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Additional file 1: Table S1. Characteristics of the 135 BC1 individuals. Table S2. Statistical analyzes comparing data between 2010 and 2011 and 2011–2012 experiments. Table S3. Spearman correlations of the four criteria (RD – RW – RF – GI) in response to X. index.Table S4. Results of the proportion test performed on 60 BC1 individuals in response to X. index.Table S5. Characteristics of the experiments in response to X. index carried out over five independent years. Table S6. Primers characteristics.

Additional file 2: Figure S1. Maternal genetic map related to VRH8771. Figure S2. Paternal genetic map related to CS. Figure S3. Variation of genetic distance depending on physical distance on the VRH8771 (A) and CS (B) genetic maps. Figure S4. Principal component analysis (PCA) of the 35 F1 individuals tested in 2010–2011 and 2011–2012 experiments with root system development (RD), root weight (RW), nematode reproduction factor (RF) and gall index (GI). Figure S5. QTL analysis of the resistance to X. index performed on 60 BC1 individuals. The results of the analysis performed on LG 9 and LG 10 are presented. The y-axis represents the LOD score obtained by the binary mapping and the x-axis represents the 19 linkage groups related to the maternal genetic map (VRH8771). Curves in plot indicate the genetic coordinate (x-axis) and LOD score (y-axis). The red dotted line represents the LOD significant threshold estimated with 1000 permutations for a level α of 0.05. Figure S6.In planta experiment (A) illustration of the experimental device with each plant grown in an individual pot covered by a transparent plastic bell and (B) example of nodosities developed on roots (red arrows).

TNL-related peptides obtained with BLASTp analysis using MEME motifs of the post-LRR domain in the Plant Genome Database website. Results are shown for Populus trichocarpa, Vitis vinifera, Medicago truncatula, Arabidopsis thaliana, Solanum tuberosum, Glycine max, Oryza sativa, Prunus persica, Sorghum bicolor, and Zea mays. Identified TNL-related sequences, unrelated TNL sequences and unknown sequences are highlighted in green, blue and yellow, respectively. (DOC 138Â kb)

Secondary-structure prediction of the PL motif-1. The table shows the consensus sequence obtained from the alignment of the peach PL sequences, the 5 PLs of the Ma protein and the WW-domain consensus sequence obtained from Vitis vinifera sequences. H signifies a helix residue. Predicted stands for extended beta sheet (E) are surrounded by the tryptophans (in blue). (DOCX 17Â kb)

Physical map of the TNL-related genes in the peach genome v1.0 and revision observed in v2.0. The map position of the 195 total TNL-related proteins is depicted within the eight scaffolds (chromosomes). Accession numbers are related to the genome glossary of the v1.0. Merged predicted peptides identified through corrected predictions are underlined and highlighted with brackets. The size of each scaffold (in Mb) and the respective number of TNL-related predicted peptides are shown under each scaffold. The Ma orthologue is indicated in red upper case. Unmapped genes in the v1.0 and mapped in the v2.0 are in green boxes. The red box shows re-localisation of TNL genes in the v2.0. Predicted peptides that are not indicated in the v2.0 are labelled with an asterisk. (PDF 167Â kb)

Structure of the Prunus TNL gene Ma predicted with the predictors Fgenesh and GENESCAN using various specific gene-finding parameters. The first row shows the exact size of each exon (and associated domain in bp) of the Ma gene. The other rows show the exon predictions. NA not appropriate. (DOCX 48Â kb)