Cattle Genome Genotyping and Quality Control

Among the animals with phenotypic records, 3,040 heifers and 4,483 cows were genotyped with Illumina BovineSNP50 BeadChip version 1 or 2 (Illumina Inc., San Diego, CA)^{23 (link)}. A total of 55,298 single nucleotide polymorphisms (SNPs) on 29 Bos taurus autosomes and the X chromosome were available. The numbers of SNPs per chromosome ranged from 894 on the X chromosome to 2,502 on the chromosome 1. A routine quality control was conducted using the software Plink^{24 (link)} to remove SNPs with minor allele frequencies <5%, call rate <90% or a significant deviation from the Hardy–Weinberg proportion (P-value < 10⁻⁵ for χ² test with one degree of freedom). After quality control, the number of SNPs remaining was 35,391. The UMD v3.1 assembly^{25 (link)} was used as the reference for genomic position of the SNPs.

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Mao X., Sahana G., Johansson A.M., Liu A., Ismael A., Løvendahl P., De Koning D.J, & Guldbrandtsen B. (2020). Genome-wide association mapping for dominance effects in female fertility using real and simulated data from Danish Holstein cattle. Scientific Reports, 10, 2953.

Publication 2020

BovineSNP50 BeadChip

Animals Bos taurus Chromosome Chromosome 1 Cows Genomic Phenotypic Single nucleotide polymorphisms X chromosome

Corresponding Organization : Chinese Academy of Sciences

Other organizations : Aarhus University, Swedish University of Agricultural Sciences

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Variable analysis

independent variables

Genotyping with Illumina BovineSNP50 BeadChip version 1 or 2

dependent variables

Phenotypic records of 3,040 heifers and 4,483 cows

control variables

Quality control procedures to remove SNPs with minor allele frequencies <5%, call rate <90% or a significant deviation from the Hardy–Weinberg proportion (P-value < 10⁻⁵ for χ² test with one degree of freedom)
Using the UMD v3.1 assembly as the reference for genomic position of the SNPs

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