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Journal of Heredity Advance Access originally published online on November 5, 2007
Journal of Heredity 2007 98(7):723-726; doi:10.1093/jhered/esm094
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© The American Genetic Association. 2007. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Brief Communications

Mitochondrial DNA Sequence and Haplotype Variation Analysis in the Chicken (Gallus gallus)

Xiaojing Guan, Tuoyu Geng, Pradeepa Silva, and Edward J. Smith

From Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061 (Guan, Geng, Silva, and Smith); and Department of Animal Sciences, University of Peradeniya, Kandy, Sri Lanka (Silva)

Address correspondence to E. J. Smith at the address above, or e-mail: esmith{at}vt.edu.

Although it is known to be useful for certain genotype:phenotype assignments, our knowledge of the nature and extent of variation in the entire chicken (Gallus gallus) mitochondrial genome (mtGenome) is limited. Here, we used experimental and in silico tools to identify nucleotide variants in the mtGenome, including the coding and non-coding (D-loop) regions. The distribution of the experimentally identified mitochondrial DNA variants in meat- (broilers) and egg-type (White Leghorn) chickens was also assessed. A total of 113 single-nucleotide polymorphisms (SNPs) were identified. The in silico analysis revealed a total of 91 SNPs, with 70 in the coding region and 21 in the non-coding region. Of the 41 experimentally identified SNPs, 27 were in the D-loop. Together, the experimentally identified SNPs in the non-coding region formed 11 haplotypes, whereas the 14 SNPs in the coding region formed 6. Though, 9 of the D-loop region haplotypes were observed only in broilers, 3 of the 6 haplotypes from the coding region occurred at a significantly higher frequency in broilers. To our knowledge, this investigation represents the first whole-mtGenome scan for variation and an evaluation, though limited in sample size, of the haplotype distribution in meat- and egg-type populations, using the SNPs and haplotypes identified.

Corresponding Editor: Rob Fleischer


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