Protocol detail

Expanding Antarctic Fur Seal Genotyping Panel

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We also added to our list of probe sequences a further set of SNPs that were previously demonstrated to be polymorphic in animals from the study colony. These included 40 SNPs derived from RAD sequencing data that were validated using Sanger sequencing (Humble et al. 2018 (link)), 102 transcriptomic SNPs that were validated using Illumina’s GoldenGate assay (Hoffman et al. 2012 (link)) and 173 cross-amplified SNPs from the Illumina Canine HD BeadChip that were previously found to be polymorphic in 24 Antarctic fur seals (Hoffman et al. 2013a (link)). In addition to these, we included a further six SNPs that were recently discovered from the second exon of the Antarctic fur seal MHC class II DQB locus based on Illumina MiSeq data from 82 Antarctic fur seals (Ottensmann 2018 ).

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Humble E., Paijmans A.J., Forcada J, & Hoffman J.I. (2020). An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3: Genes|Genomes|Genetics, 10(8), 2787-2799.

Publication 2020

GoldenGate assay Canine HD BeadChip MiSeq data

Animals Assay Canine Exon Fur seals Mhc class ii Polymorphic Snps Transcriptomic

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Variable analysis

independent variables

SNPs derived from RAD sequencing data that were validated using Sanger sequencing
Transcriptomic SNPs that were validated using Illumina's GoldenGate assay
Cross-amplified SNPs from the Illumina Canine HD BeadChip that were previously found to be polymorphic in 24 Antarctic fur seals
SNPs recently discovered from the second exon of the Antarctic fur seal MHC class II DQB locus based on Illumina MiSeq data from 82 Antarctic fur seals

dependent variables

Polymorphic SNPs in animals from the study colony

control variables

Not explicitly mentioned

controls

Sanger sequencing was used to validate the RAD sequencing data
Illumina's GoldenGate assay was used to validate the transcriptomic SNPs
The cross-amplified SNPs from the Illumina Canine HD BeadChip were previously found to be polymorphic in 24 Antarctic fur seals

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