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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #434151

Research Project: Pecan Breeding, Genomics, and Genetic Resource Management

Location: Crop Germplasm Research

2022 Annual Report

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]

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
Work by this project in fiscal year (FY) 2022 resulted in the release of new pecan varieties, the continued consolidation of historical records, and improvements to detecting and analyzing pecan diseases. In work under Objective 1, a panel of 17 genetic markers was published that can be used to distinguish between different hickory (Carya) species. In addition, the bacteria causing Pecan Bacterial Leaf Scorch (PBLS) was shown to be transmissible from the seed to germinated seedlings. This research has trade implications for pecan seed used for growing new rootstock trees but has no effects on pecans used for human consumption. Under Objective 2, seedlings of the ‘Lakota’ x 87MX3-2.11 mapping population orchard were managed and monitored for diameter, height, and bud break during the winter and spring seasons. Significant progress was made in Objective 3 work which continued the development of a database housing historical and modern records of pecan breeding, evaluation, and genetics. Multiple decades of phenotypic data, including disease, insect pest, budbreak, nut quality, and flowering records for both the Somerville and Brownwood worksites, were added to the database. The development of improved rating scales for characterizing priority pecan horticultural traits, specifically disease resistance, allowed project scientists to develop a protocol to assess leaf disease severity through image processing, a foundational step in high-throughput leaf disease analyses. Pecan breeding efforts under Objective 5 resulted in the patenting and release of three new pecan scion cultivars with good disease resistance and excellent nut quality suitable for multiple growing regions.

1. Three new patented pecan scion varieties. Pecan breeding is a long-term process that generally takes decades from initiation of breeding, through trials and evaluation, to release of a named new cultivar to growers. This is partly due to the long juvenile period pecan has before nut production, in addition to the rigorous testing required to qualify a breeding line for release as a new scion cultivar. ARS researchers at College Station, Texas, qualified and released three new scion cultivars with good to excellent leaf and nut scab disease resistance and excellent nut quality. These new cultivars are protected by plant patents, which were pursued at the recommendation of our stakeholders. The new cultivars (Pueblo, Seneca, Zuni) represent valuable new resources for commercial production of high-quality disease-resistant pecans by U.S. growers.

2. Seed transmission of Xylella fastidiosa in pecan. X. fastidiosa (XF) is a pathogenic, xylem-limited bacterium known to colonize and infect pecan with or without the expression of Pecan Bacterial Leaf Scorch (PBLS) disease symptoms. XF can be transmitted by xylem-feeding insects, including pecan spittlebug and sharpshooters, and through the grafting of clonal scions onto genetically diverse rootstocks. ARS researchers at College Station, Texas, in collaboration with researchers at New Mexico State University, discovered that XF can also be transmitted from pecan seed to seedling progeny. This research has trade implications for pecan seed used for growing new rootstock trees, but has no effects on pecan nuts used for human consumption. Continued research is being performed to better understand the seasonal patterns of XF in pecan and to develop mitigation strategies.

Review Publications
Randall, J., Cervantes, K., Ray, D.K., Sanchez, A., Mason, K., Fisk, J.N., Soneji, J.R., Sanchez, L., Grauke, L.J., Wang, X. 2021. Insights into the impact of geography and genetics on the microbiome of Carya illinoinensis. Acta Horticulturae. 1318:235-240.
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.
Wang, X., Kubenka, K.A., Chatwin, W.B., Thompson, T., Grauke, L. 2022. 'Pueblo' pecan: a compact cultivar for the western and central growing regions. HortScience. 57:7.
Wang, X., Chatwin, W.B., Hilton, A.E., Kubenka, K.A. 2022. Genetic diversity revealed by microsatellites in genus Carya. Forests. 13. Article 188.