No Specific Primer Can Independently Amplify the Complete Exon 2 of Chicken BLB1 or BLB2 Genes

Chicken BLB1 and BLB2 genes are duplicated within MHC-S region that plays a crucial role in disease resistance or susceptibility. To investigate the genetic polymorphism in chicken BLB genes, we analyzed the complete genomic DNA sequences of BLB1 and BLB2 genes from 14 published MHC-S haplotypes (59 kb). Two pairs of primers were chosen or designed to amplify the exon 2 fragments of both genes from six known MHC-S haplotypes. The PCR products were directly sequenced for a preliminary identification of specific variations that were further validated using cloning approach. We found that the specificity of the primers becomes ambiguous to nearly all of the MHC-S haplotypes. Therefore it is impossible to design specific primer according to the complete exon and intron sequences for an independent amplification of complete exon 2 of the BLB1 or BLB2 genes. This calls for an alternative strategy for the investigation of genetic variations in the BLB genes.