Location: Crop Germplasm Research2012 Annual Report
1a. Objectives (from AD-416):
Objective 1: Strategically expand and improve collections of priority Carya genetic resources and associated information. Sub-objective 1.A: Survey existing U.S. domestic collections of Carya, identify material that would fill gaps in NPGS collections, and begin strategically acquiring and characterizing them. The initial priority is to collect Carya myristiciformis (nutmeg hickory) across its range. Sub-objective 1.B: In cooperation with Federal agency collaborators, state Conservation Reserve Programs, Nature Conservancy and Heritage Programs, and private landowners, designate appropriate in situ reserves and establish additional regional Carya plantings. Objective 2: Conserve and propagate Carya genetic resources efficiently and effectively, and distribute disease-free samples and associated information worldwide. Sub-objective 2.A: With ARS collaborators, develop and apply more efficient and effective strategies for conserving the genetic integrity of Carya genetic resources. Sub-objective 2.B: Optimally maintain orchard plantations of grafted cultivar accessions at Somerville (near College Station), Texas, with duplicate plantings at Brownwood, Texas, and distribute seeds and/or cuttings to requestors. Objective 3: As resources permit, strategically genotype and phenotype Carya genetic resources for priority genetic and horticultural traits. Sub-objective 3.A: Incorporate existing characterization data for Carya into GRIN and/or other databases. Sub-objective 3.B: Incorporate existing horticultural evaluation data for Carya into GRIN and/or other databases. Sub-objective 3.C: Extend ongoing cooperative research to assess the relationship between genetic diversity and geographical distribution in Carya via molecular marker assays, and incorporate genotypic data into GRIN and/or other databases.
1b. Approach (from AD-416):
Efforts to strategically expand and improve collections of Carya genetic resources and associated information will give initial priority to collecting Carya myristiciformis (nutmeg hickory) across its range (Objective 1). Information on the distribution of nutmeg hickory will be obtained from a variety of sources, including published accounts, herbarium voucher information, USDA Forest Service Forest Inventory records, State Conservancy and Heritage programs, and personal information. When possible, seeds, graftwood, and collection records will be obtained from local cooperators. Collection trips will be conducted to targeted locations when needed. Attempts will be made in cooperation with Federal agency collaborators, State Conservation Reserve Programs, Nature Conservancy and Heritage Programs, and private landowners, to designate appropriate in situ reserves. C. floridana (scrub hickory) is the most geographically restricted hickory species in the U.S., and it will serve as a model for rational development of in situ conservation in other species. Samples will be collected from the known range of the species, characterized using available molecular tools, and data will be analyzed for patterns of genetic isolation. Implications for resource management will be interpreted and translated into guidelines for designating functional in situ reserves. Efforts to develop more efficient and effective strategies for conserving the genetic integrity of Carya genetic resources (Objective 2) will involve cooperative efforts to determine feasibility of adapting recalcitrant seed cryopreservation protocols for use in Carya. Work will involve developing protocols for harvesting, handling, shipping, viability testing and storage of pecan pollen, and cryopreservation protocols for dormant buds. To strategically genotype and phenotype Carya genetic resources for priority genetic and horticultural traits (Objective 3), there is a need to develop a relational database with capabilities for efficient management of the spatial descriptors related to original collections, spatial descriptors of repository inventories, and genetic data of the NCGR-Carya collection. A database will be structured to appropriately capture many analyses associated with one inventory, and to allow retrieval in association with other inventories of the same cultivar in forms amenable to statistical analyses. To facilitate data entry for Carya into GRIN and/or other databases, efforts will be made to integrate bar coding into field labeling, and Personal Digital Assistants (PDAs) into field data collection. Efforts to assess the relationship between genetic diversity and geographical distribution in Carya via molecular marker assays will be made using collections made from 19 native pecan populations located from Illinois to Oaxaca, Mexico, and will facilitate assessment of the extent of genetic isolation by distance and reveal patterns consistent with environmental adaptation.
3. Progress Report:
In FY 2012, a panel of 9 diverse pecan accessions (Desirable, Halbert, Mahan, Major, Starking Hardy Giant, Sumner, Western, Wichita, and 87-MX-5-1.7) was evaluated using a modern molecular technique known as Restriction-site Associated DNA sequencing (RADseq). More than 800 molecular markers known as single-nucleotide polymorphisms (SNPs) were generated for use in characterizing the genetic characteristics of various pecan types. Pecan was adopted for a pilot genetic sequencing effort by researchers at the HudsonAlpha Genome Sequencing Center. The Pawnee cultivar was chosen on the basis of utility in the breeding program. 87MX3-2.11 was chosen as the most genetically consistent cultivar observed to date, based on genetic profiling. Sample analysis as it progresses should allow estimation of genetic variation rates in the two cultivars and will generate reference material that will facilitate sequence alignment in ongoing molecular work with various phenotypes. Also in FY 2012, the project obtained valuable, historical pecan accessions that are noteworthy for their well-established age and known history. These accessions predate the commercial pecan industry and are associated with historic persons or places. Among these was 'Jefferson', from a pecan tree growing at Georgetown Visitation Preparatory School, Washington, DC, that was given to the convent by Thomas Jefferson in 1807. The project will preserve Jefferson and other historically important pecans for posterity.
1. New molecular markers for pecan. Pecan is an important U.S. nut crop that is especially critical to the success of many small farmers. There is an ongoing need for new pecan varieties that are more environmentally adaptable, productive, pest and disease resistant, and that have enhanced nutritional value. Modern tools of molecular biology can be utilized to facilitate rapid development of improved crop varieties; however, use of such tools in pecan development lags that in other crops. ARS researchers at College Station, Texas, working with Texas A&M University colleagues, have utilized molecular techniques to develop hundreds of molecular markers known as Single Nucleotide Polymorphisms or SNPs. These SNPs will be used in pecan research to identify genetically controlled traits that will be exploited to greatly speed development of new, better pecan varieties for the benefit of both producers and consumers.