Validation of the 50k Illumina goat SNP chip in the South African Angora goat

Show simple item record Lashmar, S.F. Visser, Carina Van Marle-Koster, Este 2015-06-24T06:00:01Z 2015-06-24T06:00:01Z 2015-03-12
dc.description.abstract Tools for the genomic evaluation of goats have generally lagged behind those for other species. However, the recent availability of the goat SNP50 consortium bead chip has marked a positive change for this small ruminant species. Polymorphic loci can differ greatly between breeds of the same species. Exclusion of fibre-producing breeds, such as the Angora goat, during the development of this genotyping array necessitates the validation of SNPs included on the chip to allow for genomic applications that would accelerate genetic progress in mohair yield and quality. Forty eight unrelated Angora goats, displaying phenotypic variation in two important price-determining traits, namely fibre diameter and fleece weight, were genotyped with the goat SNP50 consortium bead chip. Results revealed that 46 983 SNP (88.1%) of the 53 347 called SNPs were polymorphic (MAF>0.05). After quality control, 3 960 SNP were filtered from further analysis for violating Hardy-Weinberg and call-rate parameter thresholds, leaving 43 759 (82%) of the 53 347 SNPs to be validated for downstream analysis. Observed and expected heterozygosity values of 0.365 and 0.370, respectively, were obtained for polymorphic SNPs. A total of 30 357 SNPs in linkage disequilibrium (LD) were removed to obtain a set of independent markers, resulting in a final SNP density of 1 SNP/ ~226 kb. Results indicate that the goat SNP50 bead chip was informative in the Angora goats that were studied, and should be useful in examining the underlying genetic variation. en_ZA
dc.description.librarian am2015 en_ZA
dc.description.uri en_ZA
dc.identifier.citation Lashmar, SF, Visser, C & Van Marle-Koster, E 2014, 'Validation of the 50k Illumina goat SNP chip in the South African Angora goat', South African Journal of Animal Science, vol. 45, no. 1, pp. 56-59. en_ZA
dc.identifier.issn 0375-1589 (print)
dc.identifier.issn 2221-4062 (online)
dc.identifier.other 10.4314/sajas.v45i1.7
dc.language.iso en en_ZA
dc.publisher South African Society for Animal Science en_ZA
dc.rights Copyright resides with the authors in terms of the Creative Commons Attribution 2.5 South African Licence. en_ZA
dc.subject Call rate en_ZA
dc.subject Hardy-Weinberg equilibrium en_ZA
dc.subject Linkage disequilibrium en_ZA
dc.subject Minor allele frequency en_ZA
dc.title Validation of the 50k Illumina goat SNP chip in the South African Angora goat en_ZA
dc.type Article en_ZA

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