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Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus). BMC Genet 2020; 21:83. [PMID: 32727360 PMCID: PMC7392685 DOI: 10.1186/s12863-020-00889-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian species, it is notably different among ruminants due to a chromosomal inversion that splits MHC type II genes into two subregions (IIa, IIb). Recombination rates are reportedly high between these subregions, and a lack of linkage has been documented in domestic ruminants. However, no study has yet examined the degree of linkage between these subregions in a wild ruminant. The white-tailed deer (Odocoileus virginianus), a popular ruminant of the Cervidae family, is habitually plagued by pathogens in its natural environment (e.g. Haemonchus contortus, Elaeophora). Due to the association between MHC haplotypes and disease susceptibility, a deeper understanding of MHC polymorphism and linkage between MHC genes can further aid in this species' successful management. We sequenced MHC-DRB exon 2 (IIa) and MHC-DOB exon 2 (IIb) on the MiSeq platform from an enclosed white-tailed deer population located in Alabama. RESULTS We identified 12 new MHC-DRB alleles, and resampled 7 alleles, which along with other published alleles brings the total number of documented alleles in white-tailed deer to 30 for MHC-DRB exon 2. The first examination of MHC-DOB in white-tailed deer found significantly less polymorphism (11 alleles), as was expected of a non-classical MHC gene. While MHC-DRB was found to be under positive, diversifying selection, MHC-DOB was found to be under purifying selection for white-tailed deer. We found no significant linkage disequilibrium between MHC-DRB and MHC-DOB, suggesting that these loci are unlikely to be closely linked. CONCLUSIONS Overall, this study identified 12 new MHC-DRB exon 2 alleles and characterized a new, non-classical, MHC II gene (MHC-DOB) for white-tailed deer. We also found a lack of significant linkage between these two loci, which supports previous findings of a chromosomal inversion within the MHC type II gene region in ruminants, and suggests that white-tailed deer may have a recombination hotspot between these MHC regions similar to that found for Bos taurus.
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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: 50] [Impact Index Per Article: 4.2] [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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Ma J, Iannuccelli N, Duan Y, Huang W, Guo B, Riquet J, Huang L, Milan D. Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs. BMC Genomics 2010; 11:159. [PMID: 20211033 PMCID: PMC2850356 DOI: 10.1186/1471-2164-11-159] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 03/09/2010] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Variations in recombination fraction (theta) among chromosomal regions, individuals and families have been observed and have an important impact on quantitative trait loci (QTL) mapping studies. Such variations on porcine chromosome X (SSC-X) and on other mammalian chromosome X are rarely explored. The emerging assembly of pig sequence provides exact physical location of many markers, facilitating the study of a fine-scale recombination landscape of the pig genome by comparing a clone-based physical map to a genetic map. Using large offspring of F1 females from two large-scale resource populations (Large White male symbol x Chinese Meishan female symbol, and White Duroc male symbol x Chinese Erhualian female symbol), we were able to evaluate the heterogeneity in theta for a specific interval among individual F1 females. RESULTS Alignments between the cytogenetic map, radiation hybrid (RH) map, genetic maps and clone map of SSC-X with the physical map of human chromosome X (HSA-X) are presented. The most likely order of 60 markers on SSC-X is inferred. The average recombination rate across SSC-X is of approximately 1.27 cM/Mb. However, almost no recombination occurred in a large region of approximately 31 Mb extending from the centromere to Xq21, whereas in the surrounding regions and in the Xq telomeric region a recombination rate of 2.8-3.3 cM/Mb was observed, more than twice the chromosome-wide average rate. Significant differences in theta among F1 females within each population were observed for several chromosomal intervals. The largest variation was observed in both populations in the interval UMNP71-SW1943, or more precisely in the subinterval UMNP891-UMNP93. The individual variation in theta over this subinterval was found associated with F1 females' maternal haplotypes (Chinese pig haplotypes) and independent of paternal haplotype (European pig haplotypes). The theta between UMNP891 and UMNP93 for haplotype 1122 and 4311 differed by more than fourteen-fold (10.3% vs. 0.7%). CONCLUSIONS This study reveals marked regional, individual and haplotype-specific differences in recombination rate on SSC-X. Lack of recombination in such a large region makes it impossible to narrow QTL interval using traditional fine-mapping approaches. The relationship between recombination variation and haplotype polymorphism is shown for the first time in pigs.
