Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers
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{"title"=>"Genetic structure, linkage disequilibrium and signature of selection in sorghum: Lessons from physically anchored DArT markers", "type"=>"journal", "authors"=>[{"first_name"=>"Sophie", "last_name"=>"Bouchet", "scopus_author_id"=>"26532249800"}, {"first_name"=>"David", "last_name"=>"Pot", "scopus_author_id"=>"6603951087"}, {"first_name"=>"Monique", "last_name"=>"Deu", "scopus_author_id"=>"8416707700"}, {"first_name"=>"Jean François", "last_name"=>"Rami", "scopus_author_id"=>"7003907916"}, {"first_name"=>"Claire", "last_name"=>"Billot", "scopus_author_id"=>"6601950806"}, {"first_name"=>"Xavier", "last_name"=>"Perrier", "scopus_author_id"=>"22951885400"}, {"first_name"=>"Ronan", "last_name"=>"Rivallan", "scopus_author_id"=>"24336096100"}, {"first_name"=>"Laëtitia", "last_name"=>"Gardes", "scopus_author_id"=>"26535811700"}, {"first_name"=>"Ling", "last_name"=>"Xia", "scopus_author_id"=>"7201956029"}, {"first_name"=>"Peter", "last_name"=>"Wenzl", "scopus_author_id"=>"6603625826"}, {"first_name"=>"Andrzej", "last_name"=>"Kilian", "scopus_author_id"=>"7006511933"}, {"first_name"=>"Jean Christophe", "last_name"=>"Glaszmann", "scopus_author_id"=>"35615567100"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"364420557", "sgr"=>"84858126570", "issn"=>"19326203", "pmid"=>"22428056", "scopus"=>"2-s2.0-84858126570", "doi"=>"10.1371/journal.pone.0033470", "isbn"=>"1932-6203"}, "id"=>"5dd00e29-3656-3800-8951-7dda99c1e385", "abstract"=>"Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r(2) decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.", "link"=>"http://www.mendeley.com/research/genetic-structure-linkage-disequilibrium-signature-selection-sorghum-lessons-physically-anchored-dar", "reader_count"=>65, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>1, "Researcher"=>15, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>4, "Student > Master"=>7, "Other"=>3, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>1, "Researcher"=>15, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>4, "Student > Master"=>7, "Other"=>3, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>51, "Neuroscience"=>2, "Social Sciences"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>2}, "Social Sciences"=>{"Social Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>51}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>6}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>2, "Brazil"=>1, "Mexico"=>1, "South Africa"=>1, "Malaysia"=>1, "Spain"=>1, "India"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/668831"], "description"=>"<p>Total, intra- and intergroup accession dissimilarity correlations obtained with an increasing number of the three different marker systems (DArT, RFLP, SSR) were computed according to the data resolution statistic developed by Van Hintum <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033470#pone.0033470-vanHintum1\" target=\"_blank\">[31]</a>. An enlargement of the graph for marker numbers comprised between 0 and 150 is provided at the bottom right-hand side of the figure. For the whole CS, the description of diversity can only be considered saturated for DArT markers. An analysis of the dissimilarity correlations at the intra- and intergroup levels indicated that SSR markers were the least efficient in describing the intergroup structure.</p>", "links"=>[], "tags"=>["systems", "sorghum"], "article_id"=>339309, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ability_of_the_marker_systems_to_describe_the_genetic_structure_of_the_sorghum_Core_Sample_/339309", "title"=>"Ability of the marker systems to describe the genetic structure of the sorghum Core Sample.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-13 02:35:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/668931"], "description"=>"<p>Mean r<sup>2</sup> and the proportion of significant pairwise r<sup>2</sup> (i.e greater than P95) were computed for the CS and for subsets of accessions ranging from 25 to 150. Accessions were sampled using two strategies. Firstly, random samples of 25, 50, 75, 100, 125 and 150 genotypes were extracted to calculate LD statistics. For each sample size, 10 random samples were analysed in order to estimate standard errors of the estimations (A). Secondly, a procedure designed to define subsets of genotypes minimizing their redundancy and limiting the loss of diversity was used (MLST reported in (B)). A comparison of these two sampling approaches for three sample sizes is provided in (C) and indicates that, with both strategies, mean r<sup>2</sup> was overestimated for all distance classes in small samples (n = 25). The proportion of significant pairwise r<sup>2</sup> was always higher with the MLST, compared to the random approach, especially for small distances and small sample sizes, highlighting the efficiency of this algorithm in providing a more accurate local LD estimation through the reduction of background LD. After correcting for background structure, mean r<sup>2</sup> decreased with distance from 0.2 (for the 0–10 kb distance class) to 0.02 and stabilized after 100 kb (B). Contrary to random sampling, an increase in mean r<sup>2</sup> (B) was observed with the MLST approach when sample sizes greater than 100 accessions were considered, suggesting that redundancy, and thus background structure, was introduced after this sample size. These results indicate that, for the CS, a sample size of 100 accessions carefully selected to avoid redundancy and maximize diversity would be an optimized sample size for LD estimation.