scholarly journals Functional and population genetic features of copy number variations in two dairy cattle populations

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Young-Lim Lee ◽  
Mirte Bosse ◽  
Erik Mullaart ◽  
Martien A. M. Groenen ◽  
Roel F. Veerkamp ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Copy Number ◽  
Population Genetic ◽  
Copy Number Variations ◽  
Genetic Features

scholarly journals Functional and population genetic features of copy number variations in two dairy cattle populations

2019 ◽  
Author(s):  
Young-Lim Lee ◽  
Mirte Bosse ◽  
Erik Mullaart ◽  
Martien A. M. Groenen ◽  
Roel F. Veerkamp ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Candidate Genes ◽  
Population Differentiation ◽  
Copy Number ◽  
Copy Number Variations ◽  
Snp Markers ◽  
Functional Impact ◽  
Wide Range ◽  
Genetic Features ◽  
Differentiation Index

Abstract Background Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features. Results We discovered 14,272 autosomal CNVs, which were aggregated into 1,755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (0.05 ≤ MAF). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes , which are related to starch digestion and stature, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF>0.05) showed slightly higher LD ( r 2 =~0.1 at 10kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD ( r 2 =~0.5 at 10kb distance). Conclusions Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17 , which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers.

scholarly journals Population-genetic nature of copy number variations in the human genome

2009 ◽  
Vol 19 (5) ◽  
pp. 761-773 ◽  
Author(s):  
Mamoru Kato ◽  
Takahisa Kawaguchi ◽  
Shumpei Ishikawa ◽  
Takayoshi Umeda ◽  
Reiichiro Nakamichi ◽  
...  
Keyword(s):  
Human Genome ◽  
Copy Number ◽  
Population Genetic ◽  
Copy Number Variations ◽  
Genetic Nature

scholarly journals Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

DNA Research ◽  
2016 ◽  
Vol 23 (3) ◽  
pp. 253-262 ◽  
Author(s):  
Derek M. Bickhart ◽  
Lingyang Xu ◽  
Jana L. Hutchison ◽  
John B. Cole ◽  
Daniel J. Null ◽  
...  
Keyword(s):  
Copy Number ◽  
Population Genetic ◽  
Copy Number Variations ◽  
Multicopy Genes

scholarly journals Population-genetic properties of differentiated copy number variations in cattle

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Lingyang Xu ◽  
Yali Hou ◽  
Derek M. Bickhart ◽  
Yang Zhou ◽  
El Hamidi abdel Hay ◽  
...  
Keyword(s):  
Copy Number ◽  
Population Genetic ◽  
Copy Number Variations

scholarly journals Functional and population genetic features of copy number variations in two dairy cattle populations

2020 ◽  
Author(s):  
Young-Lim Lee ◽  
Mirte Bosse ◽  
Erik Mullaart ◽  
Martien A. M. Groenen ◽  
Roel F. Veerkamp ◽  
...  
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Dairy Cattle ◽  
Candidate Genes ◽  
Population Differentiation ◽  
Copy Number ◽  
Copy Number Variations ◽  
Functional Impact ◽  
Wide Range ◽  
Differentiation Index

Abstract Background Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features. Results We discovered 14,272 autosomal CNVs, which were aggregated into 1,755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes , which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF ≥ 0.05) showed slightly higher LD ( r 2 =~0.1 at 10kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD ( r 2 =~0.5 at 10kb distance). Conclusions Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17 , which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers. Keywords : Copy number variations, Bos taurus , Linkage disequilibrium, population genetics

scholarly journals Functional and population genetic features of copy number variations in two dairy cattle populations

2019 ◽  
Author(s):  
Young-Lim Lee ◽  
Mirte Bosse ◽  
Erik Mullaart ◽  
Martien A. M. Groenen ◽  
Roel F. Veerkamp ◽  
...  
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Dairy Cattle ◽  
Candidate Genes ◽  
Population Differentiation ◽  
Copy Number ◽  
Copy Number Variations ◽  
Functional Impact ◽  
Wide Range ◽  
Differentiation Index

Abstract Background Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features. Results We discovered 14,272 autosomal CNVs, which were aggregated into 1,755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes, which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF≥ 0.05) showed slightly higher LD (r2=~0.1 at 10kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD (r2=~0.5 at 10kb distance). Conclusions Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17, which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers. Keywords: Copy number variations, Bos taurus, Linkage disequilibrium, population genetics

scholarly journals Functional and population genetic features of copy number variations in two dairy cattle populations

2020 ◽  
Author(s):  
Young-Lim Lee ◽  
Mirte Bosse ◽  
Erik Mullaart ◽  
Martien A. M. Groenen ◽  
Roel F. Veerkamp ◽  
...  
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Dairy Cattle ◽  
Candidate Genes ◽  
Population Differentiation ◽  
Copy Number ◽  
Copy Number Variations ◽  
Functional Impact ◽  
Wide Range ◽  
Differentiation Index

Abstract Background Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features. Results We discovered 14,272 autosomal CNVs, which were aggregated into 1,755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes , which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF ≥ 0.05) showed slightly higher LD ( r 2 =~0.1 at 10kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD ( r 2 =~0.5 at 10kb distance). Conclusions Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17 , which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers. Keywords : Copy number variations, Bos taurus , Linkage disequilibrium, population genetics

scholarly journals Correction to: Analysis of Population-Genetic Properties of Copy Number Variations

2018 ◽  
pp. E1-E1
Author(s):  
Lingyang Xu ◽  
Liu Yang ◽  
Derek M. Bickhart ◽  
JunYa Li ◽  
George E. Liu
Keyword(s):  
Copy Number ◽  
Population Genetic ◽  
Copy Number Variations

Analysis of Population-Genetic Properties of Copy Number Variations

2018 ◽  
pp. 179-186 ◽  
Author(s):  
Lingyang Xu ◽  
Liu Yang ◽  
Derek M. Bickhart ◽  
JunYa Li ◽  
George E. Liu
Keyword(s):  
Copy Number ◽  
Population Genetic ◽  
Copy Number Variations

scholarly journals Functional and population genetic features of copy number variations in two dairy cattle populations

2019 ◽  
Author(s):  
Young-Lim Lee ◽  
Mirte Bosse ◽  
Erik Mullaart ◽  
Martien A. M. Groenen ◽  
Roel F. Veerkamp ◽  
...  
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Dairy Cattle ◽  
Candidate Genes ◽  
Population Differentiation ◽  
Copy Number ◽  
Copy Number Variations ◽  
Functional Impact ◽  
Wide Range ◽  
Differentiation Index

Abstract Background Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features. Results We discovered 14,272 autosomal CNVs, which were aggregated into 1,755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes, which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF 0.05) showed slightly higher LD (r2=~0.1 at 10kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD (r2=~0.5 at 10kb distance). Conclusions Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17, which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers. Keywords: Copy number variations, Bos taurus, Linkage disequilibrium, population genetics

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