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Affiliation(s)
- Junwu Ma
- Laboratoire de Génétique Cellulaire, INRA, BP52627, Castanet-Tolosan, France
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McRae AF, Beraldi D. Examination of a region showing linkage map discrepancies across sheep breeds. Mamm Genome 2006; 17:346-53. [PMID: 16596456 DOI: 10.1007/s00335-005-0087-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 01/11/2006] [Indexed: 12/23/2022]
Abstract
The availability of accurate linkage maps is an important step for the localization of genetic variants of interest. However, most studies in livestock assume the published map is applicable in their population despite the large differences between the breeds of a species. A region of sheep Chromosome 1 was previously identified as providing evidence for a marker order inconsistent with the published linkage map. In this study the identified region was investigated in more detail. Four microsatellite markers covering the central 5 cM of the inconsistent region and two flanking markers were genotyped in three sheep breeds, a commercial population (Charollais), an experimental population (Scottish Blackface), and a feral population (Soay). With the inclusion of the published linkage map, this provided evidence for three different marker orders across four sheep populations. Evidence for selection in this region was investigated using both a single-point allelic competition model and a multipoint allele-sharing statistic. Only the Charollais population provided evidence for selection, with significant transmission bias observed at marker BM7145. The implications of variation in linkage maps on the design and analysis of fine-mapping studies are discussed.
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Affiliation(s)
- Allan F McRae
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom.
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Jiang Z, Zhang X, Deka R, Jin L. Genome amplification of single sperm using multiple displacement amplification. Nucleic Acids Res 2005; 33:e91. [PMID: 15942023 PMCID: PMC1143700 DOI: 10.1093/nar/gni089] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sperm typing is an effective way to study recombination rate on a fine scale in regions of interest. There are two strategies for the amplification of single meiotic recombinants: repulsion-phase allele-specific PCR and whole genome amplification (WGA). The former can selectively amplify single recombinant molecules from a batch of sperm but is not scalable for high-throughput operation. Currently, primer extension pre-amplification is the only method used in WGA of single sperm, whereas it has limited capacity to produce high-coverage products enough for the analysis of local recombination rate in multiple large regions. Here, we applied for the first time a recently developed WGA method, multiple displacement amplification (MDA), to amplify single sperm DNA, and demonstrated its great potential for producing high-yield and high-coverage products. In a 50 mul reaction, 76 or 93% of loci can be amplified at least 2500- or 250-fold, respectively, from single sperm DNA, and second-round MDA can further offer >200-fold amplification. The MDA products are usable for a variety of genetic applications, including sequencing and microsatellite marker and single nucleotide polymorphism (SNP) analysis. The use of MDA in single sperm amplification may open a new era for studies on local recombination rates.
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Affiliation(s)
- Zhengwen Jiang
- Department of Environmental Health, Center for Genome Information, University of Cincinnati College of Medicine3223 Eden Ave, Cincinnati, OH 45267, USA
| | - Xingqi Zhang
- Department of Obstetrics and Gynecology, Northwestern University Medical SchoolChicago, IL, USA
| | - Ranjan Deka
- Department of Environmental Health, Center for Genome Information, University of Cincinnati College of Medicine3223 Eden Ave, Cincinnati, OH 45267, USA
| | - Li Jin
- Department of Environmental Health, Center for Genome Information, University of Cincinnati College of Medicine3223 Eden Ave, Cincinnati, OH 45267, USA
- State Key Laboratory of Genetic Engineering and Center for Anthropological Studies, School of Life Sciences and Morgan-Tan International Center for Life Sciences, Fudan UniversityShanghai, China
- To whom correspondence should be addressed at Liren Biology Building, Room 220, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China. Tel: +86 21 65642800; Fax: +86 21 55664388;
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Carrington M, Cullen M. Justified chauvinism: advances in defining meiotic recombination through sperm typing. Trends Genet 2004; 20:196-205. [PMID: 15041174 DOI: 10.1016/j.tig.2004.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sperm typing offers an efficient means of studying the quantitative and qualitative aspects of meiotic recombination that are virtually unapproachable by pedigree analysis. Since the initial development of the technique >10 years ago, several salient findings based on empirically derived recombination data have been described. The precise rates and distributions of recombination have been reported for specific regions of the genome, serving as the prototype for high-resolution genome-wide recombination patterns. Identification and characterization of molecular genetic events, such as unequal crossing over, gene conversion and crossover asymmetry, are under close inspection for the first time as a result of this technology. The influence of these phenomena on the evolution of the genome is of primary interest from a scientific and medical perspective. In this article, we review the novel discoveries in mammalian meiotic recombination that have been revealed through sperm typing.
