The first sequence of the swine genome will be completed thanks to funding from the US Department of Agriculture, expertise from eight academic institutions, and DNA from a dead but not forgotten Duroc sow.
Larry Schook, co-chairman of the international Swine Genome Sequencing Consortium and professor of animal sciences at the University of Illinois at Urbana-Champaign, will lead the two-year project, which is expected to cost $20 million to complete. Setting a timetable to get to this point has been "the most significant thing I've ever done in my professional life," Schook said at a workshop at the Plant and Animal Genome conference, held here this week.
Last Friday, USDA Secretary Mike Johanns announced the award of a two-year, $10-million grant from the agency's Cooperative State Research, Extension, and Education Service. One year ago, at 2005's Plant and Animal Genome conference, Joseph Jen, undersecretary for Research, Education and Economics, announced the agency's intent to issue the RFA.
Jen, who plans to leave his post in two months, said at the conference yesterday that he's "heaving a sigh of relief" as he watches the SGSC members get started on the draft sequence.
Jane Rogers at the Wellcome Trust Sanger Institute will oversee the project as it sequences the 2.7-Gb swine genome. At PAG, Rogers discussed the international effort that led to the creation of a sequencing strategy for the swine genome. The initial goal of the project is to create a BAC skim of the genome at 3x coverage. "We are looking forward to getting going," Rogers said.
Although the most recent USDA award is earmarked for creating a low-coverage draft sequence, higher coverage is still the ultimate goal. Whole-genome shotgun libraries have been constructed and are being sequenced. Rogers explained that a hybrid sequencing approach - in which 3x coverage of BACs are combined with 3x WG-shotgun libraries - will be used to develop a 6x coverage draft eventually.
All sequence traces will be deposited into trace repositories, while high-throughput data will be submitted to public databases.
Jonathan Beever, professor of animal sciences at the University of Illinois, demonstrated the completion of the first high-resolution human-pig comparative map, which provides the scaffold for BAC physical map assembly.
Beever has also characterized the pig transcriptome, which required the creation of "an autologous reagent resource for genome sequencing." That is, Beever took the DNA from a single sow, cultured fibroblasts to create cloned piglets, and either collected tissue for cDNA libraries or generated shotgun libraries from fetal fibroblasts.
The sow on which the sequence will be based died last year, but Beever's work has ensured that its genetic legacy will live on. He also had a taxidermist preserve the pig's head, which was subsequently left on Larry Schook's desk. While the resulting sequence data will be freely available to the public without restriction, the pig's head will likely stay in Schook's office.
In the meantime, SGSC members will commence sequencing. Institutions collaborating with Illinois and Sanger on the project include Iowa State University; INRA Cellular Genetics Laboratory in Toulouse, France; Roslin Institute in Edinburgh, Scotland; the University of Nevada at Reno; and the USDA Agricultural Research Service Meat Animal Research Center in Clay Center, Nebraska.
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