Genetic polymorphism within exon 2 of MHC B-G gene in nine Chinese indigenous chicken breeds

摘要

Genetic polymorphism within chicken major histocompatibility complex B-G genes was investigated by amplification of exon 2 using PCR, followed by cloning and DNA sequencing after preliminary screening on 557 individuals from nine Chinese indigenous breeds and one exotic breed. We found 31 novel alleles of B-G genes，and allele distributions at the different breeds were notably non-symmetrical. Alignment and comparison of the 29 sequences from Chinese local chickens revealed a total of 37 variable sites in the fragment of exon 2, of which 29 parsimony informative and 8 singleton variable sites were observed. The genetic distances between the alleles were estimated, 0.0013–0.1433；the variation index for per variable site was calculated as the entropy of 0.206–1.462. The relative frequencies of non-synonymous substitutions of nucleotide per non-synonymous site and synonymous substitutions per synonymous site within the region were 9.26%±1.92% and 2.34%±0.90%, respectively. The number of observed transitions versus tranversions gradually increased with genetic distances, indicating that the nucleotide substitution in the region was not saturated. Alignment of deduced amino acid sequences encoded by exon 2, showed 22 polymorphic sites of which 6 sites were parsimony informative and 16 sites were singleton variable. The amino acid properties of the immunoglobulin variable-like domain along the sequence were investigated. Its isoelectric point was 8.45, and hydrophobic amino acids accounted for 40.3% and hydrophillic 29.9%. Investigation of the dendrogram constructed using the sampled sequences revealed a preliminary phylogeny among the 29 alleles from the Chinese native chicken populations. It provided molecular data for the study on immune function and genetic evolution of chicken B-G gene [ Acta Zoologica Sinica 52(1): 160–169,2006].