83
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Windham, M. T., F. A. Hale, A. S. Windham, and Q. Cheng. 2015. A Best Management Plan for Rose Rosette. Proceedings of the Southern Nursery Research Conference. 60:165-165.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: F. M. Ochoa-Corona , A.M. Salazar Aguirre, S.G. Molina C�rdenas , A. Olmedo-Velarde, S. Dobhal, J. Olson, B. Babu, M. L. Paret. 2016. Development of efficient diagnostic tools to enable rapid, easy-to-use, accurate and affordable detection for Rose rosette virus. Oral presentation. American Phytopathological Society. Tampa, FL. July 30  August 3, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: S. G. Molina C�rdenas. A. M. Salazar Aguirre,F.M. OCHOA  CORONA, J. Olson. Fluorogenic Detection of Plant Viruses by Helicase Dependent Amplification with Self-Quenched Primers. Oral presentation. American Phytopathological Society. Tampa, FL. July 30  August 3, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: F. M. Ochoa-Corona. Diagnostics 101, Roses, biosecurity & Possibilities. Oral presentation. NCPR-Annual Tier II Meeting, Shreveport, LA. June 28-29, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: R. Ochoa, G. Otero-Colina, J. Hammond, R. Jordan, G. Bauchan. Current state of knowledge on mite transmission and control. Oral presentation. American Phytopathological Society. Tampa, FL. July 30  August 3, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Byrne, D. H., P. Klein, M. Yan, E. Roundey, and J. Lau 2016. Is breeding the answer? How long will it take? The challenges of Rose Rosette Disease (RRD). Oral presentation for the American Phytopathological Society meetings in Tampa, FL, August, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Ong, K., H. B. Pemberton, A. Windham, G. Knox, J. Olson, A. Brake, E. Roundey, and D. H. Byrne. 2016. Combating Rose Rosette  Monitoring extent and diversity of the disease. Poster presentation. American Phytopathological Society meetings in Tampa, FL, August, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Yan, M, D. H. Byrne, and P. Klein. 2016. Map construction in rose with GBS. Invited talk in the Ornamental Session at the PAG meetings, San Diego, January, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Pemberton, H. B., K. Ong, M. Windham, J. D. Olson, and D. H. Byrne. 2016. What is Rose Rosette Disease? The challenges of Rose Rosette Disease (RRD): An Update of the combating RRD SCRI project. Oral presentation for the American Society of Horticultural Sciences meetings in Atlanta, August, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Byrne, D. H., P. Klein, M. Yan, E. Roundey, and J. Lau 2016. The challenges of Rose Rosette Disease (RRD): Is breeding the answer? How long will it take?: An Update of the combating RRD SCRI project. Oral presentation for the American Society of Horticultural Sciences meetings in Atlanta, August, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Roundey, E., N. Anderson, C. Bedard, M. Scheiber, and D. H. Byrne. 2016. Evaluation of Rosa palustris as a parent for Rose Rosette Disease-resistant roses. Oral presentation for the American Society of Horticultural Sciences meetings in Atlanta, August, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Yan, M., D. H. Byrne, P. Klein, and Q. Dong. 2016. Map construction and black spot resistance QTL detection in diploid rose. Oral presentation for the American Society of Horticultural Sciences meetings in Atlanta, August, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Jennifer Olson, Tom Evans, Kevin Ong, Mark Windham, Ellen Roundey, Jeekin Lau, David H. Byrne. 2016. Is there resistance to Rose Rosette Disease among cultivated roses? National Meeting of the American Phytopathological Society. Tampa, FL. July 30-August 3. Poster.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Mark Windham, Alan Windham, Frank Hale. 2016. Management of Rose Rosette Disease. The Challenges of Rose Rosette Workshop. Oral presentation for the American Society of Horticultural Sciences meetings in Atlanta, August, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Mark Windham, Alan Windham, Frank Hale. 2016. Is Rose Rosette Manageable? 61st Southern Nursery Research Conference. Athens, GA. August 30-31.