genotyping data

Genotyping data for the five mapping population

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

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

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

SNP markers.

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

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

List of Primers.

<p>Name, sequence, position on Peach v1.0 and length of primers used to perform long-range PCR, RT-PCR and indelG assay.</p

Additional file 2: Figure S1. of The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity

Anchoring of the peach scaffolds to the three genetic maps. Colored bars represent the 8 linkage groups: pink for PxF, purple for TxE and blue for CxA. WGS scaffolds were positioned in each pseudomolecule (Pp01 to Pp08) with the corresponding genetic markers and are depicted in three different colors (dark blue, pink and pale blue); genetic markers are in the same colors of the corresponding WGS scaffolds. The zero (0) denotes the six scaffolds placed with random orientation along the pseudomolecules. The asterisk (*) indicates the two scaffolds with random order. The crosshatch (#) indicates the two scaffolds with the wrong order in Peach v2.0 that need to be inverted in a future release. (PDF 495 kb