DOI: 10.5061/dryad.zgmsbcc6f
title: Data from: The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)

description: Much of our knowledge of the drivers of immune variation, and how these
 responses vary over time, comes from humans, domesticated livestock or
 laboratory organisms. While the genetic basis of variation in immune
 responses have been investigated in these systems, there is a poor
 understanding of how genetic variation influences immunity in natural,
 untreated populations living in complex environments. Here, we examine the
 genetic architecture of variation in immune traits in the Soay sheep of St
 Kilda, an unmanaged population of sheep infected with strongyle
 gastrointestinal nematodes. We assayed IgA, IgE and IgG antibodies against
 the prevalent nematode Teladorsagia circumcincta in the blood plasma of
 &gt; 3,000 sheep collected over 26 years. Antibody levels were
 significantly heritable (h2 = 0.21 to 0.57) and highly stable over an
 individual’s lifespan. IgA levels were strongly associated with a region
 on chromosome 24 explaining 21.1% and 24.5% of heritable variation in
 lambs and adults, respectively. This region was adjacent to two candidate
 loci, Class II Major Histocompatibility Complex Transactivator (CIITA) and
 C-Type Lectin Domain Containing 16A (CLEC16A). Lamb IgA levels were also
 associated with the immunoglobulin heavy constant loci (IGH) complex, and
 adult IgE levels and lamb IgA and IgG levels were associated with the
 major histocompatibility complex (MHC). This study provides evidence of
 high heritability of a complex immunological trait under natural
 conditions and provides the first evidence from a genome-wide study that
 large effect genes located outside the MHC region exist for immune traits
 in the wild.
description: This data was collected as part of the long term individual based
 study on the Soay sheep of St Kilda in Scotland. Details of dataset
 processing is provided in the usage notes and READ ME associated with this
 repository.
description: #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~# SOAY SHEEP PROJECT DATA REUSE: The attached file(s) contain data derived from the long term field project<br> monitoring individual Soay sheep on St Kilda and their environment.  This is a<br> request to please let us know if you use them.  Several people have spent the<br> best part of their careers collecting the data.  If you plan to analyse the<br> data, there are a number of reasons why it would be very helpful if you could<br> contact Josephine Pemberton (j.pemberton@ed.ac.uk) before doing so. [NB. If you are interested in analysing the detailed project data in any depth <br> you may find it helpful to have our full relational database rather than the<br> file(s) available here.  If so, then we have a simple process for bringing you<br> onto the project as a collaborator.] 1) The data can be subject to change due to updates in the pedigree, merging of<br> records, occasional errors and so on. 2) The data are complex and workers who do not know the study system may<br> benefit from advice when interpreting it. 3) At any one time a number of people within the existing project collaboration<br> are analysing data from this project. Someone else may already be conducting<br> the analysis you have in mind and it is desirable to prevent duplication of<br> effort. 4) In order to maintain funding for the project(s), every few years we have to<br> write proposals for original analyses to funding agencies. It is therefore very<br> helpful for those running the project to know what data analyses are in<br> progress. 5) Sheep identifiers may vary relative to other data archives from papers using<br> the Soay sheep data. #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~# DATA DESCRIPTION: These data are related to the manuscript: The genetic architecture of helminth-specific immune responses in a wild<br> population of Soay sheep (Ovis aries). A. M. Sparks, K. Watt, R. Sinclair, J. G. Pilkington, J. M. Pemberton, <br> T. N. McNeilly, D. H. Nussey, S. E. Johnston For questions related specifically to this dataset, please contact Susan<br> Johnston (Susan.Johnston@ed.ac.uk) or Alexandra Sparks (A.M.Sparks@leeds.ac.uk). All analysis scripts are provided at https://github.com/sejlab/Soay_Immune_GWAS <br> and use the same directory structure as outlined in the file paths below.  Scripts are run in the following order: 1.1_BeastAnModGRM070218.R<br> 1.2_Format_Results.R<br> 1.3_BEAST_Genetic_Correlations.R<br> 1.4_Parse_Genetic_Correlations.R<br> brute_GWAS/2_BEAST_GWAS_Prepare.R <br> brute_GWAS/2_BEAST_GWAS_Run.R<br> brute_GWAS_log_Lambs/2_BEAST_GWAS_Prepare.R <br> brute_GWAS_log_Lambs/2_BEAST_GWAS_Run.R<br> 2.2.2_BEAST_GWAS_Parse_BiomaRt_log_Lambs.R<br> 2.2_BEAST_GWAS_Parse_BiomaRt.R<br> 2.3_Reparse_and_format_gene_GO_tables.R<br> 3.1_Imputation_in_Sig_Regions.R<br> 3.1_Imputation_in_Sig_Regions_log_Lambs.R<br> alphaimpute/3_Imputed_GWAS_Prepare.R<br> alphaimpute/3_Imputed_GWAS_Run.R<br> alphaimpute/3_Imputed_GWAS_Run_log_Lambs.R<br> 3.2_Parse_Genotypes_Prepare_for_GWAS.R<br> 3.2_Parse_Genotypes_Prepare_for_GWAS_log_Lambs.R<br> 3.3_Parse_Alphaimpute_GWAS.R<br> 3.3_Parse_Alphaimpute_GWAS_log_Lambs.R<br> 4_Examine_GWAS_Results_LD_Genes.R <br> 5_Variance_Attributed_to_Regions.R<br> 6_BiomaRt_SNP_functions.R<br> 6_BLAST_MHC_with_Rambouillet_Genome.R<br> 7_Sex_Specific_Effects_v1.R<br> 7_SNP_Effects.R The data files used are as follows: * data/20181107_BEAST_data_formatted.RData This is an .RData file containing the data frame `pedigree` (ID, MOTHER, FATHER<br> information) and data frame `BEASTX` which contains individual immune phenotype<br> measures.<br> [N.B. All .RData files can be read into R using the command: load("FILENAME")] <br> * data/20181107_Genabel_Data.RData This is an .RData file containing the 50K genotype data in GenABEL format after<br> quality control (N.B. requires R v3.4.3 and the R library GenABEL v1.8-0). * data/20181107_SoayGRM.Rdata This is an .RData file containing the genomic relatedness matrix used for<br> estimating trait heritability. * data/Ovis_aries.Oar_v3.1.94.genes.txt This is a text file containing the gene information for Ovis aries, as obtained<br> from Ensembl. * data/20180209_SoayPlates1-83.bed/.bim/.fam These are the PLINK files containing the 50K genotype data after quality <br> control. * data/20180209_SoayPlates1-83.bed/.bim/.fam These are the PLINK files containing the 50K genotype data after quality <br> control. * data/20140214_SheepHD_QC1_Polym.bed/.bim/.fam These are the PLINK files containing the HD genotype data after quality control. <br>