Characterization of Bovine MHC DRB3 Diversity in Global Cattle Breeds, with a Focus on Cattle in Myanmar

Overview

Journal BMC Genet

Publisher Biomed Central

Specialties Biotechnology
Molecular Biology

Date 2020 Sep 2

PMID 32867670

Citations 5

Authors

Guillermo Giovambattista

Kyaw Kyaw Moe

Meripet Polat

Liushiqi Borjigin

Si Thu Hein

Hla Hla Moe

Shin-Nosuke Takeshima

Yoko Aida

Affiliations

Soon will be listed here.

Abstract

Background: Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), 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). In addition, a database that included 2428 BoLA-DRB3 genotypes from European (Angus, Hereford, Holstein, Shorthorn, Overo Negro, Overo Colorado, and Jersey), Zebuine (Nellore, Brahman and Gir), Asian Native from Japan and Philippine and Latin-American Creole breeds was also included. Furthermore, the information from the IPD-MHC database was also used in the present analysis. 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 F analysis showed a low level of genetic differentiation between the two Myanmar native breeds (F = 0.003), and between these native breeds and the Holstein-Friesians (F < 0.021). The average F 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 from Bago, Mandalay and Yangon regions were more closely related to Zebu breeds (Gir and Brahman), populations from Kayin, Magway and Sagaing regions were more related to the Philippines native breeds. On the contrary, PCA showed that 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: This study is the first to report the genetic diversity of the BoLA-DRB3 gene in two native breeds and one exotic cattle crossbreed from Myanmar. The results obtained contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar, and increases our knowledge of the worldwide variability of cattle BoLA-DRB3 genes, an important locus for immune response and protection against pathogens.

Citing Articles

De novo genome assembly depicts the immune genomic characteristics of cattle.

Li T, Xia T, Wu J, Hong H, Sun Z, Wang M Nat Commun. 2023; 14(1):6601.

PMID: 37857610 PMC: 10587341. DOI: 10.1038/s41467-023-42161-1.

Phenotypic Selection of Dairy Cattle Infected with Bovine Leukemia Virus Demonstrates Immunogenetic Resilience through NGS-Based Genotyping of BoLA MHC Class II Genes.

Lohr C, Sporer K, Brigham K, Pavliscak L, Mason M, Borgman A Pathogens. 2022; 11(1).

PMID: 35056052 PMC: 8779071. DOI: 10.3390/pathogens11010104.

Nanovaccines against Animal Pathogens: The Latest Findings.

Celis-Giraldo C, Lopez-Aban J, Muro A, Patarroyo M, Manzano-Roman R Vaccines (Basel). 2021; 9(9).

PMID: 34579225 PMC: 8472905. DOI: 10.3390/vaccines9090988.

An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds.

Olschewsky A, Hinrichs D Animals (Basel). 2021; 11(7).

PMID: 34359144 PMC: 8300386. DOI: 10.3390/ani11072016.

Genetic Variation and Population Differentiation in the Bovine Lymphocyte Antigen Locus of South African Nguni Crossbred Cattle.

Mkize L, Zishiri O Animals (Basel). 2021; 11(6).

PMID: 34199370 PMC: 8228392. DOI: 10.3390/ani11061651.

References

Takeshima S, Miyasaka T, Polat M, Kikuya M, Matsumoto Y, Mingala C . The great diversity of major histocompatibility complex class II genes in Philippine native cattle. Meta Gene. 2015; 2:176-90. PMC: 4287811. DOI: 10.1016/j.mgene.2013.12.005. View

Takeshima S, Matsumoto Y, Aida Y . Short communication: Establishment of a new polymerase chain reaction-sequence-based typing method for genotyping cattle major histocompatibility complex class II DRB3. J Dairy Sci. 2009; 92(6):2965-70. DOI: 10.3168/jds.2008-1999. View

Bohorquez M, Ordonez D, Suarez C, Vicente B, Vieira C, Lopez-Aban J . Major Histocompatibility Complex Class II (DRB3) Genetic Diversity in Spanish Morucha and Colombian Normande Cattle Compared to Taurine and Zebu Populations. Front Genet. 2020; 10:1293. PMC: 6965167. DOI: 10.3389/fgene.2019.01293. View

Takeshima S, Ikegami M, Morita M, Nakai Y, Aida Y . Identification of new cattle BoLA-DRB3 alleles by sequence-based typing. Immunogenetics. 2001; 53(1):74-81. DOI: 10.1007/s002510000293. View

