Whole genome SNP panels for genotyping experimental chicken lines- a vital BBSRC resource

The chicken DNA sequence bridges the evolutionary gap not previously covered by any other animal, sharing a common ancestor with mammals as long as 310 million years ago. Like genetic studies in mice, the chicken may also provide important evolutionary data on vital genes and how they influence such things as disease resistance and health. Identifying these qualities is only possible when the full extent of genetic differences between animals is available. We are now entering the genetic era of livestock research, made possible by the recent publication of the genome sequence of the Chicken, and the resource of over 3 million genetic variations for the chicken genome in the publicly available Beijing Genomics Institute database. However, the data generated for these genetics variants is from only three animals - a 'typical' layer chicken, a 'typical' broiler chicken and a Chinese Silkie chicken. Although this is a very valuable tool, little is known about the level of genetic variation within and between different breeds of chicken, particularly those used in scientific research and by commercial breeders. The Institute for Animal Health (IAH) is pre-eminent in Europe in its ability to develop approaches to understand host-pathogen relationships in farm animals. The inbred chicken lines housed at IAH are a vital BBSRC-resource used by research centres throughout the EU. The 10 different chicken lines have been selectively bred and vast amounts of data collected over the past 30 years and are unique genetic resources that provide the ability to understand the genetic basis for important traits. As most of these chicken lines are of layer origin they will only contain variations that are specific that line. Our aim is to screen two panels of over 6000 variations and determine a set of variants to be used for comparative studies in each of the inbred lines. Using these genetic markers we will then be able to map traits unique by analysis of genetic crosses of the relevant lines. The tools and resources that will result from the work proposed in this application can be used to fill this knowledge gap, making the identification of genes for important traits a feasible goal. The accessibility of resources for a set of genetic variations for each of the inbred chicken lines will provide genetic tools that will support advances in poultry genomics and enable delivery of results through scientific research to the consumer. Comparisons of these inbred chicken lines may also be very important in answering immunological questions, including some topics of particular importance for human health, such as avian influenza. Furthermore, accessibility of high density maps for genetic variation in the chicken genome will provide enormous opportunities to understand and exploit the genetic control of complex traits to the benefit of poultry flocks, the UK poultry industry, the consumer and the environment.

The accessibility of genomic DNA sequence and high density SNP maps of the chicken provide enormous opportunities to understand and exploit the genetic control of complex traits to the benefit of poultry flocks, the UK poultry industry, the consumer and the environment. We now have the opportunity to correlate phenotypic variation with underlying genetic variation; however, successful mapping of these traits is will only be possible with a substantial increase in the availability of genetic markers and tools necessary to integrate genomic information with conventional breeding strategies. One of the fundamental steps in the genomic approach to animal breeding is the correlation of phenotypic data with genotypes in order to identify quantitative trait loci (QTL). To maximize the precision of genetic selection the genes underlying QTLs must be identified. This requires mapping a QTL to high resolution. Currently, there are over 3 million publicly available SNPs for the chicken genome. However, this data was generated from only three animals - a 'typical' layer chicken, a 'typical' broiler chicken and a Chinese Silkie chicken. At IAH most of the inbred lines are of layer origin and therefore will only contain SNPs that are specific to layer populations. The IAH lines have vast amounts of phenotypic data on them amassed over the past 30 years. Our specific objectives are to identify genome-wide panels of fully informative SNPs in each of our lines from existing Illumina SNP panels of over 6000 SNPs. Using these line-specific SNPs we will be able to map traits by analysis of relevant backcross generations. Additionally, we will be able to examine the Linkage Disequilibrium patterns between the divergent lines. We will provide the SNP information for each line in a publicly accessible database permitting exploitation by researchers and breeding programs to improve robustness of poultry in the UK, and thus the long-term sustainability of the UK poultry industry.