Characterization of genetic polymorphism of the bovine lymphocyte antigen DRB3.2 locus in Kankrej cattle (Bos indicus)

Allelic diversity at BoLA DRB3 locus and association with predisposition to clinical mastitis in indicus and crossbred cattle

Bovine lymphocyte antigen (BoLA) DRB3 locus in healthy and mastitis affected cattle has been genotyped by a polymerase chain reaction and restriction fragment length polymorphisms (PCR-RLFP) using RsaI restriction enzyme, followed by sequencing. In 130 farm animals, 25 BoLA DRB3 alleles have been detected by PCR-RFLP. Three distinct allelic patterns significantly associated with mastitis in Karan Fries crossbred and Sahiwal indicus cattle have been identified, whereas, four other allelic patterns were significantly high in frequency among healthy animals. Sequencing of RFLP genotypes revealed 25 and 47 alleles among healthy Sahiwal and Karan Fries, respectively, while 17 and 38 patterns observed in mastitis affected Sahiwal and Karan Fries animals, respectively. From Tajima's D-test of neutrality, it was concluded that alleles associated with mastitis were expanding in the population, whereas those of healthy were under contraction. Phylogenetic analysis carried out to delineate the evolutionary relationship of the farm and field animals at DRB3 locus, differentiating allelic patterns into six different clusters. Among the phylogenetic lineages, five patterns DRB3*028:01, DRB3*011:03, DRB3*031:01, DRB3*001:01 and DRB3*043:01, were previously reported, whereas one novel allelic variant was observed in indicus and crossbred cattle. This information will help in further exploring the association between BoLA-DRB3 genetic diversity and disease resistance in distinct cattle breeds, important in designing breeding strategies for increasing the distribution of favorable alleles.

Characterization of BoLA class II DQA and DQB by PCR-RFLP, cloning, and sequencing reveals sequence diversity in crossbred cattle

The BoLA class II DQA and DQB genes in crossbred cattle were studied using PCR-RFLP, cloning, and sequencing techniques. Seventy-two crossbred cattle (Vrindavani) were used in the current study. HaeIII and XbaI restriction enzymes digested DQA exon 2-3, revealing seven (HaeIII-A-G) and three (XbaI A-C) motifs, respectively. The BoLA-DQB gene was analyzed using PCR-RFLP with PstI and TaqI restriction enzymes, yielding five restriction motifs for each restriction enzyme (PstI-A-E and TaqI-A-E). In crossbred cattle, addition, deletion, and substitutions were observed in distinct sequences, resulting in variations in overall gene length. Changes in nucleotides at positions 64-80, 110-200, and 207-264 were largely responsible for polymorphism in DQA exon 2. The phylogenetic analysis predicted a high degree of nucleotide and amino acid changes in DQA exon 2-3 and DQB exon 2. DQA genes had a nucleotide dissimilarity of 0.3-25.4 percent, while DQB genes had a nucleotide dissimilarity of 1.5-14.3 percent. We cloned and sequenced 20 genotypes based on PCR-RFLP of the DQA and DQB genes. The current study observed variation in the DQA and DQB genes and will serve as a foundation for future research on the BoLA DQA and DQB genes.

Genetic variability and biodiversity of Ukrainian Gray cattle by the BoLA-DRB3 gene

