Source: CLEMSON UNIVERSITY submitted to NRP
ADDRESSING CRITICAL RESEARCH NEEDS FOR SUSTAINABLE PEACH PRODUCTION IN SOUTH CAROLINA
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1010409
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2016
Project End Date
Sep 30, 2020
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
CLEMSON UNIVERSITY
(N/A)
CLEMSON,SC 29634
Performing Department
Plant & Environmental Sciences
Non Technical Summary
South Carolina is the second largest peach producer in the United States and competes with California, Georgia and other states for market share. Additionally many growers make a living of small acreages selling produce from road side stands. Peach production faces many challenges that affect the tree, the fruit, and the environment. This project combines the expertise of a horticulturist, breeder, plant pathologist and virologist to generate data and science-based solutions for production challenges that currently affect the peach industry in South Carolina. These challenges include the development of best management practices to optimize fertilizer input, to manage pests and diseases sustainably, to adjust to market needs with new varieties, and to keep planting stock free of devastating viruses. In this project we will address those needs and provide the tools for our producers to compete successfully in the future.
Animal Health Component
45%
Research Effort Categories
Basic
10%
Applied
45%
Developmental
45%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2161114116020%
2161114110120%
2161114108120%
1021114101020%
5021114108120%
Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships; 216 - Integrated Pest Management Systems; 502 - New and Improved Food Products;

Subject Of Investigation
1114 - Peach;

Field Of Science
1101 - Virology; 1160 - Pathology; 1081 - Breeding; 1010 - Nutrition and metabolism;
Goals / Objectives
The goals of this project are to deliver short term and long term solutions for problems currently affecting the South Carolina peach industry. Short term solutions include improved efficiency of fertilization in fruit trees, improved disease management, and mother block virus indexing. Long term goals include the generation of cultivars of high quality standards with disease resistance, the generation and implementation of pesticide resistance guidelines and to provide our stakeholders with virus indexed trees.
Project Methods
The materials and methods below refer to the objectives of this proposalObjective 1: Develop strategies that improve the efficiency of fertilization in fruit trees, reduce cost and increase profitabilityObjective 2: Combining disease resistance with horticultural quality in new peach cultivarsObjective 3: Peach and strawberry disease and fungicide resistance managementObjective 4: Determine the occurrence and incidence of NSPV and NVM in indexed blocks and determine their incidence in the southeastern production industryObjective 1. This research comprises two field studies that will be carried out at two orchards at the Clemson University Musser Fruit Research Farm. For the first study (nutrient removal in peach trees of different cultivars and age), eighteen mature healthy trees of six different cultivars, and eight trees of two different ages will be used. All trees will be located in the same orchard and grown under the same conditions (soil, climate, irrigation and fertilization). To measure the amount of nutrients removed from the trees, samples will be taken at the following events along the season: wood at winter pruning, immature fruits at thinning, fruits at harvest, and leaves at fall. Wood pruned, flowers thinned, fruit thinned and harvested, and leaves fallen will be weighed per tree so that an accurate estimation of total nutrients removed can be done. Samples will be washed, ground, mineralized and analyzed using standard procedures. Nitrogen will be sent for analysis to the Agricultural Service Laboratory, Clemson University. Phosphorous will be measured through the Murphy-Riley method at the PI's laboratory. Potassium, calcium, magnesium, manganese, copper and zinc will be measured by atomic absorption spectrophotometry.For the second study (nanofertilization for improving leaf N and K concentrations in peach trees), baseline data on N and K leaf nutrient concentration were already taken from a block at the Musser Farm that showed K deficiency and low N content in the past year; trees in this block have been kept with minimal fertilization during this year so that trees with deficient/low N and K levels are available). Nitrogen and K nanofertilizers will be prepared at the PI's lab and will be used at spring fertilization (they will be prepared the same way during July and August, right before postharvest fertilization). Nanofertilizers will be prepared following the procedures in Corradini et al. (2010). Spring fertilization and postharvest fertilization will be performed. Bloom intensity, fruit setting, and fruit size and yield will be determined. Leaf samples will be taken and leaf analyses will be performed in July/August to assess the efficacy and efficiency of the treatments. Conventional fertilizer will be used for the grower standard.Objective 2. Activities associated with this objective include: 1) evaluation of peach germplasm for its response to the two major diseases, brown rot (Monilinia spp.) on fruit and bacterial spot (Xanthomonas arboricola pv. pruni) on leaves. Fruit will be inoculated with brown rot spores in the controlled environment and detached leaf assay (Randhawa et al., 1985) will be used for bacterial spot leaf inoculation using previously developed protocols in Dr. Schnabel's lab. Evaluation for disease response will be performed on high quality advanced selections developed in the peach breeding program and any other cultivars/selection of interest. 2) Previously acquired molecular data in combination with newly acquired phenotypic data will be used to discover alleles associated with different responses to the pathogen and develop new DNA tests for early selection using bi-parental mapping, pedigree based analysis (Bink et al 2014) and genome wide association as appropriate. 3) Existing DNA tests (www.rosbreed.org) for fruit quality and fruit response to bacterial spot and later newly developed tests will be used to evaluate and select parents for future crosses and promising seedlings from existing material. 4) Crossing design will be informed using results of existing DNA test and disease evaluation to select best parents to maximize efficiency of breeding efforts in combining disease resistance with horticultural quality. Crossing activities will be performed at the Musser Fruit Research Center, genotyping activities will be performed at the Genomics and Computational Lab, and the disease evaluation will be performed in the Gasic and Schnabel labs.Objective 3. Large scale field trials are ongoing on Armillaria root rot-infested replant sites at 3 producer locations (Fisher Orchards, Titan Farms, Hyder Farms) and at the Musser Fruit Research Farm. Yield at first, second and third pick, disease incidence, and disease severity data will be collected at each location. The number of suckers coming from the crown of the trees will be determined. The susceptibility of excavated roots to standard herbicides will be investigated to investigate potential increased susceptibility. Upon completion of this multiyear study, data will be summarized. Fungicide resistance profiles will be collected for B. cinerea from South Carolina and many other states and location-specific resistance management recommendations (Fernandez-Ortuno et al., 2014) will be provided. The method is based on discriminatory doses provides a resistance profile to 11 fungicides of 7 FRAC codes in about 5 to 7 days depending on the tissue source. A potential link between multifungicide resistance and reduced fitness and competitive ability will be examined and the molecular basis of fungicide resistance will be determined. Genotypes will be identified by amplification and sequencing of target genes, including b-tubulin, bos1, erg11, cyt b, sdhB, sdhC, and sdhD for FRAC 1, 2, 17, 11, and 7 (sdh genes), respectively. Mrr1 transcription factor sequences as well as atrB overexpression conferring resistance to FRAC 12 will be analyzed for adaptations over time. Spray strategies to minimize selection for multifungicide resistance will be evaluated at producer farms.Objective 4. As the samples are collected during the annual indexing of the bud wood blocks for the Southeastern Budwood Program, additional samples (leaf samples from 5 trees selected randomly) will be used to provide material for the extraction of total RNA using the method of Hughes and Galau, 1988. One-Step PCR (QIAGEN, Germantown, MD) will be used with the primer pairs described for NSPV [Bag et al., 2015] and Nectarine virus M (NVM) [Villamor et al., 2016]. PCR reactions will be analyzed by gel electrophoresis with selected amplicons being cloned and sequenced to confirm the identity of the products

Progress 10/01/16 to 09/30/20

Outputs
