Mizzou Hair Shedding Project

The code and analyses here are associated with "Genomic loci involved in sensing environmental cues and metabolism affect seasonal coat shedding in Bos taurus and Bos indicus cattle" (Durbin et al., 2022). Private and identifiable information including pedigrees and registration numbers has been removed. Contact Harly Durbin Rowan at harlyjaned@gmail.com or Jared Decker at deckerje@missouri.edu with questions.

Data import, joining, and cleaning

Phenotypic data

The code here is associated with "Phenotypes" heading of the Materials and methods section.

Run source_functions/import_joint_clean.R to generate data/derived_data/cleaned.rds.

• Takes a "blacklist" of farm ID/year combinations to ignore as arguments. I.e., to ignore PVF 2019 data and WAA 2018 data, Rscript --vanilla source_functions/import_join_clean.R "PVF_2019" "WAA_2018"
• Imports source_functions/first_clean.R to iteratively filter & tidy data on a farm-by-farm basis.
  • source_functions/iterative_id_search.R used to match up animals to Lab IDs using different combinations of Mizzou Hair Shedding Project identifiers and Animal Table columns
  • When an animal matches up to more than one lab ID, keeps the most recent one (unless the most recent Lab ID comes from the summer 2020 ASA/RAAA genotype share)
  • Thompson Research Farm (farm ID UMCT) data cleaned in a different way using data/derived_data/import_join_clean/umct_id_key.csv
• University of Arkansas (farm IDs BAT, SAV) data cleaned separately in source_functions/clean_arkansas.R and imported from data/derived_data/import_join_clean/ua_clean.Rds
• Uses source_functions/impute_age.R to impute missing ages when ages in other years were recorded
  • When DOB available, "age class" is (n*365d)-90d to ((n+1)*365d)-90d, where n is the age classification and d is days. This means that animals that aren't actually one year of age can still be classified as yearlings and so on.
  • Scores on animals less than 275 days (i.e., 365-90) old removed
• Miscellaneous data cleaning:
  • All records from animals with differing sexes across multiple years removed
  • All punctuation and spaces removed from animal IDs
  • "AMGV" prefix added to all American Gelbvieh Association registration numbers to match Animal Table
  • Coat colors codes, calving season codes, toxic fescue grazing status codes, and breed codes standardized

Final cleaned data stored in data/derived_data/import_join_clean/cleaned.rds. Anonymized version stored in data/derived_data/data_submission/anonymized.csv.

cleaned.rds and column descriptions

• year: Data recording year ranging from 2012-2020
• farm_id: 3-digit identifier used in UMAG Tissue Table for farm or ranch where scores was collected
• breed_code: 2-4 digit identifier used in UMAG Animal Table, reported by breeder. One of:

breed_code	Breed	Breed association
AN	Angus	American Angus Association
ANR	Red Angus	Red Angus Association of America
BG	Brangus, including UltraBlack	International Brangus Breeders Association
CHA	Charolais	American International Charolais Association
CHIA	Chianina	American Chianina Association
CROS	Mixed/crossbred cattle	Non-registered crossbred cattle
GEL	Gelbvieh, including Balancers	American Gelbvieh Association
HFD	Hereford	American Hereford Association
MAAN	Maine-Anjou	American Maine-Anjou Association
SH	Shorthorn	American Shorthorn Association
SIM	Simmental, including SimAngus	American Simmental Association
SIMB	Simbrah	American Simmental Association

• registration_number: Registration number associated with breed_code, can be NA
• animal_id: Unique identification for the animal, which must remain the same across years. Ear tag, tattoo, freeze brand, or other herd ID used when collecting the hair score. No limit on length
• sex: M or F
• color: Breeder-reported coat color. One of:

color
BLACK
BLACK ROAN
BLACK WHITE FACE
BRINDLE
BROWN
GREY
RED
RED ROAN
RED WHITE FACE
WHITE
YELLOW

• Lab_ID: Identifier used to match animal to UMAG Animal Table
• date_score_recorded: Breeder-reported date when hair shedding score was collected, formatted as YYYY-MM-DD. This in NOT the date DNA sample was collected.
• hair_score: Integer between 1-5
• age: Integer between 1-21
• calving_season: Breeder-reported season when last calf was born. One of SPRING or FALL for females, NA for bulls. June 30 is the cut-off for spring and fall calving.
• toxic_fescue: Was the animal grazed on toxic fescue during the spring of the recording year? One of TRUE or FALSE
• comment: Breeder-reported comments about the animal, including additional information about breed makeup. Comments could include descriptions such as muddy, long rear hooves, lost tail switch, black hided cattle with brown backs, etc. Producers can also note any feed supplements the animals were given.
• barcode: Barcode of blood card, hair card, or TSU submitted for genotyping through the project
• sold: Has the animal been sold, died, or left the herd? Retroactively updated for previous years once breeder indicates scores will no longer be collected on the animal
• dob: Date of birth, formatted as YYYY-MM-DD

A high level data summary including the grouped phenotype tallies mentioned in the "Phenotypes" heading can be found in html/data_summary.html.