At the current stage of genetic studies of cattle, more and more attention is being drawn to autochthonous breeds. Native cattle have a number of prominent phenotypic traits and have preserved unique genes and their combinations lost by modern commercial breeds, which would be valuable to use in selective programs. We surveyed polymorphism of the Ukrainian autochthonous Gray breed according to alleles of exon 2 of the BoLA-DRB3 gene. The uniqueness of the gene lies in the broad variability of its allele variants. Significant informativeness at DNA level is quite important for genetic studies. We surveyed allele polymorphism using the PCR-RLFP method on DNA isolated from 88 samples of blood of cows and 5 samples of sperm. We identified 28 alleles, of which 23 variants were nomenclature ones and 5 (jba, *jab, *jbb, *nad and *nda) were “without established nomenclature”, their share accounting for 8.9%. Four alleles *06, *12, *16 and *jba had a frequency above 5% and occupied 69.9% of the breed’s allele fund overall. The commonest allele was BoLA-DRB3.2*16 (44.1%). In total, we found 40 genotypes. Considering the significant dominance of variant *16, as expected, 5 genotypes with its inclusion occurred: *16/*16, *12/*16, *06/*16, *16/*24 and *jba/*16. It was present in the genotype of two out three studied animals. Parameters of heterozygosity, effective number of alleles, Shannon and Pielou indices indicate that Ukrainian Gray cattle are characterized by lowest level of genetic variability and biodiversity according to the BoLA-DRB3 gene compared with other breeds. Due to significant dominance of allele *16, the breed has no inbred motifs. We noted deviation toward increase in homozygosity without deviations from the norm of the distribution according to Hardy-Weinberg equilibrium. The obtained results will be used for genetic-populational programs with the purpose of improving the genetic potential of cattle breeds in terms of economically beneficial traits and diseases of cattle.

Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus)

BACKGROUND

The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian species, it is notably different among ruminants due to a chromosomal inversion that splits MHC type II genes into two subregions (IIa, IIb). Recombination rates are reportedly high between these subregions, and a lack of linkage has been documented in domestic ruminants. However, no study has yet examined the degree of linkage between these subregions in a wild ruminant. The white-tailed deer (Odocoileus virginianus), a popular ruminant of the Cervidae family, is habitually plagued by pathogens in its natural environment (e.g. Haemonchus contortus, Elaeophora). Due to the association between MHC haplotypes and disease susceptibility, a deeper understanding of MHC polymorphism and linkage between MHC genes can further aid in this species' successful management. We sequenced MHC-DRB exon 2 (IIa) and MHC-DOB exon 2 (IIb) on the MiSeq platform from an enclosed white-tailed deer population located in Alabama.

RESULTS

We identified 12 new MHC-DRB alleles, and resampled 7 alleles, which along with other published alleles brings the total number of documented alleles in white-tailed deer to 30 for MHC-DRB exon 2. The first examination of MHC-DOB in white-tailed deer found significantly less polymorphism (11 alleles), as was expected of a non-classical MHC gene. While MHC-DRB was found to be under positive, diversifying selection, MHC-DOB was found to be under purifying selection for white-tailed deer. We found no significant linkage disequilibrium between MHC-DRB and MHC-DOB, suggesting that these loci are unlikely to be closely linked.

CONCLUSIONS

Overall, this study identified 12 new MHC-DRB exon 2 alleles and characterized a new, non-classical, MHC II gene (MHC-DOB) for white-tailed deer. We also found a lack of significant linkage between these two loci, which supports previous findings of a chromosomal inversion within the MHC type II gene region in ruminants, and suggests that white-tailed deer may have a recombination hotspot between these MHC regions similar to that found for Bos taurus.

Sequence diversity of major histo-compatibility complex class II DQA1 in Indian Tharparkar cattle: novel alleles and in-silico analysis

Exon 2 of MHC class II gene codes for the first domain of the molecule that forms the peptide-binding groove and its polymorphism partly explains functional MHC diversity. A 850 bp DQA1 gene fragment spanning from intron I to exon III was typed by sequencing of 40 Tharparkar cattle of various agro-climatic zones of northern India along with 10 Tharparkar crossbreds. On analysis of nucleotide sequences, a total of 30 polymorphic sites (1 insertion and 29 SNPs) were identified in 14 MHC alleles leading to amino acid changes in 5 places in 249 bp (exon 2). Five new BoLa DQA1 alleles were identified and reported. The within group mean distance was highest in Tharparkar herd of Bikaner (0.045) and lowest (0.020) in that of Surathgarh (breeding tract) whereas, between groups mean distance was highest in Bikaner Tharparkar-Suratgarh Tharparkar pair. There was excess of nonsynonymous over synonymous nucleotide substitutions in the present study. The effects of these substitutions were predicted using I-Mutant and Panther online resources. The mean ratio of dN/dS was found to be >1.0 at 12 codons with two mutation hotspots at 13th codon (P = 0.002) and 64th codon (P = 0.01). The phylo-geographic analysis revealed that alleles 5, 7 and 13 formed a different cluster with alleles 7 and 13 grouped by the most frequent allele (BoLa-DQA*1401).

