In the Genetics and Genomics Group we are currently studying the genomes of Culicoides biting midges, and of inbred and out-bred lines of chickens, with the strategic aim of improving the control of viral diseases. Culicoides midges spread a number of viruses that cause severe disease in animals, including bluetongue in ruminants and African horse sickness. Analysis of the genomes of lines of chickens that differ in their susceptibility and resistance to specified pathogens is a prerequisite to understanding the basis of these differences. This, in turn, will assist in conventional chicken breeding programmes. Similarly, the analysis of the Culicoides genome will identify the genetic factors that determine why only some midges transmit viruses to animals.
Our work falls within both the Vector-borne Viral Diseases (VVD) and the Avian Viral Diseases (AVD) programmes at IAH.
Culicoides midges
Culicoides biting midges act as the biological vectors of more than 50 arboviruses including some of the most economically damaging pathogens of livestock. These include bluetongue virus (BTV), African horse sickness virus (AHSV) and epizootic haemorrhagic disease virus (EHDV). Recently BTV has had a huge impact upon European agriculture, both through trade barriers imposed in attempts to control outbreaks of the disease, and through direct fatalities and losses in productivity due to severe clinical disease in susceptible ruminants.
Recent technological advances and reduced costs have enormously increased nucleotide-sequencing throughput, facilitating the rapid analysis of entire genomes for individual arthropod vector species. One of our first goals in the Genetics & Genomics Group has been to initiate the first large-scale de novo genome sequencing project of any Culicoides biting midge. The complete Culicoides genome sequence will be of global significance, creating a new area of research, with the potential to elucidate vector-pathogen interactions, including defining the genetic drivers of vector competence. The accessibility of genomic DNA sequence data for Culicoides will provide new opportunities to analyze, understand and exploit the genetic control mechanisms underlying complex traits (such as vector-competence), within and between species, potentially leading to novel control strategies for certain vector-borne diseases.
Researchers have never before had access to such important and comprehensive data sets, in order to fully explore the range, depth and complexity of Culicoides-vector / pathogen / host relationship interactions. Sequencing and annotation of the Culicoides genome will be of global significance, creating new opportunities in Culicoides research, building on the strategically important resources generated and exploiting new genomic technologies to fully realize their potential.
Chickens
IAH is the curator of a vital BBSRC resource - 7 inbred and 2 out-bred scientifically important, chicken lines. These lines are a key resource for the AVD programme for the study of host-pathogen interactions, especially relating to susceptibility and resistance to disease.
We in the Genetics and Genomics Group have established a high-throughput genotyping facility using the Illumina platform. This work has been the focus of extensive genome-wide analysis for all IAH inbred chicken lines, leading to comprehensive haplotype analysis of the lines using the web-based chicken SNP selector software that we have implemented at IAH. Recent technological advances have enormously increased genome-sequencing throughput and reduced costs, facilitating the rapid analysis of entire genomes for individual animals, now completed for the IAH inbred lines. We have focussed our expertise in immunogenetics on the immune responses to the pathogens that infect poultry in these IAH inbred lines. Crosses between these lines, used to identify novel resistance loci, have now fine-mapped a region to 54.0 - 54.8 Mb on the long arm of Chromosome 5, and replicated the finding in commercial birds. We have filed a patent for using this marker in screening, testing and breeding (PCT/GB2010/0000850).
Publications
- Fife M.S., Howell J.S., Salmon N., Hocking P.M., van Diemen P.M., Jones M.A., Stevens M.P. and Kaiser P.
(2010)
Genome-wide SNP analysis identifies major QTL for Salmonella colonization in the chicken.
Animal Genetics, 42 (2) 134-140.
- M. Fife, N Salmon, P Hocking , P Kaiser.
(2009)
Fine mapping of the chicken salmonellosis resistance locus (SAL1).
Animal Genetics 40(6) pp 871-877.
- Kaiser P, Wu Z, Rothwell L, Fife M, Gibson M, Poh TY, Shini A, Bryden W, Shini S.
(2009)
Prospects for understanding immune-endocrine interactions in the chicken. Gen Comp Endocrinol.
Sep 1;163(1-2):83-91.
- Gibson MS, Kaiser P, Fife M.
(2009)
Identification of chicken granulocyte colony-stimulating factor (G-CSF/CSF3): the previously described myelomonocytic growth factor is actually CSF3.
J Interferon Cytokine Res. (2009) Jun;29(6):339-43.
- 5. Kaiser P, Howell J, Fife M, Sadeyen JR, Salmon N, Rothwell L, Young J, van Diemen P, Stevens M, Poh TY, Jones M, Barrow P, Swaggerty C, Kogut M, Smith J, Burt D.
(2008)
Integrated immunogenomics in the chicken: deciphering the immune response to identify disease resistance genes.
Dev Biol (Basel). (2008);132:57-66.