Progress 10/01/23 to 09/30/24
Outputs
PROGRESS REPORT Objectives (from AD-416): 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. Approach (from AD-416): 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. ARS researchers 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 the phenotypic data for fruit developmental period, date of fertilization was recorded from all trees. Date of shuck- split will be recorded when fruit matures. Period between fertilization and shuck-split will provide information on fruit developmental period. Collected leaf material from the collection and extracted DNA for sequencing to conduct genome wide association studies for 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. A fourth year⿿s collection of tree phenotypic variables was made in the ⿿Lakota x 87MX3-2.11⿿ mapping population. Variables measured included growth rate (tree height, trunk diameter), leaf area, and bud break. All transplants in the mapping population were assessed for leaf scab (recording the percentage area scabbed on the most severely diseased leaflet and providing an overall disease score for the plant). Data will be analyzed for QTL mapping. The trees are still young and will provide more comprehensive data in coming years. The trial is repeated in Texas. The two different climates in Texas and Georgia will allow environment x genotype studies, providing a basis for understanding inheritance of different phenotypic traits in pecan. 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, 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. 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 trial was set up at Shiloh Farms in Ray City, GA looking at the effect of the plant growth regulator ReTain (Valent USA, LLC) on nut retention. During the first season, nut load was assessed early, mid, and late season post application. Trees were hedged in 2022 and assessments occurred on hedged vs non-hedged sides of trees. At harvest, yield (in shell and total nutmeat) was obtained. Data collected included nut quality parameters and a second year data collection is underway. This trial will allow us to assess whether the product will lower the incidence of nut drop on cv. Desirable while following regular hedging management strategies. A new pecan block of cultivars Avalon and Lakota was successfully established. Trees that did not survive the first year⿿s planting were replaced and are being 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. Scab severity was assessed for a fourth year in a mapping population designed to better understand the inheritance of scab resistance. The cross is the two genotypes ⿿Lakota⿿ x ⿿87MX3-2.11⿿. Assessments were performed for each genotype in the experiment. As part of a multi-year, multi-location study, the information will aid understanding of scab resistance for breeding purposes. 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, growers can save substantial time and other operational cost. Laboratory experiments to ascertain effects of different phosphite fungicide formulations on growth and spore production of V. effusa were conducted. There is little detailed information on the effect of alternative phosphites (with Ni, Cu, Mn or Zn) on the growth of the fungus, but they may be more efficacious than the standard K formulation. Improved efficacy will result in better control of scab disease. A second years⿿ 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. Functional elements and genome architectures were characterized in the annotated reference genomes of three scab pathogens (Venturia effusa, V. nashicola, and V. inaequalis) to investigate alternate splicing events and intron structure of scab pre-mRNA⿿s. Sequence attributes of Venturia pre-mRNA⿿s are conserved across multiple scab species including the 5⿿ untranslated region, Kozak sequence, splice site donor/acceptor, polypyrimidine and uridine tracts, as well as the branchpoint nucleotide. RNA-sequencing data, harvested from the NCBI sequence read archives, is currently being processed for novel transcript isoform discovery in three scab pathogen species. Predictions of the branchpoint motif using a position weight matrix (in-progress) will deconvolute alternate splicing events arising from intron retention and exon skipping modules. Intron classes are being designated by covariate features including rank, length, A/T/C/G frequencies, splice donor motif, splice acceptor motif, branchpoint motif, and branchpoint distance from 3⿿ intron terminus. Together, these data will elucidate alternatively spliced isoforms of Venturia transcriptomes, and they demarcate cis-regulatory sequences involved in the regulation of scab gene expression. Work started on validating the plant hormone ethylene as playing a major role in susceptibility to pecan scab. RNA was extracted from half-sib cultivars Elliott and Desirable exogenously treated with ethylene. Quantitative PCR was run to check the expression pattern of six different genes predicted to be responsive to ethylene. Leaves of various cultivars of pecan were also checked for ethylene generation via gas chromatography at University of Georgia in Athens. Half-sibs of Elliott and Desirable were also treated with ethylene and inoculated with Venturia effusa conidia to check for increased susceptibility to the fungal pathogen. Plasmids (pRN119 & pRN120) expressing developmental regulator genes were obtained, transformed into Agrobacterium tumefaciens, and used for ⿿in soil transformation techniques. Theses plasmids have been shown to increase transformation efficiency in plants. Several phloem specific promoters have been identified and sub-cloning work started for future translating ribosomal