1
|
Ramezani A, Nikbakht Brujeni G, Sheikhi N, Parvandar Asadollahi K. MHC-linked microsatellite LEI0258 variability and population structure of chicken ecotypes in Iran. IRANIAN JOURNAL OF VETERINARY RESEARCH 2025; 25:312-318. [PMID: 40386103 PMCID: PMC12085208 DOI: 10.22099/ijvr.2024.50968.7544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/20/2025]
Abstract
Background Investigation of chicken major histocompatibility complex (MHC) genes along with their diversity across native regions and populations, as a genetic resource, can be used in the breeding programs. Important characteristics of MHC genes, such as the association with immunological and production traits, make them exceptional candidates for marker assisted selection. Aims The aim of this study was to characterize MHC based on the LEI0258 microsatellite marker to evaluate the genetic variability and diversity within and between Iranian chicken populations. Methods Blood samples were collected from six indigenous ecotypes (n=633) and Ross 308 (n=216) as a commercial breed. The MHC variability was determined based on a microsatellite marker located within MHC, LEI0258. Polymerase chain reaction and fragment analysis was used for microsatellite polymorphism detection. Results Based on the fragment analysis, 7 alleles were found in Ross 308 and 25 alleles across all 6 populations. The population with the maximum genetic diversity was Mazandaran (0.939), while the population with the minimum genetic diversity was Ross 308 (0.794). Out of the 6 Iranian chicken ecotypes, all except Arian and Khorasan, were in Hardy-Weinberg equilibrium (P<0.05). The genetic variations within (84.92%) and between (15.08%) populations were statistically significant (P<0.001). Conclusion A significant genetic structure that is not completely homogeneous among the Iranian chicken populations can be considered as distinct genetic resources. This study highlights the value of using markers such as LEI0258 to investigate the diversity of genes that play dual roles in immunity and production.
Collapse
Affiliation(s)
- A. Ramezani
- Ph.D. Student in Immunology, Department of Pathobiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - G. Nikbakht Brujeni
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - N. Sheikhi
- Department of Clinical Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - K. Parvandar Asadollahi
- Department of Clinical Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
2
|
Zhang H, Ruan P, Cong H, Xu L, Yang B, Ren T, Zhang D, Chen H, Hu P, Wang Z, Pan H, Yang X, Han Y, Zeng Y, Zhao Y, Liu D, Ceccobelli S, E G. Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets. Animals (Basel) 2024; 14:3159. [PMID: 39518882 PMCID: PMC11545170 DOI: 10.3390/ani14213159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 10/22/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024] Open
Abstract
As a global focus of animal husbandry, pigs provide essential meat resources for humans. Therefore, analyzing the genetic basis of adaptability, domestication, and artificial selection in pigs will contribute to further breeding. This study performed a genome-wide selection sweep analysis to identify candidate genes related to domestication and adaptive selection via data from 2413 public genotypes. Two complementary statistical analyses, FST (fixation index) and XP-EHH (cross-population extended haplotype homozygosity) were applied. The results revealed that numerous candidate genes were associated with high-altitude adaptability (e.g., SIRPA, FRS2, and GRIN2B) and habitat temperature adaptability (e.g., MITF, PI3KC2A, and FRS2). In addition, candidate genes related to the domestic genetic imprint of indigenous pigs (e.g., TNR, NOCT, and SPATA5) and strong artificial selection pressure in commercial breeds (e.g., ITPR2, HSD17B12, and UGP2) were identified in this study. Specifically, some MHC-related genes (e.g., ZRTB12, TRIM26, and C7H6orf15) were also under selection during domestication and artificial selection. Additionally, a phylogenetic comparative analysis revealed that the genetic divergence between populations does not fully follow the geographical distribution and management history in the major histocompatibility complex region/major histocompatibility complex II haplotypes, unlike that of the genome-wide genotypes. Furthermore, the higher heterozygosity and haplotype alleles of MHC reduce the differences between populations. Briefly, this study not only helps promote the relative theoretical understanding of environmental adaptive selection and domestication but also provides a theoretical reference for disease-resistant breeding in pigs.
