Identification of a new bovine MHC class II DRB allele by nucleotide sequencing and an analysis of phylogenetic relationships

First characterization of major histocompatibility complex class II DRB3 diversity in cattle breeds raised in Egypt

Genes encoding bovine leukocyte antigen (BoLA) enable the immune system to identify pathogens. Therefore, these genes have been used as genetic markers for infectious and autoimmune diseases as well as for immunological traits in cattle. Although BoLA polymorphisms have been reported in various cattle breeds worldwide, they have not been studied in cattle populations in Egypt. In this study, we characterized BoLA-DRB3 in two local Egyptian populations and one foreign population using polymerase chain reaction-sequence-based typing (PCR-SBT) method. Fifty-four previously reported BoLA-DRB3 alleles and eight new alleles (BoLA-DRB3*005:08, *015:07, *016:03, *017:04, *020:02:02, *021:03, *164:01, and *165:01) were identified. Alignment analysis of the eight new alleles revealed 90.7-98.9 %, and 83.1-97.8 % nucleotide and amino acid identities, respectively, with the BoLA-DRB3 cDNA clone NR-1. Interestingly, BoLA-DRB3 in Egyptian cattle showed a high degree of allelic diversity in native (na = 28, hE > 0.95), mixed (na = 61, hE > 0.96), and Holstein (na = 18, hE > 0.88) populations. BoLA-DRB3*002:01 (14.3 %), BoLA-DRB3*001:01 (8.5 %), and BoLA-DRB3*015:01 (20.2 %) were the most frequent alleles in native, mixed, and Holstein populations, respectively, indicating that the genetic profiles differed in each population. Based on the allele frequencies of BoLA-DRB3, genetic variation among Egyptian, Asian, African, and American breeds was examined using Nei's distances and principal component analysis. The results suggested that native and mixed cattle populations were most closely associated with African breeds in terms of their gene pool, whereas Holstein cattle were more distinct from the other breeds and were closely related to Holstein cattle populations from other countries.

Functional immune diversity in reindeer reveals a high Arctic population at risk

Climate changes the geographic range of both species as well as pathogens, causing a potential increase in the vulnerability of populations or species with limited genetic diversity. With advances in high throughput sequencing (HTS) technologies, we can now define functional expressed genetic diversity of wild species at a larger scale and identify populations at risk. Previous studies have used genomic DNA to define major histocompatibility complex (MHC) class II diversity in reindeer. Varying numbers of expressed genes found in many ungulates strongly argues for using cDNA in MHC typing strategies to ensure that diversity estimates relate to functional genes. We have used available reindeer genomes to identify candidate genes and established an HTS approach to define expressed MHC class I and class II diversity. To capture a broad diversity we included samples from wild reindeer from Southern Norway, semi-domesticated reindeer from Northern Norway and reindeer from the high Artic archipelago Svalbard. Our data show a medium MHC diversity in semi-domesticated and wild Norwegian mainland reindeer, and low MHC diversity reindeer in Svalbard reindeer. The low immune diversity in Svalbard reindeer provides a potential risk if the pathogenic pressure changes in response to altered environmental conditions due to climate change, or increased human-related activity.

Relationship between Allelic Heterozygosity in BoLA-DRB3 and Proviral Loads in Bovine Leukemia Virus-Infected Cattle

Simple Summary

Bovine leukemia virus (BLV) caused a severe cattle neoplastic disease called enzootic bovine leukosis (EBL). EBL causes significant economic losses in farming by reducing milk production, reproductive performance, and fertility, and through cattle culling or death. The BLV proviral load (PVL) represents the quantity of BLV genome that has integrated into the host’s genome in BLV-infected cells. It has been reported that PVLs differ according to the genetic background of the host, and some studies of BLV-associated host factors have reported on polymorphisms within the bovine major histocompatibility complex (MHC), namely bovine MHC is bovine leukocyte antigen (BoLA-DRB3). However, there is a great diversity in the PVLs associated with carrying various combinations of these alleles, especially for heterozygous alleles. Therefore, this research investigated whether heterogeneity in BoLA-DRB3 allele combinations would affect PVLs during BLV infections in different ages and breeds of cattle in Japan. This is the first report where the association between heterozygous allelic combinations and BLV PVLs phenotypes (HPLs, LPLs) was analyzed. Our findings augment current understanding about the immunological role played by BoLA heterozygosity in BLV-associated PVLs and biocontrol in BLV infections.

