Location: Crop Germplasm Research
2025 Annual Report
Objectives
Objective 1: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall NPGS Plan, apply them to priority Carya genetic resources to avoid backlogs in genetic resource and information management.
Sub-objective 1.A: Improve the accuracy of phenotyping for pecan traits, specifically pecan scab susceptibility, through improved rating scales and computer image processing.
Sub-objective 1.B: Determine the distribution of Xylella fastidiosa in pecan seeds, roots, and throughout the canopy during the growing season. Determine seed transmission rates and subspecies level differences of X. fastidiosa in various improved pecan cultivars.
Objective 2: Acquire; maintain the safety, genetic integrity, health, and viability; and distribute priority Carya genetic resources and associated descriptive information.
Sub-objective 2.A: Strategically maintain, expand, and increase the health and longevity of germplasm contained in the orchards of the NCGR-Carya.
Sub-objective 2.B: Identify and apply species-diagnostic SNPs to validate species/hybrid identity and to guide repository germplasm acquisition efforts.
Sub-objective 2.C: Validate the effectiveness of cryopreserved pollen in controlled crosses and expand the representation of Carya pollen in cryopreservation at the National Laboratory for Genetic Resources Preservation (NLGRP).
Objective 3: Characterize priority horticultural traits, genetic pathways, physiological processes, and genotypic markers to support pecan breeding, and elucidate the genomic structure for pecan and related Carya species.
Sub-objective 3.A: Identifying QTLs for growth, disease, and nut quality traits for pecan breeding using bi-parental mapping populations.
Subobjective 3.B: Validate existing QTL for bud break and scab resistance and develop GWAS trait associations in repository and breeding populations.
Sub-objective 3.C: Evaluate the contribution of non-structural carbohydrates on patterns of alternate bearing and shoot carbohydrate storage in pecan.
Objective 4: Breed pecan scion cultivars with superior horticultural traits, host-plant resistance, and tolerance to biotic and abiotic stresses, and select regionally adapted pecan rootstocks.
Sub-objective 4.A: Develop high-yielding pecan scion cultivars with a compact tree form, early nut maturity, high-quality kernels, and superior disease and/or insect resistance.
Sub-objective 4.B: Examine the effects of open-pollinated rootstocks on pecan scion vigor, nut production, and nut quality.
Approach
The USDA-ARS Pecan Breeding and Genetics program houses two major initiatives: 1) A nationally focused Pecan Breeding Program responsible for releasing 32 pecan cultivars since 1930 and 2) The National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya). Our research addresses many problems facing pecan growers, researchers, and consumers. In this research plan, we address six main concerns: Conservation of genetic diversity (Sub-objective 2.A, 2.B), pollen cryopreservation (2.C), infections of Xylella fastidiosa (1.A, 1.B), pecan breeding (4.A), associating important pecan traits with genetics (3.A, 3.B), and physiological issues affecting pecan nut yields (3.C, 4.B). Conservation of genetic diversity is the primary function of the living repository NCGR-Carya managed by the project. Items of deferred maintenance (fencing, tree removal, etc.) and structural improvements (e.g., irrigation) related to a changing climate are needed for the continued efficient operation of these diverse orchards. Pollen cryopreservation benefits the breeding program by providing another avenue of conservation and enabling crosses when pollen may not be available. Xylella fastidiosa is a major plant pathogen, and its presence in the repository and breeding material presents challenges for distribution and breeding. A better understanding of X. fastidiosa biology will facilitate the development of Integrated Pest Management approaches for control. Pecan breeding provides new varieties to the pecan industry, which are likely the best way to address the long-term challenges of a changing climate. Few associations between genetics and important pecan traits exist, and developing more will accelerate the speed and efficiency of pecan breeding. Finally, the entire pecan industry grafts scion clones onto open-pollinated seedlings as rootstocks. The degree of rootstock effects have not been fully quantified in pecan. Successful investigations in these six areas will benefit the long-term viability and usefulness of the NCGR-Carya repository and the development of high-quality varieties for the pecan industry.
Progress Report
Work by this project in FY 2025 resulted in significant progress in improving disease rating scales and screening methods, adding irrigation to repository orchards, conducting genetic characterizations (genotyping) of thousands of pecan trees for the breeding program, measuring nut and tree growth traits for genetic association mapping, and performing breeding trait evaluations. Under Objective 1, new disease rating scales for pecan diseases, including pecan bacterial leaf scorch caused by the bacterium, Xylella fastidiosa, were developed and are ready for validation. Breeding and germplasm repository orchards were screened for the presence of pecan diseases and a library of isolates of local pecan diseases is being developed to aid ongoing project work which includes increasing leaf scab disease pressure in breeding evaluations of controlled-cross seedlings. Objective 2 work addressed important deferred maintenance issues for the germplasm repository including installation of irrigation for two orchards, property perimeter fencing to exclude wild hogs, and renovation of an indoor space for the new herbarium and nut library collection. Backlogs in the breeding program were addressed by the clearing of land for a new grafted pecan breeding trial orchard, and thinning overcrowded trees from another pecan breeding orchard. Classification of wild-origin hickory trees from the Arnold Arboretum at Harvard University, using low-coverage DNA sequencing, was successful for hickories closely related to pecan (Objective 2). Hickory diversity in the germplasm repository was expanded through targeted seed collections. More than 6,000 trees (comprised of pecan breeding lines, native pecans, and hickories) were genotyped by a modern genetic approach (targeted sequencing panel) comprised of 3,100 genetic sites spread across all 16 pecan chromosomes; this work is foundational to future genomic selection analyses (Objective 2). Three years of nut collections in an 'Elliott' x 'VC1-68' pecan mapping population were measured, imaged, cracked, and processed for ongoing analysis by a molecular approach known as Quantitative Trait Loci (QTL) analysis (Objective 3). Three years of tree height and diameter measurements, taken through traditional and computational methods, were analyzed for a young 'USDA-ARS Lakota' x 87-MX-3-2.11 pecan mapping population (Objective 3). Work in the breeding program resulted in seven new controlled crosses (hundreds of seedlings expected), destructive nut quality analysis of over 9,000 pecans, detailed flowering timing for breeding selections at the final stage of evaluation, and documentation of traits required for patenting (Objective 4). The effects of 12 different rootstock families on the growth and physiological characteristics of the 'USDA-ARS-Pawnee' scion were established; there were significant increases of tree height and stem diameter for southern origin rootstocks, and delays in the timing of spring leaf burst that correlate with northern-origin rootstocks (Objective 4). Project work as a whole during FY 2025 resulted in major progress towards refining pecan research and breeding methods to facilitate accelerated development of pecan cultivars for productive and profitable use by farmers across the United States.
