Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean
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{"title"=>"Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean", "type"=>"journal", "authors"=>[{"first_name"=>"Qijian", "last_name"=>"Song", "scopus_author_id"=>"7202973814"}, {"first_name"=>"David L.", "last_name"=>"Hyten", "scopus_author_id"=>"55889370800"}, {"first_name"=>"Gaofeng", "last_name"=>"Jia", "scopus_author_id"=>"36727515000"}, {"first_name"=>"Charles V.", "last_name"=>"Quigley", "scopus_author_id"=>"7005337254"}, {"first_name"=>"Edward W.", "last_name"=>"Fickus", "scopus_author_id"=>"6507250866"}, {"first_name"=>"Randall L.", "last_name"=>"Nelson", "scopus_author_id"=>"7404560967"}, {"first_name"=>"Perry B.", "last_name"=>"Cregan", "scopus_author_id"=>"7004960538"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"368187618", "issn"=>"19326203", "pmid"=>"23372807", "sgr"=>"84872832925", "scopus"=>"2-s2.0-84872832925", "isbn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0054985"}, "id"=>"c4dac844-dd6f-3bf5-aaf2-aadc471f26eb", "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.", "link"=>"http://www.mendeley.com/research/development-evaluation-soysnp50k-highdensity-genotyping-array-soybean", "reader_count"=>129, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>11, "Researcher"=>22, "Student > Ph. D. Student"=>31, "Student > Postgraduate"=>10, "Student > Master"=>24, "Other"=>6, "Student > Bachelor"=>7, "Lecturer"=>1, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>11, "Researcher"=>22, "Student > Ph. D. Student"=>31, "Student > Postgraduate"=>10, "Student > Master"=>24, "Other"=>6, "Student > Bachelor"=>7, "Lecturer"=>1, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Biochemistry, Genetics and Molecular Biology"=>11, "Mathematics"=>1, "Agricultural and Biological Sciences"=>104, "Medicine and Dentistry"=>1, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Computer Science"=>3, "Decision Sciences"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Decision Sciences"=>{"Decision Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>104}, "Computer Science"=>{"Computer Science"=>3}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>5}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>2, "Brazil"=>6, "Germany"=>2}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/500398"], "description"=>"<p>Distribution of genetic distance based upon the proportion of polymorphic SNPs between pairs of elite cultivar, landrace and wild soybean genotypes.</p>", "links"=>[], "tags"=>["polymorphic", "snps", "pairs", "landrace", "soybean"], "article_id"=>170910, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054985.t006", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_genetic_distance_based_upon_the_proportion_of_polymorphic_SNPs_between_pairs_of_elite_cultivar_landrace_and_wild_soybean_genotypes_/170910", "title"=>"Distribution of genetic distance based upon the proportion of polymorphic SNPs between pairs of elite cultivar, landrace and wild soybean genotypes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:15:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/478851", "https://ndownloader.figshare.com/files/478872", "https://ndownloader.figshare.com/files/478873"], "description"=>"<div><p>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 (<em>Glycine max</em> L. Merr.). A total of 498,921,777 reads 35–45<b> </b>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 (<em>G. soja</em> 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.</p> </div>", "links"=>[], "tags"=>["high-density", "genotyping", "soybean"], "article_id"=>154395, "categories"=>["Biotechnology", "Genetics", "Cell Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0054985.s001", "https://dx.doi.org/10.1371/journal.pone.0054985.s002", "https://dx.doi.org/10.1371/journal.pone.0054985.s003"], "stats"=>{"downloads"=>8, "page_views"=>40, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Development_and_Evaluation_of_SoySNP50K_a_High_Density_Genotyping_Array_for_Soybean__/154395", "title"=>"Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-25 01:13:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/500438"], "description"=>"<p>Distribution of SNP minor allele frequency in elite cultivar, landrace and wild soybean populations.</p>", "links"=>[], "tags"=>["snp", "allele", "landrace", "soybean"], "article_id"=>170953, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054985.t005", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_SNP_minor_allele_frequency_in_elite_cultivar_landrace_and_wild_soybean_populations_/170953", "title"=>"Distribution of SNP minor allele frequency in elite cultivar, landrace and wild soybean populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:15:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/500242"], "description"=>"<p>(A) Significant F<sub>st</sub> values on Gm14 between SSR markers Sat_355 and Satt474 may contain loci associated with soybean domestication (B) Significant F<sub>st</sub> values between SSR markers Satt396 and Sat_140 may contain loci that were under selection in N. American soybean breeding programs.