Data from: Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach
| Main Authors: | Brown, Emily A., Pilkington, Jill G., Nussey, Dan H., Watt, Kathryn A., Hayward, Adam D., Tucker, Rachel, Graham, Andrea L., Paterson, Steve, Beraldi, Dario, Pemberton, Josephine M., Slate, Jon |
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| Format: | info dataset Journal |
| Terbitan: |
, 2012
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4993103 |
Daftar Isi:
- Identifying the genes underlying phenotypic variation in natural populations can provide novel insight into the evolutionary process. Here we test the candidate gene approach to identifying loci involved in variation in gastrointestinal parasite burden, in a wild population of Soay sheep. A comprehensive literature review, Gene Ontology databases, and comparative genomics resources were used to generate a list of candidate genes. In a pilot study these candidates, along with 50 random genes, were then sequenced in pools of Soay sheep with low and high gastrointestinal nematode burden. Further candidates were identified from SNPs that were highly differentiated between high and low resistance sheep breeds. A panel of 192 candidate and control SNPs were then typed in 960 individual Soay sheep to examine whether they individually explained variation in parasite burden, as measured as faecal egg count (FEC), as well as two immune measures. The cumulative effect of the candidate and control SNPs were estimated by fitting genetic relationship matrices (GRMs) as random effects in animal models of the three traits. No more significant SNPs were identified in the pilot sequencing experiment and association study than expected by chance. Furthermore, no significant difference was found between the proportions of candidate or control SNPs that were found to be significantly associated with parasite burden/immune measures. No significant effect of the candidate or control gene GRMs was found. There is thus little support for the candidate gene approach to the identification of loci explaining variation in parasitological and immunological traits in this population.
- sheeplow_bothpoolstemplate-singlessheephigh_bothpoolstemplate-singlesLocusXDNA_cleaned_dataCleaned SNP dataset.SNPs were genotyped on an Illumina BeadXpress platform using Goldengate Veracode technologyANA_adultsData for associations between SNPs and ANA in adultsANA_lambsData for associations between SNPs and ANA in lambsANA_senesData for associations between SNPs and ANA in senescent individuals.ANA_yearlingsData for associations between SNPs and ANA in yearlingsFEC_adultsData for associations between SNPs and FEC in adultsFEC_lambsData for associations between SNPs and FEC in lambsFEC_senesData for associations between SNPs and FEC in senescent-aged individualsFEC_yearlingsData for associations between SNPs and FEC in yearlingsTCIRC_adultsData for associations between SNPs and TCIRC in adultsTCIRC_lambsData for associations between SNPs and TCIRC in lambsTCIRC_senesData for associations between SNPs and TCIRC in senescent-aged individualsTCIRC_yearlingsData for associations between SNPs and TCIRC in yearlingsDryad statement - Brown Mol EcolGeneral information about the data used in this paper, including Soay Sheep Project contact information.ReadmeDescription of contents of files with names beginning ANA, TCIRC and FEC