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BMC Genomics

, 17:33

Plant genomics

Abstract

BackgroundA 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.

ResultsTwo high density genetic linkage maps were constructed based on 21,478 single nucleotide polymorphism loci mapped in the Williams 82 x G. soja Sieb. and 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.

ConclusionsThe 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.

KeywordsSoybean Wm82.a2.v1 assembly BARCSOYSSR 1.0 database SoySNP50K BeadChip euchromatic and heterochromatic regions linkage map AbbreviationsAFLPamplified fragment length polymorphisms

EWEssex x Williams 82 population

QTLquantitative trait loci

RAPDrandom amplified polymorphic DNA

RFLPrestriction fragment length polymorphism

RILsrecombinant inbred lines

SNPsingle nucleotide polymorphism

SSRsimple sequence repeat

WPWilliams 82 x PI479752 population

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-2344-0 contains supplementary material, which is available to authorized users.

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