Accomplishments
1. Rootstock effects on pecan performance. A critical factor influencing pecan production is rootstock selection. Rootstock choice can affect tree growth, physiology, and overall orchard performance of the grafted cultivar. The effects of rootstocks from different geographic locations have been widely tested in other nut tree crops, but have not been thoroughly tested in pecan. ARS researchers at College Station, Texas, established the impact of 12 different rootstocks on the growth and physiological characteristics of the 'USDA-ARS-Pawnee' pecan over multiple years to provide insights into optimal rootstock choices for pecan orchards. Significant increases in 'USDA-ARS-Pawnee' tree height and stem diameter were observed for southern origin rootstocks, while delays in the timing of spring leaf burst were seen in 'USDA-ARS-Pawnee' that was grafted to northern-origin rootstocks. This work provides much needed guidance to nurseries and producers in choosing the most appropriate pecan rootstocks to ensure that their pecan types will be most productive in their specific growing region and under their specific and sometimes unique environmental conditions.
2. Improved approaches to measurement of pecan tree growth. Manual and computational methods of measuring tree growth traits have been used in tree breeding; however, the comparative accuracy of these methods has not been properly measured. ARS researchers at College Station, Texas, developed a three-year dataset (2022-2025) comparing traditional and computational tools for measuring tree height and trunk diameter in a young orchard planted in 2020. Manual measurement tools were most accurate with smaller trees but showed increasing error rates with taller trees and with larger trunk size. Image measurements made by handheld cameras were more accurate than those done by traditional tools/methods, and were also easier to collect and analyze. Images taken via drones were promising but will require optimization. This work identified improved approaches/protocols for assessing pecan tree growth that are simple, accurate, more user-friendly, and that will be of significant benefit to ongoing pecan research/breeding work to improve the crop for U.S. farmers.
3. DNA sequencing array to enhance pecan breeding. Modern plant breeding methods require DNA sequence information in addition to field measurements to increase accuracy and speed of the breeding cycle. Genetic information has not historically been collected within the USDA pecan breeding program, leaving thousands of trees without sufficient information to use modern genetic approaches for pecan improvement. ARS researchers at College Station, Texas, working with cooperators at Breeding Insight, a USDA-ARS/Cornell University partnership focused on improved breeding efficiency of U.S. “specialty” crops including pecan, successfully addressed this challenge. The work developed a panel of 3,100 genetic sites distributed across the pecan genome that can be sequenced in an efficient and cost-effective manner. This sequencing array has been deployed on pecan trees across the breeding program, and includes parental lines from the project managed germplasm repository. This accomplishment establishes a very solid foundation for more efficient and more timely development of new and improved pecan types for productive use by U.S. producers.
Review Publications
Wang, X., Kubenka, K.A., Hilton, A.E., Chatwin, W.B., Cox, T.M., Tondre, B.S. 2025. The effects of freezing and stratification on pecan (Carya illinoinensis) seed germination and seedling growth. Technology in Horticulture. 5. Article e002. https://doi.org/10.48130/tihort-0024-0030.
Ren, W., Zhang, L., Maness, N., Wang, X., Tang, M., Xu, T. 2024. Changes in the diversity of pecan (Carya illinoinensis) rhizosphere microbial community with different nitrogen fertilization, a case study in Oklahoma pecan orchard. Scientia Horticulturae. 321. Article e112365. https://doi.org/10.1016/j.scienta.2023.112365.
Wang, X., Kubenka, K.A., Hilton, A.E., Chatwin, W.B., Pisani, C., Bock, C.H., Heerema, R., Randall, J., Tondre, B.S. 2025. Effect of twelve rootstocks on the scion 'Pawnee' in a 10-year-old orchard. Acta horticulturae. 1420:55-62. https://doi.org/10.17660/ActaHortic.2025.1420.8.
Ren, W., Zhang, L., Tondre, B.S., Wang, X., Xu, T. 2024. The rootstock genotype shapes the diversity of pecan (Carya illinoensis) rhizosphere microbial community. Frontiers in Microbiology. 15. https://doi.org/10.3389/fmicb.2024.1461685.
Poletto, T., Poletto, I., De Carvalloh Marques, C.E., De Sousa Silva, A.K., Kubenka, K.A., Chatwin, W.B., Gailing, O., Stefenon, V.M. 2024. CertiBase: a genetic database for cultivars certification and genetic breeding of pecan in Brazil. Crop Breeding and Applied Biotechnology. 24(3). Article e493924310.
Hilton, A.E., Bock, C.H., Brenneman, T., Chatwin, W.B., Chen, J. 2025. Whole genome resource for Xylella fastidiosa subsp. multiplex strain GaT2 causing pecan bacterial leaf scorch in Georgia, United States. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-09-24-0103-A.