Submitted to: Plant Journal
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/19/2007
Publication Date: 7/27/2007
Citation: Keller, C., Readman, C., Shin, H., Bosdet, I., Wilkin, J., Vrebalov, J., Giovannoni, J.J., Douglas, C. 2007. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant Journal. 50:1063-1078. Interpretive Summary: Populus (poplar) species are economically important crops in temperate climates throughout the world for a variety of purposes, including wood pulp, paper, biomass and for use in phytoremediation and waste water treatment. Because of its relatively small genome size (485 Mb), genetic and genomic resources, and ease of propagation and genetic manipulation, Populus provides a useful model system to study a number of biological processes of importance to woody perennial plants, such as dormancy, secondary xylem (wood) development, metabolism and responses to environmental stress. To both test general methods for plant genome assembly and to enhance resources available for poplar genomics, we undertook the generation of a poplar physical map.
Technical Abstract: As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the first maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2,802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, estimated from the genome sequence assembly to be 485+10 Mb in size. BAC ends were sequenced to aid in long-range assembly of whole genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat (SSR)-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. 2,411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa v1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced.