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Martins de Camargo M, Caetano AR, Ferreira de Miranda Santos IK. Evolutionary pressures rendered by animal husbandry practices for avian influenza viruses to adapt to humans. iScience 2022; 25:104005. [PMID: 35313691 PMCID: PMC8933668 DOI: 10.1016/j.isci.2022.104005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Commercial poultry operations produce and crowd billions of birds every year, which is a source of inexpensive animal protein. Commercial poultry is intensely bred for desirable production traits, and currently presents very low variability at the major histocompatibility complex. This situation dampens the advantages conferred by the MHC’s high genetic variability, and crowding generates immunosuppressive stress. We address the proteins of influenza A viruses directly and indirectly involved in host specificities. We discuss how mutants with increased virulence and/or altered host specificity may arise if few class I alleles are the sole selective pressure on avian viruses circulating in immunocompromised poultry. This hypothesis is testable with peptidomics of MHC ligands. Breeding strategies for commercial poultry can easily and inexpensively include high variability of MHC as a trait of interest, to help save billions of dollars as a disease burden caused by influenza and decrease the risk of selecting highly virulent strains.
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Yuan Y, Zhang H, Yi G, You Z, Zhao C, Yuan H, Wang K, Li J, Yang N, Lian L. Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations. Front Genet 2021; 12:710770. [PMID: 34484301 PMCID: PMC8414643 DOI: 10.3389/fgene.2021.710770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
The chicken major histocompatibility complex (MHC) on chromosome 16 is the most polymorphic region across the whole genome, and also an ideal model for genetic diversity investigation. The MHC B-F/B-L region is 92 kb in length with high GC content consisting of 18 genes and one pseudogene (Blec4), which plays important roles in immune response. To evaluate polymorphism of the Chinese indigenous chickens as well as to analyze the effect of selection to genetic diversity, we used WaferGen platform to identify sequence variants of the B-F/B-L region in 21 chicken populations, including the Red Jungle Fowl (RJF), Cornish (CS), White Leghorns (WLs), 16 Chinese domestic breeds, and two well-known inbred lines 63 and 72. A total of 3,319 single nucleotide polymorphism (SNPs) and 181 INDELs in the B-F/B-L region were identified among 21 populations, of which 2,057 SNPs (62%) and 159 INDELs (88%) were novel. Most of the variants were within the intron and the flanking regions. The average variation density was 36 SNPs and 2 INDELs per kb, indicating dramatical high diversity of this region. Furthermore, BF2 was identified as the hypervariable genes with 67 SNPs per kb. Chinese domestic populations showed higher diversity than the WLs and CS. The indigenous breeds, Nandan Yao (NY), Xishuangbanna Game (XG), Gushi (GS), and Xiayan (XY) chickens, were the top four with the highest density of SNPs and INDELs. The highly inbred lines 63 and 72 have the lowest diversity, which might be resulted from a long-term intense selection for decades. Collectively, we refined the genetic map of chicken MHC B-F/B-L region, and illustrated genetic diversity of 21 chicken populations. Abundant genetic variants were identified, which not only strikingly expanded the current Ensembl SNP database, but also provided comprehensive data for researchers to further investigate association between variants in MHC and immune traits.
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Affiliation(s)
- Yiming Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huanmin Zhang
- United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, United States
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhen You
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunfang Zhao
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haixu Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ling Lian
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Iglesias GM, Beker MP, Remolins JS, Canet ZE, Librera J, Cantaro H, Maizon DO, Fulton JE. MHC-B variation in maternal and paternal synthetic lines of the Argentinian Campero INTA chicken. Poult Sci 2021; 100:101253. [PMID: 34217141 PMCID: PMC8258676 DOI: 10.1016/j.psj.2021.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/16/2021] [Accepted: 05/03/2021] [Indexed: 11/30/2022] Open
Abstract
The Campero-INTA chicken of Argentina was developed to provide a robust bird that can survive under Argentinian pasture conditions with no significant additional nutrition, producing a source of animal protein for small producers or low-income families. In previous work, we described the AH paternal line of Campero and its Major Histocompatibility Complex B region (MHC-B) variation. In this work we analyzed the three remaining synthetic lines used to produce the Campero-INTA production bird: lines AS, A, and E. Because of the association between variation within the MHC of chickens and disease resistance, MHC variation within this breed is of particular interest. MHC variability within the lines used to produce the Campero-INTA chicken was examined using a 90 SNP panel encompassing the chicken MHC-B region plus the VNTR, LEI0258, located within the chicken MHC. Across all 4lines 12 haplotypes were found, with 7 of these being previously reported in North America/European breeds, reflecting the original breed sources for these birds. Three Campero unique haplotypes were found, 2 of which likely originated from MHC recombination events. MHC-B variation for all lines involved with production of the final Campero-INTA bird has now been determined.