Target Audience:Commercial peach growers Private consultants, extension agents Researchers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?-undergraduate and graduate students were trained in: PCR, in vitro fungicide sensitivity assays, in planta fungicide sensitivity assays (Schnabel); fruit quality phenotyping, DNA extraction, DNA test development and validation, detached leaf bacterial spot inoculations and brown rot fruit artificial inoculation (Gasic); physiological measurement and tissue analysis techniques (Melgar). -staff members were trained in: detached leaf bacterial spot inoculations, brown rot fruit artificial inoculation, DNA extraction and marker-assisted selection (Gasic), enzyme-linked immunosorbent assay for virus detection (Cieniewicz), RNA extraction and PCR for virus detection (Cieniewicz) How have the results been disseminated to communities of interest?Results were disseminated in the form of presentations at the: -2020 American Phytopathological Society Annual Meeting, online -2020 Southeastern Professional Fruit Workers Conference, online -2020 Extension production meetings for peach growers in Edgefield and Gaffney, SC -2020 American Society for Horticultural Sciences annual conference, online -2020 Southern Region American Society for Horticultural Sciences annual conference, Louisville, KY -2019 Southeastern Professional Fruit Workers Conference, Tifton, GA What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Objective 1: Develop strategies that improve the efficiency of fertilization in fruit trees, reduce cost and increase profitability. We recorded tree requirements were not dependent on fertilization applicationswhen trees had nutrient foliar concentrations at or above the sufficiency level; in other words, a well-nourished tree does not uptake more nutrients than needed, and when nutrient concentration of different organs (for instance, harvested fruit or pruned wood) of trees receiving rational fertilization (based on nutritional requirements) was compared to those of trees receiving excessive fertilization, the values were statistically similar, which means the excess of fertilizer is not taken up by the tree. This is relevant for reducing fertilizer waste, nutrient leaching, and pollution of below ground aquifers. Wecontinued recording a correlation between excessive concentrations of some nutrients (specifically potassium) and higher incidence of bronzing, a fruit skin disorder that causes important economic losses to our peach growers. As a consequence of these results, this year we also started assessing the concentration of potassium and calcium in bronzed areas (peach skin) and compared them with skin of fruit without bronzing. While we have not finished the tissue analyses by the time this report was written, preliminary numbers seem to indicate the excess of potassium is correlated with low concentrations of calcium in these areas. Finally, we have also evaluated the role of other mineral elements such as silicon on improving tolerance to water deficit. In a trial carried out with two-year-old plants, we recorded trees receiving foliar applications of silicon were able to cope with water deficit better than trees that did not. Data showed that silicon may have a role in reducing cuticular conductance (i.e. reducing water losses through the leaf cuticle), thus, improving water status of young trees. Objective 2: Combining disease resistance with horticultural quality in new peach cultivars. Bacterial spot fruit and leaf tolerance/resistance was evaluated in field in the peach breeding material at Musser Research Farm, due to favorable year for infection and symptoms appearing. Filed collected data have been compared with the DNA prediction for fruit response to bacterial spot infection. Genome Wide Association studies (GWAS) have been carried over with acquired detached leaf and field leaf response data to detect regions in the peach genome associated with the response to the disease and perform allele-trait analyses. DNA test for fruit response to bacterial spot infection based on SNP marker detection has been used for culling seedlings from 2020 crosses, and evaluation of hybrids planted in the experimental field from 2016-2018 crossing seasons. Metabolomic data on 15 contrasting accessions for brown rot tolerance from breeding program have been acquired and are being analyzed. Crosses between parental individuals tolerant/resistant to brown rot and bacterial spot have been made based on the phenotypic data for brown rot and genotypic data for bacterial spot, in attempt to combine the tolerance/resistance to both diseases with the high quality and horticultural performance. About 50% of the tested seedlings have been planted in the field. Eleven advanced selections with excellent horticultural quality and high tolerance and or resistance to one or both diseases have been included in replicated trials in SC (3), NC, AR and AL. Carotenoid accumulation and profile data acquired on ~300 peach accessions were included in GWAS and several regions highly associated with individual carotenoid (violaxanthin, β-cryptoxanthin and β-carotene) accumulation have been identified. Carotenoid accumulation and composition is being investigated with regards to effect on brown rot tolerance. Fruit quality has been evaluated in all advanced selection in breeding program and acquired data included in ongoing genetic studies. Objective 3: Peach and strawberry disease and fungicide resistance management. We collected Xap from shoot cankers, leaves, and fruit over two years from cultivar O'Henry of three conventional and one organic farm in South Carolina at the beginning (bud break), middle (pit hardening) and end (final swell) of production season and determined in vivo and in planta sensitivity to copper. Two phenotypes of copper tolerant Xap strains were discovered; low copper tolerance (LCT: grew up to 150 µg/ml on both media) and high copper tolerance (HCT: grew up to 200 µg/ml on both media). Spray trials conducted in greenhouse were conducted with copper rates typically applied at 'delayed dormancy' (high rate; 853.7 µg/ml Metallic Copper Equivalent; MCE), at 'shuck split' (medium rate; 209.7 µg/ml MCE), and during 'summer cover sprays' (low rate; 42 µg/ml MCE) season. Results indicated that, in contrast to a sensitive strain, LCT and HCT strains did not reduce bacterial disease incidence at the low and medium rates applied. This study confirms existence of Xap tolerance to copper in commercial peach orchards and suggests its contribution to annual yield loss due to bacterial spot disease. Mefentrifluconazole and other triazoles were examined for activity to select pathogens sensitive or resistant to DMIs using mycelial growth tests on fungicide-treated culture medium or spray trials using cucumber plants. The sensitivity of Monilinia fructicola from peach to mefentrifluconazole was higher compared to other DMIs. In contrast, the inhibitory activity of mefentrifluconazole was equal or slightly inferior compared to difenoconazole, tebuconazole, propiconazole in Colletotrichum spp., Alternaria alternaria sp. complex and Cercospora beticola isolated from peach and sugar beet, respectively. Similar tendencies (i.e. equal or slightly inferior activity and cross-resistance) were observed for cucumber powdery mildew (Podosphaera xanthii) resistant to triflumizole, myclobutanil, and difenoconazole. Despite cross-resistance to other DMIs, mefentrifluconazole is a promising fungicide for fungal disease control on peach and other crops, with a reportedly more favorable toxicity profile. Objective 4: Determine the occurrence and incidence of NSPV and NVM in indexed blocks and determine their incidence in the southeastern production industry. These viruses were not detected in the NCPN Prunus Foundation at the Clemson University Musser Fruit Research Farm. No symptoms of these virus diseases were observed in these indexed blocks. In addition to the absence of NSPV and NVM in the Prunus foundation, commercial grower blocks were surveyed visually for virus disease symptoms. Budwood blocks from which nurseries source virus-tested (negative) material for propagation were also tested for 3 important viruses (plum pox virus, prune dwarf virus, and Prunus necrotic ringspot virus) by ELISA. A total of 2,847 trees on commercial farms throughout SC and GA were tested for PPV, PNRSV, and PDV in 2020, with detection incidences of 0%, 4.0%, and 2.3% respectively. Due to COVID-19 shortages in lab personnel in spring 2020, no Budwood Program trees from commercial farms were tested for NSPV and NVM in 2020. Objective 5: Economic Analysis An enterprise budget for peaches was created in 2019 and the profitability of root collar excavation procedures was assessed. Also, an economic analysis was completed to estimate the economic loss to the South Carolina peach industry due to the March 2017 freeze in 2019.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Ishii, H., P. K. Bryson, M. Kayamori, T. Miyamoto, Y. Yamaoka, and G. Schnabel 2020. Cross-resistance to the new fungicide mefentrifluconazole in DMI-resistant fungal pathogens. Pestic. Biochem. Physiol. In press.
  • Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Adelberg, J., J. Naylor-Adelberg, S. Miller, K. Gasic, G. Schnabel, P. K. Bryson, C. Saski, S. Parris, and G. Reighard. 2020. In vitro Co-culture System for Prunus spp. and Armillaria mellea in Phenolic Foam Rooting Matric. In vitro Cellular and Developmental Biology- Plant In press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Wu, Y., C. Saski, G. Schnabel, S. Xiao, and M.J. Hu 2020. A high-quality genome resource of Botrytis fragariae, a new and rapidly spreading fungal pathogen causing strawberry gray mold in the U.S.A." Phytopathology in press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Reighard, G., J. C. Melgar, and G. Schnabel. What we know and do not know about a peach skin bronzing disorder. Acta Horticulturae, in press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Boatwright, H. and Schnabel 2020. Evaluation of the intelligent sprayer system in peach production. Plant Dis. In press.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Dowling, M. E. and G. Schnabel 2020. Understanding plant diseases with art and technology. Int. J. Hort. Sci. 20:959-966.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Miller, S. B., K. Gasic, G. R. Reighard, W. G. Henderson, P. A. Rollins, M. Vassalos, and G. Schnabel 2020. Preventative root collar excavation reduces peach tree mortality caused by Armillaria root rot on replant sites. Plant Dis. 104:1274-1279.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Abdelghafar A., Okie W., Reighard G. and K. Gasic (2020) Mapping QTLs for phytochemical compounds and fruit quality in peach. Mol Breeding 40 (3) 1-18 https://doi.org/10.1007/s11032-020-01114-y.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Rawandoozi Z., Hartmann T., Carpenedo S., Gasic K., da Silva Linge C., Van de Weg E. and Byrne D. (2020) Identification and characterization of QTLs for blush, soluble solids concentration (SSC), and titratable acidity (TA) in peach through a multi-family approach. BMC Genomics https://doi.org/10.21203/rs.3.rs-20345/v1.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Devkota P., Iezzoni A., Gasic K., Reighard G. and R. Hammerschmidt (2020) Evaluation of the susceptibility of Prunus rootstock genotypes to Armillaria and Desarmillaria species. Eur J Plant Pathol 158, 177193 (2020). https://doi.org/10.1007/s10658-020-02065-y (1.754)
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Gasic K. (2020) Advances in cultivar and rootstock breeding: A case study in peach. Acta Horticulture 1281 doi: 10.17660/ActaHortic.2020.1281.1
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Guajardo, V., Solis, S., Almada, R., Saski, C., Gasic, K., & Moreno, M. A. (2020). Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function. Sci Rep, 10(1), 1467. doi:10.1038/s41598-020-58271-5
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Li, Z., Parris, S., & Saski, C. A. (2020). A simple plant high-molecular-weight DNA extraction method suitable for single-molecule technologies. Plant Methods, 16, 38. doi:10.1186/s13007-020-00579-4.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Molin, W. T., Patterson, E. L., & Saski, C. A. (2020). Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations. PloS one, 15(9), e0233813. doi:10.1371/journal.pone.0233813
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Molin, W. T., Yaguchi, A., Blenner, M., & Saski, C. A. (2020). Autonomous replication sequences from the Amaranthus palmeri eccDNA replicon enable replication in yeast. BMC research notes, 13(1), 330. doi:10.1186/s13104-020-05169-0
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Molin, W. T., Yaguchi, A., Blenner, M. A., & Saski, C. A. (2020). The eccDNA Replicon: A Heritable, Extra-Nuclear Vehicle that Enables Gene Amplification and Glyphosate Resistance in Amaranthus palmeri. Plant Cell. doi:10.1105/tpc.20.00099
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Fuchs M., Almeyda-Becerra C., Al Rwahnih M., Atallah S.S., Cieniewicz E.J., Farrar K., Golino D.A., G�mez M., Harper S., Kelly M., Martin R.R., Martinson T., Osman F.M., Park K., Pemberton B., Scharlau V., Smith R., Tzanetakis I.E., Vidalakis G. and Welliver R. (2020) Economic studies are transformative for incentivizing and reinforcing efforts to safeguard specialty crops in the United States. Plant Disease (in press).
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Campbell, D., Sarkhosh, A., Brecht, J.K., Gillett-Kaufman, J. Liburd, O., Melgar, J.C. and Treadwell, D. (2020). Bagging of organic peaches reduces physical injuries and storage decay, but has minimal effects on fruit quality. HortScience (in press).
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Lawrence, B.T. and Melgar, J.C. (2020). Variable fall climate conditions on carbon assimilation and spring phenology of young peach trees. Plants (in press).
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Zhou, Q. and Melgar, J.C. (2020). Tree age influences nutrient partitioning among annually removed aboveground organs of peach. HortScience 55(4): 560-564. doi: 10.21273/HORTSCI14731-19
  • Type: Book Chapters Status: Published Year Published: 2020 Citation: Dowling M; Fernandez-Ortun?o D; Hu M; Schnabel G, 2020. Eight years of fungicide resistance monitoring of Botrytis cinerea from United States strawberry fields. In: Deising HB; Fraaije B; Mehl A; Oerke EC; Sierotzki H; Stammler G (Eds), "Modern Fungicides and Antifungal Compounds", Vol. IX, pp. 69-74. � 2019. Deutsche Phytomedizinische Gesellschaft, Braunschweig, ISBN: 978-3-941261-16-7.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Boatwright, H. and Schnabel, G. 2020. Evaluation of laser-guided air blast sprayer on pest and disease control in peach orchards. 2020 APS Southern Division Meeting, Charleston SC.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Schnabel, G. 10/2020. Update on research and extension activities. Southeastern Professional Fruit Workers conference, online.
  • Type: Journal Articles Status: Other Year Published: 2020 Citation: Schnabel, G. 03/2020. Disease management in peach. Production meeting; Clemson Extension. Walhalla, SC.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Schnabel, G. 03/2020. Brown rot and bacterial spot management in peach orchards. 2019 Michigan Spring peach meeting, SW Michigan Research and Extension Center. Invited Presentation.
  • Type: Journal Articles Status: Other Year Published: 2020 Citation: Schnabel, G. 03/2020. Peach and nectarine skin disorders. SW Michigan Research and Extension Center. Invited Presentation.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Schnabel, G. 02/2020. Disease management in strawberry. Production meeting; Clemson Extension. Gaffney, SC
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Schnabel, G. 02/2020. Disease management in peach. Production meeting; Clemson Extension. Edgefield, SC
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Melgar, J.C., J. M. Lawton, and G. Schnabel 02/2020. Factors inducing or exacerbating peach bronzing. Production meeting; Clemson Extension. Edgefield, SC
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Schnabel, G., and M. Dowling 02/2020. Communicating IPM with MyIPM, art, and technology. Ontario Fruit and Vegetable Conference, Niagara, Canada. Invited Presentation.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Schnabel, G. and M. Dowling 02/2020. Consequences of new REI for captan. Ontario Fruit and Vegetable Conference, Niagara, Canada. Invited Presentation.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Schnabel, G. 01/2020. Disease management in peach. Production meeting; Clemson Extension. Gaffney, SC
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Schnabel, G. and M. Dowling 2020. Anthracnose fruit rot of strawberry. Fruit and Vegetable Convention, Savannah, GA Invited Presentation.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Gasic, K, S. Miller, G. Reighard, A. Rollins, G. Henderson, J. Adelberg, C. Saski, G. Schnabel, and M. Dowling 2020. Armilllaria root rot management. Fruit and Vegetable Convention, Savannah, GA Invited Presentation.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Schnabel, G. and M. Dowling, 2020. Brown rot of peach. Fruit and Vegetable Convention, Savannah, GA Invited Presentation.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Jasinski, M., Zohar, M., Fu, W., Shemesh, K., Hatib, K., Yaakov, I. B., Holland, D., Isaacson, T., Gasic, K. (2020) Carotenoid Diversity and Accumulation in Prunus sp, Annual conference American Society of Horticultural Science.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Gasic, K., Cai, L., Rhoades, K. E.B., Linge, C. D. S., Li, Z., Saski, C. A., McCord, P., Iezzoni, A. 2020. Haplotype Diversity of a QTL Hotspot on Chromosome 4 in Peach and Sweet Cherry. Annual conference of American Society for Horticultural Science.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Adelberg, J. W., Saski, C. A., Schnabel, G., Gasic, K., Reighard, G. L. 2020. In vitro Co-culture System for Prunus spp. and Armillaria mellea in Oasis� IVE Phenolic Foam. World Congress on in vitro Biology, Society for in vitro Biology, virtual San Diego, United States.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Gasic, K., Miller, S. B., Barac, G., Saski, C. A., Schnabel, G., Reighard, G. L. 2020. Breeding for Prunus Rootstock Tolerance to Replant Diseases," Southern Regional ASHS, Louisville, KY.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Fu, W., Linge, C. D. S., Burrell III, R., Gasic, K. 2020. Feasibility of Genomic Selection for Brown Rot Tolerance in Peach. Louisville, KY. Southern Regional ASHS, (January 2020).
