An initial map of chromosomal segmental copy number variations in the chicken

Abstract

BackgroundChromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory elements. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as a model for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosomal regions that segregate for important agricultural and disease phenotypes.ResultsNinety six CNVs were identified in three lines of chickens (Cornish Rock broiler, Leghorn and Rhode Island Red) using whole genome tiling array. These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Whereas most small sized CNVs reside in none coding sequences, larger CNV regions involve genes (for example prolactin receptor, aldose reductase and zinc finger proteins). These results suggest that chicken CNVs potentially affect agricultural or disease related traits.ConclusionAn initial map of CNVs for the chicken has been described. Although chicken genome is approximately one third the size of a typical mammalian genome, the pattern of chicken CNVs is similar to that of mammals. The number of CNVs detected per individual was also similar to that found in dogs, mice, rats and macaques. A map of chicken CNVs provides new information on genetic variations for the understanding of important agricultural traits and disease.

Gene Duplication of endothelin 3 Is Closely Correlated with the Hyperpigmentation of the Internal Organs (Fibromelanosis) in Silky Chickens

“…a specific phenotype has been documented (Wright et al 2009). Intraspecific CNVs for the chicken genome were analyzed by using NimbleGen whole genome tiling arrays with 385,000 probes; the mean probe spacing was 2.6 kb (Wang et al 2010). However, the 130-kb CNV in this study was not found by them; we are, therefore, the first to report this CNV between Silky fowl and other chicken breeds.…”

“…Furthermore, recent studies have found CNVs related to various human diseases (Wain et al 2009;Zhang et al 2009;Stankiewicz and Lupski 2010). CNVs are also observed in Aves both in inter-and intraspecies (Griffin et al 2008;Skinner et al 2009;Völker et al 2010;Wang et al 2010). In addition, an association between CNVs and Figure 3 Genetic (left) and physical (right) maps of Fm on chicken chromosome 20.…”

“…However, the 130-kb CNV in this study was not found by them; we are, therefore, the first to report this CNV between Silky fowl and other chicken breeds. Since Wang et al (2010) used three fm lines (broilers, Leghorns, and Rhode Island Reds), we believe that none of these lines has a duplicated copy of the region. This may explain why the CNV was not detected by their whole chicken genome assay.…”

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

“…The NGS technology and RD method employed in our work has advantages in both technology platform and genetic diversity compared with the eight previous reports [9,[32][33][34]36,[39][40][41]. Because a significant fraction of CNVs falls into genomic regions not well-covered by microarrays, especially for SD regions lacking sufficient probes [16,23], CNV as a major source of genetic variation is complementary to SNP and could account for a substantial part of missing heritability [14].…”

Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination

“…In recent years, advances in high-throughput genome scan technologies, particularly DNA hybridization on array platforms and next-generation sequencing methods, have allowed the identification of a large number of structural variants in multiple species. Although not as comprehensive as those for human, CNV maps have been produced in cattle (2,3), horse (4), sheep (5,6), pig (7), goat (8), duck (9), and chicken (10,11).…”