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Ediriweera TK, Manjula P, Kim J, Kim JH, Nam S, Kim M, Cho E, Bhuiyan MSA, Rashid MA, Lee JH. Identification of new major histocompatibility complex-B Haplotypes in Bangladesh native chickens. Anim Biosci 2024; 37:826-831. [PMID: 38419540 PMCID: PMC11065705 DOI: 10.5713/ab.23.0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/18/2023] [Accepted: 12/15/2023] [Indexed: 03/02/2024] Open
Abstract
OBJECTIVE The major histocompatibility complex in chicken demonstrates a great range of variations within varities, breeds, populations and that can eventually influence their immuneresponses. The preset study was conducted to understand the major histocompatibility complex-B (MHC-B) variability in five major populations of Bangladesh native chicken: Aseel, Hilly, Junglefowl, Non-descript Deshi, and Naked Neck. METHODS These five major populations of Bangladesh native chicken were analyzed with a subset of 89 single nucleotide polymorphisms (SNPs) in the high-density MHC-B SNP panel and Kompetitive Allele-Specific polymerase chain reaction genotyping was applied. To explore haplotype diversity within these populations, the results were analyzed both manually and computationally using PHASE 2.1 program. The phylogenetic investigations were also performed using MrBayes program. RESULTS A total of 136 unique haplotypes were identified within these five Bangladesh chicken populations, and only one was shared (between Hilly and Naked Neck). Phylogenetic analysis showed no distinct haplotype clustering among the five populations, although they were shared in distinct clades; notably, the first clade lacked Naked Neck haplotypes. CONCLUSION The present study discovered a set of unique MHC-B haplotypes in Bangladesh chickens that could possibly cause varied immune reponses. However, further investigations are required to evaluate their relationships with global chicken populations.
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Affiliation(s)
| | - Prabuddha Manjula
- Department of Animal Science, Uva Wellassa University, Badulla 90000,
Sri Lanka
| | - Jaewon Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Jin Hyung Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Seonju Nam
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Minjun Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Eunjin Cho
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
| | | | - Md. Abdur Rashid
- Poultry Production Research Division, Bangladesh Livestock Research Institute, Dhaka-1341,
Bangladesh
| | - Jun Heon Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
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Darrington C, Lin H, Larivière JM, Fulton JE, Zhao X. Discovery of novel MHC-B haplotypes in Chantecler chickens. Poult Sci 2023; 102:102881. [PMID: 37406434 PMCID: PMC10466295 DOI: 10.1016/j.psj.2023.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic cluster of genes which contribute to immune response. Located on chromosome 16, the chicken MHC has great influence over disease resistance and susceptibility. Through the use of a high-density SNP panel which encompasses the MHC-B region, haplotypes can be easily identified. This study aims to use an MHC-B SNP panel to evaluate the MHC-B variability in the Chantecler breed. This breed is native to Quebec, Canada, and is a dual-purpose breed known for its strong resistance to extreme cold temperatures. The Chantecler breed faced a near extinction event in the 1970s, which most likely resulted in a genetic bottleneck and loss of diversity. Despite this, SNP haplotype diversity was observed among 4 Chantecler populations. A total of 8 haplotypes were observed. Of these haplotypes, 6 were previously defined in other breeds, and the other 2 were unique to the Chantecler. Within the populations, the number of haplotypes ranged from 4 to 7, with 3 haplotypes, including the novel BSNP-Chant01, being present in all the groups. This study shows existence of reasonable diversity in the MHC-B region of the Chantecler breed and our results further contribute to understanding the variability of this region in chickens.
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Affiliation(s)
| | | | | | | | - Xin Zhao
- McGill University, Montreal, QC, Canada.
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Fulton JE, Drobik-Czwarno W, Lund AR, Schmidt CJ, Taylor RL. CD99 and the Chicken Alloantigen D Blood System. Genes (Basel) 2023; 14:402. [PMID: 36833329 PMCID: PMC9957549 DOI: 10.3390/genes14020402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/09/2022] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
The chicken D blood system is one of 13 alloantigen systems found on chicken red blood cells. Classical recombinant studies located the D blood system on chicken chromosome 1, but the candidate gene was unknown. Multiple resources were utilized to identify the chicken D system candidate gene, including genome sequence information from both research and elite egg production lines for which D system alloantigen alleles were reported, and DNA from both pedigree and non-pedigree samples with known D alleles. Genome-wide association analyses using a 600 K or a 54 K SNP chip plus DNA from independent samples identified a strong peak on chicken chromosome 1 at 125-131 Mb (GRCg6a). Cell surface expression and the presence of exonic non-synonymous SNP were used to identify the candidate gene. The chicken CD99 gene showed the co-segregation of SNP-defined haplotypes and serologically defined D blood system alleles. The CD99 protein mediates multiple cellular processes including leukocyte migration, T-cell adhesion, and transmembrane protein transport, affecting peripheral immune responses. The corresponding human gene is found syntenic to the pseudoautosomal region 1 of human X and Y chromosomes. Phylogenetic analyses show that CD99 has a paralog, XG, that arose by duplication in the last common ancestor of the amniotes.
