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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Research Project #437836

Research Project: Healthy, Sustainable Pecan Nut Production

Location: Fruit and Tree Nut Research

2023 Annual Report

1. Improve pecan nut productivity by analyzing key horticultural issues that disrupt annual consistency, yield, and quality, and developing new or improved mitigation strategies. [NP305, C1, PS1B] (Previously reviewed and approved) 1.A. Determine if canopy exposure to nano-particles, in particular zinc and nickel nano-particles can improve health and longevity of pecan tree canopies. 1.B. Characterize horticultural traits of native pecan germplasm and identify genes of interest as a resource for development of new and improved cultivars. 1.C. Characterization of improved pecan rootstocks for uniformity of yield and enhanced productivity. 2. Reduce impacts of the most important pecan diseases on production, quality and uniformity of nutmeats. [NP305, C1, PS1B] (Previously reviewed and approved) 2.A. Characterize and identify novel ways to improve management of pecan scab in tree canopies based on inoculum sources, fungicide spray coverage, disease distribution and methods for disease management. 2.B. Determine dynamics of population genetic diversity of Venturia effusa in pecan orchards. 3. Develop new and improved pecan processing technologies, such as pasteurization and cracking/shelling, for improved storage, food safety, nutrition, and marketability. (NP305, C1 PS1B; NP 306, C1, PS1C) (New, for review) 3.A. Determine factors that influence the growth and/or survival of foodborne pathogens on the surface of whole and cracked pecans. 3.B. Evaluate the efficacy of novel technologies as mitigation strategies to reduce foodborne pathogens on pecans. 3.C. Identify, characterize, and model pecan and machine factors to improve halves yields in pecan cracking and shelling.

This research aims to provide pecan farmers with improved, sustainable tree and disease management practices that stabilize yield in pecan (Carya illinoinensis) orchards and maximize postharvest nutmeat quantity and quality. The management tools and strategies will enable farmers to mitigate alternate bearing (AB) and yield loss caused by disease. AB is considered the most important biological problem facing pecan production: it is economically harmful, resulting in excessive year-to-year fluctuation in nut yield and kernel quality. Many biotic and abiotic factors can induce or increase the amplitude of AB. How factors associated with canopy health, particularly nutrition, rootstock, and disease affect AB represent some of the knowledge gaps that limit development of suitable tools for stabilizing nut production and reducing yield losses. Losses postharvest include physically damaged kernels due to postharvest processing, loss to biological contaminants and poor shelf life resulting in loss of quality and salability. The research addresses 1. Whether use of nano-fertilizers can provide a basis for more efficient nutrient management, stabilize and increase production of pecan, while ensuring better environmental security. 2. Phenotyping horticultural traits of native and improved pecan germplasm in conjunction with genome wide analyses. 3. Using genomics to identify markers for horticultural traits for use in the breeding program. 4. Characterizing the role of rootstocks in tree growth and productivity, to provide a basis for more uniform, consistent and thus sustainable production of pecan nutmeats. 5. Determining how inoculum sources of pecan scab (caused by Venturia effusa) contribute to the epidemic, and using this information to develop new disease management tools, thereby reducing the impact of scab in susceptible pecan cultivars. 6. Understanding the population genetics of the scab pathogen to underpin deployment of more durable host resistance in the future. 7. Using genomics to identify effector genes involved in scab pathogen virulence. 8. Developing novel nut shelling and associated processing techniques to minimize physical nutmeat damage, contamination, and loss of quality postharvest. and 9. Improving understanding of pre-harvest and postharvest environmental factors that impact pecan color, texture, oil quality, and phytochemical content to identify conditions that maximize duration of quality. To better understand food safety risks associated with pecans, the project will address factors that influence the survival and persistence of foodborne pathogens and identify effective mitigation strategies while maintaining nut quality. In order to maximize marketability, the project will explore means to cost-effectively increase intact pecan meat extraction by modifying parametrized process variables on existing processing equipment. A series of field and laboratory studies over the project duration will address the key knowledge gaps and provide greater knowledge and understanding to develop horticultural and food safety tools and strategies required for improved management and thus long-term sustainability of pecan.

