TY - JOUR
T1 - Detection of runs of homozygosity in Norwegian Red: Density, criteria and genotyping quality control
AU - Hillestad, B.
AU - Woolliams, J. A.
AU - Boison, S. A.
AU - Grove, H.
AU - Meuwissen, T.
AU - Våge, D. I.
AU - Klemetsdal, G.
PY - 2018/7/27
Y1 - 2018/7/27
N2 - Runs of homozygosity (ROH) are long, homozygote segments of an individual’s genome, traceable to the parents and might be identical by descent. Due to the lack of standards for quality control of genotyping and criteria to define ROH, Norwegian Red was used to find the effects of SNP density, genotyping quality control and ROH criteria on the detection of ROH. A total of 384 bulls were genotyped with the Illumina HD-chip containing 777,962 SNP markers. A total of 22 data subsets were derived to examine the effects of SNP density, quality control of genotyping and ROH criteria. ROH was detected by PLINK. High SNP density led to increased resolution, fewer false-positive ROH segment, and made it possible to detect shorter ROH. Considering the ROH criteria, we demonstrated that allowing for heterozygote SNP could generate false positives. Furthermore, genotyping quality control should be tuned towards keeping as many SNP as possible, also low minor allele frequency SNP, as otherwise many ROH segments will be lost.
AB - Runs of homozygosity (ROH) are long, homozygote segments of an individual’s genome, traceable to the parents and might be identical by descent. Due to the lack of standards for quality control of genotyping and criteria to define ROH, Norwegian Red was used to find the effects of SNP density, genotyping quality control and ROH criteria on the detection of ROH. A total of 384 bulls were genotyped with the Illumina HD-chip containing 777,962 SNP markers. A total of 22 data subsets were derived to examine the effects of SNP density, quality control of genotyping and ROH criteria. ROH was detected by PLINK. High SNP density led to increased resolution, fewer false-positive ROH segment, and made it possible to detect shorter ROH. Considering the ROH criteria, we demonstrated that allowing for heterozygote SNP could generate false positives. Furthermore, genotyping quality control should be tuned towards keeping as many SNP as possible, also low minor allele frequency SNP, as otherwise many ROH segments will be lost.
KW - MAF
KW - ROH standards
KW - Runs of homozygosity
KW - SNP density
UR - http://www.scopus.com/inward/record.url?scp=85050922579&partnerID=8YFLogxK
U2 - 10.1080/09064702.2018.1501088
DO - 10.1080/09064702.2018.1501088
M3 - Article
AN - SCOPUS:85050922579
SN - 0906-4702
VL - 67
SP - 107
EP - 116
JO - Acta Agriculturae Scandinavica, Section A - Animal Science
JF - Acta Agriculturae Scandinavica, Section A - Animal Science
IS - 3-4
ER -