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Affiliation(s)
| | - Wiola Drobik-Czwarno
- Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | | | - Carl J. Schmidt
- Department of Animal and Food Science, University of Delaware, Newark, DE 19716, USA
| | - Robert L. Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
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Ediriweera TK, Manjula P, Cho E, Kim M, Lee JH. Application of next-generation sequencing for the high-resolution typing of MHC-B in Korean native chicken. Front Genet 2022; 13:886376. [DOI: 10.3389/fgene.2022.886376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
The major histocompatibility complex-B (MHC-B) region of chicken is crucially important in their immunogenesis and highly diverse among different breeds, lines, and even populations. Because it determines the resistance/susceptibility to numerous infectious diseases, it is important to analyze this genomic region, particularly classical class I and II genes, to determine the variation and diversity that ultimately affect antigen presentation. This study investigated five lines of indigenous Korean native chicken (KNC) and the Ogye breed using next-generation sequencing (NGS) data with Geneious Prime-based assembly and variant calling with the Genome Analysis Toolkit (GATK) best practices pipeline. The consensus sequences of MHC-B (BG1-BF2) were obtained for each chicken line/breed and their variants were analyzed. All of the Korean native chicken lines possessed an excessive number of variants, including an ample amount of high-impact variants that provided useful information regarding modified major histocompatibility complex molecules. The study confirmed that next-generation sequencing techniques can effectively be used to detect MHC variabilities and the KNC lines are highly diverse for the MHC-B region, suggesting a substantial divergence from red junglefowl.
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Manjula P, Fulton JE, Seo D, Lee JH. Comparison of major histocompatibility complex-B variability in Sri Lankan indigenous chickens with five global chicken populations using MHC-B SNP panel. Anim Genet 2021; 52:824-833. [PMID: 34523150 DOI: 10.1111/age.13137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 11/29/2022]
Abstract
In the present study, we investigated the major histocompatibility complex (MHC)-B haplotypes diversity of Sri Lankan indigenous chickens from three different geographical sites consisting of highly mixed populations using 90 SNPs in the MHC-B region. A total of 48 haplotypes were identified. Those included 37 novel haplotypes and 11 previously identified 'standard' haplotypes. The MHC-linked marker, LEI0258, had 23 alleles showing less diversity than defined by MHC-B SNP haplotypes. Among those identified haplotypes, five standard haplotypes-BSNP-O02, BSNP-M01, BSNP-A04, BSNP-K03, BSNP-T04-were most commonly observed, suggesting past introgression of imported breeds. Comparison of the MHC-B haplotypes of Sri Lankan and four other global populations with previously defined haplotypes indicated the sharing of 23 standard haplotypes with common origins. Novel haplotypes are population-specific and not shared among the geographical boundaries. Backyard indigenous chickens are unselected, highly crossbred, and generally thrive under dynamic environmental conditions. Hence free-range production systems may be responsible for maintaining high diversity in the MHC-B region with novel haplotypes.
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Affiliation(s)
- P Manjula
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - J E Fulton
- Hy-Line International, Dallas Center, IA, 50063, USA
| | - D Seo
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - J H Lee
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, 34134, Korea
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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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Comparison of Selection Signatures between Korean Native and Commercial Chickens Using 600K SNP Array Data. Genes (Basel) 2021; 12:genes12060824. [PMID: 34072132 PMCID: PMC8230197 DOI: 10.3390/genes12060824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Korean native chickens (KNCs) comprise an indigenous chicken breed of South Korea that was restored through a government project in the 1990s. The KNC population has not been developed well and has mostly been used to maintain purebred populations in the government research institution. We investigated the genetic features of the KNC population in a selection signal study for the efficient improvement of this breed. We used 600K single nucleotide polymorphism data sampled from 191 KNCs (NG, 38; NL, 29; NR, 52; NW, 39; and NY, 33) and 54 commercial chickens (Hy-line Brown, 10; Lohmann Brown, 10; Arbor Acres, 10; Cobb, 12; and Ross, 12). Haplotype phasing was performed using EAGLE software as the initial step for the primary data analysis. Pre-processed data were analyzed to detect selection signals using the ‘rehh’ package in R software. A few common signatures of selection were identified in KNCs. Most quantitative trait locus regions identified as candidate regions were associated with traits related to reproductive organs, eggshell characteristics, immunity, and organ development. Block patterns with high linkage disequilibrium values were observed for LPP, IGF11, LMNB2, ERBB4, GABRB2, NTM, APOO, PLOA1, CNTN1, NTSR1, DEF3, CELF1, and MEF2D genes, among regions with confirmed selection signals. NL and NW lines contained a considerable number of selective sweep regions related to broilers and layers, respectively. We recommend focusing on improving the egg and meat traits of KNC NL and NW lines, respectively, while improving multiple traits for the other lines.