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Nisbeth, J. Z., Miller, S. B., Schnabel, G., Gasic, K. 2020. Using In Vitro Screening to Find Sources of Tolerance to Armillaria spp. in Prunus Southern Regional ASHS, Louisville, KY.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: C. Saski. 2020. The eccDNA Replicon, Adaptive Potential, and Functional Genomics in Amaranthus palmeri, Plant and Animal Genome Meeting, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Cieniewicz E.J. (2020) Virus ecology in specialty crops: Progress, challenges, and plans for the Plant Virology program at Clemson. Department Seminar, University of Georgia Department of Plant Pathology, Athens, GA, February 10. (Invited)
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: C. Saski. 2020. The eccDNA Replicon, Adaptive Potential, and Functional Genomics in Amaranthus palmeri, Weed Science Society of America, Maui, HI.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: C. Saski 2020. Linking Genome Structure with Function in Herbicide Resistant Weeds, University of Illinois Plant Sciences Symposium, online.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Cieniewicz E.J. (2020) Breaking Boundaries: Perspectives on the Future of Plant Virology. Schroth Faces of the Future Special Session, American Phytopathological Society Annual Meeting (Invited, Virtual).
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Cieniewicz E.J. (2020) Southeastern Budwood Program Updates. National Clean Plant Network-Fruit Trees Tier II Annual Meeting, (Virtual) April 29.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Lawton, J.M., Melgar, J.C. and Schnabel, J.C. 2019. Factors influencing incidence and severity of bronzing skin disorder in peach. Southeastern Professional Fruit Workers Conference, Tifton, GA, November 7.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Melgar, J.C. 2020. Optimization of nutrient management in peach orchards. Upstate Commercial Peach Production Meeting, Chesnee, SC. January 23.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Lawton, J.M., Melgar, J.C. and Schnabel, J.C. 2020. Factors influencing incidence and severity of bronzing skin disorder in peach. Southern Region American Society for Horticultural Science Annual Conference, Louisville, KY, February 1.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Melgar, J.C. 2020. Irrigation management for maximum peach size and nutrient management in peach orchards. Upstate Fruit Meeting, Walhalla, SC. March 5.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Cieniewicz E.J. (2020) Southeastern Budwood Program: Update and Future Plan. Southeast Regional Fruit and Vegetable Conference, Savannah, GA, January 10.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Cieniewicz E.J. (2019) Southeastern Budwood Program and the National Clean Plant Network: Progress and Future Plans. Southeastern Professional Fruit Workers Conference, Tifton, GA, November 5.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Nascimento Silva, K., Melgar, J.C., Benlloch-Gonzalez, M., Fernandez-Escobar, R. Use of silicon as a strategy to cope with biotic and abiotic stresses. Southeastern Professional Fruit Workers Conference, Tifton, GA, November 5.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Pena, J., Melgar, J.C., Maja, J.M.J., Nascimento-Silva, K., de Castro, A. 2019. Drone-based hyperspectral discrimination of peach tree nutritional status. Southeastern Professional Fruit Workers Conference, Tifton, GA, November 5.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Lawrence, B.T., Zhou, Q. and Melgar, J.C. 2019. Exploration of potassium movement and retention in southeastern orchards. Southeastern Professional Fruit Workers Conference, Tifton, GA, November 7.


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Commercial peach growers Private consultants, extension agents Researchers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?-graduate students were trained in performing tree tissue analyses. -undergraduate and graduate students were trained in phenotyping for disease tolerance resistance for both brown rot and bacterial spot in lab conditions. -undergraduate and graduate students were trained in identification of plant pathogens, assessments of fungicide sensitivity, and in conducting scientific research. -undergraduate students and Post-Docs were trained in tissue culture and Agrobacterium mediated transformation methods and recombinant DNA techniques. How have the results been disseminated to communities of interest?Results were disseminated in the form of presentations at the: -2019 Plant and Animal Genome Conference in San Diego, CA -2019 Southeast Fruit and Vegetable conference in Savannah, GA -2019 International Peach Symposium in Prague, Check Republic -2019 American Society for Horticultural Science Annual Conference in Las Vegas, ND -2019 American Phytopathological Society Annual Meeting, Cleveland, OH -2019 Southern Agricultural Economics Association Meeting, GA -2019 National Association of Plant Breeders conference in GA -2019 Extension production meetings for peach growers in Edgefield and Gaffney, SC What do you plan to do during the next reporting period to accomplish the goals?Melgar -Continue collecting data for the activities detailed in the project, with an emphasis on the determination of potassium requirements of peach trees and disseminate any relevant piece of information to the target audience. Gasic -Create crosses to continue with combining horticultural quality with disease resistance. Continue working on detecting alleles associate with brown rot tolerance and work on developing DNA tests to be used in hybrid seedling testing. Analyze advanced selections for frequency and distribution of brown rot tolerance alleles to aid in planning future crosses and choose best parents to achieve combination of favorable alleles. Continue making crosses that combine bacterial spot tolerance/resistance with brown rot resistance by selecting parents that have favorable alleles in the high fruit quality and productivity background. Associate carotenoid profiles with the disease tolerance data to determine if there are secondary metabolites that are associated with the favorable response to the disease, and plan crosses to increase accumulation of those compounds. Schnabel -Determine copper and antibiotic resistance profiles in bacterial spot pathogen Xanthomonas arboricola -Write up results from Isprayer technology for publication -examine QoI resistant Colletotrichum spp isolates for fitness and sensitivity to alternative compounds Vassalos - Modify the budgets to evaluate potential alternative production practices. Cieniewicz -The new PI has assumed oversight of the Southeastern Budwood Program and will continue to test for viruses of economic importance, as well as monitor for the potential emergence of luteoviruses NSPV and NMV. Saski -Continue selection of the shoot apex reporter gene and FLT transformation events. We will also prepare and conduct several hundred to a thousand more transformation events. Typically, transformation and regeneration are conducted in high plex formats. We will also test constructs generated that harbor morphogenic regulators (embryogenesis transcription factors) that are driven by inducible promoters to see their effects on inducing embryogenesis in peach. An embryogenic system is the desired approach to a stable genetic transformation system. Adelberg -Develop aseptic germplasm in correct developmental stages shoot apex transformation. Continue development of media and protocols to micro-propagate accessions of Prunus with putative resistance to Armillaria spp. Develop in vitro assays for resistance based on the presence or absence of A. mellea mycelial masses in the same vessel as the resistant and susceptible Prunus genotypes (to remove the variability in fungal load as a random source of error). Broaden base of germplasm used in in vitro Armillaria screens and include A. tabescens. Develop storage technique for Prunus in vitro so plant are more readily accessible for experimental uses.