Abstract

Enzootic bovine leukosis is a lethal neoplastic disease caused by bovine leukemia virus (BLV), belongs to family Retroviridae. The BLV proviral load (PVL) represents the quantity of BLV genome that has integrated into the host’s genome in BLV-infected cells. Bovine leukocyte antigen (BoLA) class II allelic polymorphisms are associated with PVLs in BLV-infected cattle. We sought to identify relationships between BoLA-DRB3 allelic heterozygosity and BLV PVLs among different cattle breeds. Blood samples from 598 BLV-infected cattle were quantified to determine their PVLs by real-time polymerase chain reaction. The results were confirmed by a BLV-enzyme-linked immunosorbent assay. Restriction fragment length polymorphism-polymerase chain reaction identified 22 BoLA-DRB3 alleles. Multivariate negative binomial regression modeling was used to test for associations between BLV PVLs and BoLA-DRB3 alleles. BoLA-DRB3.2*3, *7, *8, *11, *22, *24, and *28 alleles were significantly associated with low PVLs. BoLA-DRB3.2*10 was significantly associated with high PVLs. Some heterozygous allele combinations were associated with low PVLs (*3/*28, *7/*8, *8/*11, *10/*11, and *11/*16); others were associated with high PVLs (*1/*41, *10/*16, *10/*41, *16/*27, and *22/*27). Interestingly, the BoLA-DRB3.2*11 heterozygous allele was always strongly and independently associated with low PVLs. This is the first reported evidence of an association between heterozygous allelic combinations and BLV PVLs.

Locus number estimation of MHC class II B in stone flounder and Japanese flounder

Members of major histocompatibility complex (MHC) family are important in immune systems. Great efforts have been made to reveal their complicated gene structures. But many existing studies focus on partial sequences of MHC genes. In this study, by gene cloning and sequencing, we identified cDNA sequences and DNA sequences of the MHC class II B in two flatfishes, stone flounder (Kareius bicoloratus) and homozygous diploid Japanese flounder (Paralichthys olivaceus). Eleven cDNA sequences were acquired from eight stone flounder individuals, and most of the polymorphic sites distributed in exons 2 and 3. Twenty-eight alleles were identified from the DNA fragments in these eight individuals. It could be deduced from their Bayesian inference phylogenetic tree that at least four loci of MHC class II B exist in stone flounder. The detailed whole-length DNA sequences in one individual were analyzed, revealing that the intron length varied among different loci. Four different cDNA sequences were identified from one homozygous diploid Japanese flounder individual, implying the existence of at least four loci. Comparison of the cDNA sequences to the DNA sequence confirmed that six exons existed in this gene of Japanese flounder, which was a common feature shared by Pleuronectiformes fishes. Our results proved the multi-locus feature of MHC class II B. The sequences we obtained would provide detailed and systematic data for further research.

The great diversity of major histocompatibility complex class II genes in Philippine native cattle

Bovine leukocyte antigens (BoLA) are extensively used as markers for bovine disease and immunological traits. However, none of the BoLA genes in Southeast Asian breeds have been characterized by polymerase chain reaction (PCR)-sequence-based typing (SBT). Therefore, we sequenced exon 2 of the BoLA class II DRB3 gene from 1120 individual cows belonging to the Holstein, Sahiwal, Simbrah, Jersey, Brahman, and Philippine native breeds using PCR-SBT. Several cross-breeds were also examined. BoLA-DRB3 PCR-SBT identified 78 previously reported alleles and five novel alleles. The number of BoLA-DRB3 alleles identified in each breed from the Philippines was higher (71 in Philippine native cattle, 58 in Brahman, 46 in Holstein × Sahiwal, and 57 in Philippine native × Brahman) than that identified in breeds from other countries (e.g., 23 alleles in Japanese Black and 35 in Bolivian Yacumeño cattle). A phylogenetic tree based on the D_A distance calculated from the BoLA-DRB3 allele frequency showed that Philippine native cattle from different Philippine islands are closely related, and all of them are closely similar to Philippine Brahman cattle but not to native Japanese and Latin American breeds. Furthermore, the BoLA-DRB3 allele frequency in Philippine native cattle from Luzon Island, located in the Northern Philippines was different from that in cattle from Iloilo, Bohol, and Leyte Islands, which are located in the Southern Philippines. Therefore, we conclude that Philippine native cattle can be divided into two populations, North and South areas. Moreover, a neutrality test revealed that Philippine native cattle from Leyte showed significantly greater genetic diversity, which may be maintained by balancing selection. This study shows that Asian breeds have high levels of BoLA-DRB3 polymorphism. This finding, especially the identification of five novel BoLA-DRB3 alleles, will be helpful for future SBT studies of BoLA-DRB3 alleles in East Asian cattle.

