Genetic polymorphism of major histocompatibility complex class II genes

Abstract

The study was conducted in 85 Malabari and 30 Attappady Black goats to analyze the PCR-RFLP polymorphism and the sequences of Major Histocompatibility Complex class II DRB and DQA2 genes. The analysis of DRB/TaqI polymorphism in Malabari and Attappady Black breeds of goats showed similar restriction patterns in both breeds with no significant changes in allele frequencies. It was also found that all the three genotypes had an equal survival capacity with respect to DRB/TaqI site as both the populations were under were under Hardy-Weinberg equilibrium. The analysis of DRB/ PstI polymorphism revealed existence of two digestion patterns (PP, Pp). The ‘pp’ pattern was absent in both Malabari and Attappady Black goats probably due to the lethal effect of ‘pp’ genotype which has prevented the survival of that genotype in the studied population. This natural selective force acting against ‘pp’ genotype resulted in significant changes in the expected genotypic frequencies and the populations were found to be not in Hardy-Weinberg equilibrium. The analysis of DQA2/EcoRV polymorphism in Malabari and Attappady Black goat populations revealed existence of all the three possible restriction patterns with a clear heterozygotic advantage (genotype frequency of 0.79 for ‘Ee’ in Malabari goats) which is expected to be due to existence of duplicate copies of DQA2 gene. The sequencing of the DRB gene second exon form Malabari and Attappady Black goats revealed four different DRB alleles having 285 bp each and were more similar to Capra aegagrus (98 to 99 percent) DRB alleles in BLASTn analysis. The sequencing of the DQA2 gene second exon and the flanking intronic sequences form Malabari and Attappady Black goats revealed four different alleles, three of which were having 304 bp each and the fourth one having 300 bp. The sequencing revealed the base changes responsible for the presence or absence of TaqI, PstI and EcoRV restriction sites in Malabari and Attappady Black goats.

The 93 and 82 amino acid compositions of DRB and DQA2 second exons revealed amino acid replacements at 23 and 21 positions respectively, many of which are present at the antigen binding region and hence affect peptide specificity. PstI genotypes significantly affected the Ig level in goats and the heterozygotic genotype was found to have higher efficiency in antigen processing.

The present study has helped to understand the variations existing in the second exon of DRB and DQA2 loci in Malabari and Attapady Black breeds of goats which has a role in the disease resistance and immunity.