Haplotype variation, recombination, and gene conversion within the turkey MHC-B locus.
The major histocompatibility complex (MHC) is a gene dense region with profound effects on the disease phenotype. In many species, characterizations of MHC polymorphisms have focused on identifying allelic haplotypes of the highly polymorphic class I and class II loci through direct immunological approaches such as monoclonal antibodies specific for the major antigens or indirectly through DNA sequence-based approaches. Invariably, these studies fail to assess the broader range of variation at the other loci within the MHC. This study examines variation in the turkey MHC by resequencing 15 interspersed amplicons ( approximately 14 kb) spaced across the MHC-B locus in a representative sampling of 52 commercial birds. Over 200 single nucleotide polymorphisms (SNPs) were identified with high levels of polymorphism (1 SNP/70 bp) and heterozygosity (average minor allele frequency of 0.15). SNP genotypes were used to identify the major haplotypes segregating in the commercial lines. Sequencing of the peptide binding region (PBR, exon 2) of the class IIB loci of select individuals identified 10 PBR alleles/isotypes among the major MHC haplotypes. Examination of pedigreed families provides direct evidence of gene conversion and recombination within the B locus. Results of this study demonstrate the MHC diversity available in commercial flocks and provide genomic resources for studying the effect of this diversity (alleles and/or haplotypes) on disease susceptibility and resistance.
Chaves
Lee D
LD
Division of Allergy & Clinical Immunology, Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA.
Faile
Gretchen M
GM
Krueth
Stacy B
SB
Hendrickson
Julie A
JA
Reed
Kent M
KM
D000595:Amino Acid Sequence; D000818:Animals; D005785:Gene Conversion / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D008285:Major Histocompatibility Complex / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D014422:Turkeys / Q000235:genetics*
Bioinformatics. 2007 Nov 1;23(21):2947-8
17846036
J Hered. 1985 May-Jun;76(3):146-54
3998437
Immunogenetics. 2006 Jun;58(5-6):407-21
16738938
Genome. 2005 Feb;48(1):12-7
15729392
J Immunol. 2004 Jun 1;172(11):6751-63
15153492
Mol Biol Evol. 2007 Aug;24(8):1596-9
17488738
Mol Biol Evol. 1999 Apr;16(4):479-90
10331274
Immunogenetics. 2008 Jan;60(1):1-18
18193213
Genet Mol Res. 2008;7(4):1267-81
19065762
J Immunol. 2008 Sep 1;181(5):3393-9
18714011
Nature. 1999 Oct 28;401(6756):923-5
10553909
Cytogenet Cell Genet. 1996;75(1):7-9
8995478
Int J Immunogenet. 2005 Apr;32(2):107-59
15787643
Immunogenetics. 1993;37(6):408-14
8436415
Immunogenetics. 2005 Jan;56(10):683-95
15605248
Anim Biotechnol. 2006;17(1):73-80
16621761
Immunogenetics. 2000 Feb;51(2):138-47
10663576
PLoS Biol. 2006 Mar;4(3):e46
16435885
Immunogenetics. 2004 Jul;56(4):261-79
15257423
Science. 1983 Feb 25;219(4587):977-9
6823560
Mol Biol Evol. 1987 Jul;4(4):406-25
3447015
Poult Sci. 2008 Mar;87(3):433-43
18281568
Anim Genet. 2009 Jun;40(3):348-52
19292710
Immunol Rev. 1999 Feb;167:305-17
10319269
Immunogenetics. 1999 Mar;49(3):215-24
9914335
Poult Sci. 2006 Apr;85(4):606-12
16615343
Poult Sci. 2004 Apr;83(4):638-49
15109061
Immunogenetics. 2009 Mar;61(3):189-97
19107380
Poult Sci. 2002 Dec;81(12):1832-41
12512574
Cytogenet Genome Res. 2007;117(1-4):213-20
17675862
Tissue Antigens. 1983 Feb;21(2):129-37
6221439
Int J Immunogenet. 2007 Apr;34(2):97-105
17373934
Immunol Rev. 1999 Feb;167:101-17
10319254
Immunogenetics. 2003 May;55(2):100-8
12692693
Immunogenetics. 2009 Apr;61(4):289-302
19212763
Immunogenetics. 2008 Aug;60(8):461-75
18574582
Immunogenetics. 1988;28(6):433-8
2903118
Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1434-9
16432226
Folia Biol (Praha). 1979;25(5):323-4
394980
J Hered. 2009 Sep-Oct;100(5):507-14
19617522
Anim Genet. 2004 Feb;35(1):18-27
14731225
Immunogenetics. 2004 Jun;56(3):178-91
15138734
J Immunol. 2007 May 1;178(9):5744-52
17442958
Immunogenetics. 1982;16(6):513-32
6763913
Cytogenet Genome Res. 2007;119(1-2):113-26
18160790
Genome. 2003 Oct;46(5):914-24
14608408
Nat Rev Genet. 2004 Dec;5(12):889-99
15573121
Tissue Antigens. 1985 May;25(5):278-82
4024061
Cytogenet Genome Res. 2003;102(1-4):331-9
14970725
Poult Sci. 1996 Aug;75(8):954-8
8829225
Immunol Rev. 1995 Feb;143:63-88
7558083
Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):3958-62
8632997
J Immunol. 2001 Mar 1;166(5):3324-33
11207288
J Immunol. 2009 Nov 15;183(10):6530-7
19864609
EMBO J. 1988 Sep;7(9):2775-85
3141149
Am J Hum Genet. 2003 Nov;73(5):1162-9
14574645