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

Abstract

Background: Myanmar cattle populations predominantly consist of native cattle breeds, characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly adapted to the harsh tropical climates of this region. Here, we analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus that has been linked to the immune response, in Myanmar cattle populations.Methods: Blood samples (n=294) were taken from two native breeds (Pyer Sein, n=163 and Shwe Ni, n=69) and a cattle crossbreed (Holstein-Friesian, n=62) distributed across six regions of Myanmar (Bago, n=38; Sagaing, n=77; Mandalay, n=46; Magway, n=46; Kayin, n=43; Yangon, n=44). DNA was genotyped using the sequence-based typing method. DNA electropherograms were analyzed using the Assign 400ATF software. Results: We detected 71 distinct alleles, including three new variants for the BoLA-DRB3 gene. Venn analysis showed that 11 of these alleles were only detected in Myanmar native breeds and 26 were only shared with Asian native and/or Zebu groups. The number of alleles ranged from 33 in Holstein-Friesians to 58 in Pyer Seins, and the observed versus unbiased expected heterozygosity were higher than 0.84 in all the three the populations analyzed. The FST analysis showed a low level of genetic differentiation between the two Myanmar native breeds (FST=0.003), and between these native breeds and the Holstein-Friesians (FST < 0.021). The average FST value for all the Myanmar Holstein-Friesian crossbred and Myanmar native populations was 0.0136 and 0.0121, respectively. Principal component analysis (PCA) and tree analysis showed that Myanmar native populations grouped in a narrow cluster that diverged clearly from the Holstein-Friesian populations. Furthermore, the BoLA-DRB3 allele frequencies suggested that while some Myanmar native populations (Bago, Mandalay and Yangon) were more closely related to Zebu breeds (Gir and Brahman), others (Kayin, Magway and Sagaing) were more related to the native breeds found in the Philippines. On the contrary, the Holstein-Friesian populations demonstrated a high degree of dispersion, which is likely the result of the different degrees of native admixture in these populations. Conclusion: These results contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar.

BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from Taurine and Zebu breeds

“…Significant differences were observed in nine out of the ten native population comparisons (p < 0.05; Table S4). Similar genetic distance values were observed among Holstein populations from different countries and between native breeds of Myanmar [24,29].…”

“…The average F ST value showed a low level of genetic differentiation (F ST = 0.0076) among native Sudanese breeds, ranging between 0.007 and 0.009 (Table S3). This average value is higher than those estimated in Myanmar native breeds (F ST = 0.003), and slightly lower than those reported for Holstein populations from different countries (F ST = 0.009) [24,29] ( Figure 4 and Table S2). When breeds were grouped in terms of the breed's geographical origin, as was done in the Venn diagram, the genetic variance among breed groups and among populations within groups accounted for 1.18% and 3.71% of the total genetic variance.…”

“…These results reveal that Sudanese cattle breeds have a particular diversity in the BoLA-DRB3 gene, as a consequence of its gene frequency profile and the presence of a high number of private alleles. [25,27,29].…”

“…Despite its central role in the immune response, the genetic diversity of the BoLA-DRB3 gene has been characterized in a limited number of breeds and cross-breeds from Europe, Asia and the Americas using polymerase chain reaction-sequence based typing (PCR-SBT; [16][17][18][19][20][21][22][23][24][25][26][27][28][29]) and target next generation sequencing (Target-NGS; [30]), the most powerful tools used to identify diversity of BoLA-DRB3 alleles in cattle breeds. Until now, private African BoLA-DRB3 alleles have been reported by authors using indirect techniques, such as PCR-RFLP, followed by cloning and sequencing [31][32][33][34].…”

“…Consequently, there are still a number of breeds that remain uncharacterized, and this number only increases when local native bovine breeds are considered [18,26,27,29,30].…”