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Affiliation(s)
- Mary Carrington
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, National Institutes of Health, SAIC-Frederick, MD 21702, USA.
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Weimann C, Kraus M, Gauly M, Erhardt G. Differences in recombination rates on chromosome 23 between German Angus and German Simmental and breed specific linkage mapping. Anim Genet 2003; 34:229-31. [PMID: 12755826 DOI: 10.1046/j.1365-2052.2003.00993.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Five paternal half sib families of German Angus (GA) (n = 428) and six of German Simmental (GS) (n = 378) including dams were genotyped with 11 microsatellites (INRA132, RM033, BM1815, BM1258, BOLA-DRB1, BM1818, BM1905, BM1443, CYP21, CSSM5 and DYMS1) derived from chromosome 23. Differences in heterozygosity between the breeds were observed. Significant differences in recombination rates between GA and GS could be demonstrated for the marker intervals INRA132-CSSM5, CYP21-BOLA-DRB1 and BOLA-DRB1-BM1818. The length of the map of GA was 90.5 cM in contrast to 117.8 cM for GS. The breed specific linkage maps show differences in length but confirmation of the order of the markers.
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Affiliation(s)
- C Weimann
- Department of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstrasse 21B, 35390 Giessen, Germany.
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Lien S, Szyda J, Leeflang EP, Hubert R, Zhang L, Schmitt K, Arnheim N. Single‐Sperm Typing. ACTA ACUST UNITED AC 2002; Chapter 1:Unit 1.6. [DOI: 10.1002/0471142905.hg0106s32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | - Rene Hubert
- University of Southern California Los Angeles California
| | - Lin Zhang
- University of Southern California Los Angeles California
| | - Karin Schmitt
- University of Southern California Los Angeles California
| | - Norman Arnheim
- University of Southern California Los Angeles California
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Frank MT, Park C, Rodriguez-Zas S, Lewin HA. Homogeneity of recombination rate within a conserved region on BTA3 that contains QTL. Anim Genet 2002; 33:56-60. [PMID: 11849138 DOI: 10.1046/j.1365-2052.2002.00814.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The D3S20-D3S34-D3S3 region on BTA3 contains quantitative trait loci (QTL) controlling milk production traits. This region also displays extensive conservation of synteny among several species including cattle, humans, mice and sheep. In this study, we evaluated the adjacent intervals D3S20-D3S34 and D3S34-D3S3 for differences in recombination rate (theta) among bulls in order to assess the suitability of population-based estimates of theta for marker assisted selection and to explore the relationship between variation in theta and chromosome breakpoints associated with mammalian evolution. Using sperm typing, thetaD3S20-D3S34 and theta D3S34-D3S3 were estimated for six triply heterozygous bulls. Recombination frequency ranged from 6.2 to 12.5% and from 9.7 to 19.2% for the D3S20-D3S34 and D3S34-D3S3 intervals, respectively. However, significant variation in theta was not detected between bulls for either interval (D3S20-D3S34 chi(2)5 d.f.=2.59, P < 0.90; D3S34-D3S3 chi(2)5 d.f.=3.72, P < 0.75). The observed differences in theta were most readily attributed to differences in allele-specific amplification efficiencies among bulls. Our results suggest that the positions of QTL in this region can be reliably determined from population data and therefore accurate marker-assisted selection can be performed for desirable alleles without concern for variation in theta. Furthermore, when considered with results of earlier studies, these findings support a correlation between the existence of evolutionary breakpoints or chromosome rearrangements and variation in theta.
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Affiliation(s)
- M T Frank
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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