Genotypic data

The code here is associated with "Genotypes & imputation" heading of the Materials and methods section.

• Parentage conflicts removed, genotypes QC'd, and genotypes reformatted using source_functions/blupf90_geno_format.snakefile
• [Link to Zenodo genotypes]

Pedigree & pedigree-based breed composition

The code here is associated with "Generation of the pedigree and genomic relatedness matrices" heading of the Materials and methods section. For privacy reasons, actual pedigrees and identifiers are not included.

• Multi-breed 3-generation pedigree construction in notebooks/3gen.Rmd using data contributed by breed associations in data/raw_data/3gen
  • Parentage for genotyped animals verified using seekparentf90 in source_functions/seekparentf90.snakefile/notebooks/seekparentf90.Rmd, discordant parents set to missing in the pedigree
• Pedigree-based breed composition data for cross-bred but registered animals cleaned in source_functions/breed_key.R and source_functions/rhf_breed_comp.R using data in data/raw_data/breed_key, output in data/derived_data/breed_key/breed_key.rds

Environmental data

The code here is associated with "The effects of temperature and photoperiod" heading of the Materials and methods section. For privacy reasons, the coordinates associated with each farm used to extract weather data are not included.

• Herd addresses converted to geographic coordinates in source_functions/coord_key.R, output in data/derived_data/environmental_data/coord_key.csv.
• Weather data for unique score dates at unique coordinates gathered using DarkSky API in source_functions/darksky.R, output in data/derived_data/environmental_data/weather.rds

Analyses

Variance component estimation

The code here is associated with the "Estimation of breeding values and genetic parameters", "The effects of temperature and photoperiod", and "Recommendations for genetic evaluations" headings of the Materials and methods section. Descriptions of models tested and associated "model IDs" can be found in notebooks/model_key.Rmd, including full models, breed-specific models, and models aimed at evaluating the effect of the environment.

• AIREML variance component estimation workflow for all models in source_functions/aireml_varcomp.snakefile
  • Calls source_functions/setup.aireml_varcomp.{model ID}.R for data formatting and setup, including contemporary group assignment
• Variance components of breed-specific models analyzed in notebooks/breeds.Rmd
• Results of models evaluating the effects of temperature and photoperiod analyzed in notebooks/environmental_data.Rmd with rendered results in html/environmental_data.html
  • Analysis of calving season, toxic fescue grazing status, and age group BLUEs in notebooks/misc_blues.Rmd

Model evaluation

The code here is associated with the "Evaluation of breeding values" heading of the Materials and methods section.

• Eigensoft smartPCA workflow in source_functions/smartpca.snakefile. Results sanity checked in notebooks/pca.Rmd
• Prediction model evaluation performed using source_functions/estimate_bias.snakefile
• Results analyzed using notebooks/estimate_bias.Rmd with rendered results for each model evaluated in html/estimate_bias.*.html

GWAA

Using de-regressed EBVs

The code here is associated with the "Deregression of breeding values and single-SNP regression" heading of the Materials and methods section.

• SNP1101 setup and workflow in source_functions/snp1101.snakefile
  • Calls source_functions/setup.snp1101.R to calculate accuracy of and de-regress breeding
• Results of full models analyzed in notebooks/general_gwas.Rmd with rendered results in html/general_gwas.html
• Results of breed-specific models analyzed in notebooks/breeds.Rmd

Meta-analysis of year-specific GWAA

The code here is associated with the "GWAA meta-analysis" and "Conditional & joint association analysis" headings of the Materials and methods section.

• GCTA-MLMA, COJO setup and workflow in source_functions/gcta_gwas.years.snakefile
• Results analyzed in notebooks/cojo.Rmd
• Rendered results can be found in html/cojo.html

GxE GWAA

The code here is associated with the "Genotype-by-environment interaction GWAA" heading of the Materials and methods section.

• GEMMA GxE GWAS setup and workflow in source_functions/gxe_gwas.snakefile
  • Calls source_functions/setup.gxe_gwas.R to pre-adjust phenotypes by subtracting contemporary group effect estimated using the gxe_gwas model (see notebooks/model_key.Rmd) and randomly select one score per year per animal

Annotation and enrichment

• Annotation and enrichment analyses performed in notebooks/annotation.Rmd

Miscellaneous

• Reference hair shedding score photos in reference_photos/