|Jenkins, Jerry - Hudsonalpha Institute For Biotechnology|
|Jia, Gaofeng - Beijing University Of Agriculture|
|Hyten, David - Dupont Pioneer Hi-Bred|
|Pantalone, Vince - University Of Tennessee|
|Jackson, Scott - University Of Georgia|
|Schmutz, Jeremy - Hudsonalpha Institute For Biotechnology|
|Cregan, Perry - Retired ARS Employee|
Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2015
Publication Date: 1/6/2016
Publication URL: http://DOI 10.1186/s12864-015-2344-0
Citation: Song, Q., Jenkins, J., Jia, G., Hyten, D., Pantalone, V., Jackson, S.A., Schmutz, J., Cregan, P. 2016. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. Biomed Central (BMC) Genomics. 17:33-44.
Interpretive Summary: The whole DNA sequence of the soybean genome was published in 2010. We provided the genetic map that allowed the segments of DNA sequence to be “anchored” to positions along the 20 soybean chromosomes. However, because the number of DNA markers and the size of the genetic mapping populations we used to create our genetic map were relatively limited, some of the segments of DNA could not be properly oriented along the soybean chromosomes and some segments did not contain a DNA marker and therefore could not be positioned in the soybean genome sequence. In order to improve the soybean genome sequence we developed two large genetic mapping populations and used many more DNA markers to create a high very density genetic map. Based upon this ultra-high density genetic map we found 37 regions in the 2010 version of the soybean genome sequence where the order of the DNA in the genome sequence needed to be corrected. In addition, 28 DNA fragments or scaffolds whose positions in the 2010 genome sequence could not be determined were positioned in the newest version of the soybean whole genome sequence, Wm82.a2.v1, which is available at the Department of Energy, Joint Genome Institute site: http://www.phytozome.org/. The new version of the soybean genome sequence will facilitate the identification of genes or quantitative trait loci controlling seed yield, seed quality and resistance to biotic or abiotic stresses as well as other genetic research and research related to the function and structure of the soybean genome.
Technical Abstract: A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines, the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, the genome positions of these markers need to be mapped. Two high density genetic linkage maps were constructed based on 21,478 single nucleotide polymorphism loci mapped in the Williams 82 x G. soja (Sieb. & Zucc.) PI479752 population with 1,083 RILs and 11,922 loci mapped in the Essex x Williams 82 population with 922 RILs. There were 37 regions or single markers where marker order in the two populations was in agreement but was not consistent with the physical position in the Glyma1.01 build. In addition, 28 previously unanchored scaffolds were positioned. Map data were used to identify false joins in the Glyma1.01 assembly and the corresponding scaffolds were broken and reassembled to the new assembly, Wm82.a2.v1. Based upon the plots of the genetic on physical distance of the loci, the euchromatic and heterochromatic regions along each chromosome in the new assembly were delimited. Genomic positions of the commonly used markers contained in BARCSOYSSR_1.0 database and the SoySNP50K BeadChip were updated based upon the Wm82.a2.v1 assembly.