Fig_2_Type_I_MADS_genes_peach

Unrooted Bayesian consensus tree of Type I MADS-box proteins from peach and Arabidopsis. Bayesian posterior probabilities for all clades are given at their respective nodes

Fig_3_Type_II_MADS_genes_peach

Unrooted Bayesian consensus tree of Type II MADS-box proteins from peach and Arabidopsis. Bayesian posterior probabilities for all clades are given at their respective nodes

Fig_5_FLC_genes

Unrooted maximum likelihood phylogenetic tree of MADS-box proteins from the FLC subfamily in peach, Arabidopsis, grapevine, poplar, maize, sorghum, and rice. Bayesian posterior probabilities for all clades are given at their respective nodes

Fig_4_SVP_AGL24_genes

Unrooted Bayesian consensus tree of MADS-box proteins from the SVP/AGL24 subfamily in peach, Arabidopsis, grapevine, poplar, maize, sorghum, and rice. Bayesian posterior probabilities for all clades are given at their respective nodes

Variant discovery in <i>PpeMYB25</i> (annotation refinement of <i>ppa023143m</i>).

<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

Alignment of Quetta reads against a 635 kb interval of Peach v1.0 pseudomolecule 5.

<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

List of 95 peach/nectarine varieties representing the diversity of cultivated <i>P. persica</i>.

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

Aminoacid alignment of the R2 and R3 MYB repeat sequences.

<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

Functional Marker indelG.

<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

Expression analysis of <i>PpeMYB25</i> in peach and nectarine flower buds.

<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