3SR – Activity Year 1 (1 May 2010-30 April 2011)
The main focus over the first year of the project as one may expect, has been data collection, including collecting DNA and phenotypes from the wide range of breeds in the project and then genotyping the DNA collected; more than enough work to keep us busy. However, the consortium’s strong international links have already played an important role in the way the project has developed both in terms of the planned genotyping strategy and sequencing.
The initial general strategy for the planned genotyping work on sheep in the project was to the genotype around 1,000 animals using the SNP50(K) chip for genome-wide association and discovery, then to develop targeted 1536 SNP chips for fine mapping, and finally to develop targeted low cost chip that could be used routinely on a commercial level. The decision to develop targeted chips was mostly driven by concerns over cost. However during the early part of the project, John McEwan from AgResearch (New Zealand) coordinated a substantial international order for Ovine SNP chips for a variety of projects run worldwide, which allowed a substantial reduction in the costs of the chips to be achieved. Participation in that order allowed us to increase the number of chips used in the project by more three-fold and to move away from the plan to develop the targeted smaller for fine mapping chips. This change in strategy should allow better results to be achieved from the project and thus better value for money, which is great news all round. This opportunity has also allowed some of the partners to increase the numbers of animals that they have been able to genotype in the same breeds as part of nationally funded projects, the data for which can (in many cases) be used to increase the power of detection in the 3SR analyses, again great news. We would like to take this opportunity to thank John for helping us make take that step forward.
A second part of the planned work on sheep was focused on sequencing to improve the reference assembly in regions of the genome that are of interest to the project, i.e. are likely to have an influence on susceptibility to mastitis or nematodes or have an effect on ovulations rate. This activity was planned initially both to help develop more useful chips for fine mapping, and also to help with the international effort to produce a good reference sequence for sheep. However, as you may have seen, since the 3SR project was initially proposed, the ISGC have made some great unexpected, but welcome, strides forward. As a result, we are currently in the process of deciding what sequencing strategy would be most beneficial for us to implement given the status of the new ovine genome assembly and the objectives oft the 3SR project. Again a good problem to have as it should result in more progress and benefits from the project than we had initially hoped to achieve.
It is also worth mentioning that the good news over the last year in terms of genomics has not just been confined to sheep. Some of the 3SR partners are also members of the International Goat Genome Consortium, who are hoping to develop their own 50K chip by early 2012. We’ll now have to wait and see if it will be possible for us to use this new resource in the 3SR project. If the timing and cost allow, it should provide another potential opportunity to increase the value for money that can be achieved through the project.