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 joinsmore »
- Authors:
-
- 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)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1615261
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genomics
- Additional Journal Information:
- Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 1471-2164
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Soybean; Wm82.a2.v1 assembly; BARCSOYSSR_1.0 database; SoySNP50K BeadChip; euchromatic and heterochromatic regions; linkage map
Citation Formats
Song, Qijian, Jenkins, Jerry, Jia, Gaofeng, Hyten, David L., Pantalone, Vince, Jackson, Scott A., Schmutz, Jeremy, and Cregan, Perry B. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. United States: N. p., 2016.
Web. doi:10.1186/s12864-015-2344-0.
Song, Qijian, Jenkins, Jerry, Jia, Gaofeng, Hyten, David L., Pantalone, Vince, Jackson, Scott A., Schmutz, Jeremy, & Cregan, Perry B. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. United States. https://doi.org/10.1186/s12864-015-2344-0
Song, Qijian, Jenkins, Jerry, Jia, Gaofeng, Hyten, David L., Pantalone, Vince, Jackson, Scott A., Schmutz, Jeremy, and Cregan, Perry B. Wed .
"Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01". United States. https://doi.org/10.1186/s12864-015-2344-0. https://www.osti.gov/servlets/purl/1615261.
@article{osti_1615261,
title = {Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01},
author = {Song, Qijian and Jenkins, Jerry and Jia, Gaofeng and Hyten, David L. and Pantalone, Vince and Jackson, Scott A. and Schmutz, Jeremy and Cregan, Perry B.},
abstractNote = {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.},
doi = {10.1186/s12864-015-2344-0},
journal = {BMC Genomics},
number = 1,
volume = 17,
place = {United States},
year = {Wed Jan 06 00:00:00 EST 2016},
month = {Wed Jan 06 00:00:00 EST 2016}
}
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Figures / Tables:
Table 1: Number of SNPs mapped to each linkage group, linkage group length based on the Williams 82 × PI479752 (WP) and the Essex × Williams 82 (EW) populations and the number of SNPs common to the two populations and SNPs unique to one population
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- Chang, Fangguo; Guo, Chengyu; Sun, Fengluan
- Frontiers in Plant Science, Vol. 9
Application of a high-resolution genetic map for chromosome-scale genome assembly and fine QTLs mapping of seed size and weight traits in castor bean
journal, August 2019
- Yu, Anmin; Li, Fei; Xu, Wei
- Scientific Reports, Vol. 9, Issue 1
Construction and comparison of three reference‐quality genome assemblies for soybean
journal, October 2019
- Valliyodan, Babu; Cannon, Steven B.; Bayer, Philipp E.
- The Plant Journal, Vol. 100, Issue 5
Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm
journal, January 2018
- Bai, Bin; Wang, Le; Zhang, Ying Jun
- Scientific Reports, Vol. 8, Issue 1
High-Throughput Screening and Characterization of a High-Density Soybean Mutant Library Elucidate the Biosynthesis Pathway of Triterpenoid Saponins
journal, February 2019
- Krishnamurthy, Panneerselvam; Fujisawa, Yukiko; Takahashi, Yuya
- Plant and Cell Physiology, Vol. 60, Issue 5
Genetic Architecture of Soybean Yield and Agronomic Traits
journal, August 2018
- Diers, Brian W.; Specht, Jim; Rainey, Katy Martin
- G3: Genes|Genomes|Genetics, Vol. 8, Issue 10
Phenotypic Variation and Genetic Architecture for Photosynthesis and Water Use Efficiency in Soybean (Glycine max L. Merr)
journal, May 2019
- Lopez, Miguel Angel; Xavier, Alencar; Rainey, Katy Martin
- Frontiers in Plant Science, Vol. 10
Genome-wide genetic diversity is maintained through decades of soybean breeding in Canada
journal, August 2019
- Bruce, Robert W.; Torkamaneh, Davoud; Grainger, Christopher
- Theoretical and Applied Genetics, Vol. 132, Issue 11
Application of a high-resolution genetic map for chromosome-scale genome assembly and fine QTLs mapping of seed size and weight traits in castor bean
journal, August 2019
- Yu, Anmin; Li, Fei; Xu, Wei
- Scientific Reports, Vol. 9, Issue 1
Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm
journal, January 2018
- Bai, Bin; Wang, Le; Zhang, Ying Jun
- Scientific Reports, Vol. 8, Issue 1
Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses
journal, July 2017
- Yan, Long; Hofmann, Nicolle; Li, Shuxian
- BMC Genomics, Vol. 18, Issue 1
Genetic Mapping and Molecular Characterization of a Broad-spectrum Phytophthora sojae Resistance Gene in Chinese Soybean
journal, April 2019
- Zhong, Chao; Li, Yinping; Sun, Suli
- International Journal of Molecular Sciences, Vol. 20, Issue 8
Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene, RpsHC18, in soybean
journal, November 2017
- Zhong, Chao; Sun, Suli; Li, Yinping
- Theoretical and Applied Genetics, Vol. 131, Issue 3
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