Generation of genome-wide CRISPR knockout libraries for pig and chicken

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The benefits of selective breeding within livestock to maintain and improve beneficial traits have long been practiced in agriculture. Traits such as increased size, milk production and resistance to infection are, for the most part, determined by relatively small differences in the DNA code of livestock animals such as pigs, cows, sheep and chickens. Recent technological advances allow scientists to read the genetic code of animals in greater detail, faster and for less money. So much so that we are beginning to understand how specific changes in the genomes of animals result in specific beneficial and detrimental characteristics. The aim in the near future is to be able to predict and select for beneficial characteristics in offspring based entirely on the animals DNA code. Although our ability to read the genetic code of animals has greatly improved our ability to translate the genetic code into physical attributes lags far behind. This is because we don't fully understand the function of most genes. A central approach to understanding the function of a particular gene involves deleting the gene and observing the effect this has on the animal or the animal's cells. Recent advances have allowed scientists to independently inhibit every individual gene within human cells, allowing them to ask how particular genes are involved in specific biological processes. These approaches allow us to link the genetic code of human cells to particular biological traits or processes. Such technologies have not been developed in livestock species due to the cost involved and comparative lack of detailed knowledge of livestock genomes compared to human genomes.In the last few years a new technology has been developed that allows scientists to rapidly and specifically edit the genomes of animals. These approaches have been shown to be more cost effective and technically superior to previous strategies for inhibiting genes. Currently the technique is limited to only a few species such as human and mouse. In this application we propose developing this technology for chicken and pig two of the most important livestock animals. Achieving this requires the latest detailed knowledge of the genome sequence of these animals and the technical skills required to develop the technology. At the Roslin institute we have two of the leading researchers involved in mapping the pig and chicken genomes as well as researchers with extensive knowledge of the newly developed technology. In addition we will be working closely with the Broad institute in the US who originally developed the technology in question. Therefore the Roslin Institute is uniquely positioned to successfully develop and apply this technology.Initially we will be asking a relatively straightforward question using the technology. Influenza virus is an important pathogen both in humans and in livestock animals. Spread of the virus in livestock such as birds and pigs contributes to outbreaks of the virus in humans, including potentially dangers pandemics. In many cases genes expressed by the host (such as human, chickens and pigs) are required by the virus and can restrict the replication of the virus. Significant amounts of work has been dedicated to understanding which genes are important following infection of human cells. Relatively little research has been performed to answer the same question in other species. We will use this technology to answer these questions. Although this will be an important aspect of the research, it is only one of many ways in which this new technology will be of benefit to scientists working on livestock animals. This technology has the potential to greatly improve our ability to understand the link between the genes encoded in a genome the functional roles they play. Such advances will have major impacts on the potential for improved breeding of livestock and will also contribute to our basic understanding of biology.