gains or losses of ≥1 kb of genomic DNA. These polymorphisms represent the most important source of variability in mammalian genomes in terms of interested nucleotides. Many CNVs represent neutral polymorphic variants, whereas several others cause or are associated with both Mendelian and complex traits. We already investigated CNVs in the ovine genome by cross-species array comparative genome hybridization and produced a first sheep CNV map based on the cattle genome. In this study we used the Illumina OvineSNP50 BeadChip data generated in Italian sheep breeds to identify CNVs in the Ovis aries genome. Genotyping data were obtained for 24 animals for each of 15 different breeds (Altamurana, Appenninica, Bagnolese, Bergamasca, Biellese, Delle Langhe, Fabrianese, Gentile di Puglia, Istrian Pramenka, Laticauda, Massese, Pinzirita, Sambucana, Sopravissana and Valle del Belice). Single nucleotide polymorphisms (SNPs) included in the Illumina OvineSNP50 BeadChip were first mapped on the Oar_v3.1 build of the sheep genome. CNVs were called after filtering genotyping data using the PennCNV software with stringent parameters and correction for waviness effects to reduce false positives. In total, we identified 656 CNV events, covering on the whole 2.62 Mb, and corresponding to 24 CNV regions (CNVRs): 21 were characterized by a loss and 3 by a gain of copy number. Some of these CNVRs harbour coding genes involved in important metabolic pathways and signalling processes. Additional studies are needed to evaluate the effects of these CNVs on phenotypic and production traits in sheep and their usefulness in defining relationships among breeds.
Analysis of copy number variations in Italian sheep breeds using the Illumina OvineSNP50 BeadChip array
CIANI, ELENA;
2013-01-01
Abstract
gains or losses of ≥1 kb of genomic DNA. These polymorphisms represent the most important source of variability in mammalian genomes in terms of interested nucleotides. Many CNVs represent neutral polymorphic variants, whereas several others cause or are associated with both Mendelian and complex traits. We already investigated CNVs in the ovine genome by cross-species array comparative genome hybridization and produced a first sheep CNV map based on the cattle genome. In this study we used the Illumina OvineSNP50 BeadChip data generated in Italian sheep breeds to identify CNVs in the Ovis aries genome. Genotyping data were obtained for 24 animals for each of 15 different breeds (Altamurana, Appenninica, Bagnolese, Bergamasca, Biellese, Delle Langhe, Fabrianese, Gentile di Puglia, Istrian Pramenka, Laticauda, Massese, Pinzirita, Sambucana, Sopravissana and Valle del Belice). Single nucleotide polymorphisms (SNPs) included in the Illumina OvineSNP50 BeadChip were first mapped on the Oar_v3.1 build of the sheep genome. CNVs were called after filtering genotyping data using the PennCNV software with stringent parameters and correction for waviness effects to reduce false positives. In total, we identified 656 CNV events, covering on the whole 2.62 Mb, and corresponding to 24 CNV regions (CNVRs): 21 were characterized by a loss and 3 by a gain of copy number. Some of these CNVRs harbour coding genes involved in important metabolic pathways and signalling processes. Additional studies are needed to evaluate the effects of these CNVs on phenotypic and production traits in sheep and their usefulness in defining relationships among breeds.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