Progress Report
ARS scientist at Byron, Georgia collected data of agronomically and horticulturally important traits from a pecan collection. Characterized bud break and flowering time in all trees in the provenance collection housed at ARS, Byron, Georgia. Additional tree phenotypic traits including trunk diameter, tree height, leaf area, nut load and tree architecture were collected and are being analyzed. Nut quality traits are being assessed. Collected leaf material from the collection and extracted DNA for sequencing to conduct genome wide association studies for single nucleotide polymorphism (SNP) identification. The traits are important for future breeding programs and will contribute to improved, sustainable production and will benefit the health value of the pecan nut. Agronomic and horticultural traits were assessed in pecan trees grafted on hickory rootstocks. Variables included tree height, trunk diameter, nut load, yield, and nut quality characteristics. The cultivars Desirable and Stuart were grafted on 12 species of hickory at the Southeastern Fruit and Tree Nut Research Station (SEFTNRS), Byron, Georgia in 1986 to establish graft compatibility. The aim now is to determine whether different species of hickory rootstock influences tree yield and nut quality of the two common pecan cultivars. The study will provide information on whether non-pecan hickories may be beneficial rootstocks to improve pecan production. A study is being conducted at the University of Georgia Ponder Farm in Tifton, Georgia to compare soil microbiome in a conventionally treated vs a low input pecan orchard. This is a two-year study, the soil has been collected, and DNA extracted. DNA is being cleaned and will be ready for sequencing. The information will give us insight of the changes in fungal and bacterial communities found in in two orchards with different management strategies. Nuts were harvested over the developmental period of nut growth including water, shell hardening, and kernel fill stages from cultivars Elliott, Pawnee, and Sumner. Allergen analysis of proteins, including RNA activity is currently in progress with the collaborator in Albany, California. This time course study will allow for a better understanding of pecan nut attributes such as lipid content, lipid oxidation, and allergens during pecan nut growth and development. A new pecan block of cultivars Avalon and Lakota was successfully established. The block comprises 328 trees planted on a 10 x 10 m spacing and is equipped with below-surface drip irrigation. This new planting will allow for studies on nutrient and irrigation management, future hedge-pruning, and other research on two new scab-tolerant cultivars that were otherwise not planted at SEFTNRS. A long-term study (12 y) was continued to explore the effect of prolonged cycles of mechanical hedge-pruning on pecan scab and tree health compared to non-hedge-pruned trees (all fungicide treated). Results are showing the benefits of hedge-pruning for management of scab susceptible cultivars in the southeastern US. The new season’s results continue to be analyzed. Mechanical hedge-pruning is beneficial to reducing tree size and maximizing canopy coverage with fungicide to reduce scab severity. An experiment was repeated in a third time over 5 years to determine characteristics of populations of the pecan scab pathogen collected from different cultivars. The experiment is designed to establish whether populations from cultivars grown alongside each other are freely recombining and conceivably have the potential to develop a “super race” of scab able to infect multiple cultivars. Results will provide valuable insights into populations genetic dynamics of scab pathogen populations to help guide resistance breeding efforts. An experiment to assess effects of tractor travel speed and spray application volume was conducted. Building on prior experiments application volumes of 114, 470 and 940 L/ha and speeds 2.4 and 3.2 km/h were compared. Samples of leaves and fruit were taken at three different heights in the canopies of the trees, and speed and volume effect on disease control explored. If fungicides can be applied at faster travel speeds and lower volumes without reducing efficacy, grower can save substantial time and other operational cost. An experiment to study scab lesions on shoots was conducted. Shoot lesions are considered to be a primary source of disease early in the season. Determinate, fruiting shoots and indeterminate shoots were collected, and the numbers of lesions counted at the end of the season. Spore production was also quantified. Better knowledge of shoot lesions and their role in the disease cycle should provide a basis for improved control. Proteins produced by the scab pathogen Venturia effusa which are predicted to play an important role in overcoming plant defenses have been identified. Preliminary work removing these genes from the