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Genetics and Genomics

Our Group

The Genetics and Genomics group is interested in understanding the underlying genetics of animal-pathogen interactions, and the natural evolution of these characteristics in birds. The group’s main area of research is the study of the genetic basis of avian viral disease resistance. Our research group has found a group of related genes called the interferon-inducible transmembrane (IFITM) genes, that are able to prevent viruses from attacking and killing host cells. The aim of our work is to determine the biology and genetic variation of these and similar immune genes in chickens; specifically, the ability of these genes to protect the host against avian viruses. The output of this project will be in identifying specific gene variants that correlate with resistance to a number of avian viruses, thus allowing poultry breeding programmes to select robust chickens, able to fight viral infections.

Our Aims

The group is involved in characterising the genetic basis of the innate immune response to viral pathogens to enhance resilience to poultry disease. The research will provide new insights into avian immunity, and provide novel tools with which to counter viral pathogens of poultry. Characterisation of the avian immune response will enhance global knowledge exchange, helping to understand the molecular and genetic basis of these important diseases of poultry. This will also help us to assess the risks to global, and the UK poultry industry. One of the main impacts of this work will be the livestock industry, and specifically poultry breeding companies. Worldwide, EU and UK policy makers in Animal Health will have an interest in our results due to the impact that the poultry industry has on food sustainability. Outcomes will also include helping select vaccine candidates early in development, and inform innovative vaccine design. We will also identify potential targets to develop more robust and resilient poultry. The work falls within both the Virus and Host Strategic Programmes at the Institute.

Our Research

The Genetics and Genomics group collaborate with a number of research groups and are currently undertaking a number of funded projects, which include:

  • Gates Foundation/Livestock Innovation Fund (LVIF) To generate chIFITM knock-out (K/O) cell lines using CRISPR/Cas9 for vaccine production
  • BBSRC Follow on Fund: Embryonic K/O of chIFITM locus for embryonated SPF eggs used in Vaccine production
  • BBSRC iCASE NPIF studentship: Transcriptional Analysis of chIFITM knockout technology for increased vaccine yields 
  • BBSRC AHRC: “Restriction of avian viruses by host IFITMs”. BB/L003996/1; including International patent application PCT/GB2014/051693.

Other research activities also include:

  • Through an EU-funded ANIHWA and BBSRC grants we are also examining genetic drivers of Culicoides-borne arboviruses. The results from these projects aim to provide fundamental insights into arbovirus:Culicoides systems which remain poorly characterised. The methods that we employ have underpinned this work, and we plan to apply for future funding to further examine the influence of genetic variation on vector competence in diverse vector species in collaboration with Simon Carpenter.
  • A collaborative project (USDA –NIFA) with the Immunogenetics group is characterising bovine immunogenetic diversity to provide a SNP chip for use in genome wide association studies, ensuring accurate studies of immune responses to both infection and vaccination.

Our Impact

We have established that chickens encode interferon-inducible transmembrane (IFITM) genes that limit influenza infection. The aim of this our work is to determine the biology and genetic variation of the IFITM genes in chickens, specifically the ability of IFITM genes to protect the host against both endemic and emerging avian viruses. The output of this project will be in identifying specific alleles that correlate with resistance to a number of avian viruses allowing poultry breeding programmes to select the beneficial alleles.

Our proposed research will also provide new insights into innate immunity, and novel tools with which to counter viral pathogens of poultry. Characterisation of the avian immune response will enhance global knowledge exchange, helping to elucidate the molecular/genetic basis for combatting these important diseases of poultry. They will also help us to assess the risks to global, and the UK poultry industry. One of the main impacts of this work will be the livestock industry, and specifically poultry breeding companies. Worldwide, EU and UK policy makers in Animal Health will have an interest in our results due to the impact that the poultry industry has on food sustainability. Outcomes will also include helping select vaccine candidates early in development and inform novel vaccine design. We will also identify potential targets for genome editing (such as IFITM), to develop more robust and resilient poultry. 

It is estimated that poultry will be the major global source of meat by 2018 and will account for 46% of meat consumed by 2022. However, infectious diseases are a continuous threat to the poultry industry. With over 60 billion chickens produced annually, it is vital that the poultry industry is protected so that food security is maintained.

Group members

Morales-Hojas R, Hinsley M, Armean I M, Silk R, Harrup L E, Gonzalez-Uriarte A, Veronesi E, Campbell L, Nayduch D, Saski C, Tabachnick W J, Kersey P, Carpenter S, Fife M (2018)

BMC Genomics 19 (1), 624
Bassano I, Ong S H, Lawless N, Whitehead T, Fife M, Kellam P (2017)

BMC Genomics 18 (1), 419
Psifidi A, Fife M, Howell J, Matika O, van Diemen P M, Kuo R, Smith J, Hocking P M, Salmon N, Jones M A, Hume D A, Banos G, Stevens M P, Kaiser P (2016)

BMC Genomics 17, e293
Staines K, Batra A, Mwangi W, Maier H J, Van Borm S, Young J R, Fife M, Butter C (2016)

PLoS ONE 11 (8), e0160173

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