Additional file 1: Table S1. SNP filtering summary for the Pinus radiata QTL and FWK mapping populations.

Additional file 3: Table S3. Descriptive statistics for the phenotypic traits measured in the QTL and FWK Pinus radiata populations in this study.

Additional file 16: Fig. S2. Synteny and collinearity between linkage groups 8 and 10 amongst the Pinus radiata parental linkage maps in this study. Vertical bars represent linkage groups, horizontal lines within bars show the position of markers within each group, lines between groups indicate homologous markers at the contig level. Scale bars shows cM (Kosambi). Fig. S1A shows perfect synteny and high collinearity between these linkage groups in three parental linkage maps. Fig. S2B...

Additional file 18: Fig. S3. Genomic predictive ability for diameter at breast height (DBH) and wood density (WD) as a function of training population size (A) and number of markers (B) used in random cross-validations of 81 Pinus radiata genotypes from the FWK population. Error bars correspond to standard deviations across 100 random cross-validations for each set of parameters. Analyses in (A) were based on all markers (M = 9353). The training population size in...

Additional file 1: Table S1. SNP filtering summary for the Pinus radiata QTL and FWK mapping populations.

Additional file 2: Table S2. SNP ranking criteria used for the Pinus radiata QTL and FWK mapping populations.

Additional file 4: Fig. S1. Frequency distributions for the phenotypic traits measured in the QTL and FWK Pinus radiata populations in this study. QTL population: (A) Ring area (mm2); (B) Density (kg/m3) Silviscan; (C) Radial cell diameter (μm); (D) Tangential cell diameter (μm); (E) Fibre coarseness (μm/m); (F) Cell wall thickness (μm); (G) Specific surface area (m2/kg); (H) Microfibril angle (degrees); (I) Modulus of elasticity (GPa); (J) Density prediction for first 5 mm core (maximum...

Additional file 5. 268,345 map file. Plain text file containing the map position (cM) of all loci on the 268,345 linkage map, in the format required for analysis using MAPQTL 6.0.

Additional file 7. 268,345 loc file. Plain text file containing the genotype codes for loci in the 268,345 parental map, in the format required for analysis using MAPQTL 6.0.

Additional file 9. All traits QTL pop. Plain text file containing the quantitative trait data of all individuals in the QTL population.

Abstract Background The growing availability of genomic resources in radiata pine paves the way for significant advances in fundamental and applied genomic research. We constructed robust high-density linkage maps based on exome-capture genotyping in two F1 populations, and used these populations to perform quantitative trait locus (QTL) scans, genomic prediction and quantitative analyses of genetic architecture for key traits targeted by tree improvement programmes. Results Our mapping approach used probabilistic error correction of the marker...

Additional file 11. 850,096 map file. Plain text file containing the map position (cM) of all loci on the 850,096 linkage map, in the format required for analysis using MAPQTL 6.0.

Additional file 11. 850,096 map file. Plain text file containing the map position (cM) of all loci on the 850,096 linkage map, in the format required for analysis using MAPQTL 6.0.

Additional file 10. 850,055 map file. Plain text file containing the map position (cM) of all loci on the 850,055 linkage map, in the format required for analysis using MAPQTL 6.0.