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Salazar Aguirre, S. Molina C�rdenas, F. Ochoa-Corona, J. Olson. Rose rosette virus detection using loop-mediated isothermal amplification (LAMP). Poster presentation. American Phytopathological Society. Tampa, FL. July 30  August 3, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: A. Olmedo-Velarde, F. Ochoa-Corona, T. Elbeaino. Toward broad detection of emaraviruses: Endpoint RT-PCR. Poster presentation. American Phytopathological Society. Tampa, FL. July 30  August 3, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: F. M. Ochoa-Corona , J. Olson. Detection and discrimination Methods you can use: virus chasers 2008-2016. Poster presentation. National Plant Diagnostic Conference. Washington D.C. March 8-10, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Ramon, J., M. A. Guaragna, and J. Hammond. 2016. Development and characterization of polyclonal and monoclonal antibodies to Rose rosette virus. Poster presentation. American Phytopathological Society. Tampa, FL. July 30  August 3, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: A. Brake and Ong, K. (2016) Monitoring and increasing awareness for Rose Rosette Disease in Texas. (Abstr.) Phytopathology 106 (Suppl.2):S2.7. Poster presentation. American Phytopathological Society. Tampa, FL. July 30  August 3, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Palma, M. 2015. Eye(ing) the customer: A Consumer Oriented Neuromarketing approach. The Rio Grande Valley Vegetable Research and Education Building Dedication. McAllen, TX. October, 2015.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Palma, M. 2015. The Brain Doesnt Lie: Using Neuromarketing Tools for Consumer Research. Ellison Chair Distinguished Lecture Series. College Station, TX. October, 2015.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: PALMA, M. 2015. Human Decision Making and the Brain. University of CEMA Invited Seminar. Buenos Aires, Argentina. September, 2015.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: PALMA, M. 2015. Pushing the bounds of rationality in Experimental Auctions. Agricultural and Applied Economics Association Annual Meeting. San Francisco, CA. July, 2015.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: PALMA, M. 2015. Coevolution of Risk Preferences and Fairness Preferences: a Structural Panel VAR Approach. Economic Science Association World Meeting. Sydney, Australia. July 2015.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: PALMA, M. 2015. Computational Search Dynamics in Discrete Choice Experiments. International Food Marketing Research Symposium. Chania, Greece. June, 2015.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: PALMA, M. 2015. Eye Tracking and Neuromeasurement tools for Marketing Research. Southern Agricultural Economics Association Invited Symposium. Atlanta, GA. February, 2015.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Binoy Babu, Washburn BK, Miller S, Poduch K, Knox G, Ochoa-Corona FM & Paret ML. A novel and rapid technique for diagnosis of Rose rosette virus using reverse transcription- recombinase polymerase amplification assay using multiple gene targets. J. Virol. Methods
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Olson, J., Schnelle, M., Ong, K. and Byrne, D. Pictorial Guide to Rose Rosette Disease Symtoms. Poster at NPDN National Meeting in Crystal City, VA. March 8-10, 2016.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Ong, K., Brake, A., and Olson, J. Monitoring: Volunteers and their Role in Data Collection and Education. American Society for Horticultural Science (ASHS), Annual conference Aug 8-11th, 2016. Atlanta, GA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Binoy Babu and Paret ML. Field based detection of Rose rosette virus using isothermal Recombinase Polymerase amplification assay. National Clean Plant Network (NCPNR)- Annual tier II rose meeting, June 28th & 29th, 2016. Shreveport, Louisiana.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Binoy Babu, Paret ML, Knox G, Ochoa-Corona FM, & Jordan R. 2016. Development of serological and molecular diagnostic tools for Rose rosette virus. American Society for Horticultural Science (ASHS), Annual conference Aug 8-11th, 2016. Atlanta, GA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Binoy Babu, Brian K. Washburn, Francisco M. Ochoa-Corona, Gary Knox and Mathews L. Paret. Development of a field-based detection technique for Rose rosette virus using isothermal reverse transcription-recombinase polymerase amplification. Poster presentation at American Phytopathological Society meetin., August, 2016. Tampa, FL, USA.
  • Type: Other Status: Published Year Published: 2015 Citation: Olson, J., and E. Rebek. 2015. Rose Rosette Disease. Oklahoma Cooperative Extension Service. EPP-7329. Updated in 2015.


