Location: Crop Germplasm Research
Project Number: 3091-21000-046-002-N
Project Type: Non-Funded Cooperative Agreement
Start Date: Mar 1, 2022
End Date: Mar 1, 2024
The National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya) houses a large germplasm repository which represents the entire genetic diversity of pecan, but its hickory diversity is limited. In the last few years, we have resequenced genomes from a large genetic diversity panel of 872 Carya (713 pecans, 129 hickories, and 30 hybrids), representing the extent of our NCGR-Carya repository collection. This project centers on expanding NCGR-Carya's genetic diversity panel with geographically diverse germplasm from the nationally accredited Carya collection at The Arnold Arboretum of Harvard University (Cooperator). This project has two main objectives. The first objective is to verify the species or hybrid identity of 194 Carya in the Cooperator's living collection. This effort will be funded by the USDA. The second objective is to use the verified species identities to select the top 40 samples for genome resequencing that represent both species and geographic diversity. This effort will be funded by the Cooperator. Both parties are investing similar amounts into this project. This joint effort would allow for the validation of a novel approach to genetically verify the species/hybrid identity of trees (in wild or ex-situ collections) before their introduction into the NCGR-Carya repository. It also supports the Cooperator's mission to create the first "genomic type collection" and be a central resource for forest tree comparative genomics, developmental biology, and phylogenetics in the future.
Collection: For this proposal, fresh young leaf tissue will be collected at the Cooperator's location in the Spring or early Summer of 2022 by ARS Researcher. It will be shipped overnight back to the USDA-ARS home location, where the tissue in tubes will be prepared and DNA will be extracted. Diploid Skim Sequencing – USDA will select the library preparation and sequencing location according to USDA procurement policies. Our target parameters for sequencing the 194 Carya from the Cooperator would be about 0.1x genome coverage (75Mb per sample) using 200bp paired-end reads. The analysis would follow the SISRS pipeline as previously described (Literman et al., 2022).