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A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle

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Prinsen, R.T.M.M.; Strillacci, M.G.; Schiavini, F.; Santus, E.; Rossoni, A.; Maurer, V.; Bieber, A.; Gredler, B.; Dolezal, M. and Bagnato, A. (2016) A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle. Livestock Science, 191, pp. 153-160.

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Online at: https://www.sciencedirect.com/science/article/abs/pii/S1871141316301779

Summary

Detecting genetic variation such as Copy Number Variants (CNVs) in cattle provides the opportunity to study their association with quantitative traits. CNVs are DNA sequences of 50 bp up to several Mb long, which can vary in copy number in comparison with a reference genome. The aim of this study was to investigate CNVs in 1410 samples of the Brown Swiss cattle breed using Illumina Bovine HD SNP chip information, which includes 777,962 SNPs. After stringent quality control, CNVs were called with the Golden Helix SVS 8.3.1 (SVS) and PennCNV software and were summarized to CNV regions (CNVRs) at a population level (i.e. overlapping CNVs), using BEDTools. Additionally, common CNVRs between the two software were set as consensus regions. Genes within consensus CNVRs were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7. In order to validate these results, quantitative PCRs were executed on 15 selected CNVRs.
The SVS software identified 25,030 CNVs summarized to 398 CNVRs, which comprised 30 gains, 344 losses and 24 complex CNVRs (i.e. containing both losses and gains), covering 3.92% of the bovine genome. The PennCNV software identified 62,341 CNVs summarized to 5578 CNVRs, which comprised 2638 gains, 2404 losses and 537 complex CNVRs, covering 7.68% of the bovine genome. The length of these CNVRs ranged from 1244 bp to 1,381,355 bp. A total of 563 consensus CNVRs were found covering 2.29% of the UMD 3.1 bovine genome assembly. Of these, 24 were gains, 300 were losses and 239 were complex CNVRs. A total of 775 official gene IDs were annotated in the consensus CNVRs. Among the 537 genes with functional information, the GO and pathway analysis was reported for those who clustered with a p-value <0.05. The quantitative PCRs successfully validated 14 (93.33%) of the selected CNVRs.
The result of this study is the first comprehensive genomic analysis of the Brown Swiss breed based on the Illumina Bovine HD SNP chip on such a large number of animals that enriches the CNV map in the bovine genome. These findings also provide valuable information for further CNV studies. Finally, the results of the CNVR map delivers new information for functional, health and productive traits considered in selection programs of the Brown Swiss breed.


EPrint Type:Journal paper
Keywords:animal breeding, dairy cattle, LowInputBreeds, FiBL45009
Agrovoc keywords:
LanguageValueURI
Englishdairy cattlehttp://aims.fao.org/aos/agrovoc/c_2108
Englishgenomeshttp://aims.fao.org/aos/agrovoc/c_3224
Subjects: Animal husbandry > Production systems > Dairy cattle
Animal husbandry > Breeding and genetics
Research affiliation: Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Animal Husbandry and Breeding
Austria > Univ. VMU Wien
European Union > LowInputBreeds > SP 1: Dairy and meat cattle
Italy > Other organizations
Italy > Univ. Milano
Switzerland > Other organizations
DOI:10.1016/j.livsci.2016.08.006
Related Links:https://www.fibl.org/en/themes/projectdatabase/projectitem/project/160.html
Deposited By: Bieber, Anna
ID Code:38548
Deposited On:30 Oct 2020 11:51
Last Modified:30 Oct 2020 11:51
Document Language:English
Status:Published
Refereed:Peer-reviewed and accepted

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