Progress 09/01/14 to 08/31/15

Outputs
Target Audience:During the first year of the project we have communicated our progress to our scientific colleagues (see journal articles, APS and ASHS oral and poster presentations), a wide audience in the green industry including producers, landscapers, garden centers, and consumers (see Workshops, extension pubs, talks to professional and gardening groups on the control of RRD, interviews (television, radio, newspaper, news release), articles in American Rose Magazine) and to rose breeders directly through their involvement in the creation of the hybrid rose populations for the project. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training was provided to 6 undergraduate students in various aspects of the research (cloning and sequencing the RRV NP, cytogenetics, genetics, horticultural evaluation). Project participants (8) and graduate students (4) participated in the annual meetings of the American Phytopathogy Society and the American Society of Horticultural Sciences. The Economics/Marketing group participated in two conferences related to the experimental design of consumer and eye tacking experiments: Institute of Food Products Marketing Annual Meeting in Chania, Greece (Eye Tracking); Economic Science Association Meeting in Sydney Australia (Consumer Experiment). How have the results been disseminated to communities of interest?During the first year of the project we have communicated our progress to our scientific colleagues (see journal articles, APS and ASHS oral and poster presentations), a wide audience in the green industry including producers, landscapers, garden centers, and consumers (see Workshops, extension pubs, talks to professional and gardening groups on the control of RRD, interviews (television, radio, newspaper, news release), social media (Facebook,Twitter), articles in American Rose Magazine), to public by diagnostic work (OSU/TAMU) and to rose breeders directly through their involvement in the creation of the hybrid rose populations for the project. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 1. In the short term, develop a set of Best Management Practices (BMPs) to combat RRD Objective 1a. Develop rapid/robust diagnostic test for Rose rosette virus Developed a single primer set based on the consensus region of the nucleocapsid gene p3 located in the RNA3 was developed. This primer set allows for the sensitive, reliable and highly specific detection of RRV by endpoint RT-PCR, TaqMan RT-qPCR, and SYBR-Green RT-qPCR. These methods are more robust/consistent than the currently available test. The selection of method to be used will depend on the user's preferences or available capabilities. Developed an artificial positive control incorporating sequences from RRV as well as multiple other common rose viruses. Developed a sensitive (to 1 fg of virus), specific, and rapid (<30 min at 42C) isothermal RT-RPA (Recombinase Polymerase Amplification) protocol for the detection of Rose rosette virus as the first step in the development of a field based detection system. Developed a sensitive and specific Real-Time RT-PCR (qRT-PCR) for the detection of Rose rosette virus using sequences from 3 of the RRV RNAs. This method is capable of measuring viral titer in both symptomatic and asymptomatic plants. Developed a sensitive (0.1 pg virus), and RRV specific DNA probe/ Riboprobe for its utilization in development of a Lateral flow device for the detection of RRV. NP (nucleo capsid protein) gene from MD isolates of RRV was cloned and deposited in the GenBank. From these, PCR primers were designed for RT-PCR detection of RRV and for cloning and expression of RRV viral proteins in a bacterial system. Begin the development of polyclonal antisera and McAb and scFv clones by using both bacterially-expressed and synthetic RRV NP protein as immunogens in mice and/or rabbits. Objective 1b. Epidemiology Establish plants in field plot to follow the development and movement of Phyllocoptes fructiphilus in the field. Established monitoring/training experiments in 4 commercial rose beds to follow the disease development to determine the major factors influencing spread as well as follow the success of a teaching program. These plots will be followed for three years. Four additional plots will be initiated in 2016. Objective 1c. Chemical/biological field control options Experimental plots have been planted at the Crossville Experiment Station in Tennessee to initiate the experiments to assess the effects of cultural (pruning and plant barriers), miticides, and antiviral applications have on mite populations, viral titer and rose rosette disease development. In the long term, identify additional sources of resistance and develop genetic tools to move resistance into commercial cultivars. Objective 2a. Identify additional sources of host plant resistance to RRD Collected observational data on 400 rose accessions. Identified ~280 that were symptomatic for RRD, 54 showed no symptoms and the rest had questionable symptoms. Planted 227 rose genotypes (cultivars, various species) in RRD resistance field evaluation plots in Tennessee (Mark Windham) and in Delaware (Tom Evans). These were also planted in Texas for evaluation for foliage fungal diseases and horticultural quality. Using light microscopy and LT-SEM the mite resistant rose (Rosa bracteata) was shown to have higher trichome density on stems and dormant buds which may provide hiding places for predatory mites and impede the entry of eriophyid mites for over wintering protection and reproduction as compared to a mite susceptible rose. Re-examination of the taxonomy of other reported species of Phyllocoptes has indicated that P. adalius is synonymous with P. fructiphilus. Two other reported species (P. linegranulatus and P. chorites) may also be synonymous. Objective 2b. Optimize Digital Genotyping Optimized DNA extraction (CTAB method) of rose leaf tissue as well as the restriction enzyme (NgoMIV - 6 base cutter) for use in high throughput genotyping by sequencing on Illumina HiSeq2500. Objective 2c. Create diploid and tetraploid consensus maps Nine diploid rose populations (~700 plants) have had their DNA extracted and sequenced. 