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Location: Corn Insects and Crop Genetics Research

Title: Integration of draft sequence and physical map as framework for genomic research in soybean (Glycine max)

item Ha, Jungmin
item Abernathy, Brian
item Grant, David
item Wu, Xiaolei
item Nelson, William
item Stacey, Gary
item Shoemaker, Randy
item Jackson, Scott

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/12/2010
Publication Date: 3/1/2012
Citation: Ha, J., Abernathy, B., Grant, D.M., Wu, X., Nelson, W., Stacey, G., Shoemaker, R.C., Jackson, S. 2012. Integration of draft sequence and physical map as framework for genomic research in soybean (Glycine max). Biomed Central (BMC) Genomics. 2(3):321-329.

Interpretive Summary: The complete hereditary code of soybean has recently been reported. Even though the whole genome sequence and Bacterial Artificial Chromosome (BAC) libraries are available, a high-resolution, chromosome-based physical map linked to the chromosomal sequence assemblies is still needed for whole-genome alignments and to facilitate gene cloning. In this paper, scientists from ARS and several other academic institutions report the integration of a physical map of soybean with the whole genome sequence of soybean.The physical map will function as an essential framework to facilitate the correct ordering and orienting of DNA fragments on chromosomes, and a minimal set of BAC clones covering the entire genome as a tool for the research community. This will be a valuable resource for legume researchers throughout the U.S. and world.

Technical Abstract: 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 scaffolds. 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 as possible gaps. This physical map will serve as the framework for ordering sequence fragments, comparative genomics, cloning genes and evolutionary analyses of legume genomes.