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Affiliation(s)
- Gabriela M Iglesias
- Universidad Nacional de Rio Negro, Sede Alto Valle y Valle Medio, Escuela de Veterinaria y Producción Agroindustrial, Cátedra de Genética, Pacheco 460, Choele Choel, Rio Negro, 8360 Argentina.
| | - María P Beker
- Universidad Nacional de Rio Negro, Sede Alto Valle y Valle Medio, Escuela de Veterinaria y Producción Agroindustrial, Cátedra de Genética, Pacheco 460, Choele Choel, Rio Negro, 8360 Argentina
| | - Jose S Remolins
- Universidad Nacional de Rio Negro, Sede Alto Valle y Valle Medio, Escuela de Veterinaria y Producción Agroindustrial, Cátedra de Genética, Pacheco 460, Choele Choel, Rio Negro, 8360 Argentina
| | - Zulma E Canet
- Universidad Nacional de Rosario, Facultad de Ciencias Veterinarias, Cátedra de Genética, Boulevard Ovidio Lagos y Ruta 33, Casilda. Santa Fe, Argentina; INTA Pergamino, Estación Experimental Agropecuaria "Ing. Agr. Walter Kugler", Av. Frondizi (Ruta 32) Km 4,5. Pergamino, Buenos Aires, Argentina
| | - José Librera
- Universidad Nacional de Rosario, Facultad de Ciencias Veterinarias, Cátedra de Genética, Boulevard Ovidio Lagos y Ruta 33, Casilda. Santa Fe, Argentina
| | - Horacio Cantaro
- Universidad Nacional de Rio Negro, Sede Alto Valle y Valle Medio, Escuela de Veterinaria y Producción Agroindustrial, Cátedra de Genética, Pacheco 460, Choele Choel, Rio Negro, 8360 Argentina; Estación Experimental Agropecuaria Alto Valle, Programa Nacional de Producción Animal, Ruta Nacional 22, Km, 1190 Argentina
| | - Daniel O Maizon
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Anguil, Ruta Nacional 5 Km 580, Anguil, Argentina
| | - Janet E Fulton
- Hy-Line International, P.O. Box 310 Dallas Center, IA 50063, USA
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4
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Haunshi S, Devara D, Ramasamy K, Ullengala R, Chatterjee RN. Genetic diversity at major histocompatibility complex and its effect on production and immune traits in indigenous chicken breeds of India. Arch Anim Breed 2020; 63:173-182. [PMID: 32760784 PMCID: PMC7397721 DOI: 10.5194/aab-63-173-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/12/2020] [Indexed: 12/03/2022] Open
Abstract
The genetic diversity at major histocompatibility complex (MHC) in indigenous chicken breeds of India
(Ghagus and Nicobari) in comparison with the White Leghorn (WLH) breed was
investigated by genotyping the MHC-linked LEI0258 marker. Altogether 38 alleles
and 96 genotypes were observed among three breeds. The observed and
effective alleles were highest in Ghagus (23, 8.3) followed by Nicobari (14,
3.2) and WLH (10 and 2.2) breeds. The size of alleles ranged from 193 to 489 bp in Ghagus, 193 to 552 bp in Nicobari and 241 to 565 bp in the WLH breed. The
number of private alleles was also highest in Ghagus (18) followed by
Nicobari (8) and WLH (5) breeds. The most frequent allele was 261 bp in WLH
(66 %), 343 bp in Nicobari (50.4 %) and 309 bp in the Ghagus (28.15 %)
breed. Observed and expected heterozygosities were highest in Ghagus (0.83,
0.88) followed by Nicobari (0.58, 0.68) and WLH (0.53, 0.54). The genetic
distance (Nei) between Ghagus and Nicobari breeds (2.24) was higher as
compared to that of Ghagus and WLH (1.23) and that between Nicobari and WLH
breeds (0.89). Association analysis revealed significant influence of MHC
alleles on body weight, egg production in Ghagus and WLH breeds and antibody
titres to Newcastle disease vaccine in the Nicobari breed.
