Genetic diversity analysis of DRB3.2 in domestic yak (Bos grunniens) in Qinghai-Tibetan Plateau

Abstract

DRB3 gene has been extensively evaluated as a candidate marker for association with many bovine disease and immunological traits. A hemi-nested polymerase chain reaction-sequencing method was used to investigate the polymorphisms of DRB3.2 gene from 209 individuals in three different domestic yak (Bos grunniens) populations (62 Tianzhu white yaks, 78 Gannan yaks and 69 Datong yaks) from the Qinghai-Tibetan Plateau. Sixty-three polymorphic sites and 143 haplotypes were detected. The percentage of polymorphic sites in Gannan Yak (GNY), Tianzhu white Yak (TWY) and Datong Yak (DTY) were 21.80, 29.95 and 12.95%, while the haplotype diversity were 0.9987, 0.9984 and 0.9855, respectively. At the amino acid level, Glu had the highest content; the percentage was 12.326%, followed by Arg (10.315%), Phe (10.804%), Val (8.346%), Gly (8.315%), Leu (6.606%) and Ala (5.851%), whereas Met and Ile were below than 1%. Only 19 amino acids were found in DTY, Met was lost. Among the synonymous codons, whose third base was G and/or C had a higher usage frequency. Most variability were found in amino acid residues 11, 13, 26, 28, 30, 32, 37, 56, 57, 59, 60, 61, 67, 70, 71, 72, 73 and 74. In GNY, the residues at positions 71, 11 and 72 were highly polymorphic with 8, 7 and 7, at 50, 58, 70, 74 and 78, the residues were selectively polymorphic than other yak populations; the other polymorphic sites were common in the populations. The results of this study indicated that the Chinese domestic yak populations in the Qinghai-Tibetan Plateau have abundant polymorphism in DRB3.2, and the GNY was the highest, followed by TWY and DTY.

Key words: Domestic Yak, Hemi-nested PCR, BoLA-DRB3.2, polymorphism.