A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach
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{"title"=>"A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach", "type"=>"journal", "authors"=>[{"first_name"=>"Elisa", "last_name"=>"Vendramin", "scopus_author_id"=>"8895712200"}, {"first_name"=>"Giorgio", "last_name"=>"Pea", "scopus_author_id"=>"11339015800"}, {"first_name"=>"Luca", "last_name"=>"Dondini", "scopus_author_id"=>"6602325366"}, {"first_name"=>"Igor", "last_name"=>"Pacheco", "scopus_author_id"=>"37075491700"}, {"first_name"=>"Maria Teresa", "last_name"=>"Dettori", "scopus_author_id"=>"7004452990"}, {"first_name"=>"Laura", "last_name"=>"Gazza", "scopus_author_id"=>"6508323851"}, {"first_name"=>"Simone", "last_name"=>"Scalabrin", "scopus_author_id"=>"24438366900"}, {"first_name"=>"Francesco", "last_name"=>"Strozzi", "scopus_author_id"=>"26021549200"}, {"first_name"=>"Stefano", "last_name"=>"Tartarini", "scopus_author_id"=>"6603900789"}, {"first_name"=>"Daniele", "last_name"=>"Bassi", "scopus_author_id"=>"55770149300"}, {"first_name"=>"Ignazio", "last_name"=>"Verde", "scopus_author_id"=>"55913729300"}, {"first_name"=>"Laura", "last_name"=>"Rossini", "scopus_author_id"=>"7006215658"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"372704247", "doi"=>"10.1371/journal.pone.0090574", "isbn"=>"10.1371/journal.pone.0090574", "pmid"=>"24595269", "issn"=>"19326203", "scopus"=>"2-s2.0-84896928165", "sgr"=>"84896928165"}, "id"=>"450362ac-6337-3990-b18a-e0bc00a81f6f", "abstract"=>"Nectarines play a key role in peach industry; the fuzzless skin has implications for consumer acceptance. The peach/nectarine (G/g) trait was described as monogenic and previously mapped on chromosome 5. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F2 progeny from the cross 'Contender' (C, peach) x 'Ambra' (A, nectarine). Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. This marker was shown to efficiently discriminate between peach and nectarine plants, indicating that a unique mutational event gave rise to the nectarine trait and providing a useful diagnostic tool for early seedling selection in peach breeding programs.", "link"=>"http://www.mendeley.com/research/unique-mutation-myb-gene-cosegregates-nectarine-phenotype-peach", "reader_count"=>50, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Researcher"=>14, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>4, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Researcher"=>14, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>4, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>43, "Social Sciences"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>43}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Czech Republic"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1405496"], "description"=>"<p>(A) The expression patterns of the R2R3-MYB gene were evaluated in ‘Contender’ [C] and ‘Ambra’ [A] buds at seven, five, four and one week before anthesis (WBA). Genomic DNA of the two cultivars was also tested as a control. The same samples were analyzed for expression of <i>RPII</i> as standard (B) and checked for DNA contamination (C).</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "Marker-assisted selection", "crops", "fruits", "developmental biology", "Cell differentiation", "Plant growth and development", "genetics", "Plant genetics", "Crop genetics", "genomics", "Genome analysis tools", "Genetic maps", "Linkage maps", "Trait locus analysis", "Plant science", "plants", "trees", "Plant genomics", "peach", "nectarine"], "article_id"=>950240, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Elisa Vendramin", "Giorgio Pea", "Luca Dondini", "Igor Pacheco", "Maria Teresa Dettori", "Laura Gazza", "Simone Scalabrin", "Francesco Strozzi", "Stefano Tartarini", "Daniele Bassi", "Ignazio Verde", "Laura Rossini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090574.g005", "stats"=>{"downloads"=>2, "page_views"=>49, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_analysis_of_PpeMYB25_in_peach_and_nectarine_flower_buds_/950240", "title"=>"Expression analysis of <i>PpeMYB25</i> in peach and nectarine flower buds.