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Affiliation(s)
- Santosh Haunshi
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad 500030, India
| | - Divya Devara
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad 500030, India
| | - Kannaki Ramasamy
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad 500030, India
| | - Rajkumar Ullengala
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad 500030, India
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5
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E GX, Chen LP, Zhou DK, Yang BG, Zhang JH, Zhao YJ, Hong QH, Ma YH, Chu MX, Zhang LP, Basang WD, Zhu YB, Han YG, Na RS, Zeng Y, Zhao ZQ, Huang YF, Han JL. Evolutionary relationship and population structure of domestic Bovidae animals based on MHC-linked and neutral autosomal microsatellite markers. Mol Immunol 2020; 124:83-90. [PMID: 32544655 DOI: 10.1016/j.molimm.2020.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 11/26/2022]
Abstract
Major histocompatibility complex (MHC) genes are critical for disease resistance or susceptibility responsible for host-pathogen interactions determined mainly by extensive polymorphisms in the MHC genes. Here, we examined the diversity and phylogenetic pattern of MHC haplotypes reconstructed using three MHC-linked microsatellite markers in 55 populations of five Bovidae species and compared them with those based on neutral autosomal microsatellite markers (NAMs). Three-hundred-and-forty MHC haplotypes were identified in 1453 Bovidae individuals, suggesting significantly higher polymorphism and heterozygosity compared with those based on NAMs. The ambitious boundaries in population differentiation (phylogenetic network, pairwise FST and STRUCTURE analyses) within and between species assessed using the MHC haplotypes were different from those revealed by NAMs associated closely with speciation, geographical distribution, domestication and management histories. In addition, the mean FST was significantly correlated negatively with the number of observed alleles (NA), observed (HO) and expected (HE) heterozygosity and polymorphism information content (PIC) (P < 0.05) in the MHC haplotype dataset while there was no correction of the mean FST estimates (P> 0.05) between the MHC haplotype and NAMs datasets. Analysis of molecular variance (AMOVA) revealed a lower percentage of total variance (PTV) between species/groups based on the MHC-linked microsatellites than NAMs. Therefore, it was inferred that individuals within populations accumulated as many MHC variants as possible to increase their heterozygosity and thus the survival rate of their affiliated populations and species, which eventually reduced population differentiation and thereby complicated their classification and phylogenetic relationship inference. In summary, host-pathogen coevolution and heterozygote advantage, rather than demographic history, act as key driving forces shaping the MHC diversity within the populations and determining the interspecific MHC diversity.
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Affiliation(s)
- Guang-Xin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Li-Peng Chen
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Dong-Ke Zhou
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Bai-Gao Yang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Jia-Hua Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Yong-Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Qiong-Hua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China
| | - Yue-Hui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ming-Xing Chu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lu-Pei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wang-Dui Basang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Science (TAAAS)), Lhasa 850002, China
| | - Yan-Bin Zhu
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Science (TAAAS)), Lhasa 850002, China
| | - Yan-Guo Han
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Ri-Su Na
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Yan Zeng
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Zhong-Quan Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Yong-Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China.
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya.
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6
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E GX, Duan XH, Yang BG, Na RS, Han YG, Zeng Y. Genetic Diversity Pattern of the MHC-LEI0258 Locus across Asian Populations of Chickens. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Tarrant KJ, Lopez R, Loper M, Fulton JE. Assessing MHC-B diversity in Silkie chickens. Poult Sci 2020; 99:2337-2341. [PMID: 32359568 PMCID: PMC7597446 DOI: 10.1016/j.psj.2020.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/20/2019] [Accepted: 01/01/2020] [Indexed: 11/06/2022] Open
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic region on chromosome 16, which contains numerous immune response genes, and is known to influence disease susceptibility and resistance in chickens. Variability of MHC-B haplotypes in various well-known and commercially utilized breeds has previously been identified. This study aims to understand MHC-B diversity in the Silkie breed using a high-density SNP panel that encompasses the chicken MHC-B region. DNA was obtained from 74 females and 27 males from a commercial Silkie breeder colony that is maintained through minimal genetic selection practices. A previously described panel of 90 SNPs, all located within the MHC-B region, was used to evaluate MHC-B variability in the commercial Silkie breeder colony. MHC-B haplotypes identified from the individual SNP information in the Silkie colony were compared to published haplotypes from the same region. Of the 27 haplotypes identified in the Silkie population, 8 have been previously described. Nineteen haplotypes are unique to the Silkie population and include one novel recombinant and 2 additional possible novel recombinants. Six haplotypes were found at a frequency greater than 5% of the population, of which 4 are novel. Finally, Hardy Weinberg Equilibrium (HWE) was calculated for the observed haplotypes, which were found to be in HWE. This study shows considerable MHC-B diversity in the Silkie breed and adds further information on variability of the MHC-B region in the chicken.
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Affiliation(s)
- Katy J Tarrant
- Department of Animal Sciences and Agricultural Education, California State University Fresno, Fresno 93740, USA.
| | - Rodrigo Lopez
- Department of Animal Sciences and Agricultural Education, California State University Fresno, Fresno 93740, USA
| | | | - Janet E Fulton
- Pitman Family Farms, Sanger, CA 93657, USA; Hy-Line International, Dallas Center, IA 50063, USA
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8
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Fulton JE. Advances in methodologies for detecting MHC-B variability in chickens. Poult Sci 2020; 99:1267-1274. [PMID: 32111304 PMCID: PMC7587895 DOI: 10.1016/j.psj.2019.11.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/08/2019] [Accepted: 11/08/2019] [Indexed: 11/19/2022] Open
Abstract
The chicken major histocompatibility B complex (MHC-B) region is of great interest owing to its very strong association with resistance to many diseases. Variation in the MHC-B was initially identified by hemagglutination of red blood cells with specific alloantisera. New technologies, developed to identify variation in biological materials, have been applied to the chicken MHC. Protein variation encoded by the MHC genes was examined by immunoprecipitation and 2-dimensional gel electrophoresis. Increased availability of DNA probes, PCR, and sequencing resulted in the application of DNA-based methods for MHC detection. The chicken reference genome, completed in 2004, allowed further refinements in DNA methods that enabled more rapid examination of MHC variation and extended such analyses to include very diverse chicken populations. This review progresses from the inception of MHC-B identification to the present, describing multiple methods, plus their advantages and disadvantages.
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Affiliation(s)
- J E Fulton
- Research and Development, Hy-Line International, Dallas Center, IA 50063, USA.
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9
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Iglesias GM, Canet ZE, Cantaro H, Miquel MC, Melo JE, Miller MM, Berres ME, Fulton JE. Mhc-B haplotypes in "Campero-Inta" chicken synthetic line. Poult Sci 2020; 98:5281-5286. [PMID: 31376352 DOI: 10.3382/ps/pez431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
The major histocompatibility complex-B (MHC-B) in chickens is a cluster of genes located on chromosome 16. The chicken MHC-B is known to be highly associated with resistance to numerous diseases caused by viruses, bacteria, and parasitic pathogens. Since the level of resistance varies with MHC-B haplotypes, identification and classification of different haplotypes within lines is important for sustaining lines. The "Campero-INTA" chicken breed is a meat-type free-range poultry breed that was developed specifically for small producers in Argentina. Campero-INTA was started by selection in populations produced by crosses between a variety of established lines. MHC-B variation was examined in 65 samples obtained in 2002 using the VNTR marker LEI0258, a marker for MHC-B region. These samples plus and an additional 55 samples from 2018 were examined for variation using the MHC-B specific SNP panel that encompasses ∼230,000 bp of the MHC-B region. Eleven MHC-B SNP haplotypes with 6 LEI0258 alleles were identified in the 120 samples representing the Campero-INTA AH (male) line. Seven haplotypes originate from the breeds originally used in the development of Campero-INTA AH line. Two appear to be recombinant haplotypes. The origin of the remaining 2 is not known, but may be associated with genes introduced from crosses with the Fayoumi breed conducted more recently to sustain the line.