Impacts
What was accomplished under these goals? Objective 1: Develop strategies that improve the efficiency of fertilization in fruit trees, reduce cost and increase profitability. Enterprise budgets for Peach Orchards were developed for the establishment and the production periods. The budgets were developed after extensive interviews with peach producers and substantial input from Clemson Cooperative Extension Service Specialists. The developed budgets were subsequently used to evaluate the economic profitability of a 40 acre peach orchard in South Carolina. In 2019, we repeatedly recorded how the current standard recommendations for fertilization of young trees (up to three years old) lead to nutrient concentrations above the optimum range established for peach trees. Concentrations of potassium above the optimum range, and specifically excessive potassium applications, did not improve tree nutritional status or its storage in reserve tissues, and did not increase soil potassium concentration in the effective root zone depth (mostly due to the fact that potassium is extremely mobile in the soil and is easily lost to leaching). On the contrary, excessive potassium was correlated with higher incidence of fruit skin disorder, which seems to indicate that fertilizer applications that include excessive potassium may be causing a nutritional imbalance in the soil and/or the tree that could induce skin disorder. Based on parallel studies, environmental factors leading to increased transpiration may be related to this imbalance, since potassium is very mobile in the xylem and, thus, easily translocated to the fruit through the transpiration stream. Results from field studies also indicated different patterns of nutrient use for trees of different age. Older peach trees were recorded to translocate more nutrients to the permanent structures than younger trees, suggesting that older trees may recycle nutrients more efficiently. Thus, the effect of tree age should be taken into account when planning fertilization programs as these differences can affect orchard productivity. Objective 2: Combining disease resistance with horticultural quality in new peach cultivars. Peach fruit flesh and skin response to brown rot infection was evaluated for progeny that in previous experiments showed high tolerance /resistance. Genome wide prediction was tested for its feasibility in breeding due to a highly polygenic control of the brown rot in peach with significant marker-trait associations across whole peach genome. Genomic prediction (GP) exhibited 50-70% predictive accuracy. Selective small-scale high throughput genotyping, Seq-SNP, with 3,000 SNP markers was performed on ~500 hybrids from 2014, 2015 and 2016 crossing seasons. Genomic prediction will be further tested using this data and ability to cull seedlings based only on genotyping data will be evaluated. Bacterial spot leaf tolerance/resistance GWAS analyses revealed several regions in the peach genome associated with the response to the disease and allele-trait analyses are in progress. DNA test for fruit response to bacterial spot infection based on SNP marker detection has been developed and used for culling seedlings from 2019 crosses. Crosses between parental individuals tolerant/resistant to brown rot and bacterial spot have been made based on the phenotypic data for brown rot and genotypic data for bacterial spot, in attempt to combine the tolerance/resistance to both diseases with the high quality and horticultural performance. Hormonal therapy has been used to break dormancy in the hybrid seeds from 2019 crosses and seedlings have been evaluated for bacterial spot fruit resistance using newly developed SNP based DNA test. About 50% of the tested seedlings have been planted in the field. Several advanced selections with excellent horticultural quality and high tolerance and or resistance to one or both diseases have been identified and used as parents in further crosses as well as included in regional trials. Selections included in the experimental orchard with the most tolerant selections for brown rot have been field tested for reduced chemical control to brown rot. Data have been included in the genomic prediction models to increase prediction accuracy. Carotenoid accumulation and profile have been evaluated on ~300 peach accessions using two year of phenotypic data. This material has also been genotyped and molecular aspect of carotenoid accumulation is being investigated with special emphasis on connection between carotenoid profiles and brown rot tolerance. Using the latest genome engineering techniques offers tremendous opportunities to study gene function in peach and can ultimately facilitate genome editing to introduce or enhance existing traits. During this reporting period, the Saski lab has established the shoot-apex method of regeneration. The shoot-apex method utilizes bisected meristematic segments that are cut, co-cultured with Agrobacterium + reporter construct and allowed to regenerate in the presence of hormones and growth factors under selection. The Saski lab (in collaboration with the Adelberg Lab) has prepared, transformed, approximately 500 shoot apex events that are currently under selection. FasTrak breeding efficiency and utility has been demonstrated in the closely related plum species but is not available for peach. The FasTrak breeding system, produces generation cycles of 1 year or less -- it can flower and fruit in 1 year. Instead of waiting 3-7 years for each generation, a generation can be made every year; which reduces variety development to 5 years from about 20 years. FasTrak is enabled through genetic engineering of the flowering time locus (FLT1) that facilitates continuous flowering. In this objective, the Saski lab has cloned the flower time locus fromCardamine flexuosa. This species contains an orthologous sequence to the FLT locus in poplar that controls flower time. An overexpression construct was prepared and initial transformations were conducted. Objective 3: Peach and strawberry disease and fungicide resistance management. Peach skin disorders reduce the marketable yield of South Carolina peaches. Our study shows that multiple factors determine the occurrence of streaking in peach orchards, including cultivar susceptibility, ripening stage, and the presence of rainwater with sufficient amounts of a yet unknown reactive agent or agent combination. Monilinia fructicola is a destructive pathogen causing brown rot on stone fruits worldwide. Cankers do present an important inoculum source. We found that a single blossom may be infected by one or more genopytes of M. fructicola, and this diversity is being preserved in the corresponding canker. This information implicates that cankers serve as diversity storehouses. Resistance management practices preserve chemical efficacy over time; but growers often lack the information or training required to implement them appropriately. A multiyear resistance monitoring program was completed. Over 50 strawberry farms across the United States were involved. Monitoring led to (1) identification of FRAC codes weakening existing programs due to widespread; qualitative resistance; (2) greater grower awareness for the need for implementing resistance management strategies; and (3) adjustments in resistance management recommendations. Objective 4: Determine the occurrence and incidence of NSPV and NVM in indexed blocks and determine their incidence in the southeastern production industry. The PI originally responsible for this project (Simon Scott) retired on June 30, 2018. The successor and new PI on this project (Elizabeth Cieniewicz) was hired in August 2019. The Southeastern Budwood Program continued testing for viruses of economic importance (plum pox virus, prune dwarf virus, and prunus necrotic ringspot virus) in spring of 2019, testing for potentially emerging viruses was paused for the year due to lack of personnel.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Zhou, Q. and Melgar, J.C. 2019. Do you know how good your peach fertilization program is? American Fruit Grower. March 2019: 24-26.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Zhou, Q. and Melgar, J.C. 2019. Where do nutrients go when you fertilize trees? Good Fruit American Fruit Grower. April 2019.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: -Allran, J., G. Schnabel, and J. C. Melgar 2019. Peach bagging in the southeastern U.S., J. AM. POMOL. SOC. 73:38-46.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: -Chechi, A., Stahlecker, J., Dowling, M. E. and G. Schnabel 2019. Diversity in species composition and fungicide resistance profiles in Colletotrichum isolates from apple. Pestic. Biochem Physiol. 158:18-24.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: -Cheng, S., G. Schnabel, H. Yuan, C. Luo 2019. LAMP detection of the genetic element Mona associated with DMI resistance in Monilinia fructicola. Pest Manag. Sci., 75: 779-786.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: -Cosseboom, S. D., K. L. Ivors, G. Schnabel, P. K. Bryson, and G. J. Holmes 2019. Within-season shift in fungicide resistance profiles of Botrytis cinerea in California strawberry fields. Plant Dis. 103:59-64.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: -Dowling, ME, Bridges, WC, Cox, BM, Sroka, T, Wilson, JR, and Schnabel, G. 2019. Preservation of Monilinia fructicola genotype diversity within fungal cankers. Plant Dis. 103:526-530.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: -Froelich, M. and G. Schnabel. 2019. Investigation of fungi causing twig blight diseases on peach trees in South Carolina. Plant Dis. 103:705-710.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: -Hu, M-J., S. D. Cosseboom, and G. Schnabel 2019. AtrB-Associated Fludioxonil Resistance in Botrytis fragariae Not Linked to Mutations in Transcription Factor Mrr1. Phytopathology 109:839-846.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: -Schmitz, L. T. and G. Schnabel, 2019. Infrequent occurrence of peach skin streaking and the role of rainwater attributes on symptom development. Plant Dis. 103:2606-2611.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: -Zhou, Q. and Melgar, J.C. 2019. Ripening season affects tissue mineral concentration and nutrient partitioning in peach trees. Journal of Plant Nutrition and Soil Science 182: 203-209. doi: 10.1002/jpln.201800304.
  • Type: Book Chapters Status: Published Year Published: 2019 Citation: -Gasic, K. and Saski CA. (2019) Advances in fruit genetics. In: Lang G. A. (ed) Achieving sustainable cultivation of temperate zone tree fruits and berries. Volume 1: Physiology, genetics and cultivation, Burleigh Dodds Science Publishing, Cambridge, UK.pp. 47 http://dx.doi.org/10.19103/AS.2018.0040.05.
  • Type: Book Chapters Status: Published Year Published: 2019 Citation: -Park, J.W., Melgar, J.C. and Kunta, M. 2019. Plant nutritional deficiency and its impact on crop production. In: Bioactive Molecules in Plant Defense. Jogaiah, S. and Abdelrahman, M. (eds.). Springer Nature Switzerland AG. doi: 10.1007/978-3-030-27165-7_12
  • Type: Book Chapters Status: Published Year Published: 2019 Citation: -Schnabel, G., P. M. Brannen, Avenot, H., T. J. Michailides, and J. E. Adaskaveg 2019. Fungicide resistance in stone fruits. In: Stevenson, K. L., McGrath, M. T., and Wyenandt, C. A. (Eds), Fungicide Resistance in North America, Vol. 21, 2nd Edition, p209-222. American Phytopathological Society, St. Paul, MN.