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-03 03:13:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1405491"], "description"=>"<p>Linkage map obtained from analysis of the CxA F<sub>2</sub> progeny. On the left side distances are indicated in cM; on the right the marker name, the physical position on Peach v1.0 and marker skewedness are reported. The peach/nectarine locus and the indelG marker are shown in bold.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "Marker-assisted selection", "crops", "fruits", "developmental biology", "Cell differentiation", "Plant growth and development", "genetics", "Plant genetics", "Crop genetics", "genomics", "Genome analysis tools", "Genetic maps", "Linkage maps", "Trait locus analysis", "Plant science", "plants", "trees", "Plant genomics", "cxa"], "article_id"=>950235, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Elisa Vendramin", "Giorgio Pea", "Luca Dondini", "Igor Pacheco", "Maria Teresa Dettori", "Laura Gazza", "Simone Scalabrin", "Francesco Strozzi", "Stefano Tartarini", "Daniele Bassi", "Ignazio Verde", "Laura Rossini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090574.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LG_5_CxA_map_around_the_G_locus_/950235", "title"=>"LG 5 CxA map around the <i>G</i> locus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-03 03:13:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1405499"], "description"=>"<p>Name, sequence, position on Peach v1.0 and length of primers used to perform long-range PCR, RT-PCR and indelG assay.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "Marker-assisted selection", "crops", "fruits", "developmental biology", "Cell differentiation", "Plant growth and development", "genetics", "Plant genetics", "Crop genetics", "genomics", "Genome analysis tools", "Genetic maps", "Linkage maps", "Trait locus analysis", "Plant science", "plants", "trees", "Plant genomics"], "article_id"=>950243, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Elisa Vendramin", "Giorgio Pea", "Luca Dondini", "Igor Pacheco", "Maria Teresa Dettori", "Laura Gazza", "Simone Scalabrin", "Francesco Strozzi", "Stefano Tartarini", "Daniele Bassi", "Ignazio Verde", "Laura Rossini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090574.t003", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_Primers_/950243", "title"=>"List of Primers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-03 03:13:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1405498"], "description"=>"<p>A marker assay was developed based on sequence information on the <i>PpeMYB25</i> gene and the Ty1<i>-copia</i> insertion. Three primers were designed to discriminate peach and nectarine genotypes (A, B). A panel of nectarines including the putative donors of the trait, show a unique fragment of about 200 bp (C). A set of peaches, of diverse pedigree and origins (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090574#pone-0090574-t001\" target=\"_blank\">Table 1</a>) (D), shows homozygous or heterozygous patterns.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "Marker-assisted selection", "crops", "fruits", "developmental biology", "Cell differentiation", "Plant growth and development", "genetics", "Plant genetics", "Crop genetics", "genomics", "Genome analysis tools", "Genetic maps", "Linkage maps", "Trait locus analysis", "Plant science", "plants", "trees", "Plant genomics"], "article_id"=>950242, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Elisa Vendramin", "Giorgio Pea", "Luca Dondini", "Igor Pacheco", "Maria Teresa Dettori", "Laura Gazza", "Simone Scalabrin", "Francesco Strozzi", "Stefano Tartarini", "Daniele Bassi", "Ignazio Verde", "Laura Rossini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090574.g006", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_Marker_indelG_/950242", "title"=>"Functional Marker indelG.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-03 03:13:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1405493"], "description"=>"<p>Five nectarine genotypes (‘Madonna di Agosto’, MdA; ‘Quetta’, Q; ‘Stark Red Gold’, SRG; ‘Goldmine’, G; ‘Ambra’, A) were analyzed to confirm the presence of the insertion within exon 3 of <i>PpeMYB25</i>. (A) Long-range amplification products reveal for all the accessions a fragment of about 7 kb (compared to 960 bp expected from the reference genome). (B) Double digestion results of the long-range PCR products show the same pattern for all the genotypes. (C) Position and structure of the Ty-<i>copia</i> retrotransposon deduced by the by the NGS analysis of ‘Quetta’ long-range amplicon. The insertion results in a truncated version of the R2R3-MYB protein.