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Additional file 2: of Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch)

Figure S1. Evolution of flesh firmness during ripening of four peach accessions with a stony hard (‘BO05030081’ and ‘IFF331’) or non-SH/MF (‘Bolero’, ‘Redhaven’) texture, as measured through a penetration-based test. (BMP 4181 kb

Additional file 3: of Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch)

Table S2. List of primers used for quantitative PCR analyses. (DOCX 12 kb

Additional file 8: of Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch)

File S1. Full list of variants annotations and effects (as calculated with SNPEff tool) from whole genome sequencing assembly of 19 accessions within the hd locus on chromosome 6. Candidate variant on PpYUC11-like gene is highlighted in black; variants associated to DEGs in yellow; high-impact variants predicted by SNPEff in red. See text for variants filtering criteria. (XLSX 41 kb

Additional file 9: of Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch)

Table S5. Phenotypic evaluation for SH trait and allelic status at YUC11 TC microsatellites of the two F2 segregating progenies BO10040 and BO10039 (issued from the SH parent ‘D4162’). (DOCX 16 kb

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

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

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

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

LG 5 CxA map around the <i>G</i> locus.

<p>Linkage map obtained from analysis of the CxA F₂ 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