Novel sources of resistance to wheat stem sawfly in five wild wheat species

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

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

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

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

Date of data collection:

2020-05-23 to 2021-08-30

Geographic location of data collection:

Orchard, Colorado, USA

Funding sources that supported the collection of the data:

Funded by the Kansas State University Wheat Genetic Resource Center

SHARING/ACCESS INFORMATION

Links to publications that cite or use the data: TBD

Was data derived from another source? yes/no

Recommended citation for this dataset: TBD

DATA & FILE OVERVIEW

File list:

00_raw_data

peirce_etal_2024_IDs_ancestralwheat_2020.csv

peirce_etal_2024_IDs_ancestralwheat_2021.csv

peirce_etal_2024_infestation_2020.csv

peirce_etal_2024_infestation_2021.csv

peirce_etal_2024_intra_clade_mono.csv

peirce_etal_2024_oviposition_2020.csv

peirce_etal_2024_oviposition_2021.csv

peirce_etal_2024_phylo_tree_spp.csv

01_r_scripts

peirce_etal_2024_infestation_code.R

peirce_etal_2024_oviposition_code.R

02_phyogenetic_tree

CSU_Hapmap_Sub.hmp.txt

CSU_Hapmap_Sub_Filt.vcf

CSU_Sub_Filt_Imp.vcf.gz

Reanalysis Markdown.Rmd

File descriptions:

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 accession

peirce_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 accession

peirce_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)

01_r_scripts

peirce_etal_2024_infestation_code.R - code used for calculating infestation and larval weight statistics

peirce_etal_2024_oviposition_code.R - code for calculating number of eggs within stems statistics

02_phyogenetic_tree

CSU_Hapmap_Sub.hmp.txt - Filtered hmp file to only keep the A genome

CSU_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 genome

peirce_etal_2024_phylo_tree_spp.csv - accessions used for the phylogenetic tree

Reanalysis Markdown.Rmd - Rmarkdown file for hmp file cleaning and phylogenetic tree building

METHODOLOGICAL INFORMATION

Description of methods used for collection/generation of data:

Methods outlined in the current article under review.