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. 2018 May 22;19(1):33.
doi: 10.1186/s12863-018-0618-7.

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

Shin-Nosuke Takeshima  1   2   3   4   5 , Claudia Corbi-Botto  6 , Guillermo Giovambattista  6 , Yoko Aida  7   8   9   10   11
Affiliations

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

Shin-Nosuke Takeshima et al. BMC Genet. .

Abstract

Background: Bovine 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.

Results: We 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.

Conclusions: The 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.

Keywords: BoLA-DRB3; Brahman; Genetic diversity; Gir; Nellore; Sequence-based typing.

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Conflict of interest statement

Ethics approval

All animals were handled by veterinarians from RIKEN, Universidad Austral de Chile and LAVET, in strict accordance with good animal practice following the Universidad Austral de Chile Institutional guidelines. This study was approved by the Committee on the Ethics of Animals for Research at the National University of LA PLATA (Certificate date May 26th, 2014) and by the Committee on the Ethics of Animals for Research at Universidad Austral de Chile (Certificate No. 153–2014). The animal has derived from private owners and the consent was taken in verbal form, because each farmer commonly contacts with veterinarian in same way.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Venn diagram showing BoLA-DRB3 allele distribution among cattle breeds grouped according to geographical origin: British, European Continental, American Creole, and Cebu
Fig. 2
Fig. 2
Cumulative gene frequency plot for Bolivian Gir (blue), Bolivian Nellore (red), and Peruvian Nellore × Brahman (green)
Fig. 3
Fig. 3
a Genetic distance between pairs of populations estimated by Wright’s F statistics (FST) (below) and Nei’s DA distance (above). b Graphical representation of calculated FST values between population pairs using an R-function: pairFstMatrix.r. HeCh = Chilean Hereford; HoJa = Japanese Holstein; ShoJa = Japanese Shorthorn; JeJa = Japanese Jersey; WaJa = Japanese Black; Ya = Yacumeño; HV = Hartón del Valle; NaPh = Philippine Native; BrPh = Philippine Brahman; GirBo = Bolivian Gir; NeBo = Bolivian Nellore; and NexBrPe = Peruvian Nellore × Brahman
Fig. 4
Fig. 4
a Neighbor-joining tree constructed from a matrix of Nei’s DA genetic distances. b Principal component analysis of 12 cattle breeds based on BoLA-DRB3 allele frequencies. HeCh = Chilean Hereford; WaJa = Japanese Black; HoJa = Japanese Holstein; ShoJa = Japanese Shorthorn; JaJe = Japanese Jersey; YA = Yacumeño; NaPh = Native Philippine; HV = Hartón del Valle; BrPh = Philippine Brahman; GirBo = Bolivian Gir; NexBrPe = Peruvian Nellore × Brahman; and NeBo = Bolivian Nellore
Fig. 5
Fig. 5
Principal component analysis of 12 cattle breeds based on the amino acid motif form antigen binding site (ABS) of BoLA-DRB3. a Pocket 1. b Pocket 4. c Pocket 6. d Pocket 7. e Pocket 9. HeCh = Chilean Hereford; WaJa = Japanese Black; HoJa = Japanese Holstein; ShoJa = Japanese Shorthorn; JaJe = Japanese Jersey; YA = Yacumeño; NaPh = Native Philippine; HV = Hartón del Valle; BrPh = Philippine Brahman; GirBo = Bolivian Gir; NexBrPe = Peruvian Nellore × Brahman; and NeBo = Bolivian Nellore. G,Glycine;P,Proline;A,Alanine;V,Valine;L,Leucine;I,Isoleucine;M,Methionine;F,Phenylalanine;Y,Tyrosine;W,Tryptophan;H,Histidine;R,Arginine;Q,Glutamine;N,Asparagine;E,Glutamic Acid;D,Aspartic Acid;S,Serine;T,Threonine
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