affinity purification sequencing (TRAP-seq) experiments of pecan. Due to Venturia effusa⿿s affinity to vascular tissue, transcripts specific to this tissue could reveal important susceptibility factors. Mislabeled plants in a previously unused genome wide association dataset have been identified and removed for more accurate results of downstream applications. A pipeline for population structure and metagenomic analysis of this dataset, and future datasets, was developed. Using population structure information generated from this dataset a tree from the Provenance collection with unique genetics compared to historical cultivars was identified that also has high resistance to pecan scab. Genetic crosses were started between this individual and susceptible cv Desirable trees for ease assessing genetic contributions to scab resistance/susceptibility. Markers for identifying successful crosses have been identified and await development. Microbiome analysis was also done using this dataset and shows unique stratification of micro- organisms associating with pecan compared to previous microbiome studies. In conjunction with past scab severity ratings, this information could be used to develop biopesticides. A pilot study was started emasculating cv Cape Fear branches to check for either improved or detrimental effects to nut development/yield. The provenance collection was also scouted for individuals producing few catkins. Future work using breeding, biotechnology techniques, or amendment application to produce female only trees could reduce alternate bearing and/or increase yield. Putative genetically transformed Venturia effusa (the organisms causing pecan scab) are awaiting materials/resources required for characterization of their genetics. The Pecan Processing Aspects of the project have been separated and documented in the report for project 6042-41000-001-000-D. ACCOMPLISHMENTS 01 Visual assessments of pecan canopy density due to late season leaf fall provided accurate and reliable estimates for comparing pecan genotypes.. Canopy density during leaf fall is important as the seasonal canopy dynamics provides insights to environmental cues and breeding potential of germplasm. ARS researchers at Byron, Georgia explored the ability of visual raters to estimate canopy foliage density in trees in the provenance collection as an indicator of leaf shed during autumn. The estimates were compared to measurements using image analysis. The results are a basis for understanding genetic control of leaf fall when combined with genotype data as part of a genome-wide association study. 02 Analysis of transcriptomes from pecan trees with wild ancestry reveal potential mechanisms of resistance/susceptibility to pecan scab.. Pecan scab disease is a key factor that limits pecan productivity in most of the eastern US growing region. ARS researchers at Byron, Georgia collected RNA from pecan trees previously shown to be either susceptible or resistant to pecan scab. Infected leaf material in addition to healthy material was collected from susceptible trees. Next-gen sequencing revealed transcriptome profiles of these different materials. Pathway enrichment analysis of this information revealed potential candidates of resistance and/or susceptibility. These genes and their associated pathways are being analyzed in further detail to guide breeding efforts for enhanced resistance to pecan scab.
Impacts
(N/A)
Publications
- Pisani, C., Bock, C.H., Randall, J. 2023. Visual rating and the use of image analysis for assessing canopy foliage density in a pecan provenance collection during leaf fall. Journal of Forestry Research. 34:1843-1834. https://doi.org/10.1007/s11676-023-01635-0.
- Toledo, P., Phillips, K., Schmidt, J., Bock, C.H., Wong, C.R., Hudson, W., Shapiro Ilan, D.I., Wells, L., Acebes-Doria, A.L. 2023. Canopy hedge pruning in pecan production differentially affects groups of arthropod pests and associated natural enemies. Crop Protection. 176. Article 106521. https://doi.org/10.1016/j.cropro.2023.106521.
- Brungardt, J.J., Alarcon, Y., Shiller, J., Monteros, M., Young, C., Randall, J.J., Bock, C.H. 2024. Transcriptome profile of pecan scab resistant and susceptible trees from a pecan provenance collection. BMC Genomics. 25:180. https://doi.org/10.1186/s12864-024-10010-0.
- Chiang, K., Chang, Y., Liu, H., Lee, J., Jarroudi, M., Bock, C.H. 2024. Survival analysis as a basis to test hypotheses when using quantitative ordinal scale disease severity data. Phytopathology. 114(2). https://doi. org/10.1094/PHYTO-02-23-0055-R.
- Johnson, K.A., Brannen, P.M., Chen, C., Bock, C.H. 2024. Visual assessment of phony peach disease: evaluating rater accuracy and reliability. Plant Disease. 108(4):930-940. https://doi.org/10.1094/PDIS-11-22-2669-RE.
- Johnson, K.A., Chen, C., Bock, C.H., Brannen, P.M. 2023. No evidence for vertical transmission of Xylella fastidiosa subsp. multiplex in peach seed. Plant Health Progress. 24(4):516-518. https://doi.org/10.1094/PHP-11-22- 0121-BR.
- Pisani, C., Cottrell, T.E. 2024. Impact of Pecan Leafroll Mite (Acari: Eriophyidae) on Pecan Foliage. Journal of Entomological Science. 59(1):86- 89. https://doi.org/10.18474/0749-8004-59.1.86.
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Progress 10/01/22 to 09/30/23
Outputs
PROGRESS REPORT Objectives (from AD-416): 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. Approach (from AD-416): 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. 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. ACCOMPLISHMENTS 01 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. 02 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. 03 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.
