W153 Goat genome assembly, Availability of an international 50K SNP chip and RH panel : an update of the International Goat Genome Consortium projects

Date: Sunday, January 15, 2012
Time: 11:30 AM
Room: San Diego
Gwenola Tosser-Klopp , INRA, France
Philippe Bardou , INRA, France
Cédric Cabau , INRA, France
Andre Eggen , Illumina, Hayward, CA
Thomas Faraut , Institut National de la Recherche Agronomique , Castanet-Tolosan, France
Henri Heuven , University of Utrecht, Netherlands
Saadiah Jamli , MARDI, Serdang, Malaysia
Christophe Klopp , INRA, France
Cindy Taylor Lawley , Illumina, Hayward, CA
John McEwan , AgResearch, Mosgiel, Otago, New Zealand
Patrice Martin , INRA, France
Carole R. Moreno , INRA, France
Philippe Mulsant , INRA, France
Ibouniyamine Nabihoudine , INRA, France
Eric Pailhoux , INRA, France
Isabelle Palhière , INRA, France
Rachel Rupp , INRA, Castanet Tolosan, France
Julien Sarry , INRA, France
Brian Sayre , Virginia State University, Petersburg, VA
Aurélie Tircazes , INRA, France
Jun Wang , Bejing Genome Institute, China
Wen Wang , Bejing Genome Institute, China
Tun-Ping Yu , DNA Landmarks, St-Jean-sur-Richelieu, QC, Canada
Wenguang Zhang , Inner Mongolia Agricultural University, China
Goat breeds, including dairy, meat and fiber breeds, are adapted to a wide range of breeding conditions, and have a large economic impact. Currently, however, they benefit from fewer genomic research tools compared to cattle or sheep. At present, the International Goat Genome Consortium (www.goat.genome.org) federates 3 projects, aiming at the improvement of knowledge of goat genome:

- de novo goat genome sequence

- RH panel and whole genome high density RH maps

- 50K SNP chip.

An update will be made on these three topics. Details will be given on the international goat SNP chip, developed using whole genome de novo sequencing and reduced representation libraries of the genome of Alpine, Saanen, Creole, Boer, Kacang and Savanna breeds. More than 500,000 SNP were chosen by filtering on flanking sequence data, minimum allele frequency, technological qualities and categorized depending on the number of breeds in which the 2 alleles were observed. 60,000 high quality SNPs were finally spaced on the goat genome, using goat contigs. 59,000 out of the 60,000 SNPs were aligned on the bovine genome. 100 % of the SNPs were observed as heterozygous in milk breeds, 97% in meat breeds. This chip, based on Illumina Infinium technology, has been used to generate cluster files on 288 animals, using both the breeds used for SNP discovery and Skopelos, Angora and Jinlan breeds. Discussion will be opened on new projects to be developed within the Consortium. Acknowledgements: CAPGENES and APIS-GENE French Breeding organizations, 3SR European project, Marcel Amills, Ilias Kyriazakis, Alessio Valentini.