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Gowane GR, Sharma P, Kumar R, Misra SS, Alex R, Vohra V, Chhotaray S, Sharma N, Chopra A, Kandalkar Y, Choudhary A, Magotra A. Population-wide genetic analysis of Ovar-DQA1 and DQA2 loci across sheep breeds in India revealed their evolutionary importance and fitness of sheep in a tropical climate. Anim Biotechnol 2023; 34:4645-4657. [PMID: 36847639 DOI: 10.1080/10495398.2023.2180010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Genetic variability at the major histocompatibility complex (MHC) is important in any species due to significant role played by MHC for antigen presentation. DQA locus has not been studied for its genetic variability across sheep population in India. In the present study, MHC of sheep at DQA1 and DQA2 loci were evaluated across 17 Indian sheep breeds. Results revealed high degree of heterozygosity (10.34% to 100% for DQA1 and 37.39 to 100% for DQA2). 18 DQA1 alleles and 22 DQA2 alleles were isolated in different breeds. Nucleotide content for DQA region revealed richness of AT content (54.85% for DQA1 and 53.89% for DQA2). DQA1 and DQA2 sequences clustered independently. We could see evidence of divergence of DQA as DQA1 and DQA2 across sheep breeds. Wu-Kabat variability index revealed vast genetic variation across DQA1 and DQA2, specifically at peptide binding sites (PBS) that consisted 21 residues for DQA1 and 17 residues for DQA2. Evolutionary analysis revealed the presence of positive and balancing selection for DQA1 locus, however DQA2 was under purifying selection across sheep breeds. Higher heterozygosity and large diversity at both loci especially at PBS indicated the fitness of the sheep population for evading pathogens and adapt to the harsh tropical climate.
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Affiliation(s)
- G R Gowane
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Priya Sharma
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Rajiv Kumar
- Animal Genetics and Breeding Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar
| | - S S Misra
- Animal Genetics and Breeding Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar
| | - Rani Alex
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - V Vohra
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Nikita Sharma
- Animal Health Section, ICAR-Central Institute for Research on Goats, Makhdoom, India
| | - Ashish Chopra
- Animal Genetics and Breeding Division, ICAR-Arid Region Campus, Central Sheep and Wool Research Institute, Bikaner, India
| | - Yogesh Kandalkar
- Deccani Sheep Breeding Unit, NWPSI at Mahatma Phule Krishi Vidyapith, Rahuri, India
| | | | - Ankit Magotra
- Animal Genetics and Breeding Division, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
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Gong Y, Guo Y, He YM, Yuan Y, Yang BG, Duan XH, Liu CL, Zhang JH, Hong QH, Ma YH, Na RS, Han YG, Zeng Y, Huang YF, Zhao YJ, Zhao ZQ, E G. Comparative analysis of the genetic diversity of the neutral microsatellite loci and second exon of the goat MHC-DQB1 gene. Anim Biotechnol 2023; 34:85-92. [PMID: 34289783 DOI: 10.1080/10495398.2021.1935980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
This study compared and analyzed the genetic diversity and population structure of exon 2 of the DQB1 gene and 13 autosomal neutral microsatellite markers from 14 Chinese goat breeds to explore the potential evolutionary mechanism of the major histocompatibility complex (MHC). A total of 287 haplotypes were constructed from MHC-DQB1 exon 2 from 14 populations, and 82 nucleotide polymorphic sites (SNPs, 31.78%) and 172 heterozygous individuals (79.12%) were identified. The FST values of the microsatellites and MHC-DQB ranged between 0.01831-0.26907 and 0.00892-0.38871, respectively. Furthermore, 14 goat populations showed rich genetic diversity in the microsatellite loci and MHC-DQB1 exon 2. However, the population structure and phylogenetic relationship represented by the two markers were different. Positive selection and Tajima's D test results showed the occurrence of a diversified selection mechanism, which was primarily based on a positive and balancing selection in goat DQB. This study also found that the DQB sequences of bovines exhibited trans-species polymorphism (TSP) among species and families. In brief, this study indicated that positive and balancing selection played a major role in maintaining the genetic diversity of DQB, and TSP of MHC in bovines was common, which enhanced the understanding of the MHC evolution.
