Genotyping Japanese Black Cows

Blood was collected from 791 Japanese Black cows. Genomic DNA was extracted using the Easy-DNA kit (Invitrogen, Cat. #K1800–01). All samples were genotyped using the BovineHD BeadChip Array (Illumina, Cat. #WG-450-1002) [41 (link)]. SNPs genotype calling were performed using GenomeStudio V2011 (Illumina, version 1.9.4). The ARS-UCD1.2 assembly was used to map the SNP position [42 ]. CNVR was detected as previously reported [15 (link)], using PennCNV software (version June 2011) [43 (link)].

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Sasaki S., Miki Y., Ibi T., Wakaguri H., Yoshida Y., Sugimoto Y, & Suzuki Y. (2021). A 44-kb deleted-type copy number variation is associated with decreasing complement component activity and calf mortality in Japanese Black cattle. BMC Genomics, 22, 107.

Publication 2021

Easy-DNA kit BovineHD BeadChip Array GenomeStudio V2011

Blood Cows Genomic Genotype Japanese

Corresponding Organization : University of the Ryukyus

Other organizations : Hyogo Prefectural Hyogo Agricultural University, Okayama University, The University of Tokyo, Institute of Livestock and Grassland Science

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Variable analysis

independent variables

Blood collection from 791 Japanese Black cows

dependent variables

Genomic DNA extraction
SNP genotyping using BovineHD BeadChip Array
SNP calling using GenomeStudio V2011
CNVR detection using PennCNV software

control variables

The ARS-UCD1.2 assembly used for SNP position mapping

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