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

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.

The major histocompatibility complex in bovines: a review

Productivity in dairy cattle and buffaloes depends on the genetic factors governing the production of milk and milk constituents as well as genetic factors controlling disease resistance or susceptibility. The immune system is the adaptive defense system that has evolved in vertebrates to protect them from invading pathogens and also carcinomas. It is remarkable in the sense that it is able to generate an enormous variety of cells and biomolecules which interact with each other in numerous ways to form a complex network that helps to recognize, counteract, and eliminate the apparently limitless number of foreign invading pathogens/molecules. The major histocompatibility complex which is found to occur in all mammalian species plays a central role in the development of the immune system. It is an important candidate gene involved in susceptibility/resistance to various diseases. It is associated with intercellular recognition and with self/nonself discrimination. It plays major role in determining whether transplanted tissue will be accepted as self or rejected as foreign.

Genetic diversity and population genetic analysis of bovine MHC class II DRB3.2 locus in three Bos indicus cattle breeds of Southern India

The present study was performed to evaluate the genetic polymorphism of BoLA-DRB3.2 locus in Malnad Gidda, Hallikar and Ongole South Indian Bos indicus cattle breeds, employing the PCR-RFLP technique. In Malnad Gidda population, 37 BoLA-DRB3.2 alleles were detected, including one novel allele DRB3*2503 (GenBank: HM031389) that was observed in the frequency of 1.87%. In Hallikar and Ongole populations, 29 and 21 BoLA-DRB3.2 alleles were identified, respectively. The frequencies of the most common BoLA-DRB3.2 alleles (with allele frequency > 5%), in Malnad Gidda population, were DRB3.2*15 (10.30%), DRB3*5702 (9.35%), DRB3.2*16 (8.41%), DRB3.2*23 (7.01%) and DRB3.2*09 (5.61%). In Hallikar population, the most common alleles were DRB3.2*11 (13.00%), DRB3.2*44 (11.60%), DRB3.2*31 (10.30%), DRB3.2*28 (5.48%) and DRB3.2*51 (5.48%). The most common alleles in Ongole population were DRB3.2*15 (22.50%), DRB3.2*06 (20.00%), DRB3.2*13 (13.30%), DRB3.2*12 (9.17%) and DRB3.2*23 (7.50%). A high degree of heterozygosity observed in Malnad Gidda (H(O) = 0.934, H(E) = 0.955), Hallikar (H(O) = 0.931, H(E) = 0.943) and Ongole (H(O) = 0.800, H(E) = 0.878) populations, along with F(IS) values close to F(IS) zero (Malnad Gidda: F(IS) = 0.0221, Hallikar: F(IS) = 0.0127 and Ongole: F(IS) = 0.0903), yielded nonsignificant P-values with respect to Hardy-Weinberg equilibrium probabilities revealing, no perceptible inbreeding, greater genetic diversity and characteristic population structure being preserved in the three studied cattle populations. The phylogenetic tree constructed based on the frequencies of BoLA-DRB3.2 alleles observed in 10 Bos indicus and Bos taurus cattle breeds revealed distinct clustering of specific Bos indicus cattle breeds, along with unique genetic differentiation observed among them. The results of this study demonstrated that the BoLA-DRB3.2 is a highly polymorphic locus, with significant breed-specific genetic diversities being present amongst the three studied cattle breeds. The population genetics and phylogenetic analysis have revealed pivotal information about the population structure and importance of the presently studied three Bos indicus cattle breeds as unique animal genetic resources, which have to be conserved for maintaining native cattle genetic diversity.