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Affiliation(s)
- Ying Gong
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yi Guo
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yong-Meng He
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Ying Yuan
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Bai-Gao Yang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Xing-Hai Duan
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Cheng-Li Liu
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Jia-Hua Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Qiong-Hua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yue-Hui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ri-Su Na
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yan-Guo Han
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yan Zeng
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yong-Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yong-Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Zhong-Quan Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Guangxin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
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3
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Kumari N, Mishra SK, Saini S, Kumar A, Loat S, Dhilor N, Niranjan SK, Sodhi M, Kataria RS. Identification of novel allelic patterns and evolutionary lineage of BoLA MHC class II DQA locus in indicine and taurine cattle. Anim Biotechnol 2022; 33:1746-1752. [PMID: 33600274 DOI: 10.1080/10495398.2021.1885426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Among different cattle types, Bos indicus are known for their ability to better resist the tropical microbial infections comparatively, wherein MHC molecules play a significant role. In this study allelic diversity at MHC locus, DQA of Bos indicus, Bos taurus and crossbred of taurine-indicus has been explored to understand the possible role of MHC region in differential immune response. Thirty nine different DQA alleles were identified, out of which 14 were novel, along with documentation of duplication of DQA alleles. Indicus cattle population presented diverse types of DQA alleles compared to crossbred and exotic. Translated amino acid sequence analysis indicated, codon 64 and 50 of peptide binding sites being highly polymorphic and most of the indicus cattle presented alanine and arginine amino acid at position 64 and 50. Within breed genetic variation found to be higher than between breeds. Because of their ability to bind and subsequently respond to a wide array of antigens, the newly identified DQA alleles with high diversity present in the form of duplicated haplotypes in different combinations in cattle populations provided significant insights into probable role of this MHC locus in better tropical disease combating ability and genetic fitness of indicus cattle.
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Affiliation(s)
- Namita Kumari
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - S K Mishra
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Shallu Saini
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Anurag Kumar
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Shubham Loat
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Nitika Dhilor
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - S K Niranjan
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Monika Sodhi
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - R S Kataria
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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4
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Mishra SK, Niranjan SK, Singh R, Kumar P, Kumar SL, Banerjee B, Kataria RS. Diversity analysis at MHC class II DQA locus in buffalo (Bubalus bubalis) indicates extensive duplication and trans-species evolution. Genomics 2020; 112:4417-4426. [PMID: 32738270 DOI: 10.1016/j.ygeno.2020.07.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/06/2020] [Accepted: 07/26/2020] [Indexed: 12/15/2022]
Abstract
Variation at MHC Class II-DQA locus in riverine and swamp buffaloes (Bubu) has been explored in this study. Through sequencing of buffalo DQA, 48 nucleotide variants identified from 17 individuals, reporting 42 novel alleles, including one pseudogene. Individual animal displayed two to seven variants, suggesting the presence of more than two Bubu-DQA loci, as an evidence of extensive duplication. dN values were found to be higher than dS values at peptide binding sites, separately for riverine and swamp buffaloes, indicating locus being under positive selection. Evolutionary analysis revealed numerous trans-species polymorphism with alleles from water buffalo assigned to at least three different loci (Bubu-DQA1, DQA2, DQA3). Alleles of both the sub-species intermixed within the cluster, showing convergent evolution of MHC alleles in bovines. The results thus suggest that both riverine and swamp buffaloes share con-current arrangement of DQA region, comparable to cattle in terms of copy number and population polymorphism.
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Affiliation(s)
- Shailendra Kumar Mishra
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India; School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201310, India.
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India.
| | - Ravinder Singh
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India
| | - Prem Kumar
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India
| | - S Lava Kumar
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India
| | - Bhaswati Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201310, India
| | - Ranjit Singh Kataria
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India.