Impacts
(N/A)
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. https://doi.org/10.1094/ PDIS-03-22-0653-RE.
- 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. https:// doi.org/10.3390/plants12020360. eArticle12020360
- Brungardt, J.J., Bock, C.H. 2023. An updated de novo transcriptome for green ash (Fraxinus pennsylvanica). Genes, Genomes, Genetics. 13(6). https://doi.org/10.1093/g3journal/jkad086.
- 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. https://doi.org/10.1094/PHYTO-03-22-0081-A.
- 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. https://doi.org/10.1111/jtxs.12723.
- 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. https://doi.org/10.1111/ppa. 13551.
- 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. https://doi.org/10.1111/1750-3841.16533.
- 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. https://doi.org/10.1016/j.cropro.2023.106234.
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Progress 10/01/21 to 09/30/22
Outputs
PROGRESS REPORT Objectives (from AD-416): 1. Improve pecan nut productivity by analyzing key horticultural issues that disrupt annual consistency, yield, and quality, and developing new or improved mitigation strategies. 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. 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. This objective will be coordinated with research on improved crop management to reduce the impact of abiotic and biotic factors causing unstable or reduced yield, and reduced quality nuts, for an integrated, systems approach to pecan production and post- harvest that benefits the profitability of the U.S. pecan industry. Anticipated products include new pecan pasteurization processes that meet market standards while maintaining nutmeat quality and nutrition. Approach (from AD-416): 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 identifying 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. A series of field and laboratory studies over the next five years will address these key areas where knowledge is lacking; the resulting information will provide the basis for novel management products that improve horticultural and disease management and favor canopy health in pecan, and improve the postharvest pipeline to maximize quantity and quality of saleable nutmeats. Data collection of agronomically and horticulturally valuable traits in a provenance collection of pecan was continued. Characterization of bud break and flowering time has been completed 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 are being analyzed. Nut quality traits are also being assessed. These traits are important for future breeding programs and will contribute to more improved, more sustainable production and will benefit the health value of the pecan nut. The second year collection of tree phenotypic variables was made in the ⿿Lakota x 87MX3-2.11⿿ mapping population. Variables measured included growth rate (tree height, trunk diameter), leaf area, and bud break. The two different climates in Texas and Georgia will allow for screening of horticultural traits in this population. These data will allow environment x genotype studies, providing a basis for understanding inheritance of different phenotypic traits in pecan. Pecan cultivars. ⿿Desirable⿿ and ⿿Stuart⿿ grafted onto 12 species of hickory in genus Carya were planted at the Southeastern Fruit and Tree Nut Research Station (SEFTNRS) in Byron, Georgia in June 1986 with the aim of assessing graft compatibility. Data collection of agronomic and horticultural traits was continued by ARS scientists at Byron, Georgia. Variables included tree height, trunk diameter, nut load, yield, and nut quality characteristics. The aim is to understand whether different species of hickory used as rootstocks have an effect on tree yield and nut quality of these two common pecan cultivars. The study will provide information on whether non-pecan hickories could have beneficial rootstock traits that can be used to improve pecan production. A field experiment with ⿿Pawnee⿿ trees was conducted to evaluate the effects of a fungicide treated/non-treated and hedged vs a non-hedged pruned orchard on nut quality, yield and gas exchange parameters. Gas exchange parameters include assimilation rate, transpiration rate, and stomatal conductance to water vapor . Second year data collection is currently in progress. The information will shed more light on tree and nut quality parameters on hedged and non-hedged pruned pecan trees. A field experiment was initiated to characterize the microbiome of a hedged vs non-hedged pruned orchard of ⿿Cherokee⿿. Shoot growth and gas exchange parameters are being collected monthly at 3 different heights within the canopy. Soil and leaf samples are being collected in order to get better insight into the bacterial and fungal microbiome. Improved knowledge on the effect hedge-pruning on soil and foliar microbiomes will help make better informed decisions regarding irrigation and fertilization programs to maximize pecan tree health by ensuring a healthy microbiome. Commenced collection of nuts of cultivars ⿿Elliott⿿, ⿿Pawnee⿿, and ⿿Sumner. Nuts are being harvested over the developmental period of nut growth, water stage, shell hardening, and kernel fill stages. Allergen analysis will at the protein and RNA levels. This time course study will allow for a better understanding of pecan nut attributes such as lipid content, lipid oxidation, and allergens during growth and development. An experiment was continued for a third season to better understand pecan scab disease epidemic development in hedge-pruned pecan trees. Trees were hedge pruned or not, and were either sprayed with fungicide + insecticide or not, and scab disease incidence and severity assessed on foliage, fruit and shoots. Results will be analyzed and will be used to ascertain how early season shoot infections vary in the differently managed trees, and the impact on scab disease development on foliage and fruit during the hedge-pruning cycle. The information will aid fungicide applications timing to better manage shoot lesions in hedge-pruned and non-hedged pecan trees. A long-term study (10 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 United States. 