Allelic variations in exon 2 of caprine MHC class II DRB3 gene in Chinese indigenous goats

Allelic variations in the second exon of caprine leukocyte antigen-DRB3 gene (CLA-DRB3*02) were investigated. A total of 459 animals from 12 Chinese indigenous goat populations were genotyped. Six alleles and 18 restriction digestion profiles were distinguished by digestion of PCR amplification product of CLA-DRB3*02 with HaeIII. The results suggested that there were significant difference (P < 0.000) in both allele frequencies and genotype frequencies of exon 2 restriction fragment length polymorphisms (RFLPs) among the breeds. The new allele CLA-DRB3*0206 was identified only in three goat populations from the three-gorge reservoir, and the breed-specific allele CLA-DRB3*0205 was merely detected in the three populations of Tibetan goat. The results also indicated that the potentially different ecological factors, such as climate, disease, topography, pasture conditions and pathogens might be account for the significantly different distribution of alleles and genotypes among the goat populations. The nucleotide and predicted amino acid sequence alignment of CLA-DRB3*02 alleles provided evidence for considerable variation among the six alleles. Phylogenetic analysis showed that the six alleles of CLA-DRB3*02 were closely related. They clustered together and were separated from the corresponding sequences of sheep and cattle, which indicated the trans-species evolution model of CLA-DRB3*02 was not present in the Chinese goat populations studied.