Genetic analysis of major histocompatibility complex (MHC) Class I Exon 4-5 in cattle and buffalo using molecular and phylogenetic approaches

Abstract

Characterization of major histocompatibility complex (MHC) Class I Exon 4-5 was carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), single-strand confirmation polymorphism (SSCP) and sequencing techniques in crossbred cattle and buffaloes. Digestion of 559 bp fragment with HinfI and HaeIII restriction enzymes produced five and three distinct PCR-RFLP patterns in cattle and buffaloes, respectively. The genotype frequencies of HinfI patterns ranged from 0.015 to 0.456 in crossbred cattle, 0.080 to 0.600 in Mehsana and 0.050 to 0.500 in Bhadawari breeds of buffaloes. Similarly, the genotype frequencies of HaeIII patterns ranged from 0.045 to 0.636. The SSCP analysis showed that the BoLA-A and BuLA-A were highly polymorphic in cattle and buffaloes. A total of 10 alleles (AA, AB, BB, AC, AD, AE, AF, BC, DD and DB) were identified by PCR-SSCP. Four partial sequences, two each for crossbred cattle (AY790633 and AY790634) and buffaloes (AY785759 and AY785760), were submitted to the GenBank, NCBI. The sequencing results showed a number of amino acid changes in Exon 4-5 region. In conclusion, MHC Class I Exon 4-5 was found to be highly polymorphic in both cattle and buffaloes which may be exploited for association with traits of economic interest.