fungus to verify their importance in pecan scab disease progression has been completed. Numerous workflows for high-throughput evaluation of pecan and pecan-related genetic information have been established. Previously generated gene expression data for pecan has been re-evaluated to give a more accurate account of pecan genes important for defense/susceptibility against genetically diverse populations of Venturia effusa; potentially preventing years or decades of misguided research. Shortcomings in previously generated genotype data have been identified. Also, a popular transformation technique was used to express transgenes in pecan leaves for verification of genetic constructs and gene delivery efficacy. Application of ultraviolet electromagnetic waves (UV) has been shown to drastically reduce germination of Venturia effusa spores under laboratory conditions. A field experiment has been started to determine the possibility of using UV for control of pecan scab in a production setting. A field study was conducted to determine the transfer of generic Escherichia coli and attenuated Salmonella to inshell pecans during harvest. Data has been collected that evaluated the effects of microbial load, time, and organism on the transfer to inshell pecans during harvest. The study will provide information regarding the potential for pathogen contamination and transfer to inshell pecans during the harvest process and can provide guidance for determining transfer risks. An industry survey was developed and distributed to gain a perspective on the food safety practices of the pecan shelling industry in the United States. From the conducted survey approximately 26 usable responses were tabulated and evaluated based on the responses from the survey and the correlations with industry practices and how it relates to food safety. The responses from the survey provided insights into industry needs and indicators of food safety practices within the shelling industry. The results will provide valuable insights on how to focus research to meet industry needs. An experiment was conducted to evaluate the effectiveness of cold plasma for reducing Salmonella populations on the surface of pecan kernels. The effects of microbial load, distance (4 and 6 cm) to the cold plasma emitter, and treatment times (10 and 20 sec) were evaluated. Preliminary data was conducted to determine how cold plasma frequency influences Salmonella and E. coli reduction on pecan kernels. The results will provide data on cold plasma as a potential non-thermal treatment for pecan kernels. Studies have been conducted to determine the effectiveness of lactic acid as an effective sanitizer in conditioning water to reduce shiga toxin-producing E. coli populations on the surface of inshell pecans. The effectiveness of lactic acid was compared against chlorine dioxide and hot water sanitizers. Preliminary studies also evaluated the effectiveness of peracetic acid as in conditioning water to reduce Salmonella on the surface of inshell pecans. Pulsed UV light has been evaluated as an effective tool to inactivate pathogens (Salmonella and E. coli) on pecan halves. The findings suggest that pulsed UV light may be a useful tool for reducing pathogen levels on pecan surfaces. The quality characteristics of treated nuts are being evaluated for color, texture, water activity, moisture content, and changes in lipid oxidation. Preliminary studies have been conducted evaluating the use of essential oils (from cinnamon bark, clove bud, etc.) in water and surface applications for inshell pecans and pecan kernels for the reduction of Salmonella and E. coli. The results may provide an alternative organic treatment to reduce populations of human pathogens on pecans. Investigations have been conducted on both established and emerging cracking mechanisms. A Myers Cracker has been used to measure cracking data including force and stress, while also enabling the control of cracker parameters such as displacement and clearance. A circumferential cracker has also been used to facilitate automated control of machine parameters. These real-time data will allow machine adjustments to preferentially generate nut halves or pieces. Alternative cracking mechanisms that integrate multiple approaches observed in the industry are being explored. One mechanism combines compression and torsion, a technique that has promise, and a machine has been built that integrates compression and torsion. A state-of-the-art imaging capability has been developed, surpassing the currently available technologies in the industry. The imaging system accurately measures crack performance, accounting for variations introduced by different cracking methods, as well as the shelling process. The measurements obtained are fed back into the equipment to facilitate adjustments. The automated feedback and control continuously learns how parameters impact cracking and shelling performance.

