Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01

Song, Qijian; Jenkins, Jerry; Jia, Gaofeng; Hyten, David L.; Pantalone, Vince; Jackson, Scott A.; Schmutz, Jeremy; Cregan, Perry B.

doi:10.1186/s12864-015-2344-0

Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01

Journal Article · Wed Jan 06 00:00:00 EST 2016 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-015-2344-0· OSTI ID:1615261

Song, Qijian ^[1]; Jenkins, Jerry ^[2]; Jia, Gaofeng ^[1]; Hyten, David L. ^[3]; Pantalone, Vince ^[4]; Jackson, Scott A. ^[5]; Schmutz, Jeremy ^[6]; Cregan, Perry B. ^[1]

US Dept. of Agriculture (USDA), Beltsville, MD (United States). Agricultural Research Service (ARS). Soybean Genomics and Improvement Lab.
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Univ. of Nebraska, Lincoln, NE (United States)
Univ. of Tennessee, Knoxville, TN (United States)
Univ. of Georgia, Athens, GA (United States). Center for Applied Genetic Technologies
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1615261

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 17; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng Figshare https://doi.org/10.6084/m9.figshare.c.3597548	collection	January 2016

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Additional file 3 of Genetic variation and genetic complexity of nodule occupancy in soybean inoculated with USDA110 and USDA123 rhizobium strains Araya, Susan; Elia, Patrick; Quigley, Charles V. figshare https://doi.org/10.6084/m9.figshare.24089173	dataset	January 2023
Additional file 5 of Genetic variation and genetic complexity of nodule occupancy in soybean inoculated with USDA110 and USDA123 rhizobium strains Araya, Susan; Elia, Patrick; Quigley, Charles V. figshare https://doi.org/10.6084/m9.figshare.24089179.v1	dataset	January 2023
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59 BASIC BIOLOGICAL SCIENCES
BARCSOYSSR_1.0 database
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Additional file 4: Table S2. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/M9.FIGSHARE.C.3597548_D2 The current record is supplemented by this dataset	dataset	January 2016
Additional file 1: Table S1. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/M9.FIGSHARE.C.3597548_D3 The current record is supplemented by this dataset	dataset	January 2016
Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/m9.figshare.c.3597548 The current record is supplemented by this collection	collection	January 2016
Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/m9.figshare.c.3597548.v1 The current record is supplemented by this collection	collection	January 2016
Additional file 2: Figure S1. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/m9.figshare.c.3597548_d1 The current record is supplemented by this text	text	January 2016
Additional file 2: Figure S1. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/m9.figshare.c.3597548_d1.v1 The current record is supplemented by this text	text	January 2016
Additional file 4: Table S2. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/m9.figshare.c.3597548_d2.v1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 1: Table S1. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/m9.figshare.c.3597548_d3.v1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 3: Figure S2. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/m9.figshare.c.3597548_d4 The current record is supplemented by this text	text	January 2016
Additional file 3: Figure S2. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Song, Qijian; Jenkins, Jerry; Jia, Gaofeng https://doi.org/10.6084/m9.figshare.c.3597548_d4.v1 The current record is supplemented by this text	text	January 2016

Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01

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