Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion.
This report describes single nucleotide polymorphisms (SNPs) in the sheep MHC class II and class III regions and provides insights into the internal structure of this important genomic complex. MHC haplotypes were deduced from sheep family trios based on genotypes from 20 novel SNPs representative...
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| Format: | Journal Article |
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Wiley-Blackwell
2012
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| Online Access: | http://hdl.handle.net/20.500.11937/9115 |
| _version_ | 1848745855932170240 |
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| author | Lee, C. Qin, J. Munyard, Kylie Subramaniam, N. Wetherall, John Stear, M. Groth, David |
| author_facet | Lee, C. Qin, J. Munyard, Kylie Subramaniam, N. Wetherall, John Stear, M. Groth, David |
| author_sort | Lee, C. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | This report describes single nucleotide polymorphisms (SNPs) in the sheep MHC class II and class III regions and provides insights into the internal structure of this important genomic complex. MHC haplotypes were deduced from sheep family trios based on genotypes from 20 novel SNPs representative of the class II region and 10 previously described SNPs spanning the class III region. All 30 SNPs exhibited Hardy Weinberg proportions in the sheep population studied. Recombination within an extended sire haplotype was observed within the class II region for 4 of 20 sheep chromosomes, thereby supporting the presence of separated IIa and IIb subregions similar to those present in cattle. SNP heterozygosity varied across the class II and III regions. One segment of the class IIa subregion manifested very low heterozygosity for several SNPs spanning approximately 120 Kbp. This feature corresponds to a subregion within the human MHC class II region previously described as a ‘SNP desert’ due to its paucity of SNPs. Linkage disequilibrium (LD) was reduced at the junction separating the putative class IIb and IIa subregions and also between the class IIa and the class III subregions. The latter observation is consistent with either an unmapped physical separation at this location, or more likely a boundary characterised by more frequent recombination between two conserved subregions, each manifesting within-block high LD. These results identify internal blocks of loci in the sheep MHC, within which recombination is relatively rare. |
| first_indexed | 2025-11-14T06:24:00Z |
| format | Journal Article |
| id | curtin-20.500.11937-9115 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T06:24:00Z |
| publishDate | 2012 |
| publisher | Wiley-Blackwell |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-91152017-09-13T16:06:10Z Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion. Lee, C. Qin, J. Munyard, Kylie Subramaniam, N. Wetherall, John Stear, M. Groth, David Class II Linkage disequilibrium SNP Class III Sheep MHC This report describes single nucleotide polymorphisms (SNPs) in the sheep MHC class II and class III regions and provides insights into the internal structure of this important genomic complex. MHC haplotypes were deduced from sheep family trios based on genotypes from 20 novel SNPs representative of the class II region and 10 previously described SNPs spanning the class III region. All 30 SNPs exhibited Hardy Weinberg proportions in the sheep population studied. Recombination within an extended sire haplotype was observed within the class II region for 4 of 20 sheep chromosomes, thereby supporting the presence of separated IIa and IIb subregions similar to those present in cattle. SNP heterozygosity varied across the class II and III regions. One segment of the class IIa subregion manifested very low heterozygosity for several SNPs spanning approximately 120 Kbp. This feature corresponds to a subregion within the human MHC class II region previously described as a ‘SNP desert’ due to its paucity of SNPs. Linkage disequilibrium (LD) was reduced at the junction separating the putative class IIb and IIa subregions and also between the class IIa and the class III subregions. The latter observation is consistent with either an unmapped physical separation at this location, or more likely a boundary characterised by more frequent recombination between two conserved subregions, each manifesting within-block high LD. These results identify internal blocks of loci in the sheep MHC, within which recombination is relatively rare. 2012 Journal Article http://hdl.handle.net/20.500.11937/9115 10.1111/j.1365-2052.2011.02268.x Wiley-Blackwell restricted |
| spellingShingle | Class II Linkage disequilibrium SNP Class III Sheep MHC Lee, C. Qin, J. Munyard, Kylie Subramaniam, N. Wetherall, John Stear, M. Groth, David Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion. |
| title | Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion. |
| title_full | Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion. |
| title_fullStr | Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion. |
| title_full_unstemmed | Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion. |
| title_short | Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion. |
| title_sort | conserved haplotype blocks within the sheep mhc and low snp heterozygosity in the class iia subregion. |
| topic | Class II Linkage disequilibrium SNP Class III Sheep MHC |
| url | http://hdl.handle.net/20.500.11937/9115 |