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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

2019 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
In FY 2019, significant progress was made in defining the genetic make-up of pecan which will greatly support work by project scientists and others in developing new and improved pecan varieties for U.S. farmers. Under Objective 1, advances were made in sequencing the pecan genome; most of this work is being done with knowledgeable cooperators who have the state-of-the art instrumentation and bioinformatics expertise to apply to the project. Also under Objective 1, work with the pecan type, Elliott X VC-168, provided genetic information that is facilitating the ongoing work to "map" the genetic traits in pecan to facilitate breeding efforts. Progress was made in gaining a fuller understanding of how pecan scab disease interacts with pecan. Work with a Lakota pecan cross on scab disease and also on the surface blotch miner, and black pecan aphid, gave valuable new insights into how this disease, and these insects affect pecan; there were significant differences observed even among sibling trees indicating genetic variation (Objective 1). In continuation of multi-year research, on-site pecan seedlings were measured for tree height and trunk diameter in early spring; these same seedlings were rated for inception of bud growth at the same time (Objective 2). Tissue collections were made from a panel of pecan cultivars for measurements of genetic diversity by modern molecular techniques. Work in FY 2019 with pecan rootstocks showed that rootstock can affect water usage by the above-ground portions of the pecan tree (Objective 2). Major progress was made in work to develop spatial maps of key pecan orchards used in project research (Objective 4). The work involves use of sophisticated software and photography and involves not only accurate definition of geographic location of given trees, but also seeks to facilitate information on plant health and other factors associated with living trees that may be relevant in enhancing pecan tree productivity. Also under Objective 4, pecan nut samples from appropriate germplasm types were analyzed for appropriate size, color, and quality factors; the data obtained were added to the master data base on nut parameters/quality maintained by the project.

1. The genome sequence of pecan. Pecan improvement has lagged behind other major crops because of the lack of genomic and genetic resources. ARS scientists at College Station, Texas, working with collaborators at a number of outside institutions, developed the first reference genome for pecan. The work focused on the prominent cultivar 'Pawnee', was developed in conjunction with a reference genome for the Chinese hickory, Carya cathayensis, and was made available for public use. As a genetic resource, the genome sequence will allow the identification of important genes that control life-history and productivity/quality traits in pecan. It will provide the structural basis for genetic mapping and association of genetic locations of important traits. This accomplishment represents a major milestone in the development of pecan genetic resources.

Review Publications
Huang, Y., Xiao, L., Zhang, Z., Zhang, R., Wang, Z., Huang, C., Huang, R., Luan, Y., Fan, T., Wang, J., Shen, C., Zhang, S., Wang, X., Randall, J., Zheng, B., Wu, J., Zhang, Q., Xia, G., Xu, C., Chen, M., Zhang, L., Jiang, W., Gao, L., Chen, Z., Leslie, C.A., Grauke, L.J., Huang, J. 2019. The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. Gigascience. 8(5):giz036.