ArticlePloS one2013
Development and evaluation of SoySNP50K, a high-density genotyping array for soybean.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 312 papers.
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312 citing papers in PubMed, 612 citations in OpenAlex.
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- Association mapping for canopy temperature under irrigated and rainfed conditions at 12 environments identified both known and novel genetic loci.The plant genome · 2026Article
- Characterization of disomic alien addition lines from an intersubgeneric cross between Glycine max and G. tomentella and phenotypic variation within those lines and their progenies.Plant molecular biology · 2026Article
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- Korean Soybean Nested Association Mapping (K-SoyNAM) population: genetic linkage map, genetic mapping, and genotype imputation.BMC genomics · 2026Article
- Quantitative trait loci analysis identifying novel genomic regions for off-target dicamba tolerance in soybean [Glycine max (L.) Merr.].BMC plant biology · 2026Article
- Genome-wide signatures of selection and genetic diversity reveal the impact of modern breeding on Brazilian soybean.Molecular breeding : new strategies in plant improvement · 2026Article
- Dissection of local haplotype diversity at soybean rust loci reveals resistance-associated and context-dependent variation patterns in diverse germplasm.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Integrative Transcriptomic Analysis and Co-Expression Network Characterization of Soybean Developmental Tissues.Plants (Basel, Switzerland) · 2026Article
- Multilocus genome-wide association study reveals genomic regions associated with resistance to red leaf blotch in soybean.BMC plant biology · 2026Article
- Development of user-selectable diverse sets of cultivated and wild soybean germplasm for genetic and breeding applications.The plant genome · 2026Article
- Classification-based genomic prediction for early identification of high-yielding and stable soybean genotypes.Frontiers in plant science · 2026Article
- Evaluation ofJournal of nematology · 2026Article
- Functional divergence of two soybean cytosolic serine hydroxymethyltransferases in development and defense against soybean cyst nematode.Frontiers in plant science · 2026Article
- Identification of candidate loci regulating seed-associated traits in soybean using genome-wide association study and image-based high-throughput phenotyping.Frontiers in plant science · 2026Article
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- Genetic mapping of novel QTL for seed protein stability in food-grade soybean (Glycine max).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Identifying canopy wilting QTLs and evaluating remote sensing approaches for selecting drought-tolerant soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
252 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The objective of this research was to identify single nucleotide polymorphisms (SNPs) and to develop an Illumina Infinium BeadChip that contained over 50,000 SNPs from soybean (Glycine max L. Merr.). A total of 498,921,777 reads 35-45 bp in length were obtained from DNA sequence analysis of reduced representation libraries from several soybean accessions which included six cultivated and two wild soybean (G. soja Sieb. et Zucc.) genotypes. These reads were mapped to the soybean whole genome sequence and 209,903 SNPs were identified. After applying several filters, a total of 146,161 of the 209,903 SNPs were determined to be ideal candidates for Illumina Infinium II BeadChip design. To equalize the distance between selected SNPs, increase assay success rate, and minimize the number of SNPs with low minor allele frequency, an iteration algorithm based on a selection index was developed and used to select 60,800 SNPs for Infinium BeadChip design. Of the 60,800 SNPs, 50,701 were targeted to euchromatic regions and 10,000 to heterochromatic regions of the 20 soybean chromosomes. In addition, 99 SNPs were targeted to unanchored sequence scaffolds. Of the 60,800 SNPs, a total of 52,041 passed Illumina's manufacturing phase to produce the SoySNP50K iSelect BeadChip. Validation of the SoySNP50K chip with 96 landrace genotypes, 96 elite cultivars and 96 wild soybean accessions showed that 47,337 SNPs were polymorphic and generated successful SNP allele calls. In addition, 40,841 of the 47,337 SNPs (86%) had minor allele frequencies ≥ 10% among the landraces, elite cultivars and the wild soybean accessions. A total of 620 and 42 candidate regions which may be associated with domestication and recent selection were identified, respectively. The SoySNP50K iSelect SNP beadchip will be a powerful tool for characterizing soybean genetic diversity and linkage disequilibrium, and for constructing high resolution linkage maps to improve the soybean whole genome sequence assembly.
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