title: Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01.
abstract: BACKGROUND
  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 (RILs), 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.
  
  
  RESULTS
  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 1083 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.
  
  
  CONCLUSIONS
  The information will facilitate the study of recombination hot spots in the soybean genome, identification of genes or quantitative trait loci controlling yield, seed quality and resistance to biotic or abiotic stresses as well as other genetic or genomic research.
authors.affiliation: USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, 20705, USA. Qijian.song@ars.usda.gov.
authors.forename: Qijian
authors.initials: Q
authors.lastname: Song
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA. jjenkins@hudsonalpha.org.
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.affiliation: USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, 20705, USA. gfjia@msn.com.
authors.forename: Gaofeng
authors.initials: G
authors.lastname: Jia
authors.affiliation: Department of Agronomy & Horticulture, Center for Plant Science Innovation, 322 Keim Hall, University of Nebraska, Lincoln, NE, 68583, USA. david.hyten@unl.edu.
authors.forename: David L
authors.initials: DL
authors.lastname: Hyten
authors.affiliation: Department of Plant Sciences, 2431 Joe Johnson Dr., University of Tennessee, Knoxville, TN, 37996-4561, USA. vpantalo@utk.edu.
authors.forename: Vince
authors.initials: V
authors.lastname: Pantalone
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602-6810, USA. sjackson@uga.edu.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA. jschmutz@hudsonalpha.org.|Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA. jschmutz@hudsonalpha.org.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, 20705, USA. perry.cregan@ars.usda.gov.
authors.forename: Perry B
authors.initials: PB
authors.lastname: Cregan
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D008040:Genetic Linkage; D018745:Genome, Plant; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D013025:Glycine max / Q000235:genetics*