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 to explore the systemic nature of phosphite fungicides in the canopy of tall pecan trees was repeated, and disease assessment performed. Knowing how the fungicide redistributes can help with understanding potential for systemic activity in relation to disease control in distal portions of the canopy, and determine how this impacts residues in nutmeats. The information can be utilized to maximize scab control while minimizing regulated phosphite residues in nutmeats. Scab severity was assessed for a second year in a mapping population designed to better understand the inheritance of scab resistance. The cross is the two genotypes ⿿Lakota⿿ x ⿿87MX3-2.11⿿. Assessments were performed for each genotype in the experiment. As part of a multi-year, multi-location study, the information will aid understanding of scab resistance for breeding purposes. An experiment was continued 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 monitoring for the sexual stage of pecan scab in leaf litter and in air samples was continued. Slides were inspected for the ascopores (which have been demonstrated in vitro) of the pecan scab pathogen. Identifying the production of sexual spores will aid understanding the epidemiology of the disease, sources of variability, and potentially additional points to apply control. An experiment was performed to test the effectiveness of pulsed ultra- violet light at reducing Salmonella on the surface of pecan kernels. Data was collected to determine the reduction of Salmonella before and after treatment. Understanding the effectiveness of PUVL at reducing pathogens will help determine if it is a feasible treatment that can be used to reduce pathogen contamination. The SEFTNRS in Byron, Georgia has established a new Biosafety Level 2 lab to perform food safety research on pecans. Construction is underway for a small scale pecan shelling facility at the location for studying processing impacts on pecan food safety and nutmeat quality. Pecan cracking mechanisms were tabulated, and a taxonomy of approaches developed through a comprehensive search of literature, patents, equipment, meeting with equipment manufacturers, and visiting facilities that use shelling equipment. Knowing the various approaches used assists in understanding the mechanics of how cracking and shelling takes place, and that can be used to improve the process for higher shell-out. A series of experiments have been designed by ARS scientists at Byron, Georgia, that will test different impactor geometry and materials during the cracking process. The design of these experiments will provide a basis for understanding and optimizing the shelling process to minimize damage of the nutmeat. ACCOMPLISHMENTS 01 Determined that pecan bacterial leaf scorch can be seed transmitted. Pecan bacterial leaf scorch can cause yield loss and decline of some pecan cultivars. The causal pathogen has a wide host range, and therefore movement of the pathogen is a concern. ARS researchers at Byron, Georgia showed that the bacteria causing pecan bacterial leaf scorch could be transmitted from infected seed to the seedlings of pecan. This information has potential ramifications for use of seed for root stocks, and the provision of pecan scion germ plasm or seed to foreign partners. 02 Determined the genetic control of resistance to demethylation inhibitor (DMI) fungicides in the pecan scab pathogen. Fungicide resistance is an issue with the scab pathogen, reducing effectiveness of control. ARS researchers at Byron, Georgia confirmed that a high level of resistance occurred in the field to DMI fungicides, and that the resistance was associated with specific mutations in two genes (CYP51A and CYP51B), that result in abnormalities of the protein, and how much of the protein is made. The knowledge identifies causes of resistance in the pathogen, and provides a basis to develop detection methods to rapidly identify and track specific resistance traits in orchard populations of the scab pathogen. 03 Characterized color change in pecan nutmeat postharvest and the kinetics of the process. Storage of pecan nutmeats is a problem as they can degrade rapidly, resulting in loss of the product. ARS researchers at Byron, Georgia confirmed that higher temperature and relative humidity, and longer storage duration resulted in darker nutmeat color, which reduces the consumer acceptability of the nutmeat. Kinetic constants for the color change (hue, lightness and chroma), and activation energies were calculated. The results allow stakeholders to predict changes in color of pecan nutmeats during storage under various conditions.
Impacts
(N/A)
Publications
- Pereira De Melo, V., Da Silva Mendonca, A.C., De Souza, H.S., Gabriel, L.C. , Bock, C.H., Eaton, M.J., Schwan-Estrada, K.R., De Carvalho Nunes, W.M. 2020. Reproducibility of the Development and Validation Process of Standard Area Diagram By Two Laboratories: An Example Using the Botrytis Cinerea/Gerbera Jamesonii Pathosystem. Plant Disease. Vol 104:2440-2448. https://doi.org/10.1094/PDIS-08-19-1708-RE.
- Hofman, C.O., Cottrell, T.E., Bock, C.H., Mizell, R.F., Wells, L., Shapiro Ilan, D.I. 2021. Impact of a biorational pesticide on the pecan aphid complex and its natural enemies. Biological Control. 161/104709. https:// doi.org/10.1016/j.biocontrol.2021.104709.
