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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

2021 Annual Report

OBJECTIVE 1: 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. Subobjective 1A: Complete four reference genomes for pecan (87MX3-2.11, 'Pawnee', 'Lakota', 'Elliott'), including sequence of the organelles (chloroplasts and mitochondria). Subobjective 1B: Develop and establish multiple mapping populations, phenotypically monitor and sequence progeny, and produce dense, high-resolution linkage maps. Subobjective 1C: Develop transcriptome sequences representing multiple tissues (dormant buds, male and female flowers, leaves and roots) of inventories of the four reference genomes. OBJECTIVE 2: Assisted by genomic information, develop more effective and efficient evaluation and selection methods for priority pecan horticultural traits (e.g., tree architecture), and apply them at diverse trial sites to select superior genotypes for pecan scion and rootstock breeding stocks. OBJECTIVE 3: 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. OBJECTIVE 4: Develop and implement a new pecan genome database that links and delivers key genomic, phenotypic, and descriptive information to pecan researchers, breeders, and producers. Record and disseminate evaluation and characterization data via that new database, GRIN-Global, and other data sources.

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) 2021 resulted in significant progress in exploiting available pecan genetic resources to develop improved pecan cultivars for U.S. producers. In work under Objective 1, seedlings of the "Lakota" x 87MX3-2.11 mapping orchard (a large population of sibling trees used to identify genetic mechanisms responsible for physical characteristics) were managed and monitored for diameter, height, and bud break during the winter and spring seasons. Multiple disease and insect susceptibilities were rated in this orchard to compare the accuracy and consistency of different rating scales. Under Objective 2, unmanned aerial vehicle drone flights over selected project orchards provided valuable photographic data of tree health and vigor. The images are being analyzed and the process for image analysis is being refined. In work under Objective 3, the leaves of four replicate trees of 1997-34-0017 (one of our upcoming cultivar releases) from Brownwood, Texas, were collected and genetically analyzed for pecan scab (a disease that severely affects pecan nut yields). Significant progress was made in the development of a database to house historical and modern data collections under Objective 4. 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 along with photos, historical documents, and links to relevant journal articles.

1. Sequencing the pecan genome. Traditional breeding efforts in pecan can take many decades because of its long juvenile period and tendency to alternate years of heavy and light nut crops. ARS researchers at College Station, Texas, working with university and industry cooperators, sequenced the genomes of four different pecan genetic types that are representative of the genetic diversity of cultivated pecan. One (Pawnee) was analyzed in sufficient detail to identify the regions of its genome that were inherited from each parent. This research, published in one of the world's most prestigious international journals, is a foundational accomplishment. It, along with projected future advancements in defining the pecan genome, will guide project efforts in the years to come toward developing better pecan cultivars, at an accelerated pace, for productive use by U.S. farmers.

2. User-friendly pecan database for researchers and producers. User-friendly pecan database for researchers and producers. The USDA pecan research program, centered in Texas, dates back almost 100 years. During that time, a wealth of valuable and irreplaceable research data has been generated; however, this important information has never been assembled into a single, widely accessible and user friendly source. ARS researchers at College Station, Texas, working with university cooperators and funded by the USDA Specialty Crops Research Initiative, developed a comprehensive database that will capture essentially all the important historical data on pecan development, as well as more contemporary information. This database will be updatable as new information is developed and will become an exceedingly valuable resource for pecan breeders and researchers, and also producers, extension personnel, etc., because it will contain photos, and other critical information that will be of practical value in making pecan orchard management decisions.

Review Publications
Bentley, N., Grauke, L.J., Ruhlman, E., Klein, R.R., Kubenka, K.A., Wang, X., Klein, P. 2020. Linkage mapping and QTL analysis of pecan (Carya illinoinensis) full-siblings using genotyping-by-sequencing. Tree Genetics and Genomes. 16. Article 83.
Hilton, A., Jeong, M., Hsu, J., Cao, F., Choi, W., Wang, X., Yu, C., Jo, Y. 2021. Thermal treatment using microwave radiation for the phytosanitation of Xylella fastidiosa in pecan graftwood. PLoS ONE. 16(1). Article e0244758.