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Affiliation(s)
- Gabriela M Iglesias
- Universidad Nacional de Río Negro, Sede Alto Valle y Valle Medio, Escuela de Veterinaria y Producción Agroindustrial, Area de Genética, Choele Choel, Rio Negro 8360, Argentina
| | - Zulma E Canet
- Cátedra de Genética, Facultad de Ciencias Veterinarias, Universidad Nacional de Rosario, Boulevard Ovidio Lagos y Ruta 33, Casilda, Santa Fe 2170, Argentina.,INTA Pergamino, Estación Experimental Agropecuaria "Ing. Agr. Walter Kugler", Pergamino, Buenos Aires 2700, Argentina
| | - Horacio Cantaro
- Universidad Nacional de Río Negro, Sede Alto Valle y Valle Medio, Escuela de Veterinaria y Producción Agroindustrial, Area de Producción Aves y Pilíferos, Choele Choel, Rio Negro 8360, Argentina.,INTA, Proyecto Nacional de Avicultura (PAVI), Estación Experimental Agropecuaria Alto Valle, Programa Nacional de Producción Animal, Ruta Nacional 22, Argentina
| | - María C Miquel
- Cátedra de Genética, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires 8332, Argentina
| | - Julián E Melo
- Facultad de Ciencias Agrícolas, Universidad Católica Pontificia Argentina (UCA), Buenos Aires, C.A.B.A 1107, Argentina.,Departamento de Tecnología, Universidad Nacional de Luján (UNLu), B6702 Luján, Buenos Aires, Argentina
| | - Marcia M Miller
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010-3000
| | - Mark E Berres
- Biotechnology Center, University of Wisconsin, Madison, WI 53706
| | - Janet E Fulton
- Biotechnology Center, University of Wisconsin, Madison, WI 53706.,Hy-Line International, Dallas Center, IA 50063
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10
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Mwambene PL, Kyallo M, Machuka E, Githae D, Pelle R. Genetic diversity of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania based on Major Histocompatibility Complex-linked microsatellite LEI0258 marker typing. Poult Sci 2019; 98:2734-2746. [PMID: 30877744 PMCID: PMC6591683 DOI: 10.3382/ps/pez076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 02/05/2019] [Indexed: 01/21/2023] Open
Abstract
Unraveling the genetic diversity of livestock species is central to understanding their value and importance for conservation and improvement in diverse production environments. In developing countries, information on genetic attributes of many livestock species is unfortunately scanty to support well-informed decision-making upon relevant management strategies. This study aimed at investigating allelic variability, genetic diversity, and genetic relationships of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania using the Major Histocompatibility Complex-linked LEI0258 marker. A total of 400 DNA samples, 40 per ecotype, were genotyped by capillary electrophoresis. Thirty different alleles with sizes ranging from 197 to 569 bp were determined. The number of alleles ranged from 17 (Itunduma) to 21 (Mbeya), with an average of 19.20 alleles per ecotype. Allelic polymorphism was further evaluated through genotyping by Sanger sequencing. Thirty-three DNA samples with different fragment sizes were re-amplified and their alleles sequenced to depict polymorphism based on a combination of two repeat regions at 12 and 13 bp, respectively, and flanking regions with SNP and indels. The repeat region at 13 bp appeared 1 to 28 times, whereas the region at 12 bp appeared 3 to 19 times in all sequenced fragments. The numbers of indels and SNP determined were 7 and 9, respectively. From capillary electrophoresis, the Chunya and Msimbazi ecotypes exhibited the highest genetic diversity (0.937), whereas the lowest value (0.910) was observed from the Mbarali ecotype, with an average of 0.925. The Namtumbo and Wanging'ombe ecotypes showed high inbreeding coefficients (FIS > 0.05), whereas a high excess heterozygote value (FIS = -0.098) was observed from the Njombe ecotype. Two percent of the genetic diversity was due to differences among ecotypes, and the rest was due to differences among individuals within the ecotypes. Despite the overall low genetic differentiation, both fragment and sequencing analyses depicted a high allelic and genetic variability across 10 chicken ecotypes. These results therefore, underscore the importance of establishing appropriate conservation and management strategies to capitalize on observed variability and maintain genetic flexibility across diverse production environments.
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Affiliation(s)
- Pius L Mwambene
- Tanzania Livestock Research Institute (TALIRI) - Uyole, Department of Research and Development, P.O. Box 6191, Mbeya, Tanzania.,Biosciences eastern and central Africa International Livestock Research Institute (BecA-ILRI) Hub, Capacity Building Unit, P.O. Box 30709-00100, Nairobi, Kenya
| | - Martina Kyallo
- Biosciences eastern and central Africa International Livestock Research Institute (BecA-ILRI) Hub, Capacity Building Unit, P.O. Box 30709-00100, Nairobi, Kenya
| | - Eunice Machuka
- Biosciences eastern and central Africa International Livestock Research Institute (BecA-ILRI) Hub, Capacity Building Unit, P.O. Box 30709-00100, Nairobi, Kenya
| | - Dedan Githae
- Biosciences eastern and central Africa International Livestock Research Institute (BecA-ILRI) Hub, Capacity Building Unit, P.O. Box 30709-00100, Nairobi, Kenya
| | - Roger Pelle
- Biosciences eastern and central Africa International Livestock Research Institute (BecA-ILRI) Hub, Capacity Building Unit, P.O. Box 30709-00100, Nairobi, Kenya
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11
