Genetic Diversity of Bovine Major Histocompatibility Complex Class II DRB3 locus in cattle breeds from Asia compared to those from Africa and America

Abstract

Genetic polymorphisms and diversity of BoLA-DRB3.2 are essential because of DRB3 gene's function in innate immunity and its association with infectious diseases resistance or tolerance in cattle. The present study was aimed at assessing the level of genetic diversity of DRB3 in the exon 2 (BoLA-DRB3.2) region in African, American and Asian cattle breeds. Amplification of exon 2 in 174 cattle revealed 15 haplotypes. The breeds with the highest number of haplotypes were Brangus (10), Sokoto Gudali (10) and Dajal (9), while the lowest number of haplotypes were found in Holstein and Sahiwal with 4 haplotypes each. Medium Joining network obtained from haplotypic data showed that all haplotypes condensed around a centric area and each sequence (except in H-3, H-51 and H-106) representing almost a specific haplotype. The BoLA-DRB3.2 sequence analyses revealed a non-significant higher rate of non-synonymous (dN) compared to synonymous substitutions (dS). The ratio of dN/dS substitution across the breeds were observed to be greater than one suggesting that variation at the antigen-binding sites is under positive selection; thus increasing the chances of these breeds to respond to wide array of pathogenic attacks. An analysis of molecular variance revealed that 94.01 and 5.99% of the genetic variation was attributable to differences within and among populations, respectively. Generally, results obtained suggest that within breed genetic variation across breeds is higher than between breeds. This genetic information will be important for investigating the relationship between BoLADRB3.2 and diseases in various cattle breeds studied with attendant implication on designing breeding programs that will aim at selecting individual cattle that carry resistant alleles.

Keywords: BoLA-DRB3.2; Cattle; Diseases; Gene polymorphism.

Fig 1

Molecular Phylogenetic analysis of the different sequences for all the breeds analyzed. Shaded areas represent each of the haplotypes defined as described in the text. The evolutionary history was inferred using the Maximum Likelihood method based on the General Time Reversible model . The tree with the highest log likelihood (-3858.8785) is shown. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.2303)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 174 nucleotide sequences.

Fig 2

Molecular diversity indices of African, Asian and American cattle. The values and standard deviations of two different diversity indices in different cattle breeds. The solid lines of different colors show the different values of the diversity indices and the dashed lines in the same color the corresponding standard deviations. Theta is a population parameter of genetic differentiation. Plot was generated in R.

Fig 3

Genetic differentiation between cattle breeds. The F_ST values are coded with a color code with the legend on the right side. The colors ranged from skye blue to deep blue and correspond to the F_ST values

Fig 4

Genetic differentiation within and between cattle breeds. Average number of pairwise differences between cattle breeds. The average number of pairwise differences between each cattle breed in the upper half of the matrix (green). The average number of pairwise differences within each cattle breed is shown in the diagonal (orange). The lower half of the matrix (blue) showed the corrected average number of pairwise differences between cattle breeds

Fig 5

A median joining network for the sequences obtained among temperate and tropical cattle. Circles represent individual sequences and have a size proportional to frequency. The red squares represent the median vector; Branch length is proportional to the number of mutations. The numbers on each edge denote the position of nucleotides within the sequence that differ between the sequences.

Fig 6

Molecular phylogenetic analysis of the cattle breeds with Sheep (Ovis aries) as outgroup. The evolutionary history was inferred using the Maximum Likelihood method based on the General Time Reversible model . The trees were build using the sequences of haplotypes 11 (A) and 15 (B), which were the most common among the breeds. The trees with the highest log likelihoods (-765.5423 and -759.5334, respectively) are shown. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.1329 and 0.1014, respectively)). The trees are drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 13 and 14 nucleotide sequences, respectively.