</p>", "links"=>[], "tags"=>["landraces", "cultivars", "chromosome", "gm14"], "article_id"=>170758, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054985.g002", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_F_st_values_of_G_soja_vs_landraces_and_elite_cultivars_vs_landraces_along_chromosome_Gm14_and_Gm04_/170758", "title"=>"F<sub>st</sub> values of <i>G. soja</i> vs. landraces and elite cultivars vs. landraces along chromosome Gm14 and Gm04.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-25 00:12:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/500118"], "description"=>"<p>(A) Selected SNPs (50,701) in euchromatic regions of SoySNP50K and the pre-selected SNPs (73,084) in euchromatic regions. (B) Selected SNPs (10,000) in heterochromatic regions and pre-selected SNPs (72,272) in heterochromatic regions.</p>", "links"=>[], "tags"=>["distances", "adjacent", "pre-selected", "snps", "euchromatic", "heterochromatic"], "article_id"=>170627, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054985.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_distances_between_adjacent_pre_selected_and_selected_SNPs_in_euchromatic_and_heterochromatic_regions_/170627", "title"=>"Distribution of distances between adjacent pre-selected and selected SNPs in euchromatic and heterochromatic regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-25 00:10:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/500516"], "description"=>"<p>Number and density of selected SNPs and the 146,161 SNPs in euchromatic and heterochromatic regions of each soybean chromosome.</p>", "links"=>[], "tags"=>["snps", "euchromatic", "heterochromatic", "regions", "soybean"], "article_id"=>171023, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054985.t003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_and_density_of_selected_SNPs_and_the_146_161_SNPs_in_euchromatic_and_heterochromatic_regions_of_each_soybean_chromosome_/171023", "title"=>"Number and density of selected SNPs and the 146,161 SNPs in euchromatic and heterochromatic regions of each soybean chromosome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:17:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/500475"], "description"=>"<p>Association of SNP selection index score, Illumina Infinium design score and priority group with the rate of SNPs with successful allele calls.</p>", "links"=>[], "tags"=>["snp", "illumina", "infinium", "snps", "allele"], "article_id"=>170992, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054985.t004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Association_of_SNP_selection_index_score_Illumina_Infinium_design_score_and_priority_group_with_the_rate_of_SNPs_with_successful_allele_calls_/170992", "title"=>"Association of SNP selection index score, Illumina Infinium design score and priority group with the rate of SNPs with successful allele calls.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:16:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/500356"], "description"=>"<p>Number of 100 kb regions across the 20 soybean chromosomes with Fst ≥0.6 in comparisons of <i>G. soja</i> vs. landraces and landraces vs. elite cultivars.</p>", "links"=>[], "tags"=>["100", "kb", "regions", "20", "soybean", "chromosomes", "fst", "comparisons", "landraces"], "article_id"=>170862, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054985.t007", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_100_kb_regions_across_the_20_soybean_chromosomes_with_Fst_0_6_in_comparisons_of_G_soja_vs_landraces_and_landraces_vs_elite_cultivars_/170862", "title"=>"Number of 100 kb regions across the 20 soybean chromosomes with Fst ≥0.6 in comparisons of <i>G. soja</i> vs. landraces and landraces vs. elite cultivars.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:14:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/500546"], "description"=>"<p>Validation rate of SNPs based on the Sanger sequence analysis of a random set of 767 SNP loci.</p>", "links"=>[], "tags"=>["snps", "sanger", "767", "snp"], "article_id"=>171064, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054985.t002", "stats"=>{"downloads"=>5, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_rate_of_SNPs_based_on_the_Sanger_sequence_analysis_of_a_random_set_of_767_SNP_loci_/171064", "title"=>"Validation rate of SNPs based on the Sanger sequence analysis of a random set of 767 SNP loci.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:17:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/500591"], "description"=>"<p>Illumina GAII DNA sequence analysis of eight genotypes and mixed DNA.</p>", "links"=>[], "tags"=>["gaii", "dna", "genotypes"], "article_id"=>171105, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Qijian Song", "David L. Hyten", "Gaofeng Jia", "Charles V. Quigley", "Edward W. Fickus", "Randall L. Nelson", "Perry B. Cregan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054985.t001", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illumina_GAII_DNA_sequence_analysis_of_eight_genotypes_and_mixed_DNA_/171105", "title"=>"Illumina GAII DNA sequence analysis of eight genotypes and mixed DNA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-25 00:18:25"}

PMC Usage Stats | Further Information

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Relative Metric

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