- Wu, S., Blackburn, M.B., Mizell, R.F., Duncan, L.W., Toews, M.D., Sparks, M., El-Borai, F., Bock, C.H., Shapiro Ilan, D.I. 2021. Pupal cell antibiosis suppresses plant and insect pathogenic fungi and is associated with a bacterium related to Serratia nematodiphila i. Journal of Invertebrate Pathology. 184/107655. https://doi.org/10.1016/j.jip.2021. 107655.
- Bock, C.H., Hotchkiss, M.W. 2021. Tractor Speed and Spray Application Volume in Tall Pecan Trees: Effect on Spray Coverage at Different Heights in the Canopy. Plant Disease. Vol 105, 2509-2520. https://doi.org/10.1094/ PDIS-11-20-2420-RE.
- Cervantes, K., Hilton, A.E., Stamler, R.A., Heerma, R., Bock, C.H., Wang, X., Jo, Y., Grauke, L.J., Randall, J.J. 2022. Evidence for seed transmission of Xylella fastidiosa in pecan (Carya illinoinensis). Frontiers in Microbiology. Article e13:780335. https://doi.org/10.3389/ fpls.2022.780335.
- Li, Z., Di Gioia, F., Zhao, X., Hong, J.C., Rosskopf, E.N., Wilson, P.C., Pisani, C., Paudel, B. 2022. Quantifying the effects of anaerobic soil disinfestation and other biological soil management strategies on nitrous oxide emissions from raised bed plasticulture tomato production. Journal of Environmental Quality. https://doi.org/10.1002/jeq2.20324.
- Pisani, C., Adkins, S.T., Turechek, W., Patel, P.C., Rosskopf, E.N. 2021. First report of Macrophomina phaseolina, Fusarium brachygibbosum, and Lasiodiplodia theobromae causing fungal watermelon vine decline in Southwest and West-Central Florida. Plant Health Progress. 22:544-551. https://doi.org/10.1094/PHP-09-20-0077-RS.
- Moore, L.C., Brenneman, T.B., Waliullah, S., Bock, C.H., Ali, M. 2022. Multiple mutations and overexpression in the CYP51A and B genes lead to decreased sensitivity of Venturia effusa to tebuconazole. International Journal of Molecular Sciences. Vol 47: 43-57. https://doi.org/10.1007/ s40858-021-00479-5.
- Del Ponte, E.M., Cazon, L.I., Alves, K.S., Pethybridge, S.J., Bock, C.H. 2022. How much do standard area diagrams improve accuracy of visual estimates of plant disease severity? A systematic review and meta-analysis. Tropical Plant Pathology. https://doi.org/10.1007/s40858-021-00479-5.
- Pravhakar, H., Kong, F., Bock, C.H., Kerr, W. 2022. Pecan color change during storage: kinetics and modeling of the processes. Food Research International. https://doi.org/10.1016/j.crfs.2022.01.015.
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Progress 10/01/20 to 09/30/21
Outputs
PROGRESS REPORT Objectives (from AD-416): Objective 1. Improve pecan nut productivity by analyzing key horticultural issues that disrupt annual consistency, yield, and quality, and developing new or improved mitigation strategies. Objective 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. Objective 1.B. Characterize horticultural traits of native pecan germplasm and identify genes of interest as a resource for development of new and improved cultivars. Objective 1.C. Characterization of improved pecan rootstocks for uniformity of yield and enhanced productivity. Objective 2. Reduce impacts of the most important pecan diseases on production, quality and uniformity of nutmeats. Objective 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. Objective 2.B. Determine dynamics of population genetic diversity of Venturia effusa in pecan orchards. Objective 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) Objective 3 will be coordinated with research on improved crop management to reduce the impact of abiotic and biotic factors causing unstable or reduced yield, and reduced quality nuts, for an integrated, systems approach to pecan production and post- harvest that benefits the profitability of the US pecan industry. Anticipated products include new pecan pasteurization processes that meet market standards while maintaining nutmeat quality and nutrition. Approach (from AD-416): 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 identifying 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. A series of field and laboratory studies over the next five years will address these key areas where knowledge is lacking; the resulting information will provide the basis for novel management products that improve horticultural and disease management and favor canopy health in pecan, and improve the postharvest pipeline to maximize quantity and quality of saleable nutmeats. Data collection of agronomically and horticulturally valuable traits in a provenance collection of pecan was continued. Characterization of bud break and flowering time has been completed in the provenance collection housed at ARS, Byron, Georgia. Additional tree phenotypic traits such as, trunk diameter, tree height, leaf area, nut load and tree architecture are being analyzed. Nut quality traits are also being assessed. These traits are important for future breeding programs and will contribute to more improved, more sustainable production and will benefit the health value of the pecan nut. A ⿿Lakota x 87MX3-2.11⿿ mapping population was created and has been planted in Somerville, Texas and replicated at Byron, Georgia. Collection of tree phenotypic variables such as: growth rate (tree height, trunk diameter), leaf area, branching pattern, and bud break has begun. This will allow environment x genotype studies to begin, providing a basis for understanding inheritance of different phenotypic traits. The two different climates in Texas and Georgia will allow for screening of horticultural traits in this population. Pecan cvs. ⿿Desirable⿿ and ⿿Stuart⿿ grafted onto 12 species of hickory in genus Carya were planted at the SOUTHEASTERN FRUIT & TREE NUT RESEARCH LABORATORY in Byron, Georgia, in June 1986 with the aim of assessing graft compatibility. Data collection of agronomic and horticultural traits was continued by ARS scientists in Byron, Georgia. Variables included tree height, trunk diameter, nut load, yield, and nut quality characteristics. The aim is to understand