Characterization of Genetic Polymorphism of Novel MHC B-LB II Alleles in Chinese Indigenous Chickens

a.
College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
b.
College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
c.
Department of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
d.
Department of Animal Husbandry and Veterinary Medicine, College of Agriculture and Animal Husbandry, Tibet University, Linzhi 860000, China

More Information

Corresponding author: E-mail address: liubang@public.wh.hb.cn (Bang Liu)

摘要

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Abstract: Genetic polymorphism of the major histocompatibility complex (MHC)B-LB II gene was studied by amplification of exon 2 using PCR, followed by cloning and DNA sequencing in eight indigenous Chinese chicken populations. To reveal the genetic variation of the B-LB II gene, 37 types of patterns detected by PCR-SSCP were investigated first, which would be used to screen novel B-LB II sequences within the breeds. The types of PCR-SSCP patterns and final sequencing allowed for the identification of 31 novel MHC B-LB II alleles from 30 unrelated individuals of Chinese chickens that were sampled. These are the first designators for the alleles of chicken MHC B-LB II gene based on the rule of assignment for novel mammalian alleles. Sequence alignment of the 31 B-LB II alleles revealed a total of 68 variable sites in the fragment of exon 2, of which 51 parsimony informative and 17 singleton variable sites were observed. Among the polymorphic sites, the nucleotide substitutions in the first and second positions of the codons accounted for 36.76% and 35.29%, respectively. The sequence similarities between the alleles were estimated to be 90.6%–99.5%. The relative frequencies of synonymous and nonsynonymous nucleotide substitutions within the region were 2.92%±0.94% and 14.64%±2.67%, respectively. These results indicated that the genetic variation within exon 2 appeared to have largely arisen by gene recombination and balancing selection. Alignment of the deduced amino acid sequences of the β1 domain coded by exon 2 revealed 6 synonymous mutations and 27 nonsynonymous substitutions at the 33 disparate sites. In particular, the nonsynonymous substitutions at the putative peptide-binding sites are considered to be associated with immunological specificity of MHC B-LB II molecule in Chinese native chickens. These results can provide a molecular biological basis for the study of disease resistance in chicken breeding.
- genetic polymorphism /
- allele /
- PCR-SSCP assay /
- indigenous Chinese chicken

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参考文献(52)

