• Asian-Australasian Journal of Animal Sciences
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• v.21 no.4
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• pp.465-470
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• 2008

This study describes genetic variability in the BoLA-DRB3 gene in Iranian native cattle (Bos Indicus and Taurus) and relationships between these breeds. This is the first study of genetic polymorphism of the BoLA-DRB3 gene in Iranian native cattle. We examined exon 2 of the major histocompatibility complex (MHC) class II DRB3 gene from 203 individuals in four populations of Iranian native cattle (52 Sarabi, 52 Najdi, 49 Sistani, 50 Golpayegani cattle) using the hemi-nested PCR-RFLP method. We identified the 36 previously reported alleles and one novel pattern (*eac). Analysis of the frequencies of the various BoLA-DRB3.2 alleles in each breed indicated that DRB3.2*52 in Sarabi cattle (23%), DRB3.2 *14 and *24 alleles in Najdi cattle (13%), DRB3.2 *8 allele in Sistani cattle (22%) and DRB3.2*16 allele in Golpayegani cattle (14%), were the most frequent alleles. Allelic frequencies ranged from 1 to 23% among the 36 alleles and there were some alleles that were found only in Iranian cattle. Effective number of alleles in the four breeds was estimated to be 7.86, 11.68, 7.08 and 3.37 in Sarabi, Najdi, Sistani and Golpayegani, respectively. Observed heterozygosities were the highest in Sarabi (94%) and Najdi (94%). A population tree based on the frequency of BoLA-DRB3.2 alleles in each breed suggested that Najdi, Sarabi and Golpayegani cattle clustered together and Najdi and Sarabi were the closest breeds. Sistani cattle differed more from these three breeds. These new data suggest that allele frequencies differ between Iranian cattle breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.12
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• pp.1691-1695
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• 2005

The bovine lymphocyte antigen (BoLA)-DRB3 gene encodes cell surface glycoproteins that initiate immune responses by presenting processed antigenic peptides to CD4 T helper cells. DRB3 is the most polymorphic bovine MHC class II gene which encodes the peptide-binding groove. Since different alleles favour the binding of different peptides, DRB3 has been extensively evaluated as a candidate marker for associations with various bovine diseases and immunological traits. For that reason, the genetic diversity of the bovine class II DRB3 locus was investigated by polymerase chain reaction-restriction fragment length polymorphism method (PCR-RFLP). This study describes genetic variability in the BoLA-DRB3 in Iranian Golpayegani Cattle. Iranian Golpayegani Cows (n = 50) were genotyped for bovine lymphocyte antigen (BoLA)-DRB3.2 allele by polymerase chain reaction and restriction fragment length polymorphism method. Bovine DNA was isolated from aliquots of whole blood. A two-step polymerase chain reaction followed by digestion with restriction endonucleases RsaI, HaeIII and BstYI was conducted on the DNA from Iranian Golpayegani Cattle. In the Iranian Golpayegani herd studied, we identified 19 alleles.DRB3.2${\times}$16 had the highest allelic frequency (14%), followed by DRB3.2${\times}$7 (11%). Six alleles (DRB3.2${\times}$25, ${\times}$24, ${\times}$22, ${\times}$20, ${\times}$15, ${\times}$3) had frequencies = 2%. Although additional studies are required to confirm the present findings, our results indicate that exon 2 of the BoLA-DRB3 gene is highly polymorphic in Iranian Golpayegani Cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.6
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• pp.752-756
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• 2011

Polymorphism of the second exon of the caprine leukocyte antigen-DRB3 gene (CLA-$DRB3^*02$) was investigated in this study. The 285 bp PCR product of 258 individuals from 10 domestic goat breeds in Southwest China was digested with restriction endonucleases PstI and HaeIII and then genotyped. Three alleles and 4 restriction digestion profiles were distinguished by digestion of the PCR fragment by PstI, and 8 alleles and 13 genotypes by HaeIII. For HaeIII restriction enzyme sites, the Chi-square ($X^2$) test showed that all goat breeds in this study did not fit with the Hardy-Weinberg equilibrium (p<0.01 or p<0.05). The highly polymorphic nature of CLA-$DRB3^*02$ was demonstrated and the ranges of gene heterozygosity (He) and polymorphism information content (PIC) were 0.36-0.63 and 0.32-0.55, respectively. Clustering analysis showed that the 10 goat breeds clustered into two groups and Dazu Black goat had a close genetic relationship with Chengdu Grey, Jintang Black and Nanjiang Yellow goats.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.12
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• pp.1791-1797
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• 2007

A study was conducted with 70 Hanwoo (Korean cattle) for genotyping bovine leukocyte antigen (BoLA)-DRB3.2 gene by using the polymerase chain reaction (PCR) and sequence based typing (SBT). Two-step PCR was carried out for amplifying a 284 bp fragment of the target gene and the PCR products were digested with three restriction enzymes namely RsaI, BstYI and HaeIII. Seventeen alleles were detected with frequencies ranging from 1.43 to 18.57% and one (x'aa) of these alleles was identified as a new allele that has not been reported before. The frequency of the new x'aa allele identified in this breed was 12.86%. In addition, the seven most frequently observed alleles (DRB3.2 *10, *15, *16, *26, *27, *54 and x'aa) accounted for 74.28% of the alleles in this population. The phylogenetic tree showed that the BoLA-DRB3.2 allele sequences of Hanwoo were shared with other Bos taurus breeds and no specific clade for Hanwoo was identified. It indicates high heterogeneity of the BoLA-DRB3 gene in this population and may give some ideas for breeding animals having better disease resistance.

• Journal of Animal Science and Technology
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• v.63 no.2
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• pp.248-261
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• 2021

Attributable to their major function in pathogen recognition, the use of bovine leukocyte antigens (BoLA) as disease markers in immunological traits in cattle is well established. However, limited report exists on polymorphism of the BoLA gene in zebu cattle breeds by high resolution typing methods. Thus, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 100 animals (Boran, n = 13; Sheko, n = 20; Fogera, n = 16; Horro, n = 19), Hanwoo cattle (n = 18) and Bangladesh Red Chittagong zebu (n = 14). Out of the 59 detected alleles, 43 were already deposited under the Immuno Polymorphism Database for major histocompatibility complex (IPD-MHC) while 16 were unique to this study. Assessment of the level of genetic variability at the population and sequence levels with genetic distance in the breeds considered in this study showed that Zebu breeds had a gene diversity score greater than 0.752, nucleotide diversity score greater than 0.152, and mean number of pairwise differences higher than 14, being very comparable to those investigated for other cattle breeds. Regarding neutrality tests analyzed, we investigated that all the breeds except Hanwoo had an excess number of alleles and could be expected from a recent population expansion or genetic hitchhiking. Howbeit, the observed heterozygosity was not significantly (p < 0.05) higher than the expected heterozygosity. The Hardy Weinberg equilibrium (HWE) analysis revealed non-significant excess of heterozygote animals, indicative of plausible over-dominant selection. The pairwise FST values suggested a low genetic variation among all the breeds (FST = 0.056; p < 0.05), besides the rooting from the evolutionary or domestication history of the cattle. No detached clade was observed in the evolutionary divergence study of the BoLA-DRB3 gene, inferred from the phylogenetic tree based on the maximum likelihood model. The investigation herein indicated the clear differences in BoLA-DRB3 gene variability between African and Asian cattle breeds.

• Korean Journal of Microbiology
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• v.44 no.3
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• pp.169-177
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• 2008

Global gene expression of Deinococcus radiodurans, a highly radiation resistant bacterium, in response to excess copper was analyzed by using oligonucleotide microarray chip. Among 3,187 open reading frames of D. radiodurans, seventy genes showed a statistically significant expression ratio of at least 2-fold changes under growth conditions of excess copper; 64 genes were induced and 6 genes were reduced. Especially, two operons ($DRB0014{\sim}DRB0017$ and $DRB0125{\sim}DRB0121$) presumably involved in the iron transport and utilization were the most highly induced genes by excess copper. A quantitative real-time PCR assay revealed that DRB00l4 and DRB0125 are highly transcribed responding to excess copper and 2,2'-dipyridyl, an iron chelator. In addition, the transcription of both genes was not changed by excess iron and bathocuproine disulphonate, a copper chelator. These results suggested that the copper metabolism may be closely connected with the iron transport and utilization in D. radiodurans. However, the disruption of each gene, DRB00l4 and DRB0125, did not affect the copper and radiation resistance, the most well-known character of this organism.

• Korean Journal of Agricultural Science
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• v.25 no.1
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• pp.79-88
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• 1998

This study was performed in order to apply to effective breeding of Korean native cattle on the molecular genetic level obtained from PCR and nucleotide sequencing analysis of BoLA DRB3 exon2 that has important roles in host immune defence. Genomic DNA used in this study was prepared from the blood of Korean native cattle in Korean Native Cattle Improvement Center of National Livestock Cooperation. The results obtained from this study are summarized as follows: 1. Genomic DNA extracted from the blood of Korean native cattle was subjected to electrophoresis on 1.5% agarose gel. Major band was bigger than 12.2kb, indicating that genomic DNA was well prepared for PCR. Amplified products of 284bp fragments was obtained the amplification of BoLA DRB3 exon2 gene by PCR. 2. Cloning of BoLA DRB3 exon2 of Korean native cattle with pCR2.1 vector was conformed by 300bp fragment from recombinent plasmid that restricted with enzyme digestion of EcoRI. 3. Homology of BoLA DRB3 exon2 alleles of parent was 82.0% between sire's alleles and 90.1% between dam's alleles. 4. In pedigree analysis using BoLA DRB3 exon2 gene, sequencing result of BoLA DRB3 exon2 genes showed inheritance by Mendelian mode through the parents to their offspring. 5. Taking together those experimental results, pedigree was confirmed on the basis of sequencing for the alleles of parents and offspring. This knowledge by the molecular biological approach could be served for the improvement of Korean native cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.9
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• pp.1226-1230
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• 2005

The present investigation was undertaken to study the genetic polymorphism of the DRB3 exon 2 in 75 crossbred cattle by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Five genotypes i.e. HaeIII-a, HaeIII-b, HaeIII-e, HaeIII-ab and HaeIII-ae were observed when the 284 bp PCR products were digested with HaeIII restriction enzyme. The corresponding frequencies of these patterns were 0.53, 0.04, 0.01, 0.38 and 0.04, respectively. Digestion with RsaI restriction enzyme resolved 24 different restriction patterns. The frequencies of these patterns ranged from 0.013 (RsaI-f, RsaI-k and RsaI-c/n) to 0.120 (RsaI-n). The results revealed that the crossbred cows belonged to the RsaI patterns namely b, k, l, a/l, d/s, l/n, l/o and m/n, whose corresponding frequencies were 0.027, 0.013, 0.040, 0.027, 0.040, 0.067, 0.027 and 0.067, respectively. Digestion of the 284 bp PCR product of DRB3.2 gene with PstI in the crossbred cattle did not reveal any restriction site. These results suggested the absence of the recognition site in some of the animals. These results also revealed that the crossbred cows studied were in homozygous as well as heterozygous condition. On the basis of the above results it can be concluded that the DRB3.2 gene was found to be highly polymorphic in the crossbred cattle population.

• Korean Journal of Agricultural Science
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• v.38 no.1
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• pp.51-63
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• 2011

BoLA (bovine leukocyte antigens) have been known as gene complex related with bovine diseases and immunological traits. This study was conducted to find out the characteristics of BoLA-DRB3 gene related to mastitis and BL(bovine leukocyte) from 280 cattle [193 animals of Holstein cattle and 87 animals of Hanwoo]. As a result, five PCR-RFLP types (b, d, e, f and g) using HaeIII restriction enzyme, three BstYI restriction patterns (b, d and e) and eight RsaI restriction types(b, d, f, I, j, n, o and w) were identified. Moreover, we identified new d' type ($197{\rightarrow}175$/22), having one more cutting site by BstYI enzyme than d type allele and n' type ($180{\rightarrow}169$/11) having one more cutting site by RsaI enzyme than n allele was additionally identified. Next, we identified 53 SNPs in BoLA-DRB3 exon2 from 280 cattle. SNP frequency and heterozygosity of Holstein and Hanwoo were investigated in all the SNP genotype. These results might be based on research for identifying marker associated with bovine diseases.

• IMMUNE NETWORK
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• v.2 no.4
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• pp.242-247
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• 2002

Background: Tumor necrosis factor-alpha (TNF-$\alpha$) is known to play an important role in various conditions such as inflammation, autoimmunity, apoptosis, insulin resistance and sleep induction. Five single nucleotide polymorphisms (SNPs) have been known to affect the transcriptional activities of TNF-$\alpha$: -1,031T/C, -863C/A, -857C/T, -308G/A and -238G/A. Methods: We have investigated 5 SNPs of the promoter region of TNF-$\alpha$ gene, the distribution of 5-locus TNF-$\alpha$ haplotypes, and their haplotypic associations with previously typed HLA-A, -B and -DRB1 loci in 107 healthy unrelated Koreans. TNF-$\alpha$ SNPs were typed using PCR-single-strand conformation polymorphism (SSCP) and PCR-restriction fragment length polymorphism (RFLP) methods. Results: The allele frequencies of -1,031C, -863A, -857T, -308A, and-238A, which are known as the high-producer-type, were 19.3%, 15.9%, 14.0%, 5.9%, and 2.9%, respectively. The frequency of -308A allele, known to be associated with autoimmune diseases, was 5.9% in Koreans which was lower than Caucasians (14~17%) and somewhat higher than Japanese (1.7%). Five most common TNF-$\alpha$ haplotypes (-1,031/-863/-857/-308/-238) comprised over 95% of total haplotypes: TCCGG (58.4%), CACGG (14.8%), TCTGG (13.7%), TCCAG (5.3%), and CCCGA (3.1%). Strong positive associations (P<0.001) were observed between TCCGG and B62; between CACGG and B51, $DRB1^*0901$; between TCTGG and B35, B54, B59, $DRB1^*1201$; and between TCCAG and A33, B58, $DRB1^*0301$, $DRB1^*1302$. Five most common extended haplotypes (>3%) comprised around 16% of total haplotypes: A33-B58-TCCAG-$DRB1^*1302$, A24-B52-TCCGG-$DRB1^*1502$, A33-B44-TCCGG-$DRB1^*1302$, A24-B7-TCCGG-$DRB1^*0101$, and A11-B62-TCCGG-$DRB1^*0406$. The distribution of extended HLA and TNF-$\alpha$ haplotypes showed that most of HLA haplotypes were almost exclusively associated with particular TNF-$\alpha$ haplotypes. Conclusion: The results obtained in this study would be useful as basic data for anthropologic studies and disease association studies in Koreans.