BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds

Abstract

Autochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agro-ecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan's harsh environment.

Characterization and genetic diversity of MHC class II DRB genes in the Arabian camel (Camelus dromedarius)

“…Contrasting with the relatively limited allelic richness, an overall intermediate level of nucleotide diversity ( π = 0.049) was observed at the DRB1 exon 2. Comparatively, this level is slightly less than that observed in cattle for example, an intensively and widely studied species, where π ranged from 0.068 to 0.09 (Salim et al 2021 ). In dromedary, much lower nucleotide diversity has been reported for both SNPs and indels (6.2 10 −4 ) and non-synonymous (1.72 10 −4 ) variants when considering all MHC genes (Lado et al 2020 ) estimated from whole genome sequences.…”

Identification of Anaplasma marginale, Babesia bovis and Babesia bigemina resistance alleles in Crioulo Lageano cattle using PCR-SBT and BoLA-DRB3 gene sequencing

“…The BoLA-DRB3*001:01 allele has been associated with mastitis resistance in Holstein cattle ( 41 ), while the BoLA-DRB3*011:01 allele has been associated with resistance to B. bigemina and also to resistance to bovine leukosis in the Hartón del Valle breed ( 29 , 40 ), in addition to being associated with resistance to mastitis ( 41 ). The BoLA-DRB3*024:06 allele has previously been described in African breeds, including Sudanese breeds ( 42 ) but has not yet been associated with any type of disease.…”

Identification of BoLA Alleles Associated with BLV Proviral Load in US Beef Cows

“…Allele *026:01 has been reported at a frequency of between 1 and 3% in populations of Baggara, Kenana, and Butana cattle [ 19 ]. However, in the current study, allele * 026:01 was present at a higher frequency (20.36%), and animals with the allele were found to have a BLV PVL approximately 3 times greater than the average of the sampled population ( Table 1 ).…”