The Flowering Repressor SVP Underlies a Novel Arabidopsis thaliana QTL Interacting with the Genetic Background
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{"title"=>"The Flowering Repressor SVP Underlies a Novel Arabidopsis thaliana QTL Interacting with the Genetic Background", "type"=>"journal", "authors"=>[{"first_name"=>"Belén", "last_name"=>"Méndez-Vigo", "scopus_author_id"=>"8516678100"}, {"first_name"=>"José M.", "last_name"=>"Martínez-Zapater", "scopus_author_id"=>"7006185591"}, {"first_name"=>"Carlos", "last_name"=>"Alonso-Blanco", "scopus_author_id"=>"6701329603"}], "year"=>2013, "source"=>"PLoS Genetics", "identifiers"=>{"doi"=>"10.1371/journal.pgen.1003289", "sgr"=>"84873513977", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pmid"=>"23382706", "issn"=>"15537390", "scopus"=>"2-s2.0-84873513977", "pui"=>"368295344"}, "id"=>"3765ebc3-5bb2-3117-99df-87269d897c51", "abstract"=>"The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments. Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species, but the molecular and evolutionary mechanisms underlying this genetic variation are mainly being determined in the model plant Arabidopsis thaliana. To find novel A. thaliana flowering QTL, we developed introgression lines from the Japanese accession Fuk, which was selected based on the substantial transgression observed in an F(2) population with the reference strain Ler. Analysis of an early flowering line carrying a single Fuk introgression identified Flowering Arabidopsis QTL1 (FAQ1). We fine-mapped FAQ1 in an 11 kb genomic region containing the MADS transcription factor gene SHORT VEGETATIVE PHASE (SVP). Complementation of the early flowering phenotype of FAQ1-Fuk with a SVP-Ler transgen demonstrated that FAQ1 is SVP. We further proved by directed mutagenesis and transgenesis that a single amino acid substitution in SVP causes the loss-of-function and early flowering of Fuk allele. Analysis of a worldwide collection of accessions detected FAQ1/SVP-Fuk allele only in Asia, with the highest frequency appearing in Japan, where we could also detect a potential ancestral genotype of FAQ1/SVP-Fuk. In addition, we evaluated allelic and epistatic interactions of SVP natural alleles by analysing more than one hundred transgenic lines carrying Ler or Fuk SVP alleles in five genetic backgrounds. Quantitative analyses of these lines showed that FAQ1/SVP effects vary from large to small depending on the genetic background. These results support that the flowering repressor SVP has been recently selected in A. thaliana as a target for early flowering, and evidence the relevance of genetic interactions for the intraspecific evolution of FAQ1/SVP and flowering time.", "link"=>"http://www.mendeley.com/research/flowering-repressor-svp-underlies-novel-arabidopsis-thaliana-qtl-interacting-genetic-background", "reader_count"=>63, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>12, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>12, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>51, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>51}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Austria"=>1, "Switzerland"=>1}, "group_count"=>2}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/496798"], "description"=>"<p>A) Frequency distribution of flowering time in an F<sub>2</sub> (L<i>er</i>×Fuk) population. Arrows and horizontal bars indicate the mean and range of variation of parental accessions. B) Flowering behaviour of ILs carrying <i>FAQ1</i>-Fuk alleles, grown under long-day and short-day photoperiods. Bars correspond to mean ± SE of 10–18 plants. Graphical genotypes are shown below the bars. In the lower panel, representative L<i>er</i> and IL-<i>FAQ1</i> plants photographed 24 days (for long-day) or 51 days (for short-day) after germination, are shown. C) Fine mapping of <i>FAQ1</i> showing the location and number of recombination events found in the 5976 gametes analysed along the BAC contig.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology"], "article_id"=>167328, "categories"=>["Genetics", "Plant Biology"], "users"=>["Belén Méndez-Vigo", "José M. Martínez-Zapater", "Carlos Alonso-Blanco"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003289.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_characterization_and_mapping_of_FAQ1_/167328", "title"=>"Identification, characterization, and mapping of <i>FAQ1</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-31 02:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/496928"], "description"=>"<p>Leaf number of independent homozygous T<sub>3</sub> transgenic lines carrying parental (A, B, F and G) or chimerical (D, E, H and I) <i>SVP</i> genomic constructs in IL-<i>FAQ1</i> (A, B, D and E) or L<i>er</i> (F–I) genetic backgrounds. Lines were grown under long-day (LD) (A, D, F and H) or short-day (SD) (B, E, G, and I) photoperiods. C) Nucleotide polymorphisms found between <i>SVP</i> genomic sequences of L<i>er</i> and Fuk. Parental and chimerical <i>SVP</i> transgenes derived from Fuk (red colour) and L<i>er</i> (green colour) are depicted in the upper part of each panel. Bars are means ± SE of 10–15 plants per line. Mean ± SE of all lines carrying the same transgene are shown above the bars. Dashed lines delimit the 95% confidence intervals of the leaf number observed in untransformed IL-<i>FAQ1</i> (red colour) and L<i>er</i> (green colour) control lines, as established by Bonferroni tests.