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Yu C, Qiu M, Jiang X, Zhang Z, Du H, Li Q, Xia B, Song X, Hu C, Xiong X, Yang L, Peng H, Chen J, Wang Y, Yang C. Genetic Diversity and Phyletic Evolution of Eleven Chinese Indigenous and Three Commercial Chicken Breeds by mtDNA Sequences. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2019. [DOI: 10.1590/1806-9061-2018-0807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- C Yu
- Sichuan Animal Science Academy, China
| | - M Qiu
- Sichuan Animal Science Academy, China
| | - X Jiang
- Sichuan Animal Science Academy, China
| | - Z Zhang
- Sichuan Animal Science Academy, China
| | - H Du
- Sichuan Animal Science Academy, China
| | - Q Li
- Sichuan Animal Science Academy, China
| | - B Xia
- Sichuan Animal Science Academy, China
| | - X Song
- Sichuan Animal Science Academy, China
| | - C Hu
- Sichuan Animal Science Academy, China
| | - X Xiong
- Sichuan Animal Science Academy, China
| | - L Yang
- Sichuan Animal Science Academy, China
| | - H Peng
- Sichuan Animal Science Academy, China
| | - J Chen
- Sichuan Animal Science Academy, China
| | - Y Wang
- Sichuan Agricultural University, China
| | - C Yang
- Sichuan Animal Science Academy, China
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12
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Sulimova GE, Oyun NY, Sevastianova AA, Alexandrov AV, Vakhrameev AB, Kuzevanova AY, Alimov AA. Evaluation of polymorphism loci associated with viral diseases in spangled Orloff chicken breed. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417100118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Esmailnejad A, Nikbakht Brujeni G, Badavam M. LEI0258 microsatellite variability and its association with humoral and cell mediated immune responses in broiler chickens. Mol Immunol 2017; 90:22-26. [PMID: 28662410 DOI: 10.1016/j.molimm.2017.06.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 05/06/2017] [Accepted: 06/12/2017] [Indexed: 11/20/2022]
Abstract
Major histocompatibility complex (MHC) has a profound influence on disease resistance or susceptibility, productivity and important economic traits in chicken. Association of the MHC with a wide range of immune responses makes it a valuable predictive factor for the disease pathogenesis and outcome. The tandem repeat LEI0258 is a genetic marker which is located within the B locus of chicken MHC and strongly associated with serologically defined haplotypes. LEI0258 microsatellite marker was applied to investigate the MHC polymorphism in Ross 308 broiler chicken (N=104). Association of LEI0258 alleles with humoral and cell mediated immune responses to Newcastle disease (ND), Infectious bursal disease (IBD) and Avian influenza (AI) vaccines were also examined. LEI0258 polymorphism was determined by PCR-based fragment analysis, and association of LEI0258 alleles with immune responses were evaluated using multivariate regression analysis and GLM procedures. A total of seven alleles ranging from 195 to 448bp were found, including two novel alleles (263 and 362bp) that were unique in Ross 308 broiler population. Association study revealed a significant influence of MHC alleles on humoral and cellular immune responses in Ross population (P<0.05). Alleles 385 and 448bp were associated with increased peripheral blood lymphocyte proliferation response. Alleles 300, 362 and 448bp had a positive effect on immune responses to Infectious bursal disease vaccine, and allele 263bp was significantly correlated with elevated antibody titer against Newcastle disease vaccine. Results obtained from this study confirmed the important role of MHC as a candidate gene marker for immune responses that could be used in genetic improvement of disease-resistant traits and resource conservation in broiler population.
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Affiliation(s)
- Atefeh Esmailnejad
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Gholamreza Nikbakht Brujeni
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Maryam Badavam
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Nguyen-Phuc H, Fulton JE, Berres ME. Genetic variation of major histocompatibility complex (MHC) in wild Red Junglefowl (Gallus gallus). Poult Sci 2016; 95:400-11. [PMID: 26839415 DOI: 10.3382/ps/pev364] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/27/2015] [Indexed: 01/09/2023] Open
Abstract
The major histocompatibility complex (MHC) is a multi-family gene cluster that encodes proteins with immuno-responsive function. While studies of MHC in domesticated poultry are relatively common, very little is known about this highly polymorphic locus in wild Red Junglefowl (Gallus gallus), the natural progenitor of domestic chickens. We investigated the diversity of MHC within and among four wild Red Junglefowl populations across diversified natural habitats in South Central Vietnam. Based on a SNP panel of 84 sites spanning 210 Kb of the MHC-B locus, we identified 310 unique haplotypes in 398 chromosomes. None of these haplotypes have been described before and we did not observe any of the wild Red Junglefowl haplotypes in domesticated chickens. Analysis of molecular variance (AMOVA) revealed that 94.51% of observed haplotype variation was accounted for at the within individual level. Little genetic variance was apportioned within and among populations, the latter accounting only for 0.83%. We also found evidence of increased recombination, including numerous hotspots, and limited linkage disequilibrium among the 84 SNP sites. Compared to an average haplotype diversity of 3.55% among seventeen lines of domestic chickens, our results suggest extraordinarily high haplotype diversity remains in wild Red Junglefowl and is consistent with a pattern of balancing selection. Wild Red Junglefowl in Vietnam, therefore, represent a rich resource of natural genomic variation independent from artificial selection.
