Genome-wide detection of copy-number variations in local cattle breeds

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Abstract

The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) andModicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker,using Illumina’s BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN thataggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with thetwo softwares contained 29 common CNVRs in CIN and 17 common CNVRs in MOD. Only a small number of CNVRsidentified in the present study have been identified elsewhere, probably because of the limitations of the array used. In total,178 and 208 genes were found within the CNVRs of CIN and MOD respectively. Gene Ontology and KEGG pathwayanalyses showed that several of these genes are involved in milk production, reproduction and behaviour, the immuneresponse, and resistance/susceptibility to infectious diseases. Our results have provided significant information for theconstruction of more-complete CNV maps of the bovine genome and offer an important resource for the investigationof genomic changes and traits of interest in the CIN and MOD cattle breeds. Our results will also be valuable for futurestudies and constitute a preliminary report of the CNV distribution resources in local cattle genomes.
Lingua originaleEnglish
Numero di pagine8
RivistaAnimal Production Science
Stato di pubblicazionePublished - 2018

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All Science Journal Classification (ASJC) codes

  • Food Science
  • Animal Science and Zoology

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