Association of BoLA-DRB3 alleles identified by a sequence-based typing method with mastitis pathogens in Japanese Holstein cows

The association of the polymorphism of bovine leukocyte antigen (BoLA-DRB3) genes identified by the polymerase chain reaction sequence-based typing (PCR-SBT) method with resistance and susceptibility to mastitis caused by pathogenic bacteria was investigated. Blood samples for DNA extraction were collected from 194 Holstein cows (41 healthy cows and 153 mastitis cows including 24 mixed-infection cows infected with 2 or 3 species of pathogens) from 5 districts of Chiba prefecture, Japan. Sixteen BoLA-DRB3 alleles were detected. The 4 main alleles of DRB3*0101, *1501, *1201, and *1101 constituted 56.8% of the total number of alleles detected. Mastitis cows were divided into 2 groups: group 1 with single-infection cows and group 2 with all mastitis cows including 24 mixed-infection cows. The differences in the frequencies of BoLA-DRB3 alleles and the number of cows homozygous or heterozygous for each BoLA-DRB3 allele between healthy cows and the 2 groups of mastitis cows were evaluated. Furthermore, similar comparisons were performed between healthy cows and the 2 groups of mastitis cows for each mastitis pathogen. It was considered that the 4 alleles, namely, DRB3*0101, *1501, *1201, and *1101 had specific resistance and susceptibility to 4 different mastitis pathogens. Thus, DRB3*0101 might be associated with susceptibility to coagulase-negative Staphylococci and Escherichia coli, and DRB3*1501 might be associated with susceptibility to Escherichia coli. However, DRB3*1101 might be associated with resistance to Streptococci and coagulase-negative Staphylococci, and DRB3*1201, with resistance to Streptococci, Escherichia coli, and Staphylococcus aureus.

Detection of bovine leukocyte antigen DRB3 alleles as candidate markers for clinical mastitis resistance in Holstein x Zebu

Bovine leukocyte antigen DRB3 alleles from Holstein x Zebu crossbred dairy cows (n = 409) were analyzed using the PCR-RFLP technique. Exon II of DRB3 was amplified using locus-specific primers (HLO30/HLO32), followed by digestion with 3 restriction enzymes (RsaI, BstyI, and HaeIII). Forty alleles were found with frequency ranging from 0.005 to 0.139. The most frequently detected alleles of Holstein x Zebu were DRB3*16, *51, *23, *11, *8, and *1, accounting for 61.12% of the alleles in the population. Detection of candidate alleles for clinical mastitis occurrence was performed by logistic regression. It was found that percentage of Holstein fraction in crossbred cows had a nonsignificant effect (P > 0.05). However, parity had a significant effect on mastitis occurrence. In addition, DRB3*1 and *52 were the most associated with the occurrence of clinical mastitis, whereas *15, *51, and *22 were associated with resistance in crossbred populations. This is the first report of association of DRB3*15 and *51 with mastitis resistance. The association was validated by examining the candidate alleles in another commercial population. Highly susceptible (n = 43) and resistant (n = 42) groups of Holstein x Zebu cows were investigated. The result confirmed that DRB3*1 and *52 could be considered as susceptibility alleles, whereas *15, *51, and *22 could be considered as resistant alleles in Holstein x Zebu raised under tropical conditions. In addition, allele effects on 305-d milk production were estimated by BLUP. It was shown that most alleles associated with high clinical mastitis occurrence were related to increased milk yield. This study revealed that allele DRB3*10 had the greatest effect on increasing milk yield with moderate resistance to clinical mastitis, which could be used as a potential marker for selection in dairy genetic evaluation.