Inclusive Composite Interval Mapping of QTL by Environment Interactions in Biparental Populations
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{"title"=>"Inclusive composite interval mapping of QTL by environment interactions in biparental populations", "type"=>"journal", "authors"=>[{"first_name"=>"Shanshan", "last_name"=>"Li", "scopus_author_id"=>"56706622400"}, {"first_name"=>"Jiankang", "last_name"=>"Wang", "scopus_author_id"=>"56503622400"}, {"first_name"=>"Luyan", "last_name"=>"Zhang", "scopus_author_id"=>"37109126100"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"605951789", "doi"=>"10.1371/journal.pone.0132414", "sgr"=>"84941363447", "isbn"=>"1932-6203", "pmid"=>"26161656", "scopus"=>"2-s2.0-84941363447"}, "id"=>"3b7dbd84-243f-3973-b2df-5caa81534bc5", "abstract"=>"Identification of environment-specific QTL and stable QTL having consistent genetic effects across a wide range of environments is of great importance in plant breeding. Inclusive Composite Interval Mapping (ICIM) has been proposed for additive, dominant and epistatic QTL mapping in biparental populations for single environment. In this study, ICIM was extended to QTL by environment interaction (QEI) mapping for multi-environmental trials, where the QTL average effect and QEI effects could be properly estimated. Stepwise regression was firstly applied in each environment to identify the most significant marker variables which were then used to adjust the phenotypic values. One-dimensional scanning was then conducted on the adjusted phenotypic values across the environments in order to detect QTL with either average effect or QEI effects, or both average effect and QEI effects. In this way, the genetic background could be well controlled while the conventional interval mapping was applied. An empirical method to determine the threshold of logarithm of odds was developed, and the efficiency of the ICIM QEI mapping was demonstrated in simulated populations under different genetic models. One actual recombinant inbred line population was used to compare mapping results between QEI mapping and single-environment analysis.", "link"=>"http://www.mendeley.com/research/inclusive-composite-interval-mapping-qtl-environment-interactions-biparental-populations", "reader_count"=>35, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>11, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>11, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>3, "Mathematics"=>1, "Agricultural and Biological Sciences"=>24, "Medicine and Dentistry"=>1, "Social Sciences"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>4}}, "reader_count_by_country"=>{"United States"=>2, "Mexico"=>2, "France"=>2, "Germany"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2170071"], "description"=>"<p>(A) <i>H</i><sup>2</sup> = 0.1. (B) <i>H</i><sup>2</sup> = 0.5. (C) <i>H</i><sup>2</sup> = 0.8. LOD scores on other chromosomes were not shown because no QTL was defined there. LOD score was close to zero on chromosomes 2 to 6.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478912, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_LOD_profiles_on_chromosome_1_across_1000_simulation_runs_for_the_linked_QTL_model_/1478912", "title"=>"Average LOD profiles on chromosome 1 across 1000 simulation runs for the linked QTL model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170074"], "description"=>"<p>Power (A) of each QTL was calculated as the proportion of runs where the QTL was identified in a 10 cM support interval. FDR (B), false discovery rate, was calculated as the proportion of false positive QTL to total QTL detected for each model and each heritability level.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478914, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Power_A_and_FDR_B_for_linked_QTL_model_/1478914", "title"=>"Power (A) and FDR (B) for linked QTL model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170075"], "description"=>"<p>(A) <i>H</i><sup>2</sup> = 0.1. (B) <i>H</i><sup>2</sup> = 0.5. (C) <i>H</i><sup>2</sup> = 0.8. Power was calculated as the proportion of runs where QTL on the interval was detected. There were 15 marker intervals defined by the 16 markers evenly distributed on chromosome 1. Power on other chromosomes were close to zero on chromosomes 2 to 6 where no QTL was predefined.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478915, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Power_analysis_by_marker_interval_of_chromosome_1_for_the_linked_QTL_model_/1478915", "title"=>"Power analysis by marker interval of chromosome 1 for the linked QTL model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170077"], "description"=>"<p>The dash line denotes the LOD threshold of 5.67 in QEI mapping.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478917, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.g007", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LOD_profiles_for_MFLW_in_the_maize_population_by_QEI_mapping_A_and_single_environment_analysis_B_/1478917", "title"=>"LOD profiles for MFLW in the maize population by QEI mapping (A) and single-environment analysis (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170078"], "description"=>"<p>A, AE<sub>1</sub> and AE<sub>2</sub> represent average additive effect, QEI effect in E<sub>1</sub> and QEI effect in E<sub>2</sub> respectively. PVE, the percentage of variance explained by individual QTL, was calculated under the assumption that the frequencies of two QTL genotypes <i>QQ</i> and <i>qq</i> are equal to 0.5.</p><p>Predefined chromosomal positions and additive effects of five unlinked QTL.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478918, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.t003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predefined_chromosomal_positions_and_additive_effects_of_five_unlinked_QTL_/1478918", "title"=>"Predefined chromosomal positions and additive effects of five unlinked QTL.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170079"], "description"=>"<p>PVE, the percentage of variance explained by individual QTL, was calculated under the assumption that the frequency of genotype <i>QQ</i> is equal to 0.5.</p><p>Predefined chromosomal positions and additive effects of two linked QTL.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478919, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.t004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predefined_chromosomal_positions_and_additive_effects_of_two_linked_QTL_/1478919", "title"=>"Predefined chromosomal positions and additive effects of two linked QTL.