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Affiliation(s)
- Hoa Nguyen-Phuc
- University of Wisconsin-Madison, Department of Animal Sciences, Madison, WI
| | | | - Mark E Berres
- University of Wisconsin-Madison, Department of Animal Sciences, Madison, WI
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15
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Fulton JE, Lund AR, McCarron AM, Pinegar KN, Korver DR, Classen HL, Aggrey S, Utterbach C, Anthony NB, Berres ME. MHC variability in heritage breeds of chickens. Poult Sci 2016; 95:393-9. [PMID: 26827122 DOI: 10.3382/ps/pev363] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/01/2015] [Indexed: 11/20/2022] Open
Abstract
The chicken Major Histocompatibility Complex (MHC) is very strongly associated with disease resistance and thus is a very important region of the chicken genome. Historically, MHC (B locus) has been identified by the use of serology with haplotype specific alloantisera. These antisera can be difficult to produce and frequently cross-react with multiple haplotypes and hence their application is generally limited to inbred and MHC-defined lines. As a consequence, very little information about MHC variability in heritage chicken breeds is available. DNA-based methods are now available for examining MHC variability in these previously uncharacterized populations. A high density SNP panel consisting of 101 SNP that span a 230,000 bp region of the chicken MHC was used to examine MHC variability in 17 heritage populations of chickens from five universities from Canada and the United States. The breeds included 6 heritage broiler lines, 3 Barred Plymouth Rock, 2 New Hampshire and one each of Rhode Island Red, Light Sussex, White Leghorn, Dark Brown Leghorn, and 2 synthetic lines. These heritage breeds contained from one to 11 haplotypes per line. A total of 52 unique MHC haplotypes were found with only 10 of them identical to serologically defined haplotypes. Furthermore, nine MHC recombinants with their respective parental haplotypes were identified. This survey confirms the value of these non-commercially utilized lines in maintaining genetic diversity. The identification of multiple MHC haplotypes and novel MHC recombinants indicates that diversity is being generated and maintained within these heritage populations.
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Affiliation(s)
- J E Fulton
- Hy-Line International, Dallas Center, IA
| | - A R Lund
- Hy-Line International, Dallas Center, IA
| | | | | | | | | | - S Aggrey
- University of Georgia, Athens, GA
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16
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Fulton JE, McCarron AM, Lund AR, Pinegar KN, Wolc A, Chazara O, Bed'Hom B, Berres M, Miller MM. A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1. Genet Sel Evol 2016; 48:1. [PMID: 26743767 PMCID: PMC4705597 DOI: 10.1186/s12711-015-0181-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/23/2015] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) is present within the genomes of all jawed vertebrates. MHC genes are especially important in regulating immune responses, but even after over 80 years of research on the MHC, much remains to be learned about how it influences adaptive and innate immune responses. In most species, the MHC is highly polymorphic and polygenic. Strong and highly reproducible associations are established for chicken MHC-B haplotypes in a number of infectious diseases. Here, we report (1) the development of a high-density SNP (single nucleotide polymorphism) panel for MHC-B typing that encompasses a 209,296 bp region in which 45 MHC-B genes are located, (2) how this panel was used to define chicken MHC-B haplotypes within a large number of lines/breeds and (3) the detection of recombinants which contributes to the observed diversity. METHODS A SNP panel was developed for the MHC-B region between the BG2 and CD1A1 genes. To construct this panel, each SNP was tested in end-point read assays on more than 7500 DNA samples obtained from inbred and commercially used egg-layer lines that carry known and novel MHC-B haplotypes. One hundred and one SNPs were selected for the panel. Additional breeds and experimentally-derived lines, including lines that carry MHC-B recombinant haplotypes, were then genotyped. RESULTS MHC-B haplotypes based on SNP genotyping were consistent with the MHC-B haplotypes that were assigned previously in experimental lines that carry B2, B5, B12, B13, B15, B19, B21, and B24 haplotypes. SNP genotyping resulted in the identification of 122 MHC-B haplotypes including a number of recombinant haplotypes, which indicate that crossing-over events at multiple locations within the region lead to the production of new MHC-B haplotypes. Furthermore, evidence of gene duplication and deletion was found. CONCLUSIONS The chicken MHC-B region is highly polymorphic across the surveyed 209-kb region that contains 45 genes. Our results expand the number of identified haplotypes and provide insights into the contribution of recombination events to MHC-B diversity including the identification of recombination hotspots and an estimation of recombination frequency.