Sequence analysis of the MHC class II DRB alleles in Alpine chamois (Rupicapra r. rupicapra)

This study characterises the expressed MHC class II DRB gene and its genetic variation in exon 2 among 59 Alpine chamois (Rupicapra r. rupicapra) from several locations in the Eastern Alps plus one population in the Western Alps. The expressed DRB gene contains all the expected characteristics including all of the conserved residues found in other mammalian species. The isolated expressed DRB gene from chamois can be considered orthologous to MHC class II DRB genes in other mammalian species. Cattle primers yielded exon 2 sequences of 284 bp length. Sequence analysis revealed 19 DRB exon 2 alleles among 59 chamois. Alleles exhibited a high degree of nucleotide and amino acid polymorphism, with most amino acid variations occurring at positions forming the peptide-binding sites. A significantly higher rate of non-synonymous (dN = 0.053+/-0.0132) than synonymous (dS = 0.007+/-0.003) substitutions indicated positive selection for diversity in the DRB locus.

The diversity of bovine MHC class II DRB3 genes in Japanese Black, Japanese Shorthorn, Jersey and Holstein cattle in Japan

We sequenced exon 2 of the major histocompatibility complex (MHC) class II DRB3 gene from 471 individuals in four different Japanese populations of cattle (201 Japanese Black, 101 Holstein, 100 Japanese Shorthorn, and 69 Jersey cattle) using a new method for sequence-based typing (SBT). We identified the 34 previously reported alleles and four novel alleles. These alleles were 80.0-100.0% identical at the nucleotide level and 77.9-100.0% identical at the amino acid level to the bovine MHC (BoLA)-DRB3 cDNA clone NR1. Among the 38 alleles, eight alleles were found in only one breed in this study. However, these alleles did not form specific clusters on a phylogenetic tree of 236-base pairs (bp) nucleotide sequences. Furthermore, these breeds exhibited similar variations with respect to average frequencies of nucleotides and amino acids, as well as synonymous and non-synonymous substitutions, in all pairwise comparisons of the alleles found in this study. By contrast, analysis of the frequencies of the various BoLA-DRB3 alleles in each breed indicated that DRB3*1101 was the most frequent allele in Holstein cattle (16.8%), DRB3*4501 was the most frequent allele in Jersey cattle (18.1%), DRB3*1201 was the most frequent allele in Japanese Shorthorn cattle (16.0%) and DRB3*1001 was the most frequent allele in Japanese Black cattle (17.4%), indicating that the frequencies of alleles were differed in each breed. In addition, a population tree based on the frequency of BoLA-DRB3 alleles in each breed suggested that Holstein and Japanese Black cattle were the most closely related, and that Jersey cattle were more different from both these breeds than Japanese Shorthorns.

Short communication: characterization of DRB3 alleles in the MHC of Japanese shorthorn cattle by polymerase chain reaction-sequence-based typing

A study was made of exon 2 of the bovine leukocyte antigen BoLA-DRB3 gene of 176 Japanese Shorthorn cattle at six farms in Japan using polymerase chain reaction-sequence-based typing (PCR-SBT). An initial round of PCR using conserved locus-specific primers, a second round of PCR using a locus-specific primer, and at least one sequence-specific primer (SSP), followed by direct sequencing of products of PCR with SSP were conducted. Twenty-one BoLA-DRB3 alleles were identified with frequencies ranging from 0.3 to 19.6% in 176 individuals, and two of these alleles were new alleles that have not been reported previously. The three most frequently observed alleles (DRB3*1201, *0301, and *0801) accounted for 43.8% of the alleles in the population of these herds. Next, we tested the products of amplification by PCR of BoLA-DRB3 exon 2 with RsaI, BstYI, and HaeIII, and identified 18 previously described PCR-restriction fragment length polymorphism (RFLP) types. The PCR-RFLP types reflected the results of PCR-SBT exactly. Our results indicate that exon 2 of the BoLA-DRB3 gene is highly polymorphic in Japanese Shorthorn cattle.

Cattle MHC genes DOA and DOB: sequence polymorphisms and assignments to the class IIb region

In a study of the genetic polymorphism of the second exons of the cattle DOA and DOB genes, two and four allelic variants were detected, respectively. In the predicted amino acid sequence, the DOA polymorphism corresponded to variation at the respective residue position, whereas the nucleotide substitutions in the DOB gene were non-informative. PCR-RFLP assays were developed for DOA and DOB typing, and both loci were genetically mapped to the BoLA class IIb region by linkage analysis in the International Bovine Reference Panel. The single nucleotide polymorphisms detected in the BoLA-DOA and -DOB genes enable these loci to be used as markers in genetic trait analyses.

Sequence and transfection of BoLA-DRB3 cDNAs

Bovine MHC (BoLA-) DRB3 alleles encoded by the DH8A, DH22A and DH24A class II haplotypes were cloned from cDNA and characterized by sequence analysis. Comparison with other full-length DRB3 sequences suggested that DRB3 alleles may have evolved through multiple lineages. All three BoLA-DRB3 alleles were shown to express on the surface of transfected cells, and the transfectants were used to define or confirm the class II specificity of a panel of monoclonal antibodies.