Genetic diversity of BoLA-DRB3 in South American Zebu cattle populations

Abstract

BackgroundBovine leukocyte antigens (BoLAs) are used extensively as markers of disease and immunological traits in cattle. However, until now, characterization of BoLA gene polymorphisms in Zebu breeds using high resolution typing methods has been poor. Here, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 421 cattle (116 Bolivian Nellore, 110 Bolivian Gir, and 195 Peruvian Nellore-Brahman). Data from 1416 Taurine and Zebu samples were also included in the analysis.ResultsWe identified 46 previously reported alleles and no novel variants. Of note, 1/3 of the alleles were detected only in Zebu cattle. Comparison of the degree of genetic variability at the population and sequence levels with genetic distance in the three above mentioned breeds and nine previously reported breeds revealed that Zebu breeds had a gene diversity score higher than 0.86, a nucleotide diversity score higher than 0.06, and a mean number of pairwise differences greater than 16, being similar to those estimated for other cattle breeds. A neutrality test revealed that only Nellore-Brahman cattle showed the even gene frequency distribution expected under a balanced selection scenario. The FST index and the exact G test showed significant differences across all cattle populations (FST = 0.057; p < 0.001). Neighbor-joining trees and principal component analysis identified two major clusters: one comprising mainly European Taurine breeds and a second comprising Zebu breeds. This is consistent with the historical and geographical origin of these breeds. Some of these differences may be explained by variation of amino acid motifs at antigen-binding sites.ConclusionsThe results presented herein show that the historical divergence between Taurine and Zebu cattle breeds is a result of origin, selection, and adaptation events, which would explain the observed differences in BoLA-DRB3 gene diversity between the two major bovine types. This allelic information will be important for investigating the relationship between the major histocompatibility complex and disease, and contribute to an ongoing effort to catalog bovine MHC allele frequencies according to breed and location.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0618-7) contains supplementary material, which is available to authorized users.

Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

“…As shown in Table 3, the values obtained in Myanmar cattle were similar to those estimated for other cattle breeds Gene diversity, HWE, and neutrality testing of BoLA-DRB3 variants found in Myanmar cattle populations As mentioned above, n a ranged from 33 in the Holstein-Friesian crossbreed to 58 in the Pyer Sein native breed, while h e and h o were both higher than 0.86 in all three populations ( Table 2). These indexes are evidence of high diversity values for Myanmar cattle populations, which is similar to the results reported for other bovine breeds which have been evaluated by PCR-SBT, and characteristic of MHC class II DR genes [18,22,23,26,29]. When we evaluated the populations using the HWE test, two of the three Myanmar populations were in equilibrium, while native breed Shwe Ni signi cantly deviated from its theoretical values (Table 2), probably because of the signi cant proportions of homozygous animals found in this study (F IS = 0.1197, p < 0.0001).…”

“…In these PCA, the rst two components accounted for 41.11% of the data variability. The rst PC accounted for 27.12% of the total variance and, as shown in a previous study [29], rst component clearly exhibited a differentiation pattern between Zebu (negative values) and Taurine (positive values) breeds, while native breeds from Myanmar and the Philippines were located near the origin of the plot (Fig. 5b).…”

“…The π values within Pyer Sein, Shwe Ni and Holstein-Friesian crossbreed were 0.090, 0.080 and 0.080, respectively, while the mean number of pairwise differences was 20.96, 17.89 and 20.09, respectively. These nucleotide diversity values all fall within the upper end of the range reported (π range = 0.068-0.083; NPD range = 16.31-20.04) for other bovine breeds when using PCR-SBT genotyping methods [18,22,23,26,29].…”

“…5b). The rst PC was primarily determined by differences in the frequency of the same alleles reported by Takeshima et al [29]. The second PC explained 13.99% of the total variation and showed a gradient among Taurine breeds, with Japanese Black and Japanese Jersey located at opposite ends.…”

“…In addition, it has been reported in cattle that immune responses and disease resistance is signi cantly related to differences in the pocket 4 motif [46,47]. Takeshima et al [29] reported that PCAs based on allelic frequencies in the amino acid motif of the ABS pockets showed a clear differentiation between Taurine and Zebu breeds, because of an enrichment for particular amino acid motifs in speci c pockets. Further studies involving structural modeling and molecular simulation of the BoLA-DRβ protein are needed to elucidate whether these differences play a role in its function.…”