[1]	Bloom, SE, Bacon, et al. Linkage of the major histocompatibility (B) complex and the nucleolar organizer in the chicken. Assignment to a microchromosome Journal of Heredity, 76 (1985),pp. 146-154
[2]	Guillemot, F, Billault, et al. A molecular map of the chicken major histocompatibility complex: the class β?genes are closely-linked to the class I genes and the nucleolar organizer EMBO J, 7 (1988),pp. 2775-2785
[3]	Bourlet, Y, Behar, et al. Isolation of chicken major histocompatibility complex class II (B-L) beta chain sequences: comparison with mammalian beta chains and expression in lymphoid organs EMBO J, 7 (1988),pp. 1031-1039
[4]	Miller, MM, Goto, et al. Proceedings of National Academy of Science USA, 93 (1996),pp. 3958-3962
[5]	Kaufman, J, Volk, et al. A “minimal essential Mhc” and an “unrecognized Mhc”: two extremes in selection for polymorphism Immunology Reviews, 143 (1995),pp. 63-88
[6]	Zoorob, R, Bernot, et al. Chicken major histocompatibility complex class II B genes: analysis of interallelic and interlocus sequence variance European Journal of Immunology, 23 (1993),pp. 1139-1145
[7]	Brown, JH, Jardetzky, et al. Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1 Nature, 364 (1993),pp. 33-39
[8]	Hedrick, PW Evolutionary genetics of the major histocompatibility complex American Naturalist, 143 (1994),pp. 945-964
[9]	Penn, DJ, Potts, et al. The evolution of mating preferences and major histocompatibility complex genes American Naturalist, 153 (1999),pp. 145-164
[10]	Nasir, L, Ndiaye, et al. Sequence polymorphism in the bovine major histocompatibility complex DQB loci Animal Genetics, 28 (1997),pp. 441-445
[11]	Snibson, KJ, Maddox, et al. Allelic variation of ovine MHC class II DQA1 and DQA2 genes Animal Genetics, 29 (1998),pp. 356-362
[12]	De, S, Singh, et al. MHC-DRB exon 2 allele polymorphism in Indian river buffalo (Bubalus bubalis) Animal Genetics, 33 (2002),pp. 215-219
[13]	Zhou, H, Hickford, et al. Allelic polymorphism in the ovine DQA1 gene Journal of Animal Science, 82 (2004),pp. 8-16
[14]	Bodmer, JG, Marsh, et al. Nomenclature for factors of the HLA system Tissue Antigens, 46 (1995),pp. 1-18
[15]	Davies, CJ, Andersson, et al. Nomenclature for factors of the BoLA system, 1996: report of the ISAG BoLA Nomenclature Committee Animal Genetics, 28 (1997),pp. 159-168
[16]	Andersson, L, Sigurdardottir, et al. Evolution of MHC polymorphism: extensive sharing of polymorphic sequence motifs between human and bovine DRB alleles Immunogenetics, 33 (1991),pp. 188-193
[17]	Mikko, S, Spencer, et al. Journal of Heredity, 88 (1997),pp. 499-503
[18]	Sena, L, Schneider, et al. Polymorphisms in MHC-DRA and -DRB alleles of water buffalo (Bubalus bubalis) reveal different features from cattle DR alleles Animal Genetics, 34 (2003),pp. 1-10
[19]	Simonsen, M, Crone, et al. The MHC haplotypes of the chicken Immunogenetics, 16 (1982),pp. 513-532
[20]	Briles, WE, Bumstead, et al. Nomenclature for chicken major histocompatibility (B) complex Immunogenetics, 15 (1982),pp. 441-447
[21]	Briles, WE, Briles, et al. Identification of haplotypes of the chicken major histocompatibility complex (B) Immunogenetics, 15 (1982),pp. 449-459
[22]	Briles, WE, Goto, et al. A polymorphic system related to but genetically independent of the chicken major histocompatibility complex Immunogenetics, 37 (1993),pp. 408-414
[23]	Zoorob, R, Behar, et al. Organization of a functional chicken class II B gene Immunogenetics, 31 (1990),pp. 179-187
[24]	Lakshmana, N, Gavora, et al. Major histocompatibility complex class ? DNA polymorphisms in chicken strains selected for Marek's disease resistance and egg production or egg production alone Poultry Science, 76 (1997),pp. 1517-1523
[25]	Li, L, Johnson, et al. Molecular characterizaton of major histocompatibility complex (B) haplotypes in broiler chickens Animal Genetics, 28 (1997),pp. 258-267
[26]	Li, L, JohnsonL, et al. The MHC of a broiler chicken line: serology, B-G genotypes, and B-F/B-LB sequences Immunogenetics, 49 (1999),pp. 215-224
[27]	Zhang, D, O'Keefe, et al. A PCR method for typing B-Lβ? family (class ? MHC) alleles in broiler chickens Animal Genetics, 30 (1999),pp. 109-119
[28]	Jacob, JP, Milne, et al. The major and a minor class II beta-chain (B-LB) gene flank the Tapasin gene in the B-F/B-L region of the chicken major histocompatibility complex Immunogenetics, 51 (2000),pp. 138-147
[29]	Livant, EJ, Zhang, et al. Three new MHC haplotypes in broiler breeder chickens Animal Genetics, 32 (2001),pp. 123-131
[30]	Iglesias, GM, Aoria, et al. Genotypic variability at the major histocompatibility complex (B and Rfp-Y) in Comperos broiler chickens Animal Genetics, 34 (2003),pp. 88-95
[31]	Xu, RF, Li, et al. Sequence Comparison of MHC Class II β (exon 2) and Phylogenetic Relationship between Poultry and Mammalian Agricultural Sciences in China, 4 (2005),pp. 299-309
[32]	Xu, RF
[33]	Sambrook, J, Fritsch, et al.
[34]	Kumar, S, Tamura, et al.
[35]	Nei, M, Gojobori, et al. Simple methods for estimating the numbers of synonymous and non-synonymous nucleotide substitutions Molecular Biological Evolution, 3 (1986),pp. 418-426
[36]	Lynch, M, Crease, et al. The analysis of population survey data on DNA sequence variation Molecular Biological Evolution, 79 (1990),pp. 377-394
[37]	Jukes, TH, Cantor, et al.
[38]	Rozas, J, Sánchez-DelBarrio, et al. DnaSP, DNA polymorphism analyses by the coalescent and other methods Bioinformatics, 19 (2003),pp. 2496-2497
[39]	International Chicken Polymorphism Map Consortium A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms Nature, 432 (2004),pp. 717-722
[40]	Nei, M
[41]	Hughes, AL
[42]	International Chicken Polymorphism Map Consortium A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms Nature, 432 (2004),pp. 695-716
[43]	Begun, DJ, Aquadro, et al. Nature, 356 (1992),pp. 519-520
[44]	Nachman, MW Single nucleotide polymorphisms and recombination rate in humans Trends Genet, 17 (2001),pp. 481-485
[45]	Shia, YC, Bradshaw, et al. Polymerase chain reaction based genotyping for characterization of SLA-DQB and SLA-DRB alleles in domestic pigs Anim Genet, 26 (1995),pp. 91-100
[46]	Paliakasis, K, Routsias, et al. Novel structural features of the human histocompatibility molecules HLA-DQ as revealed by modeling based on the published structure of the related molecule HLA-DR J Struct Biol, 117 (1996),pp. 145-163
[47]	Seidl, C, Koch, et al. HLA-DR/DQ/DP interactions in rheumatoid arthritis Eur J Immunogenet, 24 (1997),pp. 365-376
[48]	Toussirot, E, Auge, et al. HLA-DRB1 alleles and shared amino acid sequences in disease susceptibility and severity in patients from eastern France with rheumatoid arthritis J Rheumatol, 26 (1999),pp. 1446-1451
[49]	Madden, DR, Gorga, et al. The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC Cell, 70 (1992),pp. 1035-1048
[50]	Cao, MD, Qin, et al.
[51]	Chen, HL, Li, et al.
[52]	Rietsch, A, Bessette, et al. Reduction of the periplasmic disulfide bond isomerase, DsbC, occurs by passage of electrons from cytoplasmic thioredoxin J Bacteriol, 179 (1997),pp. 6602-6608