Genetic diversity and investigation of polledness in divergent goat populations using 52 088 SNPs

Abstract

The recent availability of a genome-wide SNP array for the goat genome dramatically increases the power to investigate aspects of genetic diversity and to conduct genome-wide association studies in this important domestic species. We collected and analysed genotypes from 52 088 SNPs in Boer, Cashmere and Rangeland goats that had both polled and horned individuals. Principal components analysis revealed a clear genetic division between animals for each population, and model-based clustering successfully detected evidence of admixture that matched aspects of their recorded history. For example, shared co-ancestry was detected, suggesting Boer goats have been introgressed into the Rangeland population. Further, allele frequency data successfully tracked the altered genetic profile that has taken place after 40 years of breeding Australian Cashmere goats using the Rangeland animals as the founding population. Genome-wide association mapping of the POLL locus revealed a strong signal on goat chromosome 1. The 769-kb critical interval contained the polled intersex syndrome locus, confirming the genetic basis in non-European animals is the same as identified previously in Saanen goats. Interestingly, analysis of the haplotypes carried by a small set of sex-reversed animals, known to be associated with polledness, revealed some animals carried the wild-type chromosome associated with the presence of horns. This suggests a more complex basis for the relationship between polledness and the intersex condition than initially thought while validating the application of the goat SNP50 BeadChip for fine-mapping traits in goat.

Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits

“…Similarly, fine-scale mapping of selection signatures in goats may also facilitate in the interpretation and establishment of the molecular basis of economically important goat traits. For example, the availability of the Illumina goat SNP50 array1158, as well as the rapid decrease in sequencing cost permit the identification of candidate economically important traits in goats. Our findings will facilitate the genetic dissection of phenotypic variation and aid in the future genetic improvement of production and adaptive traits in goats.…”

“…The genome of goats, which have diverse production potentials and extensive adaptation to diverse environments, provides a unique opportunity for identifying signatures associated with selection. Array- or sequencing-based detection of signatures during the selection process has been described in cattle456, chicken7, pigs8910, sheep1112, and recently in goats131415. By using whole-genome resequencing (WGS) data, Benjelloun et al .…”

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

“…The dataset used here has been previously described [19, 24]. In brief, there were between 48 (Cashmere) and 403 (Alpine) animals genotyped per breed.…”

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

“…A total of 60,000 SNPs were selected and Illumina optimized assays for a total of 53,347 SNPs that were subsequently tested in a sample of 288 goats with a high success. This SNP chip has been already used by Kijas et al [139] to carry out a genome-wide association study (GWAS) for polledness in Boer, Cashmere, and Rangeland goats. A highly significant GWAS signal was detected at chromosome 1, just at the genomic region reported by Pailhoux et al [86] as containing the causal mutation for the goat polled intersex syndrome.…”

“…A highly significant GWAS signal was detected at chromosome 1, just at the genomic region reported by Pailhoux et al [86] as containing the causal mutation for the goat polled intersex syndrome. Curiously, not all intersex goats were homozygous for the PIS deletion suggesting the existence of genetic heterogeneity for this reproductive pathology [139]. The 52K SNP chip has also been used to characterize the genetic diversity of Italian goat breeds [140], which showed a remarkable level of population structure, and it is the main tool employed in current international efforts to investigate goat genetic variation at a worldwide scale (Goat Adaptmap project, http://www.goatadaptmap.org/) as well as to develop genetic markers that can be used as selection criteria for phenotypes of economic interest (3SR project, http://www.3srbreeding.eu/ThenbspProject.aspx).…”