Detection of copy number variations in brown and white layers based on genotyping panels with different densities

Wioleta Drobik-Czwarno,Janet E Fulton,Jack C M Dekkers,Anna Wolc

doi:10.1186/s12711-018-0428-4

Abstract

BackgroundCopy number variations (CNV) are an important source of genetic variation that has gained increasing attention over the last couple of years. In this study, we performed CNV detection and functional analysis for 18,719 individuals from four pure lines and one commercial cross of layer chickens. Samples were genotyped on four single nucleotide polymorphism (SNP) genotyping platforms, i.e. the Illumina 42K, Affymetrix 600K, and two different customized Affymetrix 50K chips. CNV recovered from the Affymetrix chips were identified by using the Axiom® CNV Summary Tools and PennCNV software and those from the Illumina chip were identified by using the cnvPartition in the Genome Studio software.ResultsThe mean number of CNV per individual varied from 0.50 to 4.87 according to line or cross and size of the SNP genotyping set. The length of the detected CNV across all datasets ranged from 1.2 kb to 3.2 Mb. The number of duplications exceeded the number of deletions for most lines. Between the lines, there were considerable differences in the number of detected CNV and their distribution. Most of the detected CNV had a low frequency, but 19 CNV were identified with a frequency higher than 5% in birds that were genotyped on the 600K panel, with the most common CNV being detected in 734 birds from three lines.ConclusionsCommonly used SNP genotyping platforms can be used to detect segregating CNV in chicken layer lines. The sample sizes for this study enabled a detailed characterization of the CNV landscape within commercially relevant lines. The size of the SNP panel used affected detection efficiency, with more CNV detected per individual on the higher density 600K panel. In spite of the high level of inter-individual diversity and a large number of CNV observed within individuals, we were able to detect 19 frequent CNV, of which, 57.9% overlapped with annotated genes and 89% overlapped with known quantitative trait loci.

Highlights

Copy number variations (CNV) are an important source of genetic variation that has gained increas‐ ing attention over the last couple of years
Detection of CNV The proportion of samples that passed quality control ranged from 89.4% in line B1 genotyped on the 50K panel up to 99.6% in line W1 genotyped on the 600K panel
19 high frequency CNV region (CNVR) were detected using the 600K panel, of which 57.9% overlapped with annotated genes (Additional file 1)

Summary

Introduction

Copy number variations (CNV) are an important source of genetic variation that has gained increas‐ ing attention over the last couple of years. Copy number variations (CNV) refer to large-scale insertions, duplications, or deletions of DNA sequence segments compared to a reference assembly. Several species of farm animals have been scanned for CNV, including cattle [10,11,12], sheep [13, 14], goats [15], and pigs [16,17,18] and numerous studies have examined CNV in the chicken genome [19,20,21,22,23,24,25,26,27,28,29,30,31,32].

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Conclusion