1. Determined that maternal geographical origin influences the microbiota of progeny of pecan seedlings growing in different environments. In collaboration with others, ARS scientists at Byron, Georgia, characterized microbial communities in leaf tissues of seedlings grown from seeds obtained from the same cross in different locations. The results provide insight into the impact that geography plays on tree microbial composition and confirmed that maternal geographical location was important influencing the microbiome of the resulting progeny. This indicates ramifications for tree health and productivity of pecans when grown at location other than where the maternal tree was.

2. Characterized the genetic diversity of the pecan scab pathogen, Venturia effusa, in South America. In collaboration with scientists in Brazil and Argentina, ARS scientists at Byron, Georgia, characterized the population genetic structure and diversity of V. effusa, cause of scab in North and South America. The results showed the pathogen populations were less diverse and divergent to those in the USA. These results have ramifications for phytosanitary considerations regarding transfer of any pecan material that may harbor the scab pathogen between the different pecan production areas.

3. Characterized pecan spray coverage dependency in pecan trees due to tractor speed, volume of application, and use of a volute. Scientists at ARS Byron, Georgia, studied how tractor speed, volume of application, and use of a volute affected spray coverage from pecan sprayers. The results showed that lower volumes (470 L/Ha) at higher speeds (3.2 km/h) provided sufficient coverage for efficacious scab control at all heights to 19 m. Indeed, coverage was greater at slightly higher speeds. Use of a volute increased coverage at 15 to 19 m height. These observations are useful to stakeholders and are a basis to adjust current spray practice by applying lower volumes at higher speeds while maintaining disease control efficacy, thereby saving input costs.

Review Publications
Johnson, K.A., Bock, C.H., Vinson, E.L., Brannen, P.M. 2023. Prevalence and distribution of phony peach disease (caused by Xylella fastidiosa) in the United States. Plant Disease. 107:326-334.
Bock, C.H., Dewdney, M.M., Cox, K.D. 2022. Report on perennial fruit and nut crops in Eastern North America. Chapter in "Global Plant Health Assessment". Book Chapter. E-book 189.
Cervants, K., Grauke, L.J., Wang, X., Conner, P., Bock, C.H., Pisani, C., Randall, J. 2023. Influence of geographical orchard location on the microbiome from the progeny of a pecan controlled cross. Plants. eArticle12020360
Brungardt, J.J., Bock, C.H. 2023. An updated de novo transcriptome for green ash (Fraxinus pennsylvanica). Genes, Genomes, Genetics. 13(6).
Johnson, K., Bock, C.H., Brannen, P., Chen, J. 2022. A genome resource for Xylella fastidiosa subspecies multiplex strain P5A2 causing phony peach disease in the southeastern United States. Phytopathology. 122(11):2466-2470.
Prabhakar, H., Kerr, W., Bock, C.H., Kong, F. 2022. Effect of relative humidity, storage days, and packaging on pecan kernel texture. Journal of Texture Studies. 54:115-126.
Bock, C.H., Charlton, N.D., Shiller, J., Randall, J.J., Young, C.A. 2022. Population genetic diversity and structure of the pecan scab pathogen, Venturia efffusa, on cv. Desirable and native seedings, and the impact of marker number. Plant Pathology. 71:1103-1119.
Prabhakar, H., Stoner-Harris, T., Adhikari, K., Mishra, A., Bock, C.H., Kong, F. 2023. Changes in chemical characteristics and modeling sensory parameters of stored pecan nutmeats. Journal of Food Science. 88:1816-1834.
Bock, C.H., Cottrell, T.E., Hotchkiss, M.W. 2023. Spray coverage from pecan air-blast sprayers, with a radial air-flow and a volute-generated focused air-flow, as affected by forward speed and application volume. Crop Protection. 168:106234.