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Affiliation(s)
| | | | | | | | - Anna Wolc
- Hy-Line International, Dallas Center, IA, USA.
- Iowa State University, 239C Kildee, Ames, IA, 50011, USA.
| | - Olympe Chazara
- Department of Pathology and Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
- Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Bertrand Bed'Hom
- Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Mark Berres
- Department of Animal Sciences, University of Wisconsin, Madison, USA.
| | - Marcia M Miller
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
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17
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Nikbakht G, Esmailnejad A. Chicken major histocompatibility complex polymorphism and its association with production traits. Immunogenetics 2015; 67:247-52. [DOI: 10.1007/s00251-015-0832-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 02/17/2015] [Indexed: 10/23/2022]
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18
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Han B, Lian L, Qu L, Zheng J, Yang N. Abundant polymorphisms at the microsatellite locus LEI0258 in indigenous chickens. Poult Sci 2014; 92:3113-9. [PMID: 24235219 DOI: 10.3382/ps.2013-03416] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The chicken major histocompatibility complex (MHC) has abundant SNP and indels, and is closely related with host genetic resistance or susceptibility to disease. The LEI0258 locus is the most variable in the MHC region, and is a useful marker in reflecting the variability of MHC. In this study, we applied the LEI0258 microsatellite marker to investigate polymorphism of MHC in Chinese indigenous chickens. The size of LEI0258 fragments in 1,617 individuals from 33 Chinese chicken breeds was detected by capillary electrophoresis, and 213 samples with different fragment sizes were further sequenced. A total of 69 alleles ranging from 193 to 489 bp were found, including 21 novel alleles and 28 private alleles that existed in only one breed. Three alleles, 249 bp (7.04%), 489 bp (6.57%), and 309 bp (6.10%), were the most frequent in the indigenous chickens. A 489-bp novel allele was unique in Chinese local chicken breeds. Three indels and 4 SNP of upstream/downstream of 2 repeat regions (R13/R12) were found. Abundant variations indicate high genetic diversity at the MHC region in indigenous chickens. Rare alleles are vulnerable to genetic drift in small populations, and can be used as molecular markers for monitoring the dynamic conservation of many indigenous breeds.
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Affiliation(s)
- Bo Han
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Chazara O, Chang CS, Bruneau N, Benabdeljelil K, Fotsa JC, Kayang BB, Loukou NE, Osei-Amponsah R, Yapi-Gnaore V, Youssao IAK, Chen CF, Pinard-van der Laan MH, Tixier-Boichard M, Bed'hom B. Diversity and evolution of the highly polymorphic tandem repeat LEI0258 in the chicken MHC-B region. Immunogenetics 2013; 65:447-59. [PMID: 23529664 DOI: 10.1007/s00251-013-0697-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/10/2013] [Indexed: 12/15/2022]
Abstract
The chicken major histocompatibility complex (MHC) is located on the microchromosome 16 and is described as the most variable region in the genome. The genes of the MHC play a central role in the immune system. Particularly, genes encoding proteins involved in the antigen presentation to T cells. Therefore, describing the genetic polymorphism of this region is crucial in understanding host-pathogen interactions. The tandem repeat LEI0258 is located within the core area of the B region of the chicken MHC (MHC-B region) and its genotypes correlate with serology. This marker was used to provide a picture of the worldwide diversity of the chicken MHC-B region and to categorize chicken MHC haplotypes. More than 1,600 animals from 80 different populations or lines of chickens from Africa, Asia, and Europe, including wild fowl species, were genotyped at the LEI0258 locus. Fifty novel alleles were described after sequencing. The resulting 79 alleles were classified into 12 clusters, based on the SNPs and indels found within the sequences flanking the repeats. Furthermore, hypotheses were formulated on the evolutionary dynamics of the region. This study constitutes the largest variability report for the chicken MHC and establishes a framework for future diversity or association studies.
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Affiliation(s)
- Olympe Chazara
- Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, UMR 1313, Jouy-en-Josas, France.
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