Location: Crop Germplasm Research
2024 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 under this project during FY 2024 resulted in significant progress in pecan research facility improvement and in pecan disease research. New facilities for pecan research were completed and a ribbon-cutting ceremony was well attended by stakeholders, industry representatives, and ARS administrators. The new facility enables cutting-edge molecular and pathology research to be conducted adjacent to the orchard containing the National Clonal Repository of Carya (hickory and pecan). This proximity will facilitate project research and breeding work to address stakeholders needs. Pecan scab is the most economically important disease facing the industry; typically, management costs for the disease represent between 10-15% of annual management costs for a pecan orchard. Failure to effectively manage scab can result in complete crop loss. The best method to prevent these losses is through scab resistant germplasm; breeding resistant cultivars requires quantifiable and reproducible methodology. Up until this year, the severity of pecan leaf scab was scored on a scale of 1 to 5. Work under objectives 1 and 4 showed that breeders can reference a new visual guide to increase their accuracy and precision in performing disease ratings. This work confirmed that the new method will be instrumental for breeding resistance to pecan foliar diseases. Bacterial leaf scorch is a foliar disease caused by a resident bacterium, Xylella fastidiosa, of the pecan microbiome. This bacterium is widespread among the trees in the Repository. While a relatively minor disease for pecan, it can cause major epidemics for other trees including olive. The presence of Xylella inside pecan tissues limits the Repository's ability to share graftwood with other locations, particularly to regions where Xylella has not been found. Despite its importance, no genome sequence has existed for the strain that affects pecan. Project work under Objectives 1 and 3 assembled the first genome specific to the Xylella affecting pecan. The complete genome sequence will enable robust detection and discrimination of various strains of Xylella, and will be a significant contribution to manage the disease in pecan orchards and in the germplasm repository. Work under Objective 2 was effective in assuring ongoing integrity, maintenance, and health of critical germplasm resources, and in maintaining overall orchard health and vigor. Germplasm distribution to outside users was minimal given the limitations imposed by Xylella.
Accomplishments
1. Improved validation of leaf scab disease in pecan. Historical plant disease ratings in the pecan breeding program relied on broad estimates of disease severity (highly susceptible, moderate, resistant, etc.). Modern analysis methods using genetics to speed up breeding require more precise evaluations. ARS researchers at College Station, Texas, developed a new computer-driven rating system (Standard Area Diagram). This new system is a series of leaf images with increasing amounts of disease. Validation of this new technique established that breeders can reference these visual guides to increase accuracy and precision in performing disease ratings. These methods are being applied to other important pecan diseases, including pecan bacterial leaf scorch, and are already facilitating ongoing breeding work to develop new pecan cultivars for productive use by U.S. pecan producers.
2. New pecan genetics and plant disease laboratory. In FY 2021, a $2.5M construction project began to renovate and expand research facilities of the ARS pecan research/orchard complex at College Station, Texas. The renovation included dedicated spaces for plant disease research, controlled growth chambers, equipment for chemical storage and sterilization, and other needed capabilities. Project scientists are already using the new facilities to enhance ongoing research; effects on project pathology work have been transformative. The improvement will greatly facilitate all aspects of project work well into the future.
3. The pecan bacterial leaf scorch genome. Bacterial leaf scorch can have significant impact on pecan production. While symptoms are sporadic and not consistent from year to year, severe infections can cause canopy loss and potential tree death. Despite its importance, no genome sequence exists for the strain(s) of the Xylella fastidiosa bacterium that causes pecan bacterial leaf scorch. The bacteria requires a living tree to survive and is difficult to grow in the lab. ARS researchers at College Station, Texas, used a method that sequences DNA from the whole community of microbes living in a pecan tree, including the leaf scorch bacterium. Using known DNA sequences from Xylella that infect other tree species, the researchers assembled the complete genome sequence of this important bacterial strain that infects pecan. This accomplishment is foundational to ongoing project work to define the interactions of Xylella with living pecan trees and in developing effective management strategies.
Review Publications
Yusufali, Z., Liu, X., Wang, X., Kubenka, K.A., Du, X. 2023. Texture properties, crude fat, fatty acid profiles, total soluble solids, and total polyphenols for 21 pecan varieties and the effects of harvest year. ACS Food Science and Technology. https://doi.org/10.1021/acsfoodscitech.3c00216.
Hilton, A.E., Bock, C.H., Wang, X., Jo, Y., Conner, P., Randall, J., Chatwin, W.B. 2024. Standard area diagrams for pecan leaf scab: Effect of rater experience and location, and leaf size on reliability and accuracy of visual estimates. Plant Disease. 108:1820-1832. https://doi.org/10.1094/PDIS-09-23-1947-RE.