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Arango J, Wolc A, Owen J, Weston K, Fulton JE. Genetic Variation in Natural and Induced Antibody Responses in Layer Chickens. Animals (Basel) 2024; 14:1623. [PMID: 38891669 PMCID: PMC11171384 DOI: 10.3390/ani14111623] [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: 05/01/2024] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Selection of livestock for disease resistance is challenging due to the difficulty in obtaining reliable phenotypes. Antibodies are immunological molecules that provide direct and indirect defenses against infection and link the activities of both the innate and adaptive compartments of the immune system. As a result, antibodies have been used as a trait in selection for immune defense. The goal of this study was to identify genomic regions associated with natural and induced antibodies in chickens using low-pass sequencing. Enzyme-linked immunosorbent assays were used to quantify innate (natural) antibodies binding KLH, OVA, and PHA and induced (adaptive) antibodies binding IBD, IBV, NDV, and REO. We collected plasma from four White Leghorn (WL), two White Plymouth Rock (WPR), and two Rhode Island Red (RIR) lines. Samples numbers ranged between 198 and 785 per breed. GWAS was performed within breed on data pre-adjusted for Line-Hatch-Sex effects using GCTA. A threshold of p = 10-6 was used to select genes for downstream annotation and enrichment analysis with SNPEff and Panther. Significant enrichment was found for the defense/immunity protein, immunoglobulin receptor superfamily, and the antimicrobial response protein in RIR; and the immunoglobulin receptor superfamily, defense/immunity protein, and protein modifying enzyme in WL. However, none were present in WPR, but some of the selected SNP were annotated in immune pathways. This study provides new insights regarding the genetics of the antibody response in layer chickens.
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Affiliation(s)
- Jesus Arango
- Hy-Line International, Dallas Center, IA 50063, USA; (J.A.); (J.E.F.)
- Cobb Genetics, Siloam Springs, AR 72761, USA
| | - Anna Wolc
- Hy-Line International, Dallas Center, IA 50063, USA; (J.A.); (J.E.F.)
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jeb Owen
- Department of Entomology, Washington State University, Pullman, WA 99164, USA; (J.O.); (K.W.)
| | - Kendra Weston
- Department of Entomology, Washington State University, Pullman, WA 99164, USA; (J.O.); (K.W.)
| | - Janet E. Fulton
- Hy-Line International, Dallas Center, IA 50063, USA; (J.A.); (J.E.F.)
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2
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Zhou W, Zhang N, Huang K, Lin H, Tu J, Zheng C, Que P, Chiang CY, Martinez J, Naerhulan H, Székely T, Zhang Z, Liu Y. Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species. Mol Biol Evol 2024; 41:msae006. [PMID: 38225175 PMCID: PMC10835341 DOI: 10.1093/molbev/msae006] [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: 07/10/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
Speciation in the face of gene flow is usually associated with a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic islands. Examination of the genomic landscapes of species pairs that are still in the early stages of speciation provides an insight into this conundrum. In this study, population genomic analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (Charadrius alexandrinus) and white-faced plover (Charadrius dealbatus). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on the Taiwan Island. Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and gene flow is still ongoing in mainland coastal populations. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which contain several genes potentially associated with disease resistance, coloration, and regulation of plumage molting and thus may be relevant to the phenotypic and ecological divergence of the two nascent species. Overall, our findings suggest that divergent selection in low recombination regions may be a main force in shaping the genomic islands in two incipient shorebird species.
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Affiliation(s)
- Wenjun Zhou
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Nan Zhang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Bc, Canada
| | - Hongzhou Lin
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Jie Tu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Chenqing Zheng
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, China
| | - Chung-Yu Chiang
- Department of Environmental Science, Tunghai University, Taichung, Taiwan, China
| | | | - Halimubieke Naerhulan
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Tamás Székely
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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3
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Rice ES, Alberdi A, Alfieri J, Athrey G, Balacco JR, Bardou P, Blackmon H, Charles M, Cheng HH, Fedrigo O, Fiddaman SR, Formenti G, Frantz LAF, Gilbert MTP, Hearn CJ, Jarvis ED, Klopp C, Marcos S, Mason AS, Velez-Irizarry D, Xu L, Warren WC. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biol 2023; 21:267. [PMID: 37993882 PMCID: PMC10664547 DOI: 10.1186/s12915-023-01758-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. METHODS We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. RESULTS We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference. CONCLUSIONS We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.
