international research organisations in the International Bovine BAC Mapping Consortium and the International Bovine Genome Project. A significant reason for our decision to participate in the Bovine Genome Project was to ensure that the whole sequence of a major production species be available in the public domain for use by all interested research agencies. The first draft of the bovine sequence was released in October 2004. This first draft already provided access to increased numbers of microsatellite markers and randomly generated single nucleotide polymorphisms (SNPs), facilitating the identification of genetic polymorphisms associated with valuable traits in Qualitative Trait Loci and other studies [Barendse, 2005]. The third draft was due for release in early 2006, and will greatly enhance the quality of information available. CSIRO has built a number of databases from this work, some of which are publicly available (http://www.livestockgenomics.csiro.au). Significant progress has been made as a result of early access to the very large amount of ordered sequence covering most of the protein-coding regions of the genome. Among our early projects was the design and implementation of an interactive bovine in silico SNP database, an activity started in 2001. This project identified the need for the production of SNPs based on the bovine expressed sequence tag collections and thus also for the clustering and annotation of the clustered transcripts. The analysis pipeline and results are described in detail in Hawken et al. [2004]. Significant progress has been made in transcriptomics [Carninici et al., 2005] in recent times. CSIRO has also developed the first bovine cDNA-based microarray for the analysis of muscle and fat. This consisted of 9,600 elements derived from 2,000 expressed sequence tags and 73,000 anonymous cDNA clones [Lehnert et al., 2004]. This array has been used in a variety of experiments with muscle and fat samples from cattle of different genotypes or undergoing a range of treatments [Byrne et al., 2005; Reverter et al., 2003, 2004, 2005a, c; Wang et al., 2005a, b]. Combined, these studies have started us down the track of systems biology [Reverter et al., 2005b]. We have related work in the ovine [Dalrymple, 2005] and chicken domains [Moore et al., 2005] although the latter is focussed on disease and disease management.
Genome Information: Current Limits
The genome sequences of domestic animals and particularly the bovine sequence are incredibly valuable, as they will provide the complete repertoire of genes that are present in these species as well as the means to measure the transcriptional activities of these genes in different tissues and under different nutritional regimes.
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