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170081"], "description"=>"<p>A, AE<sub>1</sub> and AE<sub>2</sub> represent average additive effect, additive QEI effect in E<sub>1</sub> and additive QEI effect in E<sub>2</sub>, respectively. Estimated positions and effects were calculated as the average of significant QTL in the support interval. Power of each QTL was calculated as the proportion of runs where the QTL was detected in the 10 cM support interval. FDR, false positive rate, was calculated as the proportion of false QTL to the total number of QTL detected. SE: standard error.</p><p>Estimates of QTL positions and effects, and power analysis in the unlinked model based on 1000 simulation runs.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478921, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.t006", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_QTL_positions_and_effects_and_power_analysis_in_the_unlinked_model_based_on_1000_simulation_runs_/1478921", "title"=>"Estimates of QTL positions and effects, and power analysis in the unlinked model based on 1000 simulation runs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170082"], "description"=>"<p>Positive effect indicates the allele increasing trait value is from parental line CML444. Negative effect indicates the allele increasing trait value is from parental line SC-Malawi. PVE is the percentage of variance explained by individual QTL.</p><p>Estimated effects and positions of QTL detected in the maize RIL population by single-environment analysis.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478922, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.t008", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimated_effects_and_positions_of_QTL_detected_in_the_maize_RIL_population_by_single_environment_analysis_/1478922", "title"=>"Estimated effects and positions of QTL detected in the maize RIL population by single-environment analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170302", "https://ndownloader.figshare.com/files/2170303", "https://ndownloader.figshare.com/files/2170304", "https://ndownloader.figshare.com/files/2170306", "https://ndownloader.figshare.com/files/2170307", "https://ndownloader.figshare.com/files/2170308", "https://ndownloader.figshare.com/files/2170310", "https://ndownloader.figshare.com/files/2170311", "https://ndownloader.figshare.com/files/2170312"], "description"=>"<div><p>Identification of environment-specific QTL and stable QTL having consistent genetic effects across a wide range of environments is of great importance in plant breeding. Inclusive Composite Interval Mapping (ICIM) has been proposed for additive, dominant and epistatic QTL mapping in biparental populations for single environment. In this study, ICIM was extended to QTL by environment interaction (QEI) mapping for multi-environmental trials, where the QTL average effect and QEI effects could be properly estimated. Stepwise regression was firstly applied in each environment to identify the most significant marker variables which were then used to adjust the phenotypic values. One-dimensional scanning was then conducted on the adjusted phenotypic values across the environments in order to detect QTL with either average effect or QEI effects, or both average effect and QEI effects. In this way, the genetic background could be well controlled while the conventional interval mapping was applied. An empirical method to determine the threshold of logarithm of odds was developed, and the efficiency of the ICIM QEI mapping was demonstrated in simulated populations under different genetic models. One actual recombinant inbred line population was used to compare mapping results between QEI mapping and single-environment analysis.</p></div>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1479084, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0132414.s001", "https://dx.doi.org/10.1371/journal.pone.0132414.s002", "https://dx.doi.org/10.1371/journal.pone.0132414.s003", "https://dx.doi.org/10.1371/journal.pone.0132414.s004", "https://dx.doi.org/10.1371/journal.pone.0132414.s005", "https://dx.doi.org/10.1371/journal.pone.0132414.s006", "https://dx.doi.org/10.1371/journal.pone.0132414.s007", "https://dx.doi.org/10.1371/journal.pone.0132414.s008", "https://dx.doi.org/10.1371/journal.pone.0132414.s009"], "stats"=>{"downloads"=>8, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inclusive_Composite_Interval_Mapping_of_QTL_by_Environment_Interactions_in_Biparental_Populations_/1479084", "title"=>"Inclusive Composite Interval Mapping of QTL by Environment Interactions in Biparental Populations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170063"], "description"=>"<p>(A) BC<sub>1</sub> population and <i>α</i><sub><i>g</i></sub> = 0.05. (B) BC<sub>1</sub> population and <i>α</i><sub><i>g</i></sub> = 0.01. (C) F<sub>2</sub> population and <i>α</i><sub><i>g</i></sub> = 0.05. (D) F<sub>2</sub> population and <i>α</i><sub><i>g</i></sub> = 0.01.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478904, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.g001", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LOD_thresholds_of_QEI_mapping_based_on_empirical_formula_and_simulation_method_/1478904", "title"=>"LOD thresholds of QEI mapping based on empirical formula and simulation method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170065"], "description"=>"<p>LOD, LOD<sub>A</sub> and LOD<sub>AE</sub> are LOD scores for detecting QTL with both average and QEI effects, QTL only with average effect, and QTL only with QEI effects, respectively.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478906, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_LOD_profiles_across_1000_simulation_runs_for_the_unlinked_QTL_model_/1478906", "title"=>"Average LOD profiles across 1000 simulation runs for the unlinked QTL model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-10 02:53:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2170066"], "description"=>"<p>Power was calculated as the proportion of runs where QTL on the interval was detected. There were 90 marker intervals defined by the 96 markers evenly distributed on six chromosomes.</p>", "links"=>[], "tags"=>["Inclusive Composite Interval Mapping", "ICIM QEI mapping", "epistatic QTL mapping", "phenotypic values", "Biparental Populations Identification", "QEI effects", "inbred line population"], "article_id"=>1478908, "categories"=>["Biological Sciences"], "users"=>["Shanshan Li", "Jiankang Wang", "Luyan Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0132414.g003", "stats"=>{"downloads"=>5, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Power_analysis_by_marker_interval_for_the_unlinked_QTL_model_/1478908", "title"=>"Power analysis by marker interval for the unlinked QTL model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-10 02:53:12"}

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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