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5
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Ge F, Memon S, Xi D, Li S, Liu X, Li G, Wang L, Leng J, Khan S, Deng W. Cloning and characterization of MHC-DQA1 and MHC-DQA2 molecules from yak (<i>Bos grunniens</i>). Arch Anim Breed 2016. [DOI: 10.5194/aab-59-395-2016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The major histocompatibility complex (MHC) plays a crucial role in the processing and presentation of antigens and in discrimination between self and non-self. The aim of this investigation was to scrutinize the structural diversity and possible duplication of the MHC-DQA genes in yak (Bos grunniens). Two cDNA sequences were amplified and designated as Bogr-DQA1 (DQA*0101) and Bogr-DQA2 (DQA*2001) with GenBank accession numbers JQ864314 and JQ864315, respectively. The nucleotide and amino acid sequence alignment between Bogr-DQA1 and Bogr-DQA2 molecules showed that these two identified MHC-DQA gene sequences had more similarity to alleles of specific DQA1 and DQA2 genes from other Ruminantia species than to each other. The result from phylogenic investigation also revealed that there was a larger genetic distance between these two genes than between homologous genes from different species. The presence of different bovine DQA putative motifs and the large genetic distance between Bogr-DQA1 and Bogr-DQA2 suggest that these sequences are non-allelic. Further, these results indicate that DQA gene duplication occurs in ruminants. This study will be helpful in knowing MHC diversity in common ruminants and will deepen our understanding of the variation of immunological functions, evolutionary constraints, and selective forces that affect MHC variation within and between species.
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6
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High genetic diversity and distribution of Bubu-DQA alleles in swamp buffaloes (Bubalus bubalis carabanesis): identification of new Bubu-DQA loci and haplotypes. Immunogenetics 2016; 68:439-447. [DOI: 10.1007/s00251-016-0915-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
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7
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Sun Y, Zhang X, Xi D, Li G, Wang L, Zheng H, Du M, Gu Z, Yang Y, Yang Y. Isolation and cDNA characteristics of MHC-DRA genes from gayal ( Bos frontalis) and gaytle ( Bos frontalis × Bos taurus). BIOTECHNOL BIOTEC EQ 2015; 29:33-39. [PMID: 26019617 PMCID: PMC4434052 DOI: 10.1080/13102818.2014.986128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 10/13/2014] [Indexed: 11/12/2022] Open
Abstract
The mammalian major histocompatibility complex (MHC) plays important roles in pathogen recognition and disease resistance. In the present study, the coding sequence and the 5′- and 3′-untranslated regions of MHC class II DR alpha chain (the DRA gene) from rare gayal and gaytle were cloned and analyzed to dissect structural and functional variations. The nucleotide and amino acid sequences for the DRA genes in gayal (Bofr-DRA) and gaytle (Bofr × BoLA-DRA) were almost identical to those for cattle and yak (99%). Compared to yak, two amino acids substitutions in the signal peptide (SP) domain for gayal were found within all Bos animals. Except for only one replacement in the amino acid within the α2 domain of the DRA protein in gayal, the additional residues were highly conserved across the species investigated. The 20 peptide-binding sites (PBS) of Bofr-DRA and Bofr × BoLA-DRA were essentially reserved in the α1 domain among all species investigated. The lesser degree of substitution in Bofr-DRA is concordant with the concept that the DRA gene is highly conserved among all mammals. The very high degree of conservativity of the DRA gene among ruminants, including gayal, suggests its recent evolutionary separation.
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Affiliation(s)
- Yongke Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Xiaomin Zhang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Guozhi Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Liping Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Huanli Zheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Min Du
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Zhaobing Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Yulin Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Yuai Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
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8
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Sun Y, Xi D, Li G, Hao T, Chen Y, Yang Y. Genetic characterization of MHC class II DQB exon 2 variants in gayal ( Bos frontalis). BIOTECHNOL BIOTEC EQ 2014; 28:827-833. [PMID: 26019566 PMCID: PMC4434113 DOI: 10.1080/13102818.2014.960787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/07/2014] [Indexed: 11/20/2022] Open
Abstract
In the present study, exon 2 of major histocompatibility complex (MHC) class II DQB gene from 39 gayals (Bos frontalis) was isolated, characterized and compared with previously reported patterns for other bovidae. It was revealed by sequence analyses that there are 36 DQB exon 2 variants among 39 gayals. These variants exhibited a high degree of nucleotide and amino acid substitutions with most amino acid variations occurring at positions forming the peptide-binding sites (PBS). The DQB loci were analysed for patterns of synonymous (dS) and non-synonymous (dN) substitution. The gayals were observed to be under strong balancing selection in the DQB exon 2 PBS (dN = 0.094, P = 0.001). It appears that this variability among gayals could confer the ability to mount immune responses to a wide variety of peptides or pathogens.
