Jun 15, 2013

Large scale variation in DNA copy number in chicken breeds

BMC Genomics
Richard P M A CrooijmansMartien A M Groenen

Abstract

Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds. We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV. A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. Th...Continue Reading

  • References32
  • Citations17

References

  • References32
  • Citations17

Citations

Mentioned in this Paper

DNA Copy Number Changes
Genome
Dopa-Responsive Dystonia
Keratin
Array-Based Comparative Genomic Hybridization
Cytokeratin
Breeding
Gene Family
LARGE gene
Single Nucleotide Polymorphism

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