Sharif S, Mallard B, Sargeant J . Presence of glutamine at position 74 of pocket 4 in the BoLA-DR antigen binding groove is associated with occurrence of clinical mastitis caused by Staphylococcus species. Vet Immunol Immunopathol. 2000; 76(3-4):231-8. DOI: 10.1016/s0165-2427(00)00216-6. View

Rogberg-Munoz A, Wei S, Ripoli M, Guo B, Carino M, Liron J . Effectiveness of a 95 SNP panel for the screening of breed label fraud in the Chinese meat market. Meat Sci. 2015; 111:47-52. DOI: 10.1016/j.meatsci.2015.08.014. View

Xu A, Van Eijk M, Park C, Lewin H . Polymorphism in BoLA-DRB3 exon 2 correlates with resistance to persistent lymphocytosis caused by bovine leukemia virus. J Immunol. 1993; 151(12):6977-85. View

Weir B, Cockerham C . ESTIMATING F-STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE. Evolution. 2017; 38(6):1358-1370. DOI: 10.1111/j.1558-5646.1984.tb05657.x. View

Sigurdardottir S, Borsch C, Gustafsson K, Andersson L . Cloning and sequence analysis of 14 DRB alleles of the bovine major histocompatibility complex by using the polymerase chain reaction. Anim Genet. 1991; 22(3):199-209. DOI: 10.1111/j.1365-2052.1991.tb00670.x. View

10.

Chen H, Boutros P . VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics. 2011; 12:35. PMC: 3041657. DOI: 10.1186/1471-2105-12-35. View

11.

Takeshima S, Miyasaka T, Matsumoto Y, Xue G, Diaz V, Rogberg-Munoz A . Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class II BoLA-DRB3 allele. Tissue Antigens. 2014; 85(1):35-44. DOI: 10.1111/tan.12481. View

12.

Davies C, Andersson L, Joosten I, Mariani P, Gasbarre L, Hensen E . Characterization of bovine MHC class II polymorphism using three typing methods: serology, RFLP and IEF. Eur J Immunogenet. 1992; 19(5):253-62. DOI: 10.1111/j.1744-313x.1992.tb00068.x. View

13.

Takeshima S, Corbi-Botto C, Giovambattista G, Aida Y . Genetic diversity of BoLA-DRB3 in South American Zebu cattle populations. BMC Genet. 2018; 19(1):33. PMC: 5964877. DOI: 10.1186/s12863-018-0618-7. View

14.

Nei M . Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 1978; 89(3):583-90. PMC: 1213855. DOI: 10.1093/genetics/89.3.583. View

15.

Takeshima S, Matsumoto Y, Miyasaka T, Arainga-Ramirez M, Saito H, Onuma M . A new method for typing bovine major histocompatibility complex class II DRB3 alleles by combining two established PCR sequence-based techniques. Tissue Antigens. 2011; 78(3):208-13. DOI: 10.1111/j.1399-0039.2011.01708.x. View

16.

Maccari G, Robinson J, Ballingall K, Guethlein L, Grimholt U, Kaufman J . IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex. Nucleic Acids Res. 2016; 45(D1):D860-D864. PMC: 5210539. DOI: 10.1093/nar/gkw1050. View

17.

Giovambattista G, Golijow C, Dulout F, Lojo M . Gene frequencies of DRB3.2 locus of Argentine Creole cattle. Anim Genet. 1996; 27(1):55-6. DOI: 10.1111/j.1365-2052.1996.tb01178.x. View

18.

Davies C, Joosten I, Andersson L, Arriens M, Bernoco D, Bissumbhar B . Polymorphism of bovine MHC class II genes. Joint report of the Fifth International Bovine Lymphocyte Antigen (BoLA) Workshop, Interlaken, Switzerland, 1 August 1992. Eur J Immunogenet. 1994; 21(4):259-89. DOI: 10.1111/j.1744-313x.1994.tb00198.x. View

19.

Rousset F . genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour. 2011; 8(1):103-6. DOI: 10.1111/j.1471-8286.2007.01931.x. View

20.

Miyasaka T, Takeshima S, Sentsui H, Aida Y . Identification and diversity of bovine major histocompatibility complex class II haplotypes in Japanese Black and Holstein cattle in Japan. J Dairy Sci. 2011; 95(1):420-31. DOI: 10.3168/jds.2011-4621. View