Plant & Animal Genomes XVI Conference Plant & Animal Genomes XVI ConferenceJanuary 12-16, 2008
Town & Country Convention Center
San Diego, CA
Hutton Oddy1 , Chris Warkup2 , Noelle E Cockett3 , Brian P Dalrymple4 , John C McEwan5 , Frank W Nicholas6 , James Kijas4 , and the ISGC7
The International Sheep Genomics Consortium (ISGC) is working to build resources for genomics research to explore the genetic diversity in sheep in general and generate useful associations for genetic improvement in specific sheep populations. Outcomes during 2007 include a “virtual” sheep genome sequence (Dalrymple et al, 2007), resequencing of BAC-end and EST sequences for SNP discovery and positioning with RH mapping (Kijas et al, 2008) and 454 FLX sequencing of 6 sheep to a depth of 0.5 x each for SNP discovery (Payne et al, 2008; McEwan et al, 2008).
These activities will generate sufficient information to assemble 60% of the sheep genome using the genomes of other species as frameworks. However, to take advantage of the newer sequencing technologies (markedly lower cost but with shorter read length), requires a reference sequence or at least a medium coverage framework of paired-end Sanger sequence reads. The ISGC has developed a case for sequencing a single sheep genome to a depth of between 2.5 and 5x to enable de novo assembly of a reference sheep genome from the high coverage, or at the lower coverage the framework for a community sheep genome sequence. In conjunction with an expanded HapMap project and high density mapping on RH panels this information will provide the necessary foundation for genome assembly and for SNP discovery beyond the anticipated 60k SNP panel to be developed using the 454 sequencing of the 6 sheep described above.
Dalrymple, B.P. et al (2007) http://genomebiology.com/2007/8/7/R152
Kijas, J. et al (2008) These proceedings
McEwan, J.C. et al (2008) These proceedings
Payne, G. et al (2008) These proceedings