Animal health in the post-genomics era

November 24^th 2006

Natacha Voillot-Blumenthal, Sciences TV, 88, avenue de Wagram, 75017 Paris

The goal of this meeting, held by Euroscicon, was to enlarge the knowledge about host-pathogen interactions in agricultural species, because it gives us a realistic opportunity to identify disease resistance genes. Pete Kaiser, Head of the Avian Genomics group at the Institute for Animal Health opened the meeting. His project aims to identify the molecular components of the immune system that are shared between mammals and birds, and those that represent their unique evolutionary solutions. The studies try to exploit the chicken genome sequence in two ways: understanding the bird’s immune response (particularly the repertoire of immune response genes and its innate immune response) and identifying disease resistance genes . Once the genes, whose products drive innate immune responses, have been identified the study will focus on single nucleotide polymorphisms (SNPs) in these genes between different lines of chickens that differ in their resistance to pathogens (coccidiosis, salmonellosis, hbv, hbdv, mdv).

With the SNP experiment, the consortium sampled three domestic chickens (Broiler, Layer, Silkie) at one quarter coverage each and compared the resultant sequence to the draft genome of the red jungle fowl (RJF). Across the genome 2.8 million SNPs have been identified, 80% of these are expected to be informative in the inbred lines, and from previous work 500,000 are expected to differ between the lines. Differences have been observed in antibody production : some inbred lines produced higher antibody responses following vaccination, and some lines always had high antibody responses (line N),whereas others always had low responses (line 15I). Looking for SNPs on cytokine genes, they identified 40 in the coding or regulatory regions,6 of these segregated between the inbred lines, 4 were in IL-4 and IL_13 and these segregated between line N and Line 15I, which had the differential antibody expression. Further studies will try to understand if these SNPs confer functional differences on Il-4 and IL-13 in these two lines, and if those differences explain the differential Antibody responses to vaccination in these two lines. Studying resistance to visceral salmonellosis, brought Dr Kaiser's team to map locus Sal1 into the MCW29-ADL 166 interval (-20cM), they went then to exclude MCW29 and regions distal to it through analysis of 6th generation congenics. They observed that the probability peak lies between MCW81 and ADL 166 (-9cM). Collaborations such as the one between IAH and Rima Zoorob (CNRS) and the one with Mike Kogut (USDA, College station) are looking at resistance to pathogens. The first collaboration aims to study the resistance to IBDV, by doing a cross between susceptible brown leghorn (BrL) and resistant line 6 1 chickens, meanwhile the second one in a Defra-funded project compares 2 Cobb’s commercial lines, that differs in resistance to salmonella infection. Identification of genetic variation in innate immune response genes associated with resistance to chicken viral infections tries to define chickens genes and pathways that respond to viral challenge (using microarrays), intron /exon, furthermore tries to estimate dN/dS ratios for viral response genes (from chicken, turkey, zebrafish, duck),to define a chicken viral response gene set, promoter/coding sequence polymorphisms between inbred lines, to associate polymorphisms with disease resistance in inbred lines, to identify structure/function relationships of polymorphic sites within proteins. Further studies will try to improve innate robustness by understanding immune response, linking phenotype, genotype and eQTLs and studying the whole genome with SNP panels.

Livestock have a number of advantages; their population structure makes for efficient linkage analysis and high levels of linkage disequilibrium. says Michael Stear (University of Glasgow). Diseases are more challenging than production traits, they are rare, their genetic architecture probably differs there are likely to be fewer genes with more interactions and they are time dependent (because of the development of immunity and variation in parasite exposure). For efficient gene hunting you need a careful design, a good definition of phenotype and genotype, a large sample size with multiple comparisons. He studied nematodes in Blackface sheep in Scotland and Northern Ireland. His team found that the best description of the parasite distribution among lambs was the negative binomial distribution. The total variation is due to many components: date of birth, sex, the age when the egg count is done, if the lamb is a twin, but the major influences are due to additive genetic effects, and the maternal component. The components of variation change as lambs mature. Disease QTL do exist but are difficult to detect, there are interactions among alleles and loci, with the Ifng microsatellite there is a dominant susceptibility allele while in the Mhc there is heterozygote advantage.

Harry Noyes (University of Liverpool) has mapped QTL in mice and cattle that are associated with response to infection. Trypanosomiasis caused by Trypanosoma congolense is a major constraint on cattle production in Africa and like Dr Kaiser, using SNP data he is trying to identify associations with infections and to focus the networks that respond differently to infection in susceptible animals. One of the primary aims is to understand and to control disease. There has been considerable success with mendelian diseases, but quantative traits are continuously distributed due to the interaction of a large number of genes; complex traits are more interesting and challenging.

Many homologues of known mammalian cytokines are known to exist in fish (C. Secombes, University of Aberdeen). However, cytokines with no obvious homologues are also apparent, whilst some mammalian genes, such as those belonging to the Th2 cytokine cluster, have not been found. Clearly complex immune system require complex regulatory mechanisms, as seen in mammals; the control of innate or nonspecific immunity to regulate, for example, inflammation is likely to be ancient in origin. But in vertebrates, adaptive or specific immune responses are also present, and this may have required the coevolution of new regulatory mechanisms and molecules. The questions are: are all cytokine genes known in mammals present in all vertebrate groups ? Do novel cytokines genes exist in particular vertebrate groups ? Is the network as complex as in « lower » vertebrates relative to « higher » vertebrates ? Attempts to discover cytokine genes in fish have used homology cloning, EST analysis, genome analysis, and all have had some degree of success, although with homology cloning this has been restricted to genes with relatively high homology (as seen with interleukin-1 and transforming growth factor-beta ). Not all cytokine genes known in mammals are present in fish , for example, of the 33 Ils in mammals only 18 are now known to exist in fish. However, while it is clear that novel cytokines genes do exist in fish, it is debatable whether the cytokine network of fish is as complex as higher vertebrates, since expansion of different cytokine family members has occurred in each.

Studies of the behavior of CD4+ T-cells in the intestinal mucosa of the pig are relevant to humans, since the evolutionary relationships between the molecules can be determined. Michael Bailey (University of Bristol,) using multiple, fluorochrome-tagged monoclonal antibodies studied of the interactions between cells in mucosal tissue. In cases where health issues are not due to obvious diseases of major importance, an alternative approach to genetically improving animal health must be employed. Stephen Bishop ( Roslin Institute Edinburgh, UK) studied genetic variation in innate immunity traits in growing pigs from the Meishan and Large White breeds. Relationships, at the population level, between immune traits and health are ambiguous, mainly due to the difficulty of classifying animal health. However, they have successfully demonstrated consistent genetic and phenotypic correlations between PBML (peripheral blood mononuclear leucocyte) levels and growth rate.

The research (E. Glass, Roslin Institute Edinburgh, UK) also focused on host responses to a tropical protozoan parasite, Theileria annulata, a tick borne ruminant pathogen of global and economic significance. The parasite causes a devastating diseases in cattle. T .annulata resides in macrophages, and alters host genes expression which results in phenotypic changes as well as a reversible transformation of the host cell. Gene expression differences may be the key to identifying casual genes involved in disease resistance. Genomics related to animal health is coordinated by the WORLD ORGANISATION FOR ANIMAL HEALTH (OIE). It is very important to know diseases transmissible to humans, the safety of the world trade of animals and animals products. OIE plays a very important role in scientific research and the dissemination of information, developing guidelines and organizing meetings and international Symposia, improving world animal and of course human health.