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

Journal Article · · BMC Genomics
 [1];  [2];  [1];  [3];  [4];  [5];  [6];  [1]
  1. US Dept. of Agriculture (USDA), Beltsville, MD (United States). Agricultural Research Service (ARS). Soybean Genomics and Improvement Lab.
  2. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  3. Univ. of Nebraska, Lincoln, NE (United States)
  4. Univ. of Tennessee, Knoxville, TN (United States)
  5. Univ. of Georgia, Athens, GA (United States). Center for Applied Genetic Technologies
  6. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
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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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1615261
Journal Information:
BMC Genomics, Vol. 17, Issue 1; ISSN 1471-2164
Publisher:
SpringerCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 85 works
Citation information provided by
Web of Science

References (43)

Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps journal January 2013
Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean ( Glycine max ) Genome and Comparison to an Orthologous Region from Phaseolus vulgaris journal August 2010
The genomic relationship between Glycine max (L.) Merr. and G. soja Sieb. and Zucc. as revealed by pachytene chromosome analysis journal November 1988
Three Sequenced Legume Genomes and Many Crop Species: Rich Opportunities for Translational Genomics journal September 2009
An Integrated Genetic Linkage Map of the Soybean Genome journal September 1999
Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering journal May 2012
Nuclear DNA content of some important plant species journal August 1991
Identification of Quantitative Trait Loci for Sucrose Content in Soybean Seed journal March 2014
Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes journal November 2014
The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean journal February 2007
A new integrated genetic linkage map of the soybean journal February 2004
Genome sequence of the palaeopolyploid soybean journal January 2010
A genetic map of soybean (Glycine max L.) using an intraspecific cross of two cultivars: ‘Minosy’ and ‘Noir 1’ journal September 1993
An Integrated High-density Linkage Map of Soybean with RFLP, SSR, STS, and AFLP Markers Using A Single F2 Population journal January 2007
Characterization of the Soybean Genome Using EST-derived Microsatellite Markers journal January 2007
Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph journal October 2008
A genome-wide association study of seed protein and oil content in soybean journal January 2014
Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps journal April 2008
Phytophthora Root Rot Resistance in Soybean E00003 journal March 2014
Artificial selection for determinate growth habit in soybean journal April 2010
A Fine Physical Map of the Rice Chromosome 4 journal May 2002
Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean journal January 2013
Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1 -Mediated Soybean Resistance to Soybean Cyst Nematode journal April 2014
A High Density Integrated Genetic Linkage Map of Soybean and the Development of a 1536 Universal Soy Linkage Panel for Quantitative Trait Locus Mapping journal May 2010
Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean journal October 2012
Length polymorphisms of simple sequence repeat DNA in soybean. journal December 1992
A Roadmap for Functional Structural Variants in the Soybean Genome journal May 2014
Gene expression patterns are correlated with genomic and genic structure in soybean journal January 2011
Estimating the effects of population size and type on the accuracy of genetic maps journal January 2006
Fingerprinting Soybean Germplasm and Its Utility in Genomic Research journal July 2015
Palaeogenomics of plants: synteny-based modelling of extinct ancestors journal September 2010
Soybean Plastidal Omega-3 Fatty Acid Desaturase Genes GmFAD7 and GmFAD8 : Structure and Expression journal July 2011
The Genetic Architecture of Seed Composition in Soybean Is Refined by Genome-Wide Association Scans Across Multiple Populations journal September 2014
Integration of Simple Sequence Repeat DNA Markers into a Soybean Linkage Map journal September 1995
Synteny mapping between common bean and soybean reveals extensive blocks of shared loci journal January 2010
High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence journal January 2010
Genetics and Cytology of Chromosome Inversions in Soybean Germplasm journal May 2000
Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean journal January 2010
Nuclear DNA content of some important plant species journal November 1991
RFLP mapping in soybean: association between marker loci and variation in quantitative traits. journal November 1990
A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis journal March 2007
A High‐Density Soybean Genetic Map Based on AFLP Markers journal March 1997
Single-Nucleotide Polymorphisms in Soybean journal March 2003

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Fine Mapping and Identification of a Novel Phytophthora Root Rot Resistance Locus RpsZS18 on Chromosome 2 in Soybean journal January 2018
Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes journal June 2016
Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.) journal May 2019
Mapping Quantitative Trait Loci for Tolerance to Pythium irregulare in Soybean ( Glycine max L.) journal August 2018
Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance inGlycine soja, the Wild Progenitor of Cultivated Soybeans journal April 2016
Identification of Major Quantitative Trait Loci for Seed Oil Content in Soybeans by Combining Linkage and Genome-Wide Association Mapping journal July 2017
Identification and characterization of a fast-neutron-induced mutant with elevated seed protein content in soybean journal July 2019
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A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance journal March 2017
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Genome-Wide Association Studies for Dynamic Plant Height and Number of Nodes on the Main Stem in Summer Sowing Soybeans journal August 2018
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Functional analysis and development of a CRISPR/Cas9 allelic series for a CPR5 ortholog necessary for proper growth of soybean trichomes journal October 2019
Genome-Wide Association Study and QTL Meta-Analysis Identified Novel Genomic Loci Controlling Potassium Use Efficiency and Agronomic Traits in Bread Wheat journal February 2020
Exploring the performance of genomic prediction models for soybean yield using different validation approaches journal May 2019
Genetic Architecture of Soybean Yield and Agronomic Traits journal August 2018
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
Construction and comparison of three reference‐quality genome assemblies for soybean journal October 2019
Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm journal January 2018
High-Throughput Screening and Characterization of a High-Density Soybean Mutant Library Elucidate the Biosynthesis Pathway of Triterpenoid Saponins journal February 2019
Phenotypic Variation and Genetic Architecture for Photosynthesis and Water Use Efficiency in Soybean (Glycine max L. Merr) journal May 2019
Genome-wide genetic diversity is maintained through decades of soybean breeding in Canada journal August 2019
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
Genetic Mapping and Molecular Characterization of a Broad-spectrum Phytophthora sojae Resistance Gene in Chinese Soybean journal April 2019
Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene, RpsHC18, in soybean journal November 2017

Linked Research (10)

Figures / Tables (4)

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Soybean
Wm82.a2.v1 assembly
BARCSOYSSR_1.0 database
SoySNP50K BeadChip
euchromatic and heterochromatic regions
linkage map