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Affiliation(s)
- Edward S Rice
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - James Alfieri
- Department of Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, USA
| | - Giridhar Athrey
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - Jennifer R Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Philippe Bardou
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, 31326, France
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Mathieu Charles
- University Paris-Saclay, INRAE, AgroParisTech, GABI, Sigenae, Jouy-en-Josas, France
| | - Hans H Cheng
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Laurent A F Frantz
- Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4DQ, UK
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - Cari J Hearn
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Christophe Klopp
- Sigenae, Genotoul Bioinfo, MIAT UR875, INRAE, Castanet Tolosan, France
| | - Sofia Marcos
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain
| | | | | | - Luohao Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
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Bertram H, Wilhelmi S, Rajavel A, Boelhauve M, Wittmann M, Ramzan F, Schmitt AO, Gültas M. Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks. BIOLOGY 2023; 12:969. [PMID: 37508399 PMCID: PMC10375970 DOI: 10.3390/biology12070969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023]
Abstract
Avian influenza is a severe viral infection that has the potential to cause human pandemics. In particular, chickens are susceptible to many highly pathogenic strains of the virus, resulting in significant losses. In contrast, ducks have been reported to exhibit rapid and effective innate immune responses to most avian influenza virus (AIV) infections. To explore the distinct genetic programs that potentially distinguish the susceptibility/resistance of both species to AIV, the investigation of coincident SNPs (coSNPs) and their differing causal effects on gene functions in both species is important to gain novel insight into the varying immune-related responses of chickens and ducks. By conducting a pairwise genome alignment between these species, we identified coSNPs and their respective effect on AIV-related differentially expressed genes (DEGs) in this study. The examination of these genes (e.g., CD74, RUBCN, and SHTN1 for chickens and ABCA3, MAP2K6, and VIPR2 for ducks) reveals their high relevance to AIV. Further analysis of these genes provides promising effector molecules (such as IκBα, STAT1/STAT3, GSK-3β, or p53) and related key signaling pathways (such as NF-κB, JAK/STAT, or Wnt) to elucidate the complex mechanisms of immune responses to AIV infections in both chickens and ducks.
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Affiliation(s)
- Hendrik Bertram
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Selina Wilhelmi
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Marc Boelhauve
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
| | - Margareta Wittmann
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
| | - Faisal Ramzan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
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5
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Perlas A, Argilaguet J, Bertran K, Sánchez-González R, Nofrarías M, Valle R, Ramis A, Cortey M, Majó N. Dual Host and Pathogen RNA-Seq Analysis Unravels Chicken Genes Potentially Involved in Resistance to Highly Pathogenic Avian Influenza Virus Infection. Front Immunol 2022; 12:800188. [PMID: 35003125 PMCID: PMC8727699 DOI: 10.3389/fimmu.2021.800188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) cause severe systemic disease and high mortality rates in chickens, leading to a huge economic impact in the poultry sector. However, some chickens are resistant to the disease. This study aimed at evaluating the mechanisms behind HPAIV disease resistance. Chickens of different breeds were challenged with H7N1 HPAIV or clade 2.3.4.4b H5N8 HPAIV, euthanized at 3 days post-inoculation (dpi), and classified as resistant or susceptible depending on the following criteria: chickens that presented i) clinical signs, ii) histopathological lesions, and iii) presence of HPAIV antigen in tissues were classified as susceptible, while chickens lacking all these criteria were classified as resistant. Once classified, we performed RNA-Seq from lung and spleen samples in order to compare the transcriptomic signatures between resistant and susceptible chickens. We identified minor transcriptomic changes in resistant chickens in contrast with huge alterations observed in susceptible chickens. Interestingly, six differentially expressed genes were downregulated in resistant birds and upregulated in susceptible birds. Some of these genes belong to the NF-kappa B and/or mitogen-activated protein kinase signaling pathways. Among these six genes, the serine protease-encoding gene PLAU was of particular interest, being the most significantly downregulated gene in resistant chickens. Expression levels of this protease were further validated by RT-qPCR in a larger number of experimentally infected chickens. Furthermore, HPAIV quasi-species populations were constructed using 3 dpi oral swabs. No substantial changes were found in the viral segments that interact with the innate immune response and with the host cell receptors, reinforcing the role of the immune system of the host in the clinical outcome. Altogether, our results suggest that an early inactivation of important host genes could prevent an exaggerated immune response and/or viral replication, conferring resistance to HPAIV in chickens.