Collapse
Affiliation(s)
- Haoyuan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Pengcheng Ruan
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - He Cong
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Lu Xu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Baigao Yang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Tao Ren
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Dongjie Zhang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China (D.L.)
| | - Hongyue Chen
- Chongqing Animal Husbandry Technology Extension Station, Chongqing 401121, China
| | - Pengfei Hu
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130000, China
| | - Zhen Wang
- Chongqing Animal Husbandry Technology Extension Station, Chongqing 401121, China
| | - Hongmei Pan
- Chongqing Academy of Animal Sciences, Chongqing 408599, China
| | - Xiuqin Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Yanguo Han
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Yan Zeng
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China (D.L.)
| | - Simone Ceccobelli
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Guangxin E
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| |
Collapse
|
3
|
Hu J, Song L, Ning M, Niu X, Han M, Gao C, Feng X, Cai H, Li T, Li F, Li H, Gong D, Song W, Liu L, Pu J, Liu J, Smith J, Sun H, Huang Y. A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families. BMC Biol 2024; 22:31. [PMID: 38317190 PMCID: PMC10845735 DOI: 10.1186/s12915-024-01817-0] [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: 09/01/2022] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck's adaptive immune system to IAV infection is poorly characterized due to lack of a detailed gene map of the major histocompatibility complex (MHC). RESULTS We herein reported a chromosome-scale Beijing duck assembly by integrating Nanopore, Bionano, and Hi-C data. This new reference genome SKLA1.0 covers 40 chromosomes, improves the contig N50 of the previous duck assembly with highest contiguity (ZJU1.0) of more than a 5.79-fold, surpasses the chicken and zebra finch references in sequence contiguity and contains a complete genomic map of the MHC. Our 3D MHC genomic map demonstrated that gene family arrangement in this region was primordial; however, families such as AnplMHCI, AnplMHCIIβ, AnplDMB, NKRL (NK cell receptor-like genes) and BTN underwent gene expansion events making this area complex. These gene families are distributed in two TADs and genes sharing the same TAD may work in a co-regulated model. CONCLUSIONS These observations supported the hypothesis that duck's adaptive immunity had been optimized with expanded and diversified key immune genes which might help duck to combat influenza virus. This work provided a high-quality Beijing duck genome for biological research and shed light on new strategies for AIV control.
Collapse
Affiliation(s)
- Jiaxiang Hu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Linfei Song
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Mengfei Ning
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Xinyu Niu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Mengying Han
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Chuze Gao
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Xingwei Feng
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Han Cai
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Te Li
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Fangtao Li
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Huifang Li
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Weitao Song
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Juan Pu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Jinhua Liu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Honglei Sun
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China.
| | - Yinhua Huang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China.
| |
Collapse
|
4
|
Lai J, Yang L, Chen F, He X, Zhang R, Zhao Y, Gao G, Mu W, Chen X, Luo S, Ren T, Xiang B. Prevalence and Molecular Characteristics of FAdV-4 from Indigenous Chicken Breeds in Yunnan Province, Southwestern China. Microorganisms 2023; 11:2631. [PMID: 38004643 PMCID: PMC10673041 DOI: 10.3390/microorganisms11112631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Fowl adenovirus-induced hepatitis-pericardial effusion syndrome outbreaks have been increasingly reported in China since 2015, resulting in substantial economic losses to the poultry industry. The genetic diversity of indigenous chicken results in different immune traits, affecting the evolution of these viruses. Although the molecular epidemiology of fowl adenovirus serotype 4 (FAdV-4) has been well studied in commercial broiler and layer chickens, the prevalence and genetic characteristics of FAdV-4 in indigenous chickens remain largely unknown. In this study, samples were collected from six indigenous chicken breeds in Yunnan province, China. FAdV-positive samples were identified in five of the six indigenous chicken populations via PCR and 10 isolates were obtained. All FAdVs belonged to serotype FAdV-4 and species FAdV-C. The hexon, fiber, and penton gene sequence comparison analysis demonstrated that the prevalence of FAdV-4 isolates in these chickens might have originated from other provinces that exported chicks and poultry products to Yunnan province. Moreover, several distinct amino acid mutations were firstly identified in the major structural proteins. Our findings highlighted the need to decrease inter-regional movements of live poultry to protect indigenous chicken genetic resources and that the immune traits of these indigenous chickens might result in new mutations of FAdV-4 strains.