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Affiliation(s)
- Yongke Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Guozhi Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Tiantian Hao
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Yuhan Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Yuai Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
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9
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Xi D, Hao T, He Y, Leng J, Sun Y, Yang Y, Mao H, Deng W. Nucleotide sequence and polymorphism of MHC class IIDQBexon 2 alleles in Chinese yakow (Bos grunniens × Bos taurus). Int J Immunogenet 2014; 41:269-75. [DOI: 10.1111/iji.12109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 11/26/2013] [Accepted: 12/22/2013] [Indexed: 11/28/2022]
Affiliation(s)
- D. Xi
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - T. Hao
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - Y. He
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - J. Leng
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - Y. Sun
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - Y. Yang
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - H. Mao
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
| | - W. Deng
- Faculty of Animal Science and Technology; Yunnan Agricultural University; Kunming China
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10
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Genetic variability of MHC class II DQB exon 2 alleles in yak (Bos grunniens). Mol Biol Rep 2014; 41:2199-206. [PMID: 24430299 DOI: 10.1007/s11033-014-3071-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 01/04/2014] [Indexed: 11/26/2022]
Abstract
The major histocompatibility class (MHC) DQ molecules are dimeric glycoproteins revealing antigen presentation to CD(4+) T cells. In the present study, the exon 2 of the MHC class II DQB gene from 32 yaks (Bos grunniens) was cloned, sequenced and compared with previously reported patterns for other bovidae. It was revealed by sequence analyses that there are 25 DQB exon 2 alleles among 32 yaks, all alleles are found to belong to DQB1 loci. These alleles exhibited a high degree of nucleotide and amino acid polymorphisms with most amino acid variations occurring at positions forming the peptide-binding sites. The DQB loci were analyzed for patterns of synonymous (d S) and non-synonymous (d N) substitution. The yak was observed to be under strong positive selection in the DQB exon 2 peptide-binding sites (d N = 0.15, P < 0.001). It appears that this variability among yaks confers the ability to mount immune responses to a wide variety of peptides or pathogens.
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11
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Yakubu A, Salako AE, De Donato M, Takeet MI, Peters SO, Adefenwa MA, Okpeku M, Wheto M, Agaviezor BO, Sanni TM, Ajayi OO, Onasanya GO, Ekundayo OJ, Ilori BM, Amusan SA, Imumorin IG. Genetic Diversity in Exon 2 of the Major Histocompatibility Complex Class II DQB1 Locus in Nigerian Goats. Biochem Genet 2013; 51:954-66. [DOI: 10.1007/s10528-013-9620-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 02/13/2013] [Indexed: 10/26/2022]
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12
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Sun Y, Zheng H, Xi D, Zhang X, Du M, Pu L, Lin M, Yang Y. Molecular characteristics of the MHC-DRA genes from yak (Bos grunniens) and Chinese yakow (Bos grunniens × Bos taurus). Int J Immunogenet 2013; 41:69-73. [PMID: 23815277 DOI: 10.1111/iji.12072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/23/2013] [Accepted: 06/02/2013] [Indexed: 11/28/2022]
Abstract
Two full-length cDNAs (762 bp) of the DRA gene from yak and Chinese yakow were isolated and analysed to identify structural and functional variations. The sequences for DRA in yak (Bogr-DRA) and Chinese yakow (Bogr × BoLA-DRA) were essentially identical to those for cattle (99%) and buffalo (97%). Except for two substitutions in the amino acids comprising the domain for signal peptide (SP) in yak, the additional residues were highly conserved across the species investigated. Peptide-binding site (PBS) of Bogr-DRA and Bogr × BoLA-DRA was highly reserved in the α1 domain among all species investigated. The lack of mutation in Bogr-DRA is consistent with the conception that the gene is highly conserved among all mammalian species. The very high conservation of the DRA gene among ruminants, including yak, may be due to its recent evolutionary detachment.
