Piggy-BACing the human genome

Abstract

Using the INRA-Minnesota porcine radiation hybrid panel, we have constructed a human-pig comparative map composed of 2274 loci, including 206 ESTs and 2068 BAC-end sequences, assigned to 34 linkage groups. The average spacing between comparative anchor loci is 1.15 Mb based on human genome sequence coordinates. A total of 51 conserved synteny groups that include 173 conserved segments were identified. This radiation hybrid map has the highest resolution of any porcine map to date and its integration with the porcine linkage map (reported here) will greatly facilitate the positional cloning of genes influencing complex traits of both agricultural and biomedical interest. Additionally, this map will provide a framework for anchoring contigs generated through BAC fingerprinting efforts and assist in the selection of a BAC minimal tiling path and assembly of the first sequence-ready map of the porcine genome.

Characterization of the porcine differentially expressed PDK4 gene and association with meat quality

“…Alignment between pig chromosome 9 on RH map and human maps on USDA-MARC Pig Database [23], we found some QTLs associated with meat quality and production traits in this region such as body weight at 10 weeks of age (87 cM) [24], average backfat thickness (79.3-90 cM) [25], total saturated fatty acids (61.5-83.3 cM) [26], backfat at tenth rib (96-79 cM) [27]. Also, PDK4 had thought to be a key regulatory enzyme involved in switching the energy source from glucose to fatty acids in response to physiological conditions [17].…”

Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals

“…With the emergence of highthroughput sequencing projects, EST libraries were produced for the major farm animals, and the sequence data from EST projects were made available through public databases [Fadiel et al, 2005;Womack, 2005]. More recently, BAC end sequences (BES) were also used for RH mapping [Meyers et al, 2005;Tetens et al, 2007].…”

“…Altogether, more than 10,000 markers have been mapped on the porcine genome through an international participation allowing the construction of a high-resolution reference map with a res-olution down to approximately 1 Mb (available at http:// imprh.toulouse.inra.fr/) . The high-resolution RH maps have contributed to the construction of a very-high-quality BAC physical map covering the whole pig genome [Meyers et al, 2005;Humphray et al, 2007].…”

Genetic Resources, Genome Mapping and Evolutionary Genomics of the Pig (Sus scrofa)

“…Over 620K BAC end-sequences (BES) with an average read length of 635 bp have provided a previously untapped source of both coding and noncoding porcine sequence information 69. The first high-resolution, physically anchored, contiguous whole genome radiation hybrid (RH) comparative maps of the porcine autosomes were constructed by using physically anchored sequences derived from BACs 70. Furthermore, a physical map of the pig genome by integrating 265K restriction fingerprints and BES generated from 4 BAC libraries with RH markers, and contig alignments to the human genome was recently constructed with coverage across the 18 pig autosomes and the X chromosome in 176 contigs with an average length of 15 Mb as well as localised representation of the gene rich regions on Y.…”