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "Marker-assisted selection", "crops", "fruits", "developmental biology", "Cell differentiation", "Plant growth and development", "genetics", "Plant genetics", "Crop genetics", "genomics", "Genome analysis tools", "Genetic maps", "Linkage maps", "Trait locus analysis", "Plant science", "plants", "trees", "Plant genomics", "refinement"], "article_id"=>950237, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Elisa Vendramin", "Giorgio Pea", "Luca Dondini", "Igor Pacheco", "Maria Teresa Dettori", "Laura Gazza", "Simone Scalabrin", "Francesco Strozzi", "Stefano Tartarini", "Daniele Bassi", "Ignazio Verde", "Laura Rossini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090574.g003", "stats"=>{"downloads"=>2, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variant_discovery_in_PpeMYB25_annotation_refinement_of_ppa023143m_/950237", "title"=>"Variant discovery in <i>PpeMYB25</i> (annotation refinement of <i>ppa023143m</i>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-03 03:13:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1405492"], "description"=>"<p>Alignment results of reads, obtained by the resequencing of ‘Quetta’, against the peach genome region identified by the mapping interval in LG5 (from 15,853,006 bp to 16,488,104 bp). Top panel: intron-exon structure of <i>ppa023143m</i>. Central panel: plot of ‘Quetta’ paired-end distance (blue) and frequencies of single reads (yellow) at the <i>ppa023143m</i> locus. Bottom panel: blue lines are paired reads, green and red lines correspond to single reads with missing mate on the right and left side, respectively. The orange arrow points to the putative insertion inside exon 3 of <i>ppa023143m</i>.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "Marker-assisted selection", "crops", "fruits", "developmental biology", "Cell differentiation", "Plant growth and development", "genetics", "Plant genetics", "Crop genetics", "genomics", "Genome analysis tools", "Genetic maps", "Linkage maps", "Trait locus analysis", "Plant science", "plants", "trees", "Plant genomics", "quetta", "reads", "635", "kb", "peach", "pseudomolecule"], "article_id"=>950236, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Elisa Vendramin", "Giorgio Pea", "Luca Dondini", "Igor Pacheco", "Maria Teresa Dettori", "Laura Gazza", "Simone Scalabrin", "Francesco Strozzi", "Stefano Tartarini", "Daniele Bassi", "Ignazio Verde", "Laura Rossini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090574.g002", "stats"=>{"downloads"=>2, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_Quetta_reads_against_a_635_kb_interval_of_Peach_v1_0_pseudomolecule_5_/950236", "title"=>"Alignment of Quetta reads against a 635 kb interval of Peach v1.0 pseudomolecule 5.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-03 03:13:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1405501"], "description"=>"a<p>(B)  =  breeding materials (L)  =  landrace.</p>b<p>-  =  unknown donor of the nectarine allele.</p><p>For each accession the following information is reported: name, genotype at the indelG marker (941 bp reference peach allele, 197 bp nectarine allele carrying the retrotransposon insertion), phenotype, pedigree, country of origin and year of release/discovery when known, putative donor of the nectarine allele in <i>P.persica</i> if pedrigree information was available.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "Marker-assisted selection", "crops", "fruits", "developmental biology", "Cell differentiation", "Plant growth and development", "genetics", "Plant genetics", "Crop genetics", "genomics", "Genome analysis tools", "Genetic maps", "Linkage maps", "Trait locus analysis", "Plant science", "plants", "trees", "Plant genomics", "95", "varieties", "cultivated"], "article_id"=>950245, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Elisa Vendramin", "Giorgio Pea", "Luca Dondini", "Igor Pacheco", "Maria Teresa Dettori", "Laura Gazza", "Simone Scalabrin", "Francesco Strozzi", "Stefano Tartarini", "Daniele Bassi", "Ignazio Verde", "Laura Rossini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090574.t001", "stats"=>{"downloads"=>5, "page_views"=>40, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_95_peach_nectarine_varieties_representing_the_diversity_of_cultivated_P_persica_/950245", "title"=>"List of 95 peach/nectarine varieties representing the diversity of cultivated <i>P. persica</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-03 03:13:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1405500"], "description"=>"a<p>SNP detection was performed by Sequenom MassArray technology, except for the SNPs in italics that were genotyped by Sanger sequence.</p>b<p>the genetic distances estimated by the analysis of informative recombinant plants are reported in italics.</p>c<p>the first nucleotide correspond to the reference allele in the peach genome (Peach v1.0).</p>d<p>lower case bases correspond to the tails added to the SNP extension primer for Sequenom MassArray analysis.</p><p>For each marker the following information is reported: marker name, position in cM with respect to the map in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090574#pone-0090574-g001\" target=\"_blank\">Figure 1</a>, position in bp with respect to the peach genome sequence (Peach v1.0), SNP allele and the primer sequences used.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "Marker-assisted selection", "crops", "fruits", "developmental biology", "Cell differentiation", "Plant growth and development", "genetics", "Plant genetics", "Crop genetics", "genomics", "Genome analysis tools", "Genetic maps", "Linkage maps", "Trait locus analysis", "Plant science", "plants", "trees", "Plant genomics"], "article_id"=>950244, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Elisa Vendramin", "Giorgio Pea", "Luca Dondini", "Igor Pacheco", "Maria Teresa Dettori", "Laura Gazza", "Simone Scalabrin", "Francesco Strozzi", "Stefano Tartarini", "Daniele Bassi", "Ignazio Verde", "Laura Rossini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090574.t002", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNP_markers_/950244", "title"=>"SNP markers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-03 03:13:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1405495"], "description"=>"<p>MYB domains (pfam00249) of peach PpeMYB25, cotton GhMYB25 (ACJ07153.1, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090574#pone.0090574-Li1\" target=\"_blank\">[39]</a>) and <i>Antirrhinum</i> AmMYBML1 (CAB433991.1, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090574#pone.0090574-Finn1\" target=\"_blank\">[54]</a>) were aligned using the Muscle on line tool at EBI (<a href=\"http://www.ebi.ac.uk/Tools/msa/muscle/\" target=\"_blank\">http://www.ebi.ac.uk/Tools/msa/muscle/</a>). Graphic display of the alignment was obtained using BoxShade (<a href=\"http://www.ch.embnet.org/software/BOX_form.html\" target=\"_blank\">http://www.ch.embnet.org/software/BOX_form.html</a>). Black shaded residues are identical, grey shaded residues are similar. Coordinates in the protein sequences are indicated.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "Marker-assisted selection", "crops", "fruits", "developmental biology", "Cell differentiation", "Plant growth and development", "genetics", "Plant genetics", "Crop genetics", "genomics", "Genome analysis tools", "Genetic maps", "Linkage maps", "Trait locus analysis", "Plant science", "plants", "trees", "Plant genomics", "alignment", "r2", "r3", "myb"], "article_id"=>950239, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Elisa Vendramin", "Giorgio Pea", "Luca Dondini", "Igor Pacheco", "Maria Teresa Dettori", "Laura Gazza", "Simone Scalabrin", "Francesco Strozzi", "Stefano Tartarini", "Daniele Bassi", "Ignazio Verde", "Laura Rossini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090574.g004", "stats"=>{"downloads"=>0, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Aminoacid_alignment_of_the_R2_and_R3_MYB_repeat_sequences_/950239", "title"=>"Aminoacid alignment of the R2 and R3 MYB repeat sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-03 03:13:51"}

PMC Usage Stats | Further Information

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