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Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array.
- Source :
-
BMC genomics [BMC Genomics] 2012 Aug 06; Vol. 13, pp. 376. Date of Electronic Publication: 2012 Aug 06. - Publication Year :
- 2012
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Abstract
- Background: Btau&#95;4.0 and UMD3.1 are two distinct cattle reference genome assemblies. In our previous study using the low density BovineSNP50 array, we reported a copy number variation (CNV) analysis on Btau&#95;4.0 with 521 animals of 21 cattle breeds, yielding 682 CNV regions with a total length of 139.8 megabases.<br />Results: In this study using the high density BovineHD SNP array, we performed high resolution CNV analyses on both Btau&#95;4.0 and UMD3.1 with 674 animals of 27 cattle breeds. We first compared CNV results derived from these two different SNP array platforms on Btau&#95;4.0. With two thirds of the animals shared between studies, on Btau&#95;4.0 we identified 3,346 candidate CNV regions representing 142.7 megabases (~4.70%) of the genome. With a similar total length but 5 times more event counts, the average CNVR length of current Btau&#95;4.0 dataset is significantly shorter than the previous one (42.7 kb vs. 205 kb). Although subsets of these two results overlapped, 64% (91.6 megabases) of current dataset was not present in the previous study. We also performed similar analyses on UMD3.1 using these BovineHD SNP array results. Approximately 50% more and 20% longer CNVs were called on UMD3.1 as compared to those on Btau&#95;4.0. However, a comparable result of CNVRs (3,438 regions with a total length 146.9 megabases) was obtained. We suspect that these results are due to the UMD3.1 assembly's efforts of placing unplaced contigs and removing unmerged alleles. Selected CNVs were further experimentally validated, achieving a 73% PCR validation rate, which is considerably higher than the previous validation rate. About 20-45% of CNV regions overlapped with cattle RefSeq genes and Ensembl genes. Panther and IPA analyses indicated that these genes provide a wide spectrum of biological processes involving immune system, lipid metabolism, cell, organism and system development.<br />Conclusion: We present a comprehensive result of cattle CNVs at a higher resolution and sensitivity. We identified over 3,000 candidate CNV regions on both Btau&#95;4.0 and UMD3.1, further compared current datasets with previous results, and examined the impacts of genome assemblies on CNV calling.
- Subjects :
- Animals
Base Sequence
Cattle classification
Comparative Genomic Hybridization veterinary
Gene Dosage
Oligonucleotide Array Sequence Analysis veterinary
Polymorphism, Single Nucleotide
Sequence Analysis, DNA veterinary
Cattle genetics
Chromosome Mapping veterinary
DNA Copy Number Variations
Genome
Subjects
Details
- Language :
- English
- ISSN :
- 1471-2164
- Volume :
- 13
- Database :
- MEDLINE
- Journal :
- BMC genomics
- Publication Type :
- Academic Journal
- Accession number :
- 22866901
- Full Text :
- https://doi.org/10.1186/1471-2164-13-376