Work package 1

The principal objective of work package 1 is to develop a computational environment for handling and exploiting the massive amount of data that will be generated by the new generation of highly parallel sequencing technology with particular emphasis on resequencing issues of relevance to complex trait research.

Through in-house activity and international collaboration, we currently have access to thousands of putative SNPs in cattle, pigs and salmon. However, in order to determine haplotype structures and fine-map QTLs (Quantitative Trait Loci) down to the resolution where causal associations between the SNPs and phenotypes can be discovered, and since a QTN (Quantitative Trait Nucleotide) can only be found if it is typed, there is an urgent need for increasing this number to hundreds of thousands or even millions of SNPs. The availability of high-quality genome reference sequences for a number of species (soon available in cattle and pigs) provides new opportunities for SNP detection by generating massive amounts of additional sequence data that can be aligned to the reference sequence. The new generation of highly parallel sequencing technologies (such as 454; www.454.com or Solexa; www.illumina.com) is particularly useful for such an approach. Even in species lacking a reference sequence (like salmon) these technologies can be exploited to generate hundreds of thousands of SNPs by sequencing genome-wide distributed fragments generated through genome complexity reduction
 
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