</p>", "links"=>[], "tags"=>["linkage", "disequilibrium", "sizes"], "article_id"=>339412, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolution_of_linkage_disequilibrium_for_different_sample_sizes_and_distances_/339412", "title"=>"Evolution of linkage disequilibrium for different sample sizes and distances.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-13 02:36:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/669134"], "description"=>"<p>The data for the photoperiod sensitivity index (Kp, which corresponds to the decrease in the duration of the vegetative phase between two sowing dates) presented in (A) were obtained from Clerget <i>et al. </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033470#pone.0033470-Clerget1\" target=\"_blank\">[70]</a> who used the same collection of accessions. Kp varies from 0 for photoperiod-insensitive varieties, which do not change the duration of their vegetative phase with the sowing date, to 1.0 for the most strongly photoperiod-sensitive varieties which maintain their calendar date of flowering constant by reducing the duration of their vegetative phase. A total of 136 accessions with a membership coefficient greater than the 0.6 threshold were considered. These accessions corresponded to 40 accessions from group A, 27 from group B, 21 from group C, 11 from group D, 17 from group E and 22 from group F. An Anova analysis indicated highly significant differences between the genetic groups (p value<2.2e-16) with genetic group F harbouring a low photoperiod sensitivity index. An analysis of the variability in the allelic frequency of the DArT marker SbMITE-188058 (FI847787) located at 11.7 kb from a homologue of the FAR-RED IMPAIRED RESPONSE 1 protein isolated in <i>Arabidopis thaliana</i> (B) highlighted the specificity of group F, suggesting a potential role of this gene in the genetic control of variability in photoperiod sensitivity.</p>", "links"=>[], "tags"=>["variability", "photoperiod", "allelic", "dart"], "article_id"=>339607, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.g005", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concomitant_variability_of_the_photoperiod_sensitivity_index_with_the_allelic_frequency_of_the_DArT_SbMITE_188058_/339607", "title"=>"Concomitant variability of the photoperiod sensitivity index with the allelic frequency of the DArT SbMITE-188058.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-13 02:40:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/669252"], "description"=>"a<p>Decay of LD with physical distance were fitted according to Ohta and Kimura (1969) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033470#pone.0033470-Ohta1\" target=\"_blank\">[37]</a> model: E (r<sup>2</sup><sub>ij</sub>) = 1/(1+4Neρd<sub>ij</sub>ρ). Where, r<sup>2</sup><sub>ij</sub> stands for the LD value between markers i and j, Ne for the effective population size, ρ for the per base recombination rate and d<sub>ij</sub> for the distance in base pairs between markers i and j. The analysis was performed with the nls function in R. The composite parameter a = Neρ was estimated for the whole CS and the different genetic groups.</p>b<p>Achieved convergence tolerance obtained with the nls function in R.</p>", "links"=>[], "tags"=>["markers"], "article_id"=>339732, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.t004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_markers_required_for_association_mapping_studies_/339732", "title"=>"Number of markers required for association mapping studies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-13 02:42:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/342185", "https://ndownloader.figshare.com/files/342225", "https://ndownloader.figshare.com/files/342249", "https://ndownloader.figshare.com/files/342287", "https://ndownloader.figshare.com/files/342312"], "description"=>"<div><p>Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r<sup>2</sup> decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.