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Affiliation(s)
- Y Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
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13
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Stafuzza NB, Greco AJ, Grant JR, Abbey CA, Gill CA, Raudsepp T, Skow LC, Womack JE, Riggs PK, Amaral MEJ. A high-resolution radiation hybrid map of the river buffalo major histocompatibility complex and comparison with BoLA. Anim Genet 2012; 44:369-76. [PMID: 23216319 DOI: 10.1111/age.12015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2012] [Indexed: 02/03/2023]
Abstract
The major histocompatibility complex (MHC) in mammals codes for antigen-presenting proteins. For this reason, the MHC is of great importance for immune function and animal health. Previous studies revealed this gene-dense and polymorphic region in river buffalo to be on the short arm of chromosome 2, which is homologous to cattle chromosome 23. Using cattle-derived STS markers and a river buffalo radiation hybrid (RH) panel (BBURH5000 ), we generated a high-resolution RH map of the river buffalo MHC region. The buffalo MHC RH map (cR5000 ) was aligned with the cattle MHC RH map (cR12000 ) to compare gene order. The buffalo MHC had similar organization to the cattle MHC, with class II genes distributed in two segments, class IIa and class IIb. Class IIa was closely associated with the class I and class III regions, and class IIb was a separate cluster. A total of 53 markers were distributed into two linkage groups based on a two-point LOD score threshold of ≥8. The first linkage group included 32 markers from class IIa, class I and class III. The second linkage group included 21 markers from class IIb. Bacterial artificial chromosome clones for seven loci were mapped by fluorescence in situ hybridization on metaphase chromosomes using single- and double-color hybridizations. The order of cytogenetically mapped markers in the region corroborated the physical order of markers obtained from the RH map and served as anchor points to align and orient the linkage groups.
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Affiliation(s)
- N B Stafuzza
- Department of Biology, UNESP - São Paulo State University, IBILCE, Sao Jose do Rio Preto, SP, 15054-000, Brazil
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Yasukochi Y, Kurosaki T, Yoneda M, Koike H, Satta Y. MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus. BMC Evol Biol 2012. [PMID: 23190438 PMCID: PMC3575356 DOI: 10.1186/1471-2148-12-230] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background The major histocompatibility complex (MHC) genes are one of the most important genetic systems in the vertebrate immune response. The diversity of MHC genes may directly influence the survival of individuals against infectious disease. However, there has been no investigation of MHC diversity in the Asiatic black bear (Ursus thibetanus). Here, we analyzed 270-bp nucleotide sequences of the entire exon 2 region of the MHC DQB gene by using 188 samples from the Japanese black bear (Ursus thibetanus japonicus) from 12 local populations. Results Among 185 of 188 samples, we identified 44 MHC variants that encoded 31 different amino acid sequences (allotypes) and one putative pseudogene. The phylogenetic analysis suggests that MHC variants detected from the Japanese black bear are derived from the DQB locus. One of the 31 DQB allotypes, Urth-DQB*01, was found to be common to all local populations. Moreover, this allotype was shared between the black bear on the Asian continent and the Japanese black bear, suggesting that Urth-DQB*01 might have been maintained in the ancestral black bear population for at least 300,000 years. Our findings, from calculating the ratio of non-synonymous to synonymous substitutions, indicate that balancing selection has maintained genetic variation of peptide-binding residues at the DQB locus of the Japanese black bear. From examination of genotype frequencies among local populations, we observed a considerably lower level of observed heterozygosity than expected. Conclusions The low level of observed heterozygosity suggests that genetic drift reduced DQB diversity in the Japanese black bear due to a bottleneck event at the population or species level. The decline of DQB diversity might have been accelerated by the loss of rare variants that have been maintained by negative frequency-dependent selection. Nevertheless, DQB diversity of the black bear appears to be relatively high compared with some other endangered mammalian species. This result suggests that the Japanese black bears may also retain more potential resistance against pathogens than other endangered mammalian species. To prevent further decline of potential resistance against pathogens, a conservation policy for the Japanese black bear should be designed to maintain MHC rare variants in each local population.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Evolutionary Studies of Biosystems, the Graduate University for Advanced Studies (SOKENDAI), Shonan Village, Hayama, Kanagawa 240-0193, Japan.
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Behl JD, Verma NK, Tyagi N, Mishra P, Behl R, Joshi BK. The major histocompatibility complex in bovines: a review. ISRN VETERINARY SCIENCE 2012; 2012:872710. [PMID: 23738132 PMCID: PMC3658703 DOI: 10.5402/2012/872710] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 03/29/2012] [Indexed: 11/23/2022]
Abstract
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.
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Affiliation(s)
- Jyotsna Dhingra Behl
- Animal Genetics Division, National Bureau of Animal Genetics Resources, P.O. Box 129, GT Bypass Road, Haryana, Karnal 132001, India
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