whether different species of hickory used as rootstocks have an effect on tree yield and nut quality of two common pecan cultivars ⿿Stuart⿿ and ⿿Desirable⿿. A greenhouse pot study using two cultivars ⿿Pawnee and ⿿Elliott was established by ARS scientists in Byron, Georgia. The goal is to observe the effects a root-knot nematode Melodogyne partityla and beneficial entomopathogenic nematode Steinernema rarum have on plant physiological responses such as plant growth parameters (stem diameter, seedling height) , plant gas exchange, chlorophyll content, leaf area, fresh and dry weight of leaves, stems, and roots, and root galling. This information will allow us to assess the effects root-knot nematodes can have on two common pecan cultivars (one of which is a commonly used rootstock) and whether entomopathogenic nematodes could be a solution to mitigate the problem. An experiment was repeated by ARS scientists in Byron, Georgia, to better understand pecan scab disease epidemic development in pecan trees. Trees were hedge pruned or not, and were either sprayed with fungicide + insecticide or not, and scab disease incidence and severity assessed on foliage, fruit and shoots. Results will be analyzed by ARS scientists in Byron, Georgia, and will be used to ascertain how early season shoot infections vary in the differently managed trees, and how this impacts scab disease development on foliage and fruit early in the season. The information will aid fungicide applications timing to better manage shoot lesions in hedge-pruned and non-hedged pecan trees. A long-term study was continued by ARS scientists in Byron, Georgia, to explore the effect of prolonged cycles of mechanical hedge-pruning on pecan scab and tree health compared to non-hedge-pruned trees. Results confirm that hedging benefits scab management by allowing a greater proportion of the fruit to be effectively protected by efficacious fungicide coverage. This has ramifications for management of scab susceptible cultivars in the southeastern United States. But long-term effects of hedge pruning on pecan disease development are not known. Results are being analyzed by ARS scientists in Byron, Georgia. Mechanical hedge-pruning is beneficial to maximizing canopy coverage with fungicide to reduce scab severity of the nut crop. A field experiment was repeated by ARS scientists in Byron, Georgia, to monitor the activity of pecan scab disease lesions throughout the year on three cultivars of pecan. The numbers of spores produced on lesions on shoot samples were monitored to determine periods of lesion activity. The information will help identify the critical period of conidial production from shoot lesions, particularly early in the season which is considered the primary source of infection for the epidemic, which will pave the way for more appropriately targeted fungicide applications. An experiment was conducted by ARS scientists in Byron, Georgia, to determine characteristics of populations of the pecan scab pathogen collected from different cultivars. This is part of a study to establish whether populations from cultivars grown alongside each other are freely recombining and conceivably have the potential to develop ⿿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 exploring the systemic nature of phosphites fungicides in the canopy of tall pecan trees was conducted by ARS scientists in Byron, Georgia, and disease assessment performed. Knowing how the fungicide redistributes can help with understanding potential for systemic-activity in relation to disease control in distal portions of the canopy, and determine how this impacts residues in nutmeats. The information can be utilized to maximize scab control while minimizing phosphite residues in nutmeats. Record of Any Impact of Maximized Teleworking Requirement: Critical work to get the project experiments initiated were achieved. Impact on milestones is expected to be minimal. The project commenced on 3 Apr 2020. ACCOMPLISHMENTS 01 Developed the first four high quality genomes of pecan. ARS scientists at Byron, Georgia, developed the first four high quality genomes of pecan genotypes. Comparative genome analysis revealed substantial adaptive introgressions. The outbred nature of the genomes provided targets for variants segregating within breeding pedigrees. Presence- absence and functional variants were used to identify candidate genes for pathogen resistance. Combined, the analyses and genome resources take a crucial step towards exploiting molecular targets in the pecan genome to accelerate breeding efforts in pecan and form a foundation for functional and quantitative genomics in a highly diverse and outbred crop. 02 Optimizing scab control in mature pecan canopies. ARS scientists at Byron, Georgia, characterized the distribution of fungicide and consequent scab disease control in the canopies of tall pecan trees receiving fungicide sprays applied at different volumes and speeds. The results demonstrated that applying fungicide at 2.5 mph and 50 GPA was as efficacious as slower speeds and higher volumes usually used by the industry. This information is valuable as it provides growers the option to travel faster and apply lower volumes thereby saving time, labor costs, equipment operation and maintenance costs, and water. 03 Use of zinc and nickel nano-fertilizers on pecan physiology. ARS scientists at Byron, Georgia, assessed whether nano-fertilizers of two essential micronutrients to pecan nickel and zinc could supplement traditional salt-based fertilizers. The results demonstrated that nickel was more easily absorbed into the leaf when supplied by nano- fertilizers for both cultivars in the study ⿿Zinner⿿ and ⿿Byrd⿿. Additionally, nano-fertilizers showed a positive impact on gas exchange parameters on ⿿Zinner⿿ plants. Based on these data, nano-fertilizers could be beneficial in pecan production systems in developing new orchard management tools.
