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Additional file 9: Supplementary Table S2. Analysis of allelic variant on WGS data retrieved from NCBI SRA database of 41 peach accessions. The presence of di1/di1, di2/di2 and di1/di2 genotypes or of PET alleles in Prupe.6G242400 was assessed. References to phenotype information about double-flower and other ornamental traits are also indicated. Accessions with unclear genotype at either di or Di2 loci were also included.

Additional file 7: Supplementary File S1. DNA sequence of the diΔ, di1 and di2 variants. Prupe.2G237700 is highlighted in green with the boxed pre-miR172 sequence. The deletion is indicated in diΔ with strikethrough text while the insertions in di1 and di2 are highlighted in orange and yellow, respectively. Primers used for genotyping are marked as bold, underlined sequences. Primers used for RT-qPCR analysis are shown on a portion of the pre-miR172d sequence.

Table S3. SRA accession number of assembled Illumina Whole-Genome libraries. (DOCX 13Â kb)

Table S4. List of candidate genes identified on the chromosome 6 region comprised between SNP_IGA_652659 (13,743,178Â bp) and SNP_IGA_534275 (15,609,595Â bp). (DOCX 17Â kb)

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

Table S1. List of analyzed peach accessions and respective texture phenotype. (DOCX 19Â kb)

List of candidate genes identified on the chromosome 2 region associated to SNP_IGA_214703 (from 8.5 to 9.1Â Mb) (DOCX 9 kb)

MareyMap plot of TxE linkage map. Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 236Â kb)

Figure S2. QTLs for Fusarium ear rot (FER), fumonisin B1 contamination (FB1) and days to silking (DTS). Marker names are listed on the right side of each LG and the corresponding genetic distances (in centiMorgan) on the left side. QTLs are drawn at the right of each LG and are represented as central bars indicating the 1-LOD confidence interval and external thin lines indicating the 2-LOD confidence interval. QTLs are identified by the trait code, followed by the year (2011/2012), the sowing time (A/B) and the inoculation technique (F/T) for which the QTL was detected. QTLs for FER are reported with red bars, FB1 in black and DTS in green. (PPTX 152Â kb)

Figure S1. Weekly means of A) temperature, B) relative humidity and C) weekly sums of rain precipitation in years 2011 and 2012. First week corresponds to the first 7Â days of flowering in the early sowing of both 2011 and 2012. Last week corresponds to the week of the harvest day for both 2011 and 2012, in the early and late sowings. (PPTX 72Â kb)

Coefficient of variation of the predictive ability vs heritability. Figure reporting, for each trait, the coefficient of variation of predictive ability as function of the heritability of the trait in each progeny. Fruit weight in red, Sugar content in green and Titratable acidity in blue. (PDF 5 kb)

MareyMap plot of TxE linkage map. Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 236Â kb)

List of candidate genes identified on the chromosome 3 region associated to the SNP_IGA_366639 (from 26.2 to 26.5Â Mb) (DOCX 10 kb)

List of primers used in this study. (DOCX 8 kb)

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 495Â kb)

Effect of sample size. Figure reporting, for each trait, the coefficient of variation of heritability, predictive ability, and repeatability as functions of sample size. (PDF 6 kb)

MareyMap plot of CxA linkage map. Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 233Â kb)

SRA accession number (DOCX 8 kb)

MareyMap plot of CxA linkage map. Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 233Â kb)

MareyMap plot of PxF linkage maps (including the F1 and recurrent parent maps). Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 405Â kb)

Figure S3. Rating scale of Fusarium ear rot severity on the F. verticillioides inoculated maize ears. (PPTX 1340Â kb)

Candidate genes identified on the chromosome 2 associated to the SNP_IGA_185608 (from 5.6 to 6.0Â Mb) (DOCX 9 kb)

Effect of phenotypic variability. Figure reporting, for each trait, the coefficient of variation of heritability, predictive ability, and repeatability as functions of the coefficient of variation of each phenotipic trait. (PDF 6 kb)

MareyMap plot of PxF linkage maps (including the F1 and recurrent parent maps). Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 405Â kb)

Candidate genes identified on the chromosome 2 associated to the SNP_IGA_185608 (from 5.6 to 6.0Â Mb) (DOCX 9 kb)

List of primers used in this study. (DOCX 8 kb)