Detection of CNVs in layer chickens using 42K, 50K and 600K SNP chips A. Wolc1,2, W. Drobik- Czwarno 1,3, J.E. Fulton2, P. Settar2, J. Arango2, D. Lubritz2, J.C.M. Dekkers1 1Department of Animal Science, Iowa State University, 806 Stange Road, 239E Kildee Hall, Ames, Iowa 50011, USA. awolc@iastate.edu (Corresponding Author) 2Hy-Line International, 2583 240th Street, Dallas Center, Iowa 50063, USA. 3Department of Animal Genetics and Breeding, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland. The development of SNP chips has enabled rapid genotyping of hundreds of thousands of loci at a relatively low cost. In addition to providing SNP genotype information, copy number variation (CNV) can also be inferred from intensity data generated by the same chips. The aim of this study was to detect and describe CNVs in five lines of layer chickens using different SNP chips. A total of 18,719 individuals from four pure lines and one commercial cross were genotyped using four different SNP chips (Illumina 42K, Affymetrix 600K, and two customized Affymetrix 50K chips). Analysis software Axiom® CNV Summary Tools and PennCNV were used to identify CNVs from Affymetrix chips and cnvPartition in Genome Studio was used to identify CNV’s from the Illumina chip. The CNV regions (CNVR) within lines were defined using the BedTools software, through merging CNVs overlapping by at least 1 bp. CNVRs identified across all panels were selected with BedTools intersect to choose regions with highest confidence. Gene enrichment analysis was performed for genes that overlap identified CNVs to detect overrepresented biological processes and pathways. The mean number of detected CNVs per individual varied depending on the population and size of the SNP set, from 0.50 with the 50K chip in one of the white layer lines up to 4.87 with the 600K chip in one of the brown layer lines. There were considerable differences in the number of detected CNVs between lines, probably due to breeding history. The length of detected CNVs ranged from 1.16 kb to 3.16 Mb. The mean length of detected CNVs was higher for the 42K and 50K chips than for the 600K chip, which is most likely a result of low detectability of shorter CNVs due to larger distances between markers in comparison to the 600K chip. The low frequency of CNVs detected on the 50K panels could also result from their custom design, which intentionally eliminated poorly clustering SNPs. Most of the detected CNVs had low population frequencies. In total CNVs were merged into 2687 CNVRs and overlapped 495.73 Mb of the genome. Intersecting CNVRs across all lines and panels yielded 4131 CNVRs from which 2139 were observed in at least two individuals. In conclusion, commonly used SNP chip platforms and analysis using relevant software can be used to identify CNVs in commercially relevant chicken layer lines. The number of detected CNVs and their length depends on the population and density of SNP on the chip. Keywords: CNV, SNP chip, layer chicken, association study

Anna Wolc, Wioleta Drobik- Czwarno, Janet Fulton, Petek Settar, Jesus Arango, Danny Lubritz, Jack Dekkers

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Technologies - Genotyping, , 85, 2018
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