  • Type: Book Chapters Status: Published Year Published: 2019 Citation: -Schnabel, G., D. Fern�ndez-Ortu�o, A. Amiri, and N. A. Peres 2019. Fungicide resistance in pathogens of strawberry. In: Stevenson, K. L., McGrath, M. T., and Wyenandt, C. A. (Eds), Fungicide Resistance in North America, Vol. 21, 2nd Edition, p251-264. American Phytopathological Society, St. Paul, MN.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Boatwright, H. and G. Schnabel 2019. Characterization of Cytospora species from South Carolina peach trees. Annual Meeting APS, Cleveland OH.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Boatwright, H. and Schnabel, G. 2019.Evaluation of laser-guided air blast sprayer on pest and disease control in peach orchards. Southeastern Professional Fruit Workers Meeting, Tifton, GA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Cody White (Graduate Student) presented: a research poster on breakeven analysis based on the enterprise budgets developed, at the Southern Agricultural Economics Association Annual Meeting, February 2-5, 2019, Birmingham, AL.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Cody White (Graduate Student) presented: a research paper on the Overall Economic Loss to the South Carolina Peach Industry due to the March 2017 Freeze, at the Southern Agricultural Economics Association Annual Meeting, February 2-6, 2018, Jacksonville, FL
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Cox, B. and G. Schnabel 2019 Bacterial spot of peach: Chemical sensitivity in strains from cankers, leaves, and fruit. Annual Meeting APS, Cleveland OH.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Cox, B. Schnabel, G. Wang, H. 2019 Bacterial spot of peach: Spring Canker, field incidence and chemical sensitivity. Southeastern Professional Fruit Workers Meeting, Tifton, GA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Dowling, M. and G. Schnabel 2019. Extension education using animated illustrations and time-lapse videos of disease progression. Annual Meeting APS, Cleveland OH. Invited Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Gasic presented Impact on Peach Breeding: Elite Selections Combining Disease Resistance and Superior Fruit Quality, at the American Society for Horticultural Science Annual Conference, July 21  25, 2019, Las Vegas, NV, U.S.A.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Hu, M. G. Schnabel, and S. Cosseboom 2019. Competitiveness of multifungicide resistant Botrytis cinereal isolates under field conditions. Annual Meeting APS, Cleveland OH.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Ishii, H. and Schnabel, G. 2019 Comparative inhibitory activity of mefentrifluconazole with other DMI fungicides against peach pathogens in vitro. Southeastern Professional Fruit Workers Meeting, Tifton, GA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Lawrence, B.T. and Melgar, J.C. Retention of potassium following high annual application rates in peach trees (Prunus persica (L.) Batsch). Poster. American Society for Horticultural Science Annual Conference. July 21 - 25. Las Vegas, NV, United States.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Lawton, J. M., Melgar, J. C. and Schnabel, G 2019. Factors influencing incidence and severity of bronzing skin disorder in peach. Southeastern Professional Fruit Workers Meeting, Tifton, GA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Munoz, M. and G. Schnabel 2019. Fungicide resistance profiles in Botrytis cinerea from commercial cut flower roses and influence of cultural practices on spore movement. Annual Meeting APS, Cleveland OH.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: -Schnabel, G. 2019. The use of SDHI fungicides in premixtures; successes and concerns. Annual Meeting APS, Cleveland OH.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Schnabel, G. and M. Dowling 2019. Integrated approaches to manage gray mold and fungicide resistance with focus on producer education and involvement. Resistance 2019, Rothamsted Research, West Common, Harpenden, UK.


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Commercial peach growers Private consultants, extension agents Researchers Changes/Problems:Insufficient chilling and late spring frost decreased the number of hybrids achieved in this year's crossing. We will increase the efforts next year to reach desirable number of progeny to ensure favorable recombination is achieved. What opportunities for training and professional development has the project provided?-Undergraduate and graduate students were trained in phenotyping for disease tolerance resistance for both brown rot and bacterial spot in lab conditions. -Two undergraduate students were trained on skills to establish in vitro cultures for co-culture screenings. How have the results been disseminated to communities of interest?-results for objective 1 were disseminated at four conferences: the Southeast Regional Fruit and Vegetable Conference in Savannah, GA; the Southern Region - American Society for Horticultural Science Annual Conference in Jacksonville, FL; the American Society for Horticultural Science Annual Conference in Washington, DC; and the Southeastern Professional Fruit Workers Conference in Manchester, TN. -results for objective 2 were disseminated at the Southern Region - American Society for Horticultural Science Annual Conference in Jacksonville, FL; the American Society for Horticultural Science Annual Conference in Washington, DC; the Southeastern Professional Fruit Workers Conference in Manchester, TN; and internationally at the 9th Rosaceae Genomic Conference in Nanjing, China and 30th International Horticultural Congress in Istanbul, Turkey. -results for objective 3 were shared in form of presentations at the strawberry Expo in Winstem Salem, NC; the Southeastern Professional Fruit Workers Conference in Manchester, TN; at production meetings in Gaffney and Edgefield, SC; at the Arkansas Peach grower meeting, Fayetteville, AR; at the North Carolina Bramble School, Shelby, NC; at the North Carolina Apple Fruit School, Flat Rock, NC; at the Chilton Area Peach Production Meeting in Clanton, AL; at the North Amercian Strawberry Grower Association Annual Meeting in New Orleans, LA. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. -Continue collecting data for the activities detailed in the project, with an emphasis on the determination of potassium and phosphorus requirements of peach trees, and disseminate any relevant piece of information to the target audience. Objective 2 -Create crosses to continue with combining horticultural quality with disease resistance. Continue working on detecting alleles associate with brown rot tolerance and work on developing DNA tests to be used in hybrid seedling testing. Analyze advanced selections for frequency and distribution of brown rot tolerance alleles to aid in planning future crosses and choose best parents to achieve combination of favorable alleles. Continue making crosses that combine bacterial spot tolerance/resistance with brown rot resistance by selecting parents that have favorable alleles in the high fruit quality and productivity background. Associate carotenoid profiles with the disease tolerance data to determine if there are secondary metabolites that are associated with the favorable response to the disease, and plan crosses to increase accumulation of those compounds. -The co-culture system for determining resistance of Prunus to Armillaria will be standardized in a repeatable protocol. The identification of putative resistance in Prunus spp. will be determined. Objective 3. -identify and characterize causal organisms of peach limb and twig dieback; continue to investigate peach skin streaking; find new approaches for anthracnose disease management; provide resistance monitoring service to fruit growers.