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Manjula P, Kim M, Cho S, Seo D, Lee JH. High Levels of Genetic Variation in MHC-Linked Microsatellite Markers from Native Chicken Breeds. Genes (Basel) 2021; 12:240. [PMID: 33567601 PMCID: PMC7915948 DOI: 10.3390/genes12020240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic gene region that regulates cellular communication in all specific immune responses. In this study, we investigated 11 microsatellite (MS) markers in the MHC-B region of chicken populations from four countries: Sri Lanka, Bangladesh, South Korea, and Nigeria. The MS markers were divided into two sets. Set 1 included five novel MS markers, which we assessed using 192 samples from 21 populations. Set 2 included six previously reported markers, which we assessed using 881 samples from 29 populations. The Set 1 MS markers had lower polymorphism (polymorphic information content (PIC) < 0.5) than the Set 2 markers (PIC = 0.4-0.9). In all populations, the LEI0258 marker was the most polymorphic, with a total of 38 alleles (PIC = 0.912, expected heterozygosity (He) = 0.918). Local populations from Sri Lanka, Bangladesh, and Nigeria had higher allele diversity and more haplotypes for Set 2 MS markers than Korean and commercial populations. The Sri Lankan Karuwalagaswewa village population had the highest MHC diversity (mean allele number = 8.17, He = 0.657), whereas the white leghorn population had the lowest (mean allele number = 2.33, He = 0.342). A total of 409 haplotypes (89 shared and 320 unique), with a range of 4 (Rhode Island red) to 46 (Karuwalagaswewa village (TA)), were identified. Among the shared haplotypes, the B21-like haplotype was identified in 15 populations. The genetic relationship observed in a neighbour-joining tree based on the DA distance agreed with the breeding histories and geographic separations. The results indicated high MHC diversity in the local chicken populations. The difference in the allelic pattern among populations presumably reflects the effects of different genotypes, environments, geographic variation, and breeding policies in each country. The selection of MHC allele in domestic poultry can vary due to intensification of poultry production. Preserved MHC diversity in local chicken provides a great opportunity for future studies that address the relationships between MHC polymorphisms and differential immune responses.
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Affiliation(s)
| | | | | | | | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (P.M.); (M.K.); (S.C.); (D.S.)
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Cho SH, Lee SS, Manjula P, Kim M, Lee SH, Lee JH, Seo D. Population structure analysis of Yeonsan Ogye using microsatellite markers. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:790-800. [PMID: 33987560 PMCID: PMC7721577 DOI: 10.5187/jast.2020.62.6.790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022]
Abstract
The Yeonsan Ogye (YO) chicken is a natural heritage of Korea, characterized by
black feathers, skin, bones, eyes, and comb. The purebred of YO population has
been reared under the natural mating system with no systematic selection and
breeding plan. The purpose of this study was to identify the genetic diversity
and find the optimal number of population sub-division using 12 polymorphic
microsatellite (MS) markers to construct a pedigree-based breeding plan for the
YO population. A total of 509 YO birds were used for this study. Genetic
diversity and population structure analysis were conducted based on the MS
marker genotype information. The overall average polymorphic information content
value and expected heterozygosity of the population were 0.586, and 0.642,
respectively. The K-mean cluster analysis based on the genetic distance result
confirmed that the current YO population can be divided into three ancestry
groups. Individuals in each group were evaluated based on their genetic distance
to identify the potential candidates for a future breeding plan. This study
concludes that a future breeding plan with known pedigree information of
selected founder animals, which holds high genetic diversity, could be the best
strategy to ensure the conservation of the Korean YO chicken population.
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Affiliation(s)
- Sung Hyun Cho
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | | | - Prabuddha Manjula
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Minjun Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
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