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A genome-wide association study using CNVs for production traits in Brown Swiss dairy cattle

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Prinsen, R.T.M.M.; Strillacci, M.G.; Schiavini, F.; Rossoni, A.; Gredler, B.; Dolezal, M.A.; Bagnato, A. and Bieber, A. (2016) A genome-wide association study using CNVs for production traits in Brown Swiss dairy cattle. In: Book of Abstracts of the 67th Annual Meeting of the European Federation of Animal Science, p. 344.

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Summary

Detecting genetic variation such as Copy Number Variation (CNV) in cattle provides the opportunity to study their association with productive traits. The aim of this study was to investigate CNVs in 1,410 samples of the Brown Swiss cattle breed using Illumina BovineHD Genotyping BeadChip data and to perform a genomewide association analysis for three production traits: milk yield (MY), fat yield (FY) and protein yield (PY).
After severe quality control, CNVs were called with the Golden Helix SVS 8.3.1 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. CNV-association studies were executed with the CNVRuler software using a linear regression model. Genes within significant associated CNVRs for each trait were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7. The quality control filtered out 294 samples. The GoldenHelix software identified 25,030 CNVs summarized to 398 CNVRs while PennCNV identified 62,341 CNVs summarized to 5,578 CNVRs. A total of 132 CNVRs were identified to be significantly associated with one or more of the three evaluated traits. The greatest association signal was given by a CNVR on chromosome 4 for MY. The associated regions overlap with 256 genes annotated on the Bos taurus genome assembly (UMD3.1). The result of this study is a comprehensive genomic analysis of the Brown Swiss breed, which enriches the bovine CNV map in its genome. Finally, the results of the association studies deliver new information for productive traits considered in selection programs of the Brown Swiss breed.


EPrint Type:Conference paper, poster, etc.
Type of presentation:Poster
Keywords:Brown Swiss, dairy cattle, animal breeding, selecetion
Agrovoc keywords:
LanguageValueURI
Englishcattlehttp://aims.fao.org/aos/agrovoc/c_1391
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
"Organics" in general > Countries and regions > Switzerland
Research affiliation: Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Animal Husbandry and Breeding
Austria > Univ. VMU Wien
Italy > Other organizations
Switzerland > Other organizations
ISSN:1382-6077
ISBN:978-90-8686-284-9
DOI:DOI: 10.3920/978-90-8686-830-8
Deposited By: Bieber, Anna
ID Code:38543
Deposited On:30 Oct 2020 09:39
Last Modified:30 Oct 2020 09:39
Document Language:English
Status:Published
Refereed:Peer-reviewed and accepted

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