</p> </div>", "links"=>[], "tags"=>["linkage", "disequilibrium", "lessons", "anchored", "dart", "markers"], "article_id"=>127639, "categories"=>["Biotechnology", "Genetics", "Cell Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033470.s001", "https://dx.doi.org/10.1371/journal.pone.0033470.s002", "https://dx.doi.org/10.1371/journal.pone.0033470.s003", "https://dx.doi.org/10.1371/journal.pone.0033470.s004", "https://dx.doi.org/10.1371/journal.pone.0033470.s005"], "stats"=>{"downloads"=>4, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genetic_Structure_Linkage_Disequilibrium_and_Signature_of_Selection_in_Sorghum_Lessons_from_Physically_Anchored_DArT_Markers/127639", "title"=>"Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-03-13 02:07:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/668720"], "description"=>"<p>(A) Genome composition of accessions for different levels of structure. Each sample is represented in K dimensions, with K being the number of hypothetical genetic groups that compose the collection (K ranging from 2 to 10). Three different datasets were tested: 713 DArTs, 60 RFLPs, and 40 SSRs. Each accession on the X-axis is represented by K colours (each corresponding to a genetic group) ordered according to a decreasing genome fraction on the Y-axis. For each dataset, 171 accessions were ordered according to DArT assignments, with a decreasing proportion of genome assigned to the main groups according to STRUCTURE at K = 10. (B) Neighbour-Joining tree of the CS with colour projection of the six groups obtained with the model-based method at the 0.6 membership threshold at K = 6. The Neighbour-Joining tree is based on the genetic similarities between accessions calculated as the proportion of shared alleles of the DArT markers (Sokal and Michener modality index). The colours correspond to the genetic groups obtained at K = 6 in (A). Accessions assigned at a proportion <0.6 are coloured in grey. Group A in pink includes D and B from India, C and CB from China. Group B in blue includes C and D from Africa. Group C in red includes G from Western Africa. Group D in spring green includes Gm from Western Africa. Group E in orange includes G from Southern Africa and Asia. Group F in green includes K and KC from Southern Africa. Clusters were identified by Deu <i>et al.</i> (2006).</p>", "links"=>[], "tags"=>["groups", "model-based", "revealed", "systems", "distance-based"], "article_id"=>339188, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequential_identification_of_the_genetic_groups_through_model_based_analysis_as_revealed_by_the_different_marker_systems_and_comparison_of_the_most_relevant_model_based_structure_K_8202_8202_6_with_distance_based_method_analysis_/339188", "title"=>"Sequential identification of the genetic groups through model-based analysis as revealed by the different marker systems and comparison of the most relevant model-based structure (K = 6) with distance-based method analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-13 02:33:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/669378"], "description"=>"<p>Genetic differentiations were calculated among the genetic groups considering only those accessions assigned with a membership > = 0.6. For DArT, RFLP and SSR markers, F<i>st</i> values (Weir and Cockerham, 1984) were computed with GENETIX.</p>", "links"=>[], "tags"=>["differentiation", "groups", "systems"], "article_id"=>339856, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_differentiation_Fst_between_the_six_genetic_groups_as_obtained_with_three_different_marker_systems_DArT_RFLP_SSR_/339856", "title"=>"Pairwise differentiation (Fst) between the six genetic groups as obtained with three different marker systems (DArT, RFLP, SSR).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-13 02:44:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/668513"], "description"=>"<p>(A) Average log-likelihood and standard errors obtained with STRUCTURE software. For the three marker systems, the log-likelihood reached a plateau around K = 6. (B) The ΔK parameter <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033470#pone.0033470-Evanno1\" target=\"_blank\">[69]</a> enabled the identification of high values at K = 2 (DArTs, RFLPs) and K = 4 (DArTs, SSRs), and lower peaks at K = 7 (DArTs, SSRs) and K = 6 (RFLPs, although this peak was not visible with the Y axis-scale used). (C) Proportion of unassigned accessions at the 0.6 membership threshold for each marker system. This proportion varied with the marker systems and the number of groups, K. To assess the stability of accession assignments to the different genetic groups between runs for the different marker systems, the average dissimilarity indices between runs for all accessions were computed and are reported in (D) according to calculations presented in the Material and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033470#s2\" target=\"_blank\">Methods</a> section. This analysis revealed that SSR markers provided the least stable assignment across runs for the same K level. Lastly, assignment stability across marker systems is reported in (E) through the calculation of the average dissimilarity index for all accessions for each pair of marker systems (see text for details). This analysis indicated that the assignments obtained with the SSRs were the most divergent from the other marker systems (DArTs and RFLPs).