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Towards a high density SNP International Goat Chip
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According to FAO, in 2009, the world population of goats was estimated to be around 868 million animals and was steadily growing either in developed or developing countries. Goat breeds include dairy, meat and fiber breeds, are adapted to a wide range of breeding conditions and have thus a great economic importance. However, they benefit from fewer genomic research tools, as compared to cattle or sheep. Recently, several research projects were conducted in different laboratories to improve goat genome knowledge and develop new research tools. Goat genome was sequenced de novo (see W. Zhang presentation, this meeting), a RH panel was developed (see B. Sayre presentation, this meeting). In France, a collaborative SNP discovery research programme, CAPRISNIP, was launched by INRA and breeding organisations CAPGENES and APIS-GENE in 2009. At least two other SNP discovery projects were launched in other countries, using either reduced representations of the genome (University of Utrecht, Netherlands) or whole genome de novo sequencing (Malaysian Agricultural Research and Development Institute). RNA-sequencing projects conducted by different research groups at INRA may also be a valuable source for SNP discovery and annotation. We propose to federate these several SNP discovery and RNA-seq research programmes within the frame of the International Goat Genome Consortium in order to develop an international versatile high density SNP chip. Collection of the data is underway. SNP detection will be done in early 2011. The work plan includes i) alignment of the different sequences on de novo assembled goat contigs ii) ordering of contigs on ovine or bovine genome reference sequenceiii)SNP discovery and annotation iv) small set SNP test generation v) determination of the SNP panel vi) raw data access to all partners. A first international chip order is planned for autumn 2011.
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