Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome

Abstract

The Swine Genome Sequencing Consortium (SGSC) was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC's mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP) that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA), presentations demonstrated that a human-pig comparative map has been completed, BAC fingerprint contigs (FPC) for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG) shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3× coverage of BACs comprising the MTP and 3× of the WG-shotgun libraries will be used to develop a draft 6× coverage of the pig genome.

The genome and the nucleus: a marriage made by evolution

“…human (Venter et al 2001) and chicken (Hillier et al 2004). This will hopefully change in the next few years due to initiatives to sequence the pig genome (Schook et al 2005). We would certainly relish this because the authors of this review have mapped the positioning of porcine interphase chromosomes in a variety of cell types making the pig the organism that has the most whole chromosomes mapped to their interphase position than any other organism (Foster et al 2004(Foster et al , 2005Foster, Griffin and Bridger, manuscript in preparation).…”

Mining the pig genome to investigate the domestication process

“…This strategy has also been used to identify candidate regions for domestication traits. The Swine Genome Sequencing Consortium (SGSC) began in 2003 (Schook et al, 2005) and published the assembly of the genome sequence of a domestic pig 9 years later (Groenen et al, 2012). Before the completion of the genome sequence, several methodologies for retrieving genome information were applied, such as the sequencing of reduced genomic libraries and the construction of dense genotyping panels (for example, Ramos et al, 2009).…”

An animal model to evaluate the function and regulation of the adaptively evolving stress protein SEP53 in oesophageal bile damage responses

“…The pig SEP53 locus present in the CH242-126j8 BAC clone (CU076058) is currently being sequenced as part of the pig genome sequencing project led by the Swine Genome Sequencing Consortium (Schook et al 2005). The SEP53 locus found in the PigE-67g7 clone sequence (DQ910536) is missing 168 bp present in the CH242-126j8 clone (CU076058).…”