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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

2018 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
This is a new project that replaced 3091-21000-035-00D and which is continuing and expanding upon the work of the precursor project. Work under this new project in FY 2018 largely addressed FY 2019 milestones relevant to Objective 1. Seed from controlled crosses ('Lakota' X 87MX3-2.11), collected earlier, was measured using the standard methods of the breeding program and planted in FY 2018 in the ARS greenhouse at the Brownwood, Texas, worksite. Date of seed germination was subsequently monitored and diameters and heights measured. Immature leaf tissue was collected in duplicate from over 1,000 controlled cross seedlings, placed in DNA extraction tubes, and immediately quenched in liquid nitrogen using revised methods developed in previous research. One complete set of these samples is in archival, -80C storage, and the other is being processed by cooperators in order to use microsatellite markers to confirm parentage. After tissue sampling in Brownwood, all seedlings were transported to the ARS Somerville worksite where they were deployed in a randomized test under an outdoor, overhead irrigation system established to induce an epidemic of pecan scab (Venturia effusum). Seedlings were rated for scab disease expression in late FY 2018.