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. 2010 Jun 3:11:351.
doi: 10.1186/1471-2164-11-351.

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

Xiaofei Wang  1 , Samuel Nahashon, Tromondae K Feaster, Ann Bohannon-Stewart, Nathaniel Adefope
Affiliations

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

Xiaofei Wang et al. BMC Genomics. .

Abstract

Background: Chromosomal 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.

Results: Ninety 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.

Conclusion: An 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.

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Figures

Figure 1
Figure 1
Quantitative PCR analysis of CNVs in 20 birds. DNA samples were diluted to 10 ng/μl and the conecentrations were meassured with Nanodrop spectrophotometer. Relative copy number was obtained by comparing threshold cyles of test DNA with a reference DNA that was serial diluted to 80, 20, 10 and 2.5 ng/μl. One unit of relative copies is the amount in 1 ng of reference DNA. Values represent mean ± SD of four reactions. Data were not normalized to the reference locus and copy number was not rounded. Numbers on x-axis are bird ID.
Figure 2
Figure 2
Organization of CNV region at locus 17 located on GGA 10 (Chr10: 125113-157964). A block of sequence (Chr10:125051-149999) was aligned with chicken genome assembly build 2.1 using BLAT algorithm at UCSC genome database. Numbers at the top of the graph represent nucleotide positions in the chicken genome assembly. Long arrows indicate higher order repeat organization and orientation. Short green arrows indicate orientation and location of human olfactory receptor homologs aligned to GGA 10. Symbols of the same style (line color and fillings) on the same side of the blue line represent sequence blocks sharing >95% identity.
Figure 3
Figure 3
Relationship between copy number and transcript levels at RHACD8 locus. (A) Plot of spleen CD8α and RHACD8 mRNA levels. Spleen RNA samples were isolated from adult broilers and Leghorns. (B) Plot of GAPDH mRNA levels in spleen of the same 10 chickens. (C) Pearson correlation between CD8α and RHACD8 mRNA levels. (C) Pearson correlation between RHACD8 mRNA level and of RHACD8 DNA copy number.
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