Location: Crop Germplasm Research
2023 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
This is a new project which replaced 3091-21000-039-000D and which is continuing and expanding upon the work of the precursor project. Work by this project in FY 2023 resulted in substantial progress on improving phenotype (observable physical traits) ratings, repository management, quantifying rootstock effects on scion (tree) growth, and compiling historical phenotypic data to detect molecular trait associations for use in pecan breeding. A newly developed Standard Area Diagram (SAD) improved all measures of agreement, accuracy, precision, and bias among 37 evaluators with various experience levels; these cooperating scientists/evalulators were from Texas, Georgia, and New Mexico (Objective 1). The presence of the bacterial pathogen, Xylella fastidiosa, was assessed in pecan seeds, roots, and throughout the canopy during the growing season. About 4% of seedlings tested positive for the bacterium and transmission rates were relatively stable across all seedstocks; further testing is ongoing (Objective 1). Tree removal and thinning of disqualified seedling plantings from the breeding program is underway to prepare land for the establishment of new replicated breeding evaluations (Objective 2). Analysis to determine species identity of wild-origin Carya (the pecan and hickory Genus) from the accredited Carya collection at the Arnold Arboretum at Harvard University is underway using an existing bioinformatic pipeline (Objective 2). Cryopreserved pollen was used to make successful crosses that will be evaluated in FY 2024 (Objective 2). Phenotype collections in both biparental mapping populations were successfully completed and were used to validate image analysis methods to obtain higher accuracy (Objective 3). A genome-wide association study (GWAS) of ~700 repository cultivars was conducted, and historical phenotypic data for bud break, scab ratings, and 16 seed quality traits was shown to have too much missing historical data to be properly analyzed. Appropriate statistical methods for rescuing and combining scab data are being evaluated (Objective 3). First- and second-year shoots of three pecan lines with different alternate bearing habits were collected and, in collaboration with academic colleagues, are undergoing analysis for carbohydrate and sugar levels. Crosses to construct a multi-parent mapping population were conducted; these consisted of 100 full siblings from 6 crosses that represent the phenotypic diversity under active selection in our breeding program (Objective 3). Preliminary project work in FY 2023 also established that the geographic origin of seedstocks/rootstocks influences tree growth, architecture, and the nutrient content of the scion leaves (Objective 4).
Accomplishments
1. Improved methodology to assess pecan growth and vigor. Ongoing efforts to improve pecan performance and productivity must rely on accurate methodology to define and monitor growth characteristics that are critical in developing improved cultivars. Historical field methods for characterizing important traits such as tree height, trunk diameter, canopy width, and total leaf area were done manually and required significant commitment of time and personnel. ARS researchers at College Station, Texas, utilized a modern software program (ImageJ) to measure appropriate parameters and process the large datasets quickly and accurately. ImageJ was fully comparable to traditional methods but was much more efficient. This software will greatly facilitate ongoing project work focused on developing new pecan types for productive use by U.S. farmers.
