Sex misassignment of animals in breeding programmes can arise from sources such as misidentification and data-entry errors. The objective of this study was to develop a test for checking sex using Single Nucleotide Polymorphism (SNP) chip genotypes on chromosome X. All animals in this study were genotyped using the GeneSeek Genomic Profiler LD v3 (GGPv3) SNP chip. After filtering, 16478 sex-verified animals (15703 cows and 775 bulls) were available in the training set. The proportion of heterozygous SNPs on chromosome X was used to predict sex. The distribution of heterozygosity was bimodal in the training population with a clear gap between 0.01 and 0.03. Using the heterozygosity cutoff of 0.02 resulted in 100% and 99.6% prediction accuracy for males and females, respectively. Additional analysis determined that four incorrectly classified females were either XO or inbred. The test was validated on an independent set of 2212 animals, which resulted in seven animals for which the predicted sex differed to the recorded sex. Physical examination of these animals revealed that the predicted sex was correct in all cases. The method developed is a useful addition to quality control of genotypes obtained as part of a genomic selection programme.
Proceedings of the New Zealand Society of Animal Production, Volume 76, Adelaide, 26-30, 2016
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