Impacts
(N/A)
Publications
- Standish, J.R., Brenneman, T.B., Bock, C.H., Stevenson, K.L. 2021. Spatial variation and temporal dynamics of fungicide sensitivity in Venturia effusa within a pecan orchard. Plant Disease. 105: 377-383. https://doi. org/10.1094/PDIS-04-20-0889-RE.
- Bock, C.H., Alarcon, Y., Conner, P.J., Young, C.A., Randall, J.J., Pisani, C., Grauke, L.J., Wang, X., Monteros, M.J. 2020. Foliage and fruit susceptibility of a pecan provenance collection to scab, caused by Venturia effusa. Center for Agriculture and Biosciences International (CABI) Invasive Species Compendium. 1:19. https://doi.org/10.1186/s43170- 020-00020-9.
- Bock, C.H., Young, C.A., Zhang, M., Chen, C., Brannen, P.M., Adaskaveg, J. A., Charlton, N.D. 2021. Mating type idiomorphs and genetic diversity of venturia carpophila, cause of peach scab. Phytopathology. 111(2):408-424. https://doi.org/10.1094/PHYTO-12-19-0485-R.
- Luo, W., Posny, D., Kriss, A.B., Graham, J.H., Poole, G.H., Taylor, E.L., Mccollum, G., Gottwald, T.R., Bock, C.H. 2020. Seasonal and post-harvest population dynamics of the Asiatic citrus canker pathogen Xanthomonas axonopodis pv. citri on grapefruit in Florida. Crop Protection. 137:105277. https://doi.org/10.1016/j.cropro.2020.105227.
- Charlton, N.D., Yi, M., Bock, C.H., Zhang, M., Young, C.A. 2021. First description of the sexual stage of Venturia effusa, causal agent of pecan scab. Mycologia. 112:711-721. https://doi.org/10.1080/00275514.2020. 1759998.
- Hilton, A.E., Wang, X., Zhang, M., Cervantes, K., French, J., Randall, J.J. , Bock, C.H., Grauke, L.J., Jo, Y.K. 2020. Improved methods for detecting Xylella fastidiosa in pecan and related Carya species. European Journal of Plant Pathology. https://doi.org/10.1007/s10658-020-02050-5.
- Bock, C.H., Rains, G.C., Hotchkiss, M.W., Chen, C., Brannen, P.M. 2020. The effect of tractor speed and canopy position on fungicide spray deposition and peach scab incidence and severity. Plant Disease. 104(7): 2014-2022. https://doi.org/10.1094/PDIS-11-18-1950-RE.
