Location: Crop Germplasm Research
2023 Annual Report
Objectives
Objective 1: Efficiently and effectively acquire Carya genetic resources; maintain their safety, genetic integrity, health and viability; and distribute them and associated information worldwide. [NP301, C2, PS2A]
Objective 2: Complete the sequencing and assembly of the pecan reference genome, and apply genomic information from it, from mapping populations, and from diverse pecan genotypes and phenotypes to map and characterize the genetic bases for key pecan horticultural traits. [NP301, C1, PS1A]
Objective 3: Develop and implement new pecan data management systems that link and deliver key genotypic, phenotypic, and descriptive information to pecan researchers, breeders, and producers. Record and disseminate evaluation and characterization data via GRIN-Global and other data sources. [NP301, C4, PS4A]
Objective 4: Assisted by genomic information, develop more effective and efficient evaluation, characterization, and selection methods for priority pecan horticultural traits (e.g., tree architecture), and apply them to priority Carya genetic resources as well as diverse trial sites to select superior genotypes for pecan scion and rootstock breeding stocks. [NP301, C1, PS1A]
Objective 5: Guided by new genomic and trait evaluation data, breed and release superior pecan scion and rootstock cultivars that produce trees with reduced size, excellent nut quality and yield, tolerance to environmental extremes, and resistance to disease and pests. [NP301, C1, PS1B]
Approach
The primary goal of this project is to increase pecan production through the development of improved cultivars and rootstocks. This is a sister project to "Management of the National Collection of Carya Genetic Resources and Associated Information" (3091-21000-042-00D) and benefits from observations made on range-wide provenance collections maintained in that effort, as well as from verified inventories of parent cultivars to generate controlled crosses. Objectives will be achieved through coordinated research in cooperation with national and international researchers working with pecan and hickory to improve genomic tools and refine the methods of phenotypically selecting improved scion cultivars and regionally adapted rootstocks. This project works in cooperation with national nursery and nut crop producers to ensure improved regional performance of introduced materials. These improvements will be accomplished through improved phenotypic selection techniques, supplemented with molecular tools to develop and release pecan scion cultivars producing high nut yield and quality on trees of reduced size, and possessing regionally appropriate levels of disease and insect resistance. Similar approaches will be used to select regionally adapted pecan seedstocks with improved vigor, uniformity, salt tolerance, disease and insect resistance, and specific geographical adaptation which will ultimately contribute to increased yields of grafted scions. Qualitative and quantitative techniques, in conjunction with molecular techniques, will be used to elucidate the genetic control of certain key horticultural traits. This project will fill key knowledge gaps regarding the genetic control of pecan flowering (that impacts alternate bearing), disease resistance, seasonal phenology, tree size, and nut quality.
Progress Report
Project work in FY 2023 included assessment of nut maturation and performance of nut harvest for various research blocks and projects (Objective 1). The collections of seed from controlled crosses included nine cultivars in the germplasm repository with confirmed infections of Xylella fastidiosa, a potentially serious pecan disease organism. The infected samples were from the 'Elliott' x 'VC1-68' bi-parental mapping population, and from the breeding lines and controls in the grafted replicated test (stage IV) of our breeding program. Harvested seed from the controlled crosses and repository cultivars were stratified and prepared for planting (Objective 1, 5). Seed from the breeding program and mapping population were processed and prepared for analysis of nut quality traits and yield (Objective 4, 5). DNA extraction and low-coverage sequencing were also completed from leaf tissue of wild-origin Carya (the pecan and hickory Genus) obtained from the accredited Carya collection at The Arnold Arboretum at Harvard University (Objective 1). Repository management was improved by the attachment of permanent tree labels to hundreds of trees in the breeding blocks and germplasm repository (Objective 1). All data obtained were archived into our central pecan database and cloud drives (Objective 3). During the life of this project, major accomplishments in pecan germplasm enhancement and breeding were made; all key milestones were met. The multi-institution collaboration published four high-quality nuclear pecan genome sequences and two chloroplast genome sequences. Additionally, the development of diagnostic methods for Xylella fastidiosa in Carya and documentation of seed transmission were achieved and will be critical to effective disease management and exploitation of Carya germplasm worldwide. A large full-sibling mapping population of 'Lakota' x 87MX3-2.11 was created, parentage was genetically established or confirmed, and the accessions within the population were planted in three environments (College Station, Texas; Byron and Tifton, Georgia). Over the next decade, this population will be critical in identifying genetic mechanisms for physical characteristics. A centralized database was established to house the decades of phenotypic (observable physical traits), photographic, and genotypic data accumulated over the lifetime of this project. Three pecan cultivars, 'Pueblo', 'Seneca', and 'Zuni', were released and patented at the request of stakeholders, marking the first time pecan cultivars developed by the USDA have been patented. This project expired in FY 2023 and was replaced by 3091-21000-046-000D, which is continuing and expanding upon the work.
Accomplishments
1. Pecan rootstocks to improve pecan growth and vigor. Pecan is one of the most important nut crops in the U.S. Open-pollinated seedling rootstocks (seedstocks) are commonly used throughout the pecan industry, but the effects of rootstocks on scion performance have not been properly studied. Scion is generally defined as the improved pecan germplasm that is grafted to the rootstock at or somewhat above ground level. To establish the effects of different rootstocks on growth and development of the 'Pawnee' scion, ARS researchers at College Station, Texas, conducted experiments using progeny generated by mother trees from different geographical regions. Data were collected over a three-year period, focusing on various growth parameters of ten-year-old 'Pawnee'-grafted trees. The results indicated that seedstock families from southern areas showed better performance growth, with Mexican seedstocks significantly increasing scion height, trunk diameter, and canopy width. Conversely, the northern seedstocks showed significantly delayed budbreak time. These results clearly demonstrate that seedstock choice can affect long-term orchard productivity, and emphasize the importance of choosing a proper seedstock for appropriate regions. This accomplishment is important to the pecan production industry in its ongoing efforts to improve pecan productivity and profitability.
Review Publications
Wang, X., Chatwin, W.B., Kubenka, K.A., Hilton, A.E., Thompson, T., Grauke, L. 2022. 'Zuni' pecan: A cultivar of large nuts for the central and western growing regions. HortScience. https://doi.org/10.21273/HORTSCI16827-22.
Pham, T., Yusufali, Z., Wang, X., Kubenka, K.A., Du, X. 2023. Impact of room temperature storage on the pecan kernel color, carotenoids, polyphenols, and physicochemical properties. ACS Food Science and Technology. 3(6):1077-1089. https://doi.org/10.1021/acsfoodscitech.3c00087.
Wang, X., Chatwin, W.B., Kubenka, K.A., Hilton, A.E., Thompson, T., Grauke, L. 2022. 'Seneca' pecan: A compact cultivar for the northern region. HortScience. 57(11):1490-1493. https://doi.org/10.21273/HORTSCI16825-22.
Xi, J., Lv, S., Zhang, W., Zhang, J., Wang, K., Guo, H., Hu, J., Yang, Y., Wang, J., Xia, G., Fan, G., Wang, X., Xiao, L. 2022. Comparative plastomes of the critically endangered Carya poilanei and other Carya species provide new insights into the maternal relationship and phylogeny of the genus. Frontiers in Plant Science. 13. Article 990064. https://doi.org/10.3389/fpls.2022.
Ren, W., Zhang, L., Maness, N., Wang, X., Tang, M., Xu, T. 2023. 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 112365. https://doi.org/10.1016/j.scienta.2023.112365.