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Affiliation(s)
- Albert Perlas
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Jordi Argilaguet
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Kateri Bertran
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Raúl Sánchez-González
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Miquel Nofrarías
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Rosa Valle
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Antonio Ramis
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Martí Cortey
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Natàlia Majó
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
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6
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Direct and indirect contributions of molecular genetics to farm animal welfare: a review. Anim Health Res Rev 2021; 22:177-186. [PMID: 34842522 DOI: 10.1017/s1466252321000104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Since domestication, farm animals have played a key role to increase the prosperity of humankind, while animal welfare (AW) is debated even today. This paper aims to comprehensively review the contributions of developing molecular genetics to farm animal welfare (FAW) and to raise awareness among both scientists and farmers about AW. Welfare is a complex trait affected by genetic structure and environmental factors. Therefore, the best welfare status can be achieved not only to enhance environmental factors such as management and feeding practices, but also the genetic structure of animals must be improved. In this regard, advances in molecular genetics have made great contributions to improve the genetic structure of farm animals, which has increased AW. Today, by sequencing and/or molecular markers, genetic diseases may be detected and eliminated in local herds. Additionally, genes related to diseases or adaptations are investigated by molecular techniques, and the frequencies of desired genotypes are increased in farm animals to keep welfare at an optimized level. Furthermore, stress on animals can be reduced with DNA extraction from stool and feather samples which reduces physical contact between animals and veterinarians. Together with molecular genetics, advances in genome editing tools and biotechnology are promising to improve FAW in the future.
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7
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Drobik-Czwarno W, Wolc A, Kucharska K, Martyniuk E. Genetic determinants of resistance to highly pathogenic avian influenza in chickens. ROCZNIKI NAUKOWE POLSKIEGO TOWARZYSTWA ZOOTECHNICZNEGO 2019. [DOI: 10.5604/01.3001.0013.5065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Highly pathogenic avian influenza (HPAI) poses a huge threat to poultry production and also introduces an epidemiological risk in the human population. Thus far, HPAI has been controlled mainly through widespread implementation of biosecurity, and in the case of an outbreak, liquidation of flocks and establishment of protection zones. Alternative strategies for combating HPAI include the use of vaccines, genetic modification, and genetic selection for increased general and specific immunity in birds. These kinds of strategies often require identification of the genes involved in the immune response to the pathogen. Many genes have been identified as potentially associated with differences in the response to HPAI between poultry species and between individuals. Thus far, the most attention has been focused on genes taking part in regulating the innate immune response, which is responsible for preventing infection and limiting the replication and spread of the virus. The most commonly mentioned candidates for layer chickens include interferon-stimulated genes (ISGs) and RIG-I-like receptors. Proteins encoded by genes of the BTLN family, defensins, and proteins involved in apoptosis have also been associated with differences in the response to HPAI. Recent years have seen an increasing number of studies on the genetic determinants of individual differences in the response to HPAI in chickens. Data from HPAI outbreaks in the US in the spring of 2015 and Mexico in the years 2012-2016 have enabled a more precise analysis of this problem. A number of genes have been identified as associated with the immune response, but their specific role in determining the survival of birds requires further study. Preliminary results indicate that genetic determinants of resistance to HPAI are highly complex and can vary depending on the virus strain and the genetic line of birds.