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Progress 10/01/19 to 09/30/20
Outputs
Progress Report Objectives (from AD-416): 1. Improve pecan nut productivity by analyzing key horticultural issues that disrupt annual consistency, yield, and quality, and developing new or improved mitigation strategies. 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. 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. Approach (from AD-416): This research aims to provide pecan farmers with improved, sustainable tree and disease management practices that stabilize yield in pecan (Carya illinoinensis) orchards. The management tools and strategies will enable farmers to mitigate alternate bearing (AB) and further loss in yield 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. The research targets 1. Whether use of nano- fertilizers can provide a basis for more efficient nutrient management, stable and greater production of pecan, while ensuring better environmental security. 2. Characterizing phenotypic traits of native pecan germplasm in conjunction with genome wide analyses to identify traits to incorporate into improved cultivars. 3. Characterization of the role rootstocks in tree growth and productivity, to provide a basis for more uniform, consistent and thus sustainable production of pecan nutmeats. 4. 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, and 5. Understanding the population genetics of the scab pathogen to underpin deployment of more durable host resistance in the future. A series of field and laboratory studies over the next five years will address these key areas where knowledge is lacking; the resulting information will provide the basis for novel management products that improve horticultural and disease management and favor canopy health in pecan. ARS researchers at Byron, Georgia, initiated a greenhouse study to determine the effect of canopy exposure to nano-particles, in particular essential micronutrients zinc and nickel. The experiment was carried out on two cultivars �Byrd� and �Zinner�. The effects of foliar application of zinc and nickel nano-particles is being compared to conventional micronutrient applications on pecan seedlings as a means to improve health and longevity of pecan trees, while reducing wastage and cost of application. The use of nano-fertilizers will allow more economic, sustainable and precise fertilization for pecan production. ARS researchers at Byron, Georgia, initiated data collection of agronomically and horticulturally valuable traits in a provenance collection of pecan. Characterization of bud break and flowering time has been completed in the provenance collection housed at ARS, Byron, Georgia. Additional tree canopy data based on remote sensing technology is being analyzed. Nut traits, including fatty acid profiles of trees resistant to scab are being assessed. These traits are important for future breeding programs and will contribute to more improved, more sustainable production and will benefit the health value of the pecan nut. ARS researchers at Byron, Georgia, conducted research to evaluate dwarfing hickory rootstocks on tree productivity, and graft compatibility and assess tree yield. The effect of hickory species as rootstocks can provide useful information on their value for tree dwarfing and other traits, including drought tolerance, while maintaining tree productivity and overall tree health. The trees have been characterized using remote sensing and mapping technology to compare various horticultural parameters. The information will contribute to future, more efficient, improved pecan production systems. Pecan root-knot nematode (Meloidogyne partityla) is a constraint to pecan cultivation. Nematode parasitism was previously reported to be associated with zinc and nickel deficiency and mouse ear disorder. The evaluation of three different rootstock susceptibilities to pecan root- knot nematode was carried out in a greenhouse at University of Georgia in Athens, Georgia. The susceptibility of pecan rootstocks to pathogenic nematodes will allow for a better understanding of mouse ear severity related to nickel and other cation deficiencies and selection of appropriate rootstocks to enhance orchard productivity where nematode parasitism is an issue. An experiment was established by ARS researchers at Byron, Georgia, to better understand pecan scab disease epidemic development in pecan trees. Trees were hedge pruned or not, and will either be sprayed with fungicide or not, and scab disease incidence and severity assessed on foliage, fruit and shoots. Results will be analyzed and will be used to ascertain how early season shoot infections vary in the differently managed trees, and how this impacts scab disease development on foliage and fruit early in the season. The information will aid fungicide applications timing to better manage shoot lesions in hedge-pruned and non-hedged pecan trees. Field experiments were established by ARS researchers at Byron, Georgia, to monitor the activity of pecan scab disease lesions throughout the year on three cultivars of pecan. The numbers of spores produced on lesions on shoot samples will be monitored to determine periods of lesion activity. This will help identify the critical period of conidial production from shoot lesions, particularly that early in the season which is considered the primary source of infection for the epidemic, which will pave the way for more appropriately targeted fungicide applications. A long-term study was continued by ARS researchers at Byron, Georgia, to explore the effect of prolonged cycles of mechanical hedge-pruning on pecan scab and tree health compared to non-hedge-pruned trees. Results confirm that hedging benefits scab management by allowing a greater proportion of the fruit to be effectively protected by efficacious fungicide coverage. This has ramifications for management of scab susceptible cultivars in the southeastern United States. But long-term effects of hedge pruning on pecan disease development are not known. Results are being analyzed. Mechanical hedge-pruning is beneficial to maximizing canopy coverage with fungicide to reduce scab severity of the nut crop. Samples of scab-diseased overwintering shoot, leaf and shuck material were collected and examined by ARS researchers at Byron, Georgia, for evidence of structures that could be the sexual stage of the scab pathogen (Venturia effusa). A spore sampler was operated in the field by ARS researchers at Byron, Georgia, to collect samples of air-borne spores to determine whether any could be identified as the sexually produced ascospore of the pecan scab pathogen. Identification of the sexual stage in the field will have major ramifications for our understanding of the epidemiology of the disease, and may provide useful new points for control. An experiment was continued by ARS researchers at Byron, Georgia, to determine characteristics of populations of the pecan scab pathogen collected from different cultivars. No studies have been done to establish whether populations from cultivars grown alongside each other are freely recombining and conceivably have the potential to develop �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. Research was initiated by ARS researchers at Byron, Georgia, to develop improved approaches to analyzing data from ordinal scales used for the assessment of pecan scab and other plant diseases. The ramifications of rating methods and analysis, particularly when using disease ordinal scales, can be problematic. The work aims to ensure accurate and reliable estimation and analysis of pecan scab and other diseases.
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