Impacts
What was accomplished under these goals? Objective 1: Peach trees of different ripening seasons had different nutrient allocation patterns, and the amount of nutrients removed through each event differed among peach trees of different ripening seasons.Overall, early-season peach trees are capable of accumulating and mobilizing more nutrients back to the branches, trunks and roots during the period between postharvest and leaf senescence, meaning early-season peach trees might need less fertilization than what is often applied. Under the same fertilization conditions, early-season peach trees had more nutrients removed from pruning and leaf fall, but fewer nutrients removed through harvesting. Total removed DW from each tree also showed this pattern: early-season cultivars had more DW of pruned wood and fallen leaves but less fruit yield. Furthermore, pruned wood and fallen leaves account for a remarkable content of nutrients that are removed from the tree. Fertilization practices for young peach trees (one-three years old) are also being evaluated under this project. Standard fertilization guidelines (as suggested by the cooperative extension services of universities in the Southeast) are being compared with a reduced rate (70% of the standard) and a split rate (same as standard but split in five times/year instead of three). Results so far have showed similar tree growth (tree trunk-crossectional area), fruit yield on year three (the first year trees bear fruit), and leaf nutrient analyses among treatments, which indicates that fertilizer applications could probably be reduced 30% without any impact on productivity. In any case, the impact of fertilization during these three years of tree establishment on tree performance after year four is yet to be evaluated. Dry conditions during fall season (before leaf abscission occurs) as well as an extended senescence season increased nutrient concentration in reserve (dormant) organs. These are conditions that occur in the southeastern U.S. in years when La Niña climatic cycle is predominant, as it brings dry and warm conditions during fall and winter to the Southeast. Nevertheless, these are results on juvenile trees and need to be confirmed with field studies. Objective 2: Peach fruit flesh and skin response to brown rot infection was evaluated for progeny with the 'Contender' source of tolerance/resistance. Genome wide association studies (GWAS) have revealed 32 SNP markers across whole peach genome associated with the response to brown rot infection. Candidate gene studies revealed genes associated with resistance response and haplotype - trait analyses revealed several alleles that increase susceptibility of the peach fruit to brown rot. Genomic prediction (GP) is being explored as a method to select material that has potential to increase brown rot tolerance in the progeny and use it in breeding. Bacterial spot leaf tolerance/resistance in peach has also been evaluated with detached leaf phenotyping protocol. GWAS analyses revealed several regions in the peach genome associated with the response to the disease and allele-trait analyses are in progress. In addition, DNA test for fruit response to bacterial spot infection is being improved using newer technologies to improve precision and decrease application cost. Crosses between parental individuals tolerant/resistant to brown rot and bacterial spot have been made in attempt to combine the tolerance/resistance to both diseases with the high quality and horticultural performance. Several advanced selections have been found that have desirable horticultural quality and high tolerance and or resistance to one or both diseases. Experimental orchard with the most tolerant selections for brown rot have been established and field testing for reduced chemical control to brown rot will be initiated next year. Carotenoid accumulation and profile have been evaluated on ~300 peach accessions, and fruit samples have been collected for a second season. About 2/3 of that material has also been phenotyped for brown rot tolerance. Data analyses for connection between carotenoid profile and disease resistance in peach are ongoing. Recently discovered secondary metabolic structures involvement in increased tolerance to brown rot (B. Quilot pers. comm) will be evaluated in most tolerant material from the Clemson peach breeding program in collaboration with the INRA, France. An in vitro assay was developed to screen Prunus rootstocks for tolerance and potential resistance to Armillaria spp, a soil borne fungal pathogen. This co-culture system establishes fungal colonies in a phenolic foam, and overlays the fungal mass with Prunus microplants rooted in a larger block phenolic foam. This matrix can be infused with fresh nutrient solution as frequently as needed. The plant fungus community remains vigorous for 12 weeks, at which time resistance is scored. Four species of Prunus rootstocks, and two species of Armillaria fungus have been demonstrated to thrive in this system. Objective 3: Isolates of C. truncatum were collected from the United States and China from peach, soybean, citrus, and begonia and sensitivity to six DMIs was determined. Compared with DMI sensitive isolates of C. fructicola, C. siamense, and C. fioriniae (EC50 value ranging from 0.03 to 16.2 µg/ml to six DMIs), C. truncatum and C. nymphaeae were resistant to flutriafol and fenbuconazole (with EC50 values of more 50 µg/ml). Moreover, C. truncatum was resistant to tebuconazole and metconazole (with resistance factors of 27.4 and 96.0) and displayed reduced sensitivity to difenoconazole and propiconazole (with resistance factors of 5.1 and 5.2). Analysis of the Colletotrichum spp. genome revealed two potential DMI targets, CYP51A and CYP51B, that putatively encode P450 sterol 14α-demethylases. Both genes were identified and sequenced from C. truncatum and other species and no correlation between CYP51 gene expression levels and fungicide sensitivity was found. Fungi in the genus Monilinia cause brown rot disease of stone and pome fruits. We report the draft genome assemblies of four important phytopathogenic species: M. fructicola, M. fructigena, M. polystroma, and M. laxa. The draft genome assemblies were 39 Mb (M. fructigena), 42 Mb (M. laxa), 43 Mb (M. fructicola), and 45 Mb (M. polystroma) with as few as 550 contigs (M. laxa). These are the first draft genome resources publicly available for M. laxa, M. fructigena, and M. polystroma. Botrytis isolates (188) were obtained from flowers and fruit collected from multiple states. B. fragariae made up 35.1% of the entire collection, and composed close to half of the Botrytis population in North Carolina (43.4%), South Carolina (61.0%), and Georgia (42.9%). One isolate of B. mali was also found, and the rest of the isolates were B. cinerea (sensu lato). We detected B. fragariae resistance to the active ingredients thiophanate-methyl, iprodione, fludioxonil, and fenhexamid. We also detected B. fragariae isolates with resistance to up to four chemical classes of fungicides, though most isolates were resistant to one or two chemical classes.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Chen, S. Y. Wang, G.Schnabel, C. A. Peng, S. Lagishetty, K. Smith, C. X. Luo, and H. Yuan. 2018. Inherent Resistance to 14?-Demethylation Inhibitor Fungicides in Colletotrichum truncatum Is Likely Linked to CYP51A and/or CYP51B Gene Variants. Phytopathology, 108:1263-1275.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Rivera, Y., K. Zeller, S. Srivastrava, J. Sutherland, M. Galvez, M. Nakhla, A. Poniatowska, G. Schnabel, G. Sundin, and Z. G. Abad. 2018. Draft genome resources for the phytopathogenic fungi Monilinia fructicola, M. fructigena, M. polystroma and M. laxa, the causal agents of brown rot. Phytopathology, in press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Dowling, M. E., Hu, M-J., and G. Schnabel. 2018. Fungicide resistance in Botrytis fragariae and species prevalence in the Mid-Atlantic United States. Plant Dis. 102:964-969.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Da Silva Linge C., Antanaviciute L., Abdelghafar A., Arus P., Bassi D., Rossini L. and Gasic K. (2017) High density, multi-population consensus genetic linkage map for peach (Prunus persica L. Batsch) - a novel reference genetic linkage map for Prunus. PLOS ONE 10.1371/journal.pone.0207724.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Fu W.*, Burrell R., Da Silva Linge C., Schnabel G. and Gasic K. (2018) Breeding for brown rot (Monilinia spp.) tolerance in Clemson University peach breeding program. Journal of American Pomological Society 72(2):94-100.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Abdelghafar A.*, Reighard G. and Gasic K. (2018) Antioxidant capacity and bioactive compounds accumulation in modern peach breeding germplasm. Journal of American Pomological Society 72(1):40-69.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Fernandez i Marti A., Saski C.A., Manganaris G.A., Gasic K. and Crisosto C.H. (2018) Genomic Sequencing of Japanese Plum (Prunus salicina Lindl.) Mutants Provides a New Model for Rosaceae Fruit Ripening Studies. Front. Plant Sci. 9:21. doi: 10.3389/fpls.2018.00021.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Fruit producers in South Carolina County agents and private consultants in South Carolina Researchers in public breeding programs, plant pathology programs, private plant breeders Changes/Problems:Some of the measurements were affected by the devastating freeze events peach orchards suffered last spring (2017). For instance, as a consequence of these late freezes, some varieties did not have enough fruit to sample and some data were lost. In any case, it also provided an interesting and unexpected situation (regarding nutritional status of the trees, as nutrients had been partially uptaken by the tree but were not used in producing fruit) that is worthy of exploration. What opportunities for training and professional development has the project provided?Dr. Melgar participated in a USAID - Farmer-to-Farmer program in Guatemala where he provided recommendations on fertilization of fruit trees to peach producers in field visits, grower meetings and a workshop. This was not directly provided by the project but the experience gained with this project has definitely been an asset to carry out this opportunity. Several undergraduate and graduate students were trained to do meaningul research in the area of plant pathology, breeding, and horticulture. For example, on brown rot fruit inoculations and evaluation of resistance/tolerance. Graduate student was trained to analyze and understand the phenotypic performance of fruit inoculations and to detect the regions in peach genome associated with brown rot response. Growers were trained through presentations and workshops to use FRAC codes effectively using the new interactive tables in MyIPM, how the new species B. fragariae may impact production, and how peach trees can be planted on replant sites for increased longevity. How have the results been disseminated to communities of interest?We have disseminated these partial results in different fruit worker meetings and scientific symposia. Specifically at a peach growers meeting in Edgefield, SC, at the Southeastern Professional Fruit Workers Conference, the American Society for Horticultural Science Annual Conference, at the Hershey's Fruit and Vegetable convention in PA, at the national American Phytopathological Society Annual meeting, and the Southern Region - American Society for Horticultural Science Annual Conference. Results have been disseminated to the stakeholders via report to Peach Council and presentations at the regional and national meetings. Material transfer agreements (MTA) has been established for testing the advanced selections in different environments with one grower and two universities. Two advanced selections have been shared via the MTA for field testing. Fungicide resistance monitoring results were disseminated via email to more than 50 farms in the southeast together with locations specific research reports. Extension recommendations were shared in MyIPM, which reaches hundreds of fruit growers. What do you plan to do during the next reporting period to accomplish the goals?We will continue collecting data for the activities detailed in the project, and disseminate any relevant piece of information to the target audience. We will create crosses to combine the horticultural quality with disease resistance. Continue working on detecting alleles associated with brown rot tolerance and work on developing DNA tests to be used in hybrid seedling testing. Determine haplotypes associated with brown rot tolerance and analyze advance selections for tolerance allele frequency and distribution to plan future crosses and choose bets parents to achieve combination of favorable alleles. Combine bacterial spot tolerance/resistance with brown rot resistance in future crosses by selecting parents that have favorable alleles in the high fruit quality and productivity background. We will continue to provide location specific resistance monitoring, characterize genetic determinants in B. fragariae conferring resistance to fungicides, add more resistance management tools to MyIPM, and continue to develop a mechanical sweeper to free soil from the collar of excavated roots. We will make modifications to the sampling procedure and a detailed examination of the distribution of the viruses in peach trees will be completed to insure the reliability of the detection of these viruses.

