Genetic diversity and evolutionary significance of Cahi-DRB1 gene in Indian goat from semi-arid regions

Unlocking the genetic diversity of the Cahi-DRB1 gene in Indian goat breeds sheds light on their immune system's resilience. While extensive studies have elucidated MHC diversity in cattle and sheep, research on goats remains limited. Thus, this study aimed to investigate the genetic diversity of cahi-DRB1 across five goat breeds in India, encompassing a total of 233 individual goats. Using a PCR sequence-based typing approach, DRB1 fragments (285 bp) were amplified and sequenced. The PCR products were purified and sequenced. Amino acid variability within breeds was evaluated using the Wu-Kabat index at peptide-binding pockets. Selection analysis included assessing positive selection through relative rates of nonsynonymous and synonymous mutations, Z-test, and Tajima's test of neutrality. The findings revealed notable heterozygosity across breeds (mean: 100 %), with nucleotide content averaging 22.51 % for A, 18.62 % for T, 24.33 % for C, and 34.35 % for G. The GC content was rich (59.26 %) across breeds for the DRB1 region. The mean distance for DRB1 was highest in Barbari (0.20) and lowest in Osmanabadi goat (0.12), with a higher rate of transversions observed. The Wu-Kabat index assessments underscored substantial genetic variation within the peptide binding sites (PBS) of DRB1, with specific residues (12, 14, 33, 58, and 87) showing polymorphism relevant to antigen presentation. Positive selection pressure was evident across all breeds for the DRB1 locus (dN>dS), highlighting its evolutionary significance. The rich diversity of the DRB1 gene underscores the fitness of the population and the significance of this locus for future selection programs. These results highlight the highly polymorphic nature of the DRB1 locus in Indian goat breeds, emphasizing its crucial role in modulating immune responses. Consequently, our study offers valuable insights for developing targeted breeding strategies to enhance disease resistance in goats, thereby providing practical implications for sustainable livestock management.