The Affymetrix Bovine Axiom Array 640k SNP chips were used for genotyping the Hanwoo steers. Quality controls were tested to screen available SNPs with PLINK software version 1.07 (Purcell et al., 2007 (link)), and those SNPs were removed with the following four criteria; i) the frequency of the least genotype was less than ten, ii) the call rate was smaller than 95%, iii) p-value of Hardy-Weinberg equilibrium test was less than 0.001, iv) minor allele frequency was less than 5%.
Bovine axiom array 640k snp chips
Manufactured by Thermo Fisher Scientific
The Bovine Axiom Array 640k SNP chips are a high-density genotyping array developed by Thermo Fisher Scientific. The array contains approximately 640,000 single nucleotide polymorphism (SNP) markers that can be used to genotype bovine samples. The core function of this product is to enable researchers to conduct genome-wide association studies and other genetic analyses in cattle.
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2 protocols using bovine axiom array 640k snp chips
1
Hanwoo Steer Genotyping with Bovine Axiom Array
2
Hanwoo Steer Genotyping with Bovine Axiom Array
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Blood samples of 140 Hanwoo steers were collected for genotyping using Affymetrix Bovine Axiom Array 640k SNP chips. Quality controls were tested to screen available SNPs with PLINK version 1.07 [9 (link)], and the SNPs meeting the following criteria were removed: i) the frequency of the least genotype was less than ten, ii) the call rate was smaller than 95%, iii) p-value of the Hardy-Weinberg equilibrium test was less than 0.001, and iv) minor allele frequency was less than 5%.
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