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Chantier qualité GA; International audience; Until recently, the construction of a reference genome was performed using Sanger sequencing alone. The emergence of next-generation sequencing platforms now means reference genomes may incorporate sequence data generated from a range of sequencing platforms, each of which have different read length, systematic biases and mate-pair characteristics. The objective of this review is to inform the mammalian genomics community about the experimental strategy being pursued by the International Sheep Genomics Consortium (ISGC) to construct the draft reference genome of sheep (Ovis aries). Component activities such as data generation, sequence assembly and annotation are described, along with information concerning the key researchers performing the work. This aims to foster future participation from across the research community through the coordinated activities of the consortium. The review also serves as a ‘marker paper’ by providing information concerning the pre-publication release of the reference genome. This ensures the ISGC adheres to the framework for data sharing established at the recent Toronto International Data Release Workshop and provides guidelines for data users.

Parasitism by fasciolosis affects cattle and buffalo production throughout the tropical regions in the world with and estimated economic impact of $US2billion/pa. In a unique research strategy we aim to exploit the extreme genetic resistance of the Indonesian Thin Tail (ITT) sheep to undertake molecular characterisation of a putative major gene for Fasciola gigantica (FGR) resistance in these sheep by a combined functional genomics and positional cloning approach, and through comparative mapping, identify homologous genes in cattle and buffalo for commercial application. The strategy for the immunological programme developed in parallel with the genome screen, is to provide function/identity of putative candidate genes through understanding the mechanisms of resistance determined by the FGR gene. This approach is now used in contemporary genome biology as a "functional genomics" approach for gene identification and isolation to open new avenues in genetic control or identification of new regulatory factors for control of internal parasites in ruminants. Our gene mapping approach uses 10 resource families which are a highly heterozygous cross between resistant (ITT) and susceptible (Merino) genotypes. These families are used to create 600 backcross progeny to obtain gene expression in a susceptible (Merino) background. All progeny are being phenotyped for expression of resistance by challenge with 300 viable Fasciola gigantica metacercaria. Following measurement of an extensive range of immunological and haernatological parameters during infection, all sheep are slaughtered at 16 weeks for assessment of parasite parameters (resistance). Preliminary segregation analysis in 400 progeny from 7 sires, supports the presence of a gene with large effect for resistance to F gigantica. A strong sex x major gene interaction was evident, in which males expressed the putative gene, whereas females did not in 4 out of the 5 families in which segregation was evident. The major gene effect was consistent for male progeny groups with approximately a 50% reduction in fluke burden (20-28 flukes). Genome analysis is undertaken in all progeny by a full genome scan using a panel of 85 highly polymorphic micro-satellite markers to obtain a chromosomal location of the putative major gene as the first step in a positional candidate cloning approach. A complete analysis of our first 3 families, revealed a putative QTL in males but not female progeny. Based on a functional assessment of the genetic mechanism for resistance, a fine mapping approach in extended families, and detailed comparative mapping to man, mouse and other ruminant systems, we intend to obtain a positional clone for all major candidate genes as potential FGR resistance genes. Through a novel in-vitro killing assay of juvenile Fasciola parasites, our in vitro studies have demonstrated the effector cells mediating killing of F. gigantica immature parasites include ITT macrophages and eosinophils and the molecular mechanism of killing involves superoxide radicals. Furthermore IgG2 responses correlated with susceptibility to infection. Results from our immunological approach, using in vitro and in vivo experimental approaches, collectively suggests Th1-like responses are associated with the susceptibility of Merino sheep to F. gigantica infection while, conversely, Th2-like responses are associated with the resistance of ITT sheep to F. gigantica infection. (Texte intégral)

Dexter cattle are a small breed of cattle originating in Ireland that have been bred in Australia for several decades. There have been reports of mutant, aborted foetuses in this breed of cattle, described as chondrodysplastic foetuses (or "bulldog" calves). The affected foetuses display disproportionate dwarfism, a short vertebral column, marked micromelia, a relatively large head with a retruded muzzle, cleft palate, protruding tongue and a large abdominal hernia. Dexter chondrodysplasia is inherited in an incompletely dominant manner. As part of an approach to controlling the disease in Australia, Dexter Cattle Australia (DCA) chose to initiate and support research to develop a DNA-test to identify carrier animals, prevent carrier x carrier matings, and hence reduce the incidence of chondrodysplastic foetuses. The aim was to find the gene responsible for chondrodysplasia, and develop a DNA-test. Potential candidate genes were identified, and homozygosity mapping in regions predicted to contain candidate genes identified a region of interest. A candidate gene predicted to be in the region of interest was mapped on the bovine linkage map confirming location in the region of interest. The candidate gene was screened for disease causing mutations. One disease causing mutation was identified in the candidate gene. The mutation is a 4 bp insertion causing a frame shift which leads to a premature termination codon. The resulting protein was predicted to contain less than one third of the original amino acid sequence. A DNA-test was developed to identify animals heterozygous for the mutation. The PCR test is based on fragment length analysis and will be available to Dexter breeders this year. There is an indication of a second, yet unidentified mutation in an unrelated bull, causing chondrodysplasia. The search for the second mutation will continue and if found will add accuracy to the initial DNA-test. (Texte intégral)