GWAS and Genome Resequencing Provide Insights into Polled and Intersex Goats

The newly developed GoatSNP50 chip provides the opportunity to explore the genetic basis of phenotypic traits in this important livestock species. We collected and analysed genotypes from 52,088 SNP in Boer, Cashmere and Rangeland goats that had both polled and horned individuals. Genome wide association mapping of the poll locus was performed both within-breed and across-breeds, revealing a strong signal on goat chromosome 1. The 769 Kb critical interval contained the poll intersex syndrome (PIS) locus, confirming the genetic basis in non-European animals is the same as identified previously in Saanen goats. Analysis using a PCR-based deletion test and SNP haplotypes carried by a small set of sex reversed animals, known to be associated with poll, revealed some animals carried the wild-type chromosome associated with the presence of horns. This prompted whole genome sequencing of 5 animals to an average depth of 10-fold coverage of Illumina reads. Analysis of the PIS locus confirmed the homozygous presence of a deleted region in some, but not all of the intersex individuals. This confirms a more complex basis for the relationship between poll and the intersex condition than initially thought, while validating the application of the GoatSNP50 chip for fine-mapping traits in goat.