</p>", "links"=>[], "tags"=>["sorghum", "cs", "rflps"], "article_id"=>338986, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_sorghum_CS_using_DArTs_RFLPs_and_SSRs_/338986", "title"=>"Analysis of sorghum CS using DArTs, RFLPs and SSRs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-13 02:29:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/669293"], "description"=>"a<p>group number as defined in the text. UN corresponds to unassigned accessions. CS: Whole Core Sample.</p>b<p>number of accessions assigned to the different genetic groups. Assignment was based on full congruence between the three marker systems (cf <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033470#pone.0033470.s004\" target=\"_blank\">Table S1</a>, column “Group Consensus Schemes”).</p>c<p>races present in the group defined according to grain and spikelet morphology (Harlan and De Wet, 1972). B: bicolor, C: caudatum, D: durra, G: guinea, K: kafir, Gm: guinea margaritiferum sub-race defined according to Snowden's classification.</p>d<p>Af: Africa, As: Asia, ME: Middle East, SAf: Southern Africa, WAf: Western Africa.</p>e<p>allelic richness and private allelic richness computed with HP-Rare are normalized values.</p>f<p>expected heterozygosity estimated with PowerMarker. Standard deviations estimated with 1000 bootstraps are shown in brackets.</p>", "links"=>[], "tags"=>["parameters", "groups"], "article_id"=>339767, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_diversity_parameters_within_the_Core_Sample_171_accessions_and_within_the_6_genetic_groups_identified_/339767", "title"=>"Genetic diversity parameters within the Core Sample (171 accessions) and within the 6 genetic groups identified.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-13 02:42:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/669335"], "description"=>"a<p>number of pairs of markers.</p>b<p>proportion of r<sup>2</sup> values greater than the P95 threshold (this threshold corresponded to r<sup>2</sup>>0.11 for the whole Core Sample).</p>", "links"=>[], "tags"=>["linkage", "disequilibrium"], "article_id"=>339813, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.t003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolution_of_linkage_disequilibrium_with_physical_distance_in_the_Core_Sample_/339813", "title"=>"Evolution of linkage disequilibrium with physical distance in the Core Sample.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-13 02:43:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/669205"], "description"=>"a<p>Type of selection detected, b stands for balancing selection whereas d stands for diversifying selection.</p>b<p>Method used to identify the considered locus, b stands for BAYESCAN (log10(Bayesfactor)>1, l for LOSITAN (CI>0.99) and bl corresponds to loci detected with both methods.</p>c<p>The DArT marker name corresponding to the genebank accession provided can be found in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033470#pone.0033470.s005\" target=\"_blank\">Table S2</a> (Marker_Name column).</p>d<p>The F<i>st</i> value obtained with BAYESCAN, the log 10 (Bayes factor) is provided in brackets.</p>e<p>The F<i>st</i> value obtained with LOSITAN, the Pvalue corresponding to P(Simul Fstf</p><p>Distance between DArT marker and the closest gene in kb.</p>g<p>Protein presenting the highest similarity with the gene located in the vicinity of the DArT marker as detected by a BlastP against the Swissprot database, the Evalue and Similarity percentage at the amino acid level are provided in the following columns.</p>h<p>Biological process in which the gene is involved: D: Disease resistance, S: Abiotic stress resistance, F: Flowering regulation, CW: Cell wall establishment, M: plant morphology, R: reproduction, DR: DNA repair or Regulation of transcription or Regulation of translation, o: others.</p>", "links"=>[], "tags"=>["markers", "presenting"], "article_id"=>339679, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Sophie Bouchet", "David Pot", "Monique Deu", "Jean-François Rami", "Claire Billot", "Xavier Perrier", "Ronan Rivallan", "Laëtitia Gardes", "Ling Xia", "Peter Wenzl", "Andrzej Kilian", "Jean-Christophe Glaszmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033470.t005", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DArT_markers_presenting_evidence_of_selection_/339679", "title"=>"DArT markers presenting evidence of selection.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-13 02:41:19"}

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Relative Metric

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