Impacts
What was accomplished under these goals? The field study for objective 1 is ongoing. We have collected and processed samples and analyzed data in Fall 2016, and in every season of 2017. From these data we have already started to see interesting trends in the amounts of nutrients used from peach trees of different ripening seasons. For ojbective 2, regions of the peach genome associated with brown rot tolerance have been detected. Determining variability in these regions in the peach germplasm and their phenotypic performance is in progress. Phenotypic data for additional source of resistance/tolerance for brown rot have been collected as well as the genotypic data for all advanced selections in the breeding program. Parental genotypes with high horticultural quality and tolerance to brown rot and bacterial spot have been detected. These will be used as parents in future crosses. We have found that the fungus can grow and is virulent in the semi-solid tissue culture media that supports the plantlet growth, but these conditions are distant from actual field conditions. The roots have not lignified, and the cellular matrix organization appears to be less organized than typical developed roots; and access to the roots is difficult. We are now in the early phases of advancing the plantlet growth system into an advanced environment that uses an aerated matrix for plantlet growth that supports root lignification, rather than semi-solid agar, easy access, and is scalable for larger screens. We have also established several putative resistant and susceptible clonal plantlet populations for future work. These efforts will advance our basic understanding of cell biology, tree defense mechanisms, and make significant strides toward the common goal of securing the peach crop through development of a stable peach rootstock. For objective 3 cultural control methods for Armillaria root rot control were improved. Specifically we implemented more grower demonstration trials and assessed efficacy of the practice in established trials. Results indicate the practice extends the life of peach trees on replant sites. We improved resistance management programs for farmers that will sustain disease management. Specifically, we investigated differential efficacy of FRAC 7 and 3 fungicides and recommended the ones with enhanced intrinsic activity to farmers. We also did regionwide resistance monitoring to farmers of South Carolina and 9 more states and resistance profiles helped identify fungicides of low or no efficacy. Alternative FRAC codes for rotations were identified and assessed. Polyoxin D was found suitable for gray mold control when combined with captan and thus provides resistance management opportunities. We found a new species of Botrytis in the USA and characterized for its distribution and occurrence. Research is ongoing to clarify its importance for strawberry producers. We also identified resistance determinants in target genes in this new species and currently characterize their effects on fungicide efficacy. For objective 4, PCR tests for Little cherry virus 1 (LCV-1) (Lim et al., 2015), Cherry Virus A (CVA) and two recently described viruses (a luteovirus, tentatively named nectarine stem pitting virus- NSPV [Bag et al.,2015] and a marafivirus; Nectarine virus M (NVM) [Villamor et al., 2016] were completed with mixed success. Although confirming the efficiency of the PCR process by assaying for the presence of "house keeping" genes [NADH dehydrogenase (NADH)], detection of the viruses was inconsistent.

Publications

  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Schnabel, G., F. MJ Hu, G. Edison, and R. Pargas. 2017. Communication of FRAC code principles with fruit producers via smartphone. In: H.B. Deising, B. Fraaije, A. Mehl, E.C. Oerke, H. Sierotzki, G. Stammler (Eds). Modern Fungicides and Antifungal Compounds, Vol. VIII, pp 73-76. 2017 DPG Verlag, Braunschweig, ISBN: 978-3-941261-15-0.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Cosseboom, S.D., K. Ivors, G. Schnabel, and G. Holmes 2017. First Report of Botrytis mali causing gray mold on strawberry in California. Plant Dis. In press.
  • Type: Journal Articles Status: Accepted Year Published: 2018 Citation: Rupp, S., C. Plesken, S. Rumsey, M. Dowling, G. Schnabel, R. Weber and M. Hahn 2017. Botrytis fragariae, a new species causing gray mold on strawberries, shows high frequencies of specific and efflux-based fungicide resistance. Applied and Environmental Microbiology. 83: In press.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Cordova, L. G., L. V. Madden, A. Amiri, G. Schnabel, and N.A. Peres 2017. Meta-analysis of a web-based disease forecast system for control of anthracnose and botrytis fruit rots of strawberry in southeastern United States. Plant Dis. 101:1910-1917.
  • Type: Book Chapters Status: Accepted Year Published: 2017 Citation: Dowling, M.E., M.-J. Hu, and G. Schnabel 2017. Identification and characterization of Botrytis fragariae isolates on strawberry in the United States. Plant Dis. 101:1769-1773.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Samarakoon, S. C., G. Schnabel, J. E. Faust, K. Bennett, J. Jent, M. J. Hu, S. Basnagala, and M. Williamson 2017. First report of resistance to multiple chemical classes of fungicides in Botrytis cinerea, the causal agent of gray mold from greenhouse-grown petunia in Florida. Plant Dis. 101:1052.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Hu, M-J., C. Peng, J.C. Melgar and G. Schnabel 2017. Investigation of potential causes of peach skin streaking. Plant Dis. 101:1601-1605.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Dowling, M.E., Schnabel, G., Boatwright, H.G., and S. Everhart 2017. Novel gene-sequence markers for isolate tracking within Monilinia fructicola lesions. Pest Manag. Sci. 73:1822-1829.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Dowling, M. E. and G. Schnabel 2017. First report of Botrytis mali causing gray mold on strawberry in the United States. Plant Dis. 101:1034.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Hao, X.J., Hu, M.J., Chen, S.N., and G. Schnabel 2017. Challenges in assessing efficacy of polyoxin-D zinc salt against Colletotrichum species. J. Plant Pathol. 99:513-516.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Melgar, J.C., J. Corbin, and D. Ouellette. 2017. Optimizing fertilization for peach tree establishment in the Southeastern United States. HortScience 52(9):S194. (Abstr.)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Fu W, Burrell R., Da Silva Linge C, Schnabel G. and Gasic K. (2017) Breeding for brown rot (Monilinia spp.) in peach. IX International Peach Symposium, July 2-6, 2017, Bucharest, Romania.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Fu* W, Burrell R., and Gasic K. (2017) Enabling Breeding for Brown Rot (Monilinia spp.) Resistance in Peach. 81st SR-ASHS annual meeting, February 3-5, 2017, Mobile AL
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Schnabel, G. 2017. Multifungicide resistance in Botrytis cinerea; Evolution and Management. Seminar Department of Plant Pathology and Entomology, North Carolina State University, Raleigh, NC. Invited Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: The advent and spread of prodigious multi-fungicide resistance in Botrytis species. 2017 Annual American Phytopathological Society, San Antonio TX. Invited Symposium Speaker.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Hu, M.J., and G. Schnabel 2017. High levels of fludioxonil resistance in Botrytis fragariae and investigation of potential resistance mechanisms. 2017 Annual American Phytopathological Society, San Antonio TX.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Schnabel, G. 2017. Evolution and mechanisms of resistance to multiple chemical classes of fungicides in Botrytis cinerea. 2017 Potomac Division 73rd Annual Meeting, American Phytopathological Society, Morgantown, WV. Invited Symposium Speaker.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Poudel, B. and Scott, S.W. 2017. A report of cherry rusty mottle-associated virus in South Carolina. Australasian Plant Dis. Notes 12:15
  • Type: Journal Articles Status: Accepted Year Published: 2017 Citation: B. Poudel, P. Rollins, D.T. Bishop & S.W. Scott, (2018) Incidence of Viruses in Two Large-Scale Plantings of Blackberry in South Carolina as Detected Through the Use of Sentinel Plants and RT-PCR. Plant Health Progress