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Affiliation(s)
- Wioleta Drobik-Czwarno
- Szkoła Główna Gospodarstwa Wiejskiego w Warszawie Wydział Nauk o Zwierzętach Katedra Genetyki i Ogólnej Hodowli Zwierząt
| | - Anna Wolc
- Iowa State University Department of Animal Science
| | - Kornelia Kucharska
- Szkoła Główna Gospodarstwa Wiejskiego w Warszawie Wydział Nauk o Zwierzętach Katedra Biologii Środowiska Zwierząt, Zakład Zoologii
| | - Elżbieta Martyniuk
- Szkoła Główna Gospodarstwa Wiejskiego w Warszawie; Wydział Nauk o Zwierzętach
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8
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Creating Disease Resistant Chickens: A Viable Solution to Avian Influenza? Viruses 2018; 10:v10100561. [PMID: 30326625 PMCID: PMC6213529 DOI: 10.3390/v10100561] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 11/16/2022] Open
Abstract
Influenza A virus (IAV) represents an ongoing threat to human and animal health worldwide. The generation of IAV-resistant chickens through genetic modification and/or selective breeding may help prevent viral spread. The feasibility of creating genetically modified birds has already been demonstrated with the insertion of transgenes that target IAV into the genomes of chickens. This approach has been met with some success in minimising the spread of IAV but has limitations in terms of its ability to prevent the emergence of disease. An alternate approach is the use of genetic engineering to improve host resistance by targeting the antiviral immune responses of poultry to IAV. Harnessing such resistance mechanisms in a “genetic restoration” approach may hold the greatest promise yet for generating disease resistant chickens. Continuing to identify genes associated with natural resistance in poultry provides the opportunity to identify new targets for genetic modification and/or selective breeding. However, as with any new technology, economic, societal, and legislative barriers will need to be overcome before we are likely to see commercialisation of genetically modified birds.
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9
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Wolc A, Drobik-Czwarno W, Fulton JE, Arango J, Jankowski T, Dekkers JCM. Genomic prediction of avian influenza infection outcome in layer chickens. Genet Sel Evol 2018; 50:21. [PMID: 29720082 PMCID: PMC5930871 DOI: 10.1186/s12711-018-0393-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
Avian influenza (AI) is a devastating poultry disease that currently can be controlled only by liquidation of affected flocks. In spite of typically very high mortality rates, a group of survivors was identified and genotyped on a 600K single nucleotide polymorphism (SNP) chip to identify genetic differences between survivors, and age- and genetics-matched controls from unaffected flocks.
In a previous analysis of this dataset, a heritable component was identified and several regions that are associated with outcome of the infection were localized but none with a large effect. For complex traits that are determined by many genes, genomic prediction models using all SNPs across the genome simultaneously are expected to optimally exploit genomic information. In this study, we evaluated the diagnostic value of genomic estimated breeding values for predicting AI infection outcome within and across two highly pathogenic avian influenza viral strains and two genetic lines of layer chickens using receiver operating curves. We show that genomic prediction based on the 600K SNP chip has the potential to predict disease outcome especially within the same strain of virus (area under receiver operating curve above 0.7), but did not predict well across genetic varieties (area under receiver operating curve of 0.43).
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Affiliation(s)
- Anna Wolc
- Department of Animal Science, Iowa State University, 806 Stange Road, 239E Kildee Hall, Ames, IA, 50010, USA. .,Hy-Line International, 2583 240th Street, Dallas Center, IA, 50063, USA.
| | - Wioleta Drobik-Czwarno
- Department of Animal Genetics and Breeding, Faculty of Animal Science, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Janet E Fulton
- Hy-Line International, 2583 240th Street, Dallas Center, IA, 50063, USA
| | - Jesus Arango
- Hy-Line International, 2583 240th Street, Dallas Center, IA, 50063, USA
| | - Tomasz Jankowski
- Hy-Line International, 2583 240th Street, Dallas Center, IA, 50063, USA.,Nutribiogen, Witkowska 15/1, 61-039, Poznan, Poland
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 806 Stange Road, 239E Kildee Hall, Ames, IA, 50010, USA
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