</p>", "links"=>[], "tags"=>["phenotypes", "transgenic", "lines", "chimerical"], "article_id"=>167449, "categories"=>["Genetics", "Plant Biology"], "users"=>["Belén Méndez-Vigo", "José M. Martínez-Zapater", "Carlos Alonso-Blanco"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003289.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowering_phenotypes_of_transgenic_lines_for_parental_and_chimerical_SVP_alleles_/167449", "title"=>"Flowering phenotypes of transgenic lines for parental and chimerical <i>SVP</i> alleles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-31 02:04:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/497022"], "description"=>"<p>Leaf numbers of independent homozygous T<sub>3</sub> transgenic lines carrying Fuk (red colour) or L<i>er</i> (green colour) <i>SVP</i> transgenes grown under long-day (LD) (A) or short-day (SD) (B) photoperiod. Genetic backgrounds are indicated in the horizontal axis. Bars are means ± SE of 10–15 plants per line. Mean ± SE of all lines carrying the same transgene and background are shown above the bars. Dashed lines delimit the 95% confidence intervals of the leaf numbers observed in the corresponding untransformed control lines as established by Bonferroni tests.</p>", "links"=>[], "tags"=>["phenotypes", "transgenic", "lines", "developed"], "article_id"=>167543, "categories"=>["Genetics", "Plant Biology"], "users"=>["Belén Méndez-Vigo", "José M. Martínez-Zapater", "Carlos Alonso-Blanco"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003289.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowering_phenotypes_of_SVP_transgenic_lines_developed_in_multiple_genetic_backgrounds_/167543", "title"=>"Flowering phenotypes of <i>SVP</i> transgenic lines developed in multiple genetic backgrounds.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-31 02:05:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/497165"], "description"=>"<p>A) Geographic distribution of <i>SVP/FAQ1</i> causal polymorphism. B) Sliding window plot of nucleotide diversity along <i>SVP</i> region derived from 18 world-wide accessions. Nucleotide diversities in <i>SVP</i> coding region are shown inside the panel. C) N-J tree showing the genetic relationships among <i>SVP</i> sequences. D) N-J tree showing the genome-wide genetic relationships among 54 Asian accessions, as estimated from a set of 237 polymorphic SNPs. In C and D, accessions carrying Fuk allele for <i>SVP/FAQ1</i> causal polymorphism are shown in red color. E) Frequency distribution of leaf numbers in an F<sub>2</sub> (Fuk×YGU) population. Average leaf number ± SE and sample size (<i>N</i>) of the three <i>SVP</i> genotypic classes, established based on Ala/Val<sup>32</sup> CAPS marker, is given inside the panel.</p>", "links"=>[], "tags"=>["patterns"], "article_id"=>167688, "categories"=>["Genetics", "Plant Biology"], "users"=>["Belén Méndez-Vigo", "José M. Martínez-Zapater", "Carlos Alonso-Blanco"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003289.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographic_and_genetic_diversity_patterns_of_natural_SVP_alleles_/167688", "title"=>"Geographic and genetic diversity patterns of natural <i>SVP</i> alleles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-31 02:08:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/497248"], "description"=>"<p>For each background is shown: the endogenous and transgenic <i>SVP</i> alleles analysed, the number of independent homozygous transgenic lines evaluated, and the average <i>FAQ1/SVP</i> allelic effects in long-day (LD) and short-day (SD) photoperiod. Allelic effects were estimated in two experiments as the mean difference between the leaf number of transgenic lines carrying <i>SVP</i> transgenes from L<i>er</i> and Fuk. Only transgenic lines differing significantly from the corresponding untransformed control were used for allelic effect estimates.</p>1<p>: The allelic effect of the original <i>FAQ1</i> locus (detected in L<i>er</i> and IL-<i>FAQ1</i> lines) was estimated as the leaf number difference between L<i>er</i> and IL-<i>FAQ1</i> untransformed plants.</p>", "links"=>[], "tags"=>["allelic", "flowering", "initiation"], "article_id"=>167772, "categories"=>["Genetics", "Plant Biology"], "users"=>["Belén Méndez-Vigo", "José M. Martínez-Zapater", "Carlos Alonso-Blanco"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003289.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FAQ1_SVP_allelic_effects_on_flowering_initiation_in_different_genetic_backgrounds_/167772", "title"=>"<i>FAQ1/SVP</i> allelic effects on flowering initiation in different genetic backgrounds.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-31 02:09:32"}

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Agriculture", "average_usage"=>[241, 422, 551, 659, 765, 866, 954, 1043, 1142, 1235, 1311, 1397, 1462]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"subject_area"=>"/Biology and life sciences/Plant science", "average_usage"=>[269, 451, 577, 699, 812, 922, 1019, 1126, 1225, 1309, 1404, 1493, 1563]}]}
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