DOI: 10.6084/m9.figshare.24977937
title: <b>Novel sources of resistance to wheat stem sawfly in five wild wheat species</b>

description: Identifying novel sources of resistance to wheat stem sawfly in five wild wheat species Erika S. Peirce, Byron Evers, Zachary J. Winn, W. John Raupp, Mary Guttieri, Allan K. Fritz, Jesse Poland, Eduard Akhunov, Scott Haley, Esten Mason, and Punya Nachappa<br>Title of Dataset: R script and data used to analyze the data for a wheat stem sawfly (Cephus cinctus) to evaluate triticale as a suitable trap crop, field and cone-tainer data<br>Author Information: A. Principal Investigator Contact Information Name: Punya Nachappa Institution: Department of Agricultural Biology, Colorado State University Address: 307 University Ave, Fort Collins, CO 80523 Email: punya.nachappa@colostate.edu<br> B. Associate or Co-investigator Contact Information Name: Erika S. Peirce Institution: Rangeland Resources and Systems Research Unit Address: USDA-ARS, Fort Collins, CO, USA Email: erika.peirce@usda.gov<br><br>Date of data collection:2020-05-23 to 2021-08-30Geographic location of data collection: Orchard, Colorado, USAFunding sources that supported the collection of the data: Funded by the Kansas State University Wheat Genetic Resource Center<br>SHARING/ACCESS INFORMATIONLinks to publications that cite or use the data: TBDWas data derived from another source? yes/noRecommended citation for this dataset: TBD<br>DATA & FILE OVERVIEWFile list:00_raw_data peirce_etal_2024_IDs_ancestralwheat_2020.csvpeirce_etal_2024_IDs_ancestralwheat_2021.csvpeirce_etal_2024_infestation_2020.csvpeirce_etal_2024_infestation_2021.csvpeirce_etal_2024_intra_clade_mono.csvpeirce_etal_2024_oviposition_2020.csvpeirce_etal_2024_oviposition_2021.csvpeirce_etal_2024_phylo_tree_spp.csv<br>01_r_scriptspeirce_etal_2024_infestation_code.Rpeirce_etal_2024_oviposition_code.R<br>02_phyogenetic_treeCSU_Hapmap_Sub.hmp.txtCSU_Hapmap_Sub_Filt.vcfCSU_Sub_Filt_Imp.vcf.gzReanalysis Markdown.Rmd<br>File descriptions: <br>00_raw_data peirce_etal_2024_IDs_ancestralwheat_2020.csv - Accession IDs, wheat is the unique identifier, name is accession number or cultivar name, species is the species of the accession, sub_species is the subspecies of the accessionpeirce_etal_2024_IDs_ancestralwheat_2021.csv - Accession IDs, wheat is the unique identifier, name is accession number or cultivar name, species is the species of the accession, sub_species is the subspecies of the accessionpeirce_etal_2024_infestation_2020.csv - Infestation data for WSS, Date sampled is the date the stems were cut, wheat is unique identifier associated with the ID csv file, tray is the tray number plants were in, letter is the planting and infestation date, zadoks is stem maturity, sd is stem diameter in milimeters, larva is number of larva found, frass is presence of WSS frass, stub is if stem was cut or not, weight is weight of larva in grams.peirce_etal_2024_infestation_2021.csv - Infestation data for WSS, Date sampled is the date the stems were cut, wheat is unique identifier associated with the ID csv file, tray is the tray number plants were in, letter is the planting and infestation date, zadoks is stem maturity, sd is stem diameter in milimeters, larva is number of larva found, frass is presence of WSS frass, stub is if stem was cut or not, weight is weight of larva in grams.peirce_etal_2024_intra_clade_mono.csv - Denoting which clade accessions belonged to. peirce_etal_2024_oviposition_2020.csv - eggs found within stems of wheat accessions and cultivars, Date is when stem was dissected, tray is tray plants were grown in, letter is planting and infestation date, sd is stem diameter in milimeters, eggs is number of eggs in the stem, eggs_present is whether an egg was present or not, name is name of accession or cultivar, sub_species is the sub species and species of accession. peirce_etal_2024_oviposition_2021.csv - eggs found within stems of wheat accessions and cultivars, Date is when stem was dissected, tray is tray plants were grown in, letter is planting and infestation date, sd is stem diameter in milimeters, eggs is number of eggs in the stem, eggs_present is whether an egg was present or not, name is name of accession or cultivar, sub_species is the sub species and species of accession. X1, X2, X3, X4 are the nodes within the wheat scored for solidness with 1-5, Stem.solidness is the total solidness score of the whole stem (5-25)<br><br>01_r_scriptspeirce_etal_2024_infestation_code.R - code used for calculating infestation and larval weight statisticspeirce_etal_2024_oviposition_code.R - code for calculating number of eggs within stems statistics<br>02_phyogenetic_treeCSU_Hapmap_Sub.hmp.txt - Filtered hmp file to only keep the A genomeCSU_Hapmap_Sub_Filt.vcf - fixed VCF and to do hierarchical clustering with CSU_Sub_Filt_Imp.vcf.gz -Filtered hmp file for monomorphic sites amd only keep the A genomepeirce_etal_2024_phylo_tree_spp.csv - accessions used for the phylogenetic treeReanalysis Markdown.Rmd - Rmarkdown file for hmp file cleaning and phylogenetic tree building<br><br>METHODOLOGICAL INFORMATIONDescription of methods used for collection/generation of data: Methods outlined in the current article under review.