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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

2020 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
Significant progress was made in fiscal year 2020 on defining the genetic make-up of pecan so as to facilitate improvement of the crop for U.S. farmers. Under Objective 1, four pecan types (87MX3-2.11, 'Lakota', 'Pawnee', and 'Elliott') were sequenced and the gene annotations have been completed. Leaf samples of a panel of 500 different pecan types were collected and re-sequenced. A linkage map of the controlled cross between 'Elliott' x VC1-68 was constructed. Genetic tools known as quantitative trait loci (QTL) of phenotypic traits were located on this linkage map. Also under Objective 1, more than 1,000 seedlings of a selected population were dug and 482 were transplanted in the nursery at the College Station, Texas, worksite in January 2020. Another set of 482 seedlings were shipped to ARS collaborators in Bryon, Georgia, in February 2020. Before digging the seedlings, trunk diameter, plant height, and infestation levels by a fungal pathogen (Venturia effuse), the upper surface blotch miner (Cameraria caryaefoliella Clemens), and the black pecan aphid (Melanocallis caryaefoliae Davis) were measured. Also under Objective 1, seasonal collections were made from a panel of cultivars representing genetic diversity, and were saved for subsequent RNA extraction and re-sequencing. The RNA samples were sequenced and the datasets are currently being analyzed. Under Objective 2, active season tree positions were determined by unmanned-autonomous vehicle (UAV) images and were added to our georeferenced database. Descriptors are being developed for tree form. Under Objective 3, pollen was collected and deposited at the Fort Collins, Colorado, facility for preservation of genetic diversity of pecan. Under Objective 4, a local database of pecan breeding information was developed. This database interfaces with other databases (Botanical Garden (BG)-Base, Germplasm Resource Information Network (GRIN)-Global, and a genomic database developed by New Mexico State University). A prototype that links relational and image data to spatial maps was developed. Handheld data recording devices were acquired, and a method for collection by handheld units was developed to facilitate importation of data to a Structured Query Language (SQL) database. In addition, Bluetooth enabled measuring devices (digital calipers, etc.) were used to interface with the handheld units for improved accuracy and efficiency. Project work overall in fiscal year 2020 added significantly to the knowledge base on pecan genetics that is relevant to breeding better pecans for U.S. producers and consumers.

1. The nuclear genome sequence of pecan. Understanding the detailed genetic make-up of pecan is critical to advancing the crop by breeding. ARS researchers at College Station, Texas, sequenced the whole genomes of the pecan cultivars, 87MX3-2.11, 'Lakota', 'Elliott', and 'Pawnee', including identification of critical genes. This accomplishment is a major advancement because the genome sequence provides the genetic blueprint of gene location and function, establishing foundational information to support pecan genetic research and breeding efforts for many years to come.

2. The chloroplast genome sequence of pecan. In addition to the nuclear genome, plants also have a chloroplast genome. It is a small, extra-nuclear genome that is critical for photosynthesis and which is generally passed from the mother to the offspring. Because of the unique inheritance pattern, chloroplast genomes can be used to trace maternal origin over many generations. ARS researchers at College Station, Texas, established the chloroplast genome sequences from two different pecan populations. This accomplishment is critical in future work to establish the origin of pecan in North America, to define evolution of the species, and to guide ongoing efforts at pecan improvement.

3. Pecan genes controlling budbreak and pecan scab. Understanding the detailed genetic control of important characteristics and traits in pecan is critical to advancing the crop and protecting it from destructive pests and diseases. ARS researchers at College Station, Texas, identified specific genes that control budbreak in pecan and also susceptibility to scab, a very destructive pecan disease. The work which focused on budbreak identified a gene that is significantly responsible for variation observed in the timing of budbreak in the spring. A gene controlling scab susceptibility was also identified. This accomplishment begins the process of definitively characterizing the genomic make-up of pecan which, as the work progresses, will greatly accelerate pecan improvement through much more tightly focused breeding efforts.

Review Publications
Cao, F., Wei, Y., Wang, X., Li, Y., Peng, F. 2019. A study of the evaluation of the pecan drought resistance of grafted 'Pawnee' trees from different seedling rootstocks. HortScience. 54(12):2139-2145.
Wang, X., Rhein, H., Jenkins, J., Schmutz, J., Grimwood, J., Grauke, L.J., Randall, J. 2020. Chloroplast genome sequences of Carya illinoinensis from two distinct geographic populations. Tree Genetics and Genomes. 16:48.
Cao, F., Wang, X., Liu, Z., Li, Y., Peng, F. 2019. Differential protein analysis of pecan hardwood cuttings. HortScience. 54(9):1551-1557.