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Supplemental Material for Pincot et al., 2020 (in review)

dataset
posted on 14.07.2021, 17:45 by Dominique D.A. Pincot, Mirko Ledda, Mitchell J. Feldmann, Michael A. Hardigan, Thomas J. Poorten, Daniel E. Runcie, Christopher Heffelfinger, Stephen L. Dellaporta, Glenn S. Cole, Steven J. Knapp
File S1 contains the pedigree database with parents and offspring in a standard trio format (offspring, mother, father) with the following passport data: (a) alphanumeric identification number; (b) common names or aliases; (c) accession types (e.g., cultivars, breeding materials, or wild ecotypes); (d) birth years (years of origin); (e) geographic origins; (f) inventor (breeder or institution) names; (g) taxonomic classifications, and (h) DNA-authenticated pedigrees for genotyped UCD accessions. File S2 contains pedigrees of in the Helium format with parents and offspring identified by common names or aliases (Shaw et al. 2014; https://github.com/cardinalb/helium-docs/wiki). File S3 is a complete bibliography of the databases and documents we referenced to build the pedigree database. Files S4 and S5 contain betweenness (B), in-degree (di), and out-degree (do) statistics, structural role assignments, giant or halo component assignments, and coancestry-based estimates of the genetic contributions of founders and ancestors to cultivars in the California and Cosmopolitan populations, respectively. File S6 contains R code developed to estimate H from A and G as described by Legarra et al. (2009). The example input files from Legarra et al. (2009) for computing the H matrix are included. File S7 contains R code developed for exclusion (paternity-maternity) analyses. Table S1 details the most prominent ecotype founders and their coancestry-based estimates of genetic contribution to the California and Cosmopolitan populations.

History

Article title

Social Network Analysis of the Genealogy of Strawberry: Retracing the Wild Roots of Heirloom and Modern Cultivars

Manuscript #

G3-2020-402012-T