Collapse
Affiliation(s)
- Jinyu Lai
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Liangyu Yang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Fashun Chen
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Xingchen He
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Rongjie Zhang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Yong Zhao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Gan Gao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Weiwu Mu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Xi Chen
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Shiyu Luo
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| | - Tao Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Bin Xiang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Center for Poultry Disease Control and Prevention, Yunnan Agricultural University, Kunming 650201, China
| |
Collapse
|
5
|
Lestari D, Murtini S, Ulupi N, Gunawan A, Sumantri C. Novel MHC BLB2 gene polymorphism and its association with IgY concentration and Newcastle disease antibody titer in IPB-D2 chickens. Arch Anim Breed 2023; 66:275-283. [PMID: 37782567 PMCID: PMC10539726 DOI: 10.5194/aab-66-275-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 08/11/2023] [Indexed: 10/04/2023] Open
Abstract
This study aimed to identify the polymorphism of the B Locus Beta 2 (BLB2) gene and its association with immunoglobulin Y (IgY) concentration and Newcastle disease (ND) antibody titer; we analyzed BLB2 gene expression in different categories of ND antibody titers in IPB-D2 chickens. The total sample used was 100 IPB-D2 chickens. Blood samples were collected at 21 weeks old for an ELISA (enzyme-linked immunoassay) test, an HI (hemagglutination inhibition) test, and genotyping. The method for BLB2 polymorphism was Sanger sequencing. Analysis of BLB2 gene expression was performed using the cecal tonsil tissue of IPB-D2 chickens. Polymorphism data were analyzed using SNPstats and DNAsp (DNA Sequence Polymorphism) software. The association of the single-nucleotide polymorphisms (SNPs) with IgY concentration and ND antibody titer was analyzed using SAS software (version 9.2). The genotype mean values were compared by means of a T test. The relative mRNA expression analysis was performed using a quantitative real-time polymerase chain reaction (qRT-PCR). The results showed that 13 SNPs were found in exon 2 and exon 3 in the BLB2 gene. As many as 4 out of the 13 SNPs were associated with IgY concentration. As many as 9 out the 13 SNPs may have changed amino acids. The Δ Ct value showed that the expression of the BLB2 gene in IPB-D2 chickens with high ND antibody titers is higher than IPB-D2 chickens with low ND antibody titers. In conclusion, the AA genotype of g.458 T > A was associated with high IgY concentrations, and the BLB2 gene presented with a high expression in IPB-D2 chickens with high ND antibody titers.
Collapse
Affiliation(s)
- Dwi Lestari
- Graduate School of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor, 16680, Indonesia
| | - Sri Murtini
- Department of Animal Disease and Veterinary Public Health, Faculty of Veterinary Medicine, IPB University, Bogor, 16680, Indonesia
| | - Niken Ulupi
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor, 16680, Indonesia
| | - Asep Gunawan
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor, 16680, Indonesia
| | - Cece Sumantri
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor, 16680, Indonesia
| |
Collapse
|
6
|
Localization of Chicken Rab22a in Cells and Its Relationship to BF or Ii Molecules and Genes. Animals (Basel) 2023; 13:ani13030387. [PMID: 36766276 PMCID: PMC9913282 DOI: 10.3390/ani13030387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Rab22a is an important small GTPase protein the molecule that is involved in intracellular transportation and regulation of proteins. It also plays an important role in antigens uptake, transportation, regulation of endosome morphology, and also regulates the transport of antigens to MHC (Major Histocompatibility Complex) molecules. To investigate the role of Rab22a, the intracellular co-localization of chicken Rab22a (cRab22a) molecule and its relationship to BF and chicken invariant chain (cIi) molecules was studied. A 3D protein structure of Rab22a was constructed by using informatics tools (DNASTAR 4.0 and DNAMAN). Based on the model, the corresponding recombinant eukaryotic plasmids were constructed by point mutations in the protein's structural domains. HEK 293T cells were co-transfected with plasmids pEGFP-C1-cIi to observe the intracellular co-localization. Secondly, the DC2.4 Mouse Dendritic Cell and Murine RAW 264.7 cells were transfected with recombinant plasmids of pmCherry-cRab22a and pmCherry-mRab22a respectively. Subsequently, the intracellular localization of cRab22a in early and late endosomes was observed with specific antibodies against EEA1 and LAMP1 respectively. For gene expression-based studies, the cRab22a gene was down-regulated and up-regulated in HD11 cells, following the detection of transcription levels of the BFa (MHCIa) and cIi genes by real-time quantitative PCR (RT-qPCR). The interactions of the cRab22a gene with BFa and cIi were detected by co-immunoprecipitation (Co-IP) and Western blot. The results showed that the protein structures of chicken and mouse Rab22a were highly homologous (95.4%), and both localize to the early and late endosomes. Ser41 and Tyr74 are key amino acids in the Switch regions of Rab22a which maintain its intracellular localization. The down-regulation of cRab22a gene expression significantly reduced (p < 0.01) the transcription of BFa (MHCIa) and cIi in HD11 cells. However, when the expression of the cRab22a gene was increased 55 times as compared to control cells, the expression of the BFa (MHCIa) gene was increased 1.7 times compared to the control cells (p < 0.01), while the expression of the cIi gene did not significantly differ from control (p > 0.05). Western blot results showed that cRab22a could not directly bind to BFa and cIi. So, cRab22a can regulate BFa and cIi protein molecules indirectly. It is concluded that cRab22a was localized with cIi in the endosome. The Switch regions of cRab22a are the key domains that affect intracellular localization and colocalization of the cIi molecule.
Collapse
|
7
|
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.
Collapse
|
8
|
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: 0.3] [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.
Collapse
|