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Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs
Year:
2010
Source of publication :
BMC Genomics
Authors :
Seroussi, Eyal
;
.
Shirak, Andrey
;
.
Weller, Joel Ira
;
.
Yakobson, Emanuel
;
.
Volume :
11
Co-Authors:
Seroussi, E., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Glick, G., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Shirak, A., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Yakobson, E., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Weller, J.I., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Ezra, E., Israel Cattle Breeders Association, Caesaria Industrial Park 38900, Israel
Zeron, Y., Sion, AI Institute, Shikmim 79800, Israel
Facilitators :
From page:
To page:
(
Total pages:
1
)
Abstract:
Background: Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV's potential as a major source for heritable variation in complex traits. Genomic selection is a newly developed tool based on the estimation of breeding values for quantitative traits through the use of genome-wide genotyping of SNPs. Over 30,000 Holstein bulls have been genotyped with the Illumina BovineSNP50 BeadChip, which includes 54,001 SNPs (~SNP/50,000 bp), some of which fall within CNV regions.Results: We used the BeadChip data obtained for 912 Israeli bulls to investigate the effects of CNV on SNP calls. For each of the SNPs, we estimated the frequencies of occurrence of loss of heterozygosity (LOH) and of gain, based either on deviation from the expected Hardy-Weinberg equilibrium (HWE) or on signal intensity (SI) using the PennCNV "detect" option. Correlations between LOH/CNV frequencies predicted by the two methods were low (up to r = 0.08). Nevertheless, 418 locations displayed significantly high frequencies by both methods. Efficiency of designating large genomic clusters of olfactory receptors as CNVs was 29%. Frequency values for copy loss were distinguishable in non-autosomal regions, indicating misplacement of a region in the current BTA7 map. Analysis of BTA18 placed major quantitative trait loci affecting net merit in the US Holstein population in regions rich in segmental duplications and CNVs. Enrichment of transporters in CNV loci suggested their potential effect on milk-production traits.Conclusions: Expansion of HWE and PennCNV analyses allowed estimating LOH/CNV frequencies, and combining the two methods yielded more sensitive detection of inherited CNVs and better estimation of their possible effects on cattle genetics. Although this approach was more effective than methodologies previously applied in cattle, it has severe limitations. Thus the number of CNVs reported here for the Holstein breed may represent as little as one-tenth of inherited common structural variation. © 2010 Seroussi et al; licensee BioMed Central Ltd.
Note:
Related Files :
Animal
Animals
cattle
gene mapping
Genetic Loci
genetic markers
Genetics
Israel
Mammalia
Receptors, Odorant
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Related Content
More details
DOI :
10.1186/1471-2164-11-673
Article number:
673
Affiliations:
Database:
Scopus
Publication Type:
article
;
.
Language:
English
Editors' remarks:
ID:
19391
Last updated date:
02/03/2022 17:27
Creation date:
16/04/2018 23:28
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Scientific Publication
Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs
11
Seroussi, E., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Glick, G., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Shirak, A., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Yakobson, E., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Weller, J.I., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Ezra, E., Israel Cattle Breeders Association, Caesaria Industrial Park 38900, Israel
Zeron, Y., Sion, AI Institute, Shikmim 79800, Israel
Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs
Background: Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV's potential as a major source for heritable variation in complex traits. Genomic selection is a newly developed tool based on the estimation of breeding values for quantitative traits through the use of genome-wide genotyping of SNPs. Over 30,000 Holstein bulls have been genotyped with the Illumina BovineSNP50 BeadChip, which includes 54,001 SNPs (~SNP/50,000 bp), some of which fall within CNV regions.Results: We used the BeadChip data obtained for 912 Israeli bulls to investigate the effects of CNV on SNP calls. For each of the SNPs, we estimated the frequencies of occurrence of loss of heterozygosity (LOH) and of gain, based either on deviation from the expected Hardy-Weinberg equilibrium (HWE) or on signal intensity (SI) using the PennCNV "detect" option. Correlations between LOH/CNV frequencies predicted by the two methods were low (up to r = 0.08). Nevertheless, 418 locations displayed significantly high frequencies by both methods. Efficiency of designating large genomic clusters of olfactory receptors as CNVs was 29%. Frequency values for copy loss were distinguishable in non-autosomal regions, indicating misplacement of a region in the current BTA7 map. Analysis of BTA18 placed major quantitative trait loci affecting net merit in the US Holstein population in regions rich in segmental duplications and CNVs. Enrichment of transporters in CNV loci suggested their potential effect on milk-production traits.Conclusions: Expansion of HWE and PennCNV analyses allowed estimating LOH/CNV frequencies, and combining the two methods yielded more sensitive detection of inherited CNVs and better estimation of their possible effects on cattle genetics. Although this approach was more effective than methodologies previously applied in cattle, it has severe limitations. Thus the number of CNVs reported here for the Holstein breed may represent as little as one-tenth of inherited common structural variation. © 2010 Seroussi et al; licensee BioMed Central Ltd.
Scientific Publication
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