ARS | Publication request: Integration of the draft sequence and physical map as a framework for genomic research in soybean (Glycine max (L.) Merr.) and wild soybean (Glycine soja Sieb. and Zucc.)

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 19, 2011
Publication Date: March 1, 2012
Citation: Ha, J., Abernathy, B., Nelson, W., Grant, D.M., Wu, X., Nguyen, H., Stacey, G., Wing, R., Shoemaker, R.C., Jackson, S. 2012. Integration of the draft sequence and physical map as a framework for genomic research in soybean (Glycine max (L.) Merr.) and wild soybean (Glycine soja Sieb. and Zucc.). Genes, Genomes, Genetics. 2(3):321-329.

Interpretive Summary: Although the entire complement of hereditary material in soybean has been decoded, a high-resolution physical map integrated to that DNA sequence is still needed. The physical map will help researchers assemble the sequence and will facilitate gene cloning. In this manuscript, the authors report on the development of a high resolution physical map using three independent clone libraries. They created a physical bridge of overlapping DNA clones that covered as much as 95% of all the soybean chromosomes. This physical map will serve as a framework for finishing the assembly of the soybean DNA sequence, for comparing chromosome structure with other plants, and for evolutionary analysies.

Technical Abstract: Soybean is a model for the legume research community due to its importance as a crop, a well populated genetic map, and the availability of a genome sequence. Even though a whole genome shotgun sequence and Bacterial Artificial Chromosome (BAC) libraries are available, a high-resolution chromosome-based physical map linked to the sequence assemblies is still needed for whole-genome alignments and to facilitate gene cloning. The physical map will function as an essential framework to facilitate the correct ordering and orienting of DNA fragments on chromosomes, and provide a minimal set of BAC clones covering the entire genome as a tool for the research community. Three independent BAC libraries, consisting of 223,640 clones, combined with genetic and gene-based markers were used to construct a minimal tiling path (MTP) of BAC clones. Out of the 134,182 fingerprinted clones, 107,214 clones were assembled into contigs and 1,355 FPC contigs were aligned to build the FPC map, incorporating a total of 4,628 markers and aligned to 838,932,828 bp of the genome sequence. Four different MTPs were selected to obtain maximum genome coverage by spanning gaps in the sequence coverage. The MTPs covered from 92.8% to 95.5% of the soybean draft genome sequence (Gmax1.01) that consists of 950,068,807 bp assembled in 20 chromosome-level pseudomolecules. The MTPs were selected from an improved chromosome-based physical map combined with the genome sequence. Since our purpose was to pick the most reliable MTP, and not the MTP with the minimal number of clones, we integrated the FPC map and draft sequence and added clones with unpaired BES in order to build a high-quality, reliable physical map with as few gaps as possible. This physical map will serve as the framework for ordering sequence fragments, comparative genomics, cloning genes and evolutionary analyses of legume genomes.