120 bp sequences were collected and put through the GBS pipeline developed in TASSEL and in the CLC Genomics workbench using the strawberry genome as a "proxy" reference genome for SNP/INDEL discovery. Preliminary maps were constructed using JoinMap with about 1,000 SNPs. Objective 2d. Discover markers associated with RRD resistance The collaborating breeders made about 3,000 pollination among various RRD resistant and susceptible roses. Initial set with these accessions of Rosa palustris(a RRD resistant species) was low to fair which indicates that breeding with this species may be challenging. We will put more emphasis in the pollination work on other species (Rosa setigera) and some putatively resistant rose cultivars. Scott Trees of Ball Horticulture has agreed to collaborate in the production of hybrids for this work this coming year. Create an information and demonstration pipeline. Objective 3a. Develop a RRD Monitoring Network We have more than 200 volunteers located in 38 of the 48 continental states who are interested in participating in the RRD Monitoring Network. Have developed 4 fact sheets for the training for volunteers participating in the RRD Monitoring Network. The RRD reporting app should be available in the spring of 2016. Established relationships for sites to conduct on-site monitoring for resistance/tolerance. Thus far 3 sites in North Texas (Denton, Wichita, and Dallas county) have agreed to plant monitoring sites in the spring of 2016. Objective 3b. Develop national RRD BMP training materials Extension fact sheets developed in Oklahoma and Florida. Working on fact sheet for national audience A scripted PowerPoint is 80% complete for Rose Rosette Disease training. This presentation includes information about the history, symptoms, vector, and detailed of management in different settings and be available for educators and managers to use for training purposes. In addition, the poster showing RRD symptomology, "Combating Rose Rosette: A Pictorial Guide to Rose Rosette Disease" was published Objective 3c. Develop an information pipeline Developed a Combating Rose Rosette logo. Established a "Combating Rose Rosette Disease" Facebook page. It currently has about 200 followers. During the first year of the project we have communicated our progress to our scientific colleagues (see journal articles, APS and ASHS oral and poster presentations), a wide audience in the green industry including producers, landscapers, garden centers, and consumers (see Workshops, extension pubs, talks to professional and gardening groups on the control of RRD, interviews (television, radio, newspaper, news release), articles in American Rose Magazine) and to rose breeders directly through their involvement in the creation of the hybrid rose populations for the project. Improve our understanding of consumer and industry preferences and barriers to rose sales. Objective 4a. Assess U.S. consumer preferences Demographic analysis of consumption of green industry products is ongoing. Eye tracking and other behavioral response equipment is available and ready to go. We are currently developing pilot tests for the consumer experiments to analyze the external validity of responses. Review of the literature for discrete choice experiments and eye tracking in ornamental plants is ongoing. Objective 4b Identify market barriers inhibiting sales of new roses No progress Objective 4c. Socioeconomic impacts of RRD research No progress

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Babu, B., H. Dankers, E. Newberry, C. Baker, T. Schubert, G. Knox and M. Paret. 2014. First Report of Rose rosette virus Associated with Rose Rosette Disease Infecting Knockout Roses in Florida. Plant Disease 98(10):1449. October 2014.
  • Type: Journal Articles Status: Under Review Year Published: 2015 Citation: Shefali Dobhal; Jennifer D Olson; Mohammad Arif, Ph.D; Johnny A Garcia Suarez; Francisco M Ochoa-Corona. A simplified strategy for sensitive detection of Rose rosette virus compatible with three RT-PCR Chemistries. Journal of Virological Methods
  • Type: Journal Articles Status: Submitted Year Published: 2015 Citation: Binoy Babu, Brian K. Washburn, Kristina Poduch, Gary Knox and Mathews Paret. Identification and characterization of two novel genomic RNA segments RNA5 and RNA6 in Rose rosette virus infecting roses (Acta Virologica),
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2015 Citation: Bolques, A., M. Paret, G. Knox, B. Babu, H. Dankers, T. Schubert, C. Baker, & M. Orwat. Rose rosette disease in Florida. Proc. Fla. State Hort. Soc., 127, xxxxxx.
  • Type: Other Status: Published Year Published: 2015 Citation: Olson, J., Rebek, E., and Schnelle, M. 2015. Rose Rosette Disease. Oklahoma State University Cooperative Extension Service. Fact Sheet No. EPP-7329.
  • Type: Other Status: Published Year Published: 2015 Citation: Babu, Binoy, Mathews L. Paret, Tim Schubert, Carlye Baker, Gary Knox, Fanny Iriarte, James Aldrich, Laura Ritchie, Carrie L. Harmon and Svetlana Y. Folimonova. 2015. Rose rosette disease: A new disease of roses in Florida, PP317. Florida Cooperative Extension Service, University of Florida, Institute of Food and Agricultural Science, Gainesville, FL. 6 pp. May 2015.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2016 Citation: M. Windham. Unraveling Rose Rosette. International Plant Propagators Society  Southern Region. Hickory, NC. (Invited). Oct. 24-28, 2014
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2016 Citation: M. Windham, F. Hale, A. Windham and Q. Cheng. 2015. A Best Management Plan for Rose Rosette. 60th Southern Nursery Association Research Conference. Alanta, GA. July 22-22.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Binoy Babu, Brian K. Washburn, Kristina Poduch, Gary Knox, Timothy S. Schubert, Carlye Baker, Jeyaprakash Ayyamperumal, Debra Jones and Mathews L. Paret. Genomic characterisation and development of TaqMan� Real-Time RT-PCR assay for Rose rosette virus. American Phytpathological Society meeting, Pasadena, California July 1st-August 5th.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Binoy Babu, Jeyaprakash Ayyemperumal, Debra Jones, Timothy S. Schubert, Carlye Baker, Gary Knox and Mathews L. Paret. Diagnostic tools for Rose rosette virus: TaqMan� qRT-PCR and Recombinase polymerase assay. 14th Biennial Meeting of the Florida Phytopathological Society. June 4-6, 2015, University of Florida.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: R. Jordan, J. Hammond, M. L. Paret, B. Babu, F. Ochoa-Corona, J. Olson, R. Ochoa, E. Roundey, D. Byrne. Combating Rose Rosette Disease: Development of rapid, efficient, easy-to-use virus diagnostic tools and studying virus-vector interactions. American Phytopathological Society, Pasadena CA,Aug 1-5, 2015. Poster 464-P.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Roundey, Anderson, Byrne, Olson, Windham, Windham, Miller, Graves, Bedard, and Dobres. Search for genetically conditioned resistance to rose rosette disease among garden roses. Oral presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper21683.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Jordan, Hammond, Paret, Babu, Ochoa, Olson, Ochoa, Roundey and Byrne. Combating Rose Rosette Disease: Development of rapid, efficient, user-friendly virus diagnostic tools and studying virus-vector interactions. Poster presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper21684.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Olson, Schnelle, Ong, Roundey, and Byrne. Combating Rose Rosette: Pictorial Guide to Rose Rosette Disease Symptoms. Poster presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper22173.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Ong, Pemberton, Olson, Windham, Knox, Brake, Roundey, and Byrne. Combating Rose Rosette Monitoring extent and diversity of the disease. Poster presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper22183.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Palma, Ribera, Hall, Byrne, and Roundey. Combating Rose Rosette Disease: Economics and Marketing. Poster presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper22090.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Byrne, Klein, Roundey, Yan, et al. Combating Rose Rosette: Breeding for Resistance. Poster presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper21563.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Yan, Dong, Byrne, and Klein. Applying genotyping by sequencing technology on Rosa spp. Oral presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper21224.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Wu, Liang, and Byrne. Heritability of Rosa spp. Plant Architecture in Diploid Rose. Oral presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper21045.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Liang, Wu, and Byrne. Characterization of 11 hybrid rose populations for petal number under cool and warm season conditions. Oral presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper21343.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Pemberton, H. D. H. Byrne, A. wind ham, J. O)lson, G. Knox, and K. Ong. 2015. Combating Rose Rosette: The information pipeline. Poster presentation for the American Society of Horticultural Sciences meetings in New Orleans, August, 2015. https://ashs.confex.com/ashs/2015/webprogram/Paper22000.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Orwat, M., Bolques, A., Paret, M., Knox, G., Babu, B., Dankers, H., Schubert, T., Baker C. 2014. Early Detection: Rose Rosette Disease Workshop and Inservice Training. Extension Professionals Association of Florida. Annual Conference. Panama City, FL., Abstract Book, p. 32 http://epaf.ifas.ufl.edu/documents/2014abstractbookFINAL.pdf
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Byrne, D. H. 2015. Rose Breeding and Genetics Research at Texas A&M University. Presented at the conference, An Afternoon with Roses, at the FPS, University of California, Davis, CA. May 2, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Bolques, A., Paret, M., Knox, G., Babu, B., Dankers, H., Schubert, T., Baker, C., Orwat, M. 2014. Rose Rosette Disease Alert. 50th Anniversary Meeting of the Caribbean Food Crop Society. St. Thomas, USVI, Abstract Book, p. 17. http://cfcs.eea.uprm.edu/sites/default/files/file_attach/CFCS%20Program%20Bookr.pdf