Title: Admixture and linkage disequilibrium analysis of meat goat breeds Authors
Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: December 26, 2012
Publication Date: January 12, 2013
Citation: Sayre, B., Soelkner, J., Van Tassell, C.P., Sonstegard, T.S. 2013. Admixture and linkage disequilibrium analysis of meat goat breeds. Plant Animal Genome XXI, paper PO711, pp. 251. Technical Abstract: Understanding the population structure and variation within the genome will assist with efforts to make genetic gains for meat goat production. A recently developed Illumina Goat 50K SNP panel containing 52,295 SNP loci was created primarily from SNPs identified in European dairy goat breeds and Asian meat goats. Four goat breeds important to the US meat goat industry, Boer (n=34), Kiko (n=12), Myotonic (n=14), and Spanish (n=20) goats were genotyped. Data were initially analyzed to compare the quality of the SNP panel for genotyping breeds in the US. The quality trimmed data (49,163 SNPs) were used to identify admixture effects and estimates of linkage disequilibrium (LD) across and within breeds. Mapping of LD and runs of homozygozity (ROI) was conducted to look for genomic recombination effects. Overall inbreeding was approximately 7.5% with the highest inbreeding in Boer and Myotonic (12%) and lowest in Spanish and Kiko (3%) populations. Admixture results indicate a variety of low percentage mixing in the Boer population which fits with the history of the importation of this breed and the grade up from other breeds. A strong relationship was found between the Kiko and Spanish breeds, as both have been suggested to have Spanish origins. Interestingly, the Myotonic data does not indicate a similarity to either the Boer or Spanish meat goats. The background of this breed is not clear in the historical record. Future comparisons to breeds genotyped for the Goat AdaptMap project will be necessary to trace the origin of the Myotonic breed.