Dataset

 

Dataset for predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation Public Deposited

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https://ir.library.oregonstate.edu/concern/datasets/tq57nx45z

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Abstract
  • The legality of wood products in trade often depends on their geographic origin, creating a need for forensic tools that can verify claims of provenance for wood and wood products. Cedrela odorata L. or Spanish cedar is a target of illegal logging. We developed a 140 SNP Agena™ MassARRAY® assay for geographic assignment of C. odorata specimens to their origin. Hybridization capture, target enrichment, and short-read sequencing of 192 Cedrela specimens allowed us to identify 140 spatially informative SNPs that differentiate C. odorata specimens by latitude, temperature, and precipitation. These SNPs were validated using 356 Cedrela specimens from eight species, and genetic clusters from discriminant analysis of principal components corresponded roughly to species groups. We used random forest classification and the R package SPASIBA to perform discrete and continuous spatial assignment of C. odorata sensu stricto specimens and to evaluate classification error. In this supplementary directory, a reduced representation nuclear genome reference for C. odorata, a VCF file containing 144,083 high quality SNPs for C. odorata which may be used to further refine out SNP genotyping assay for geographic assignment or other purposes, 140 SNP primers used for the Agena™ MassARRAY®, and data sets to replicate our statistical analysis using R. By sharing these resources, we hope to enable future research on this widespread Neotropical tree genus.
  • Keywords: Logging; Cedrela; Forensic biology; Plants; Mahogany--South America; Meliaceae; Spanish cedar
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  • Finch, K. N. (2019). Dataset for predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation (Version 1) [Data set]. Oregon State University. https://doi.org/10.7267/TQ57NX45Z
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  • The generation of these resources was supported by the United States Agency for International Development (19318814Y0010-140001), the United States Forest Service International Programs, and the United States Forest Service Pacific Northwest Research Station.
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