Additional file 1: of Identification of recombination events in outbred species with next-generation sequencing data

Table S1. Summary of parental blocks from the intermediate files of ‘parent1.abxaa.5snps.blocks’, ‘parent2.aaxab.5snps.blocks’, ‘parent1.long.haplotype’ and ‘parent2.long.haplotype’, created by findGCO. Table S2. The number of SNPs contained in the long parental haplotypes from the intermediate files of ‘parent1.long. Haplotype’ and ‘parent2.long.haplotype’ created by findGCO. Table S3. Distribution of the number of gene conversion events detected in each of the 10 progeny and inherited from the male parent based on the reference genome sequences. Figure S1. CO patterns identified in each progeny on all chromosomes in the female parent P. deltoides. Figure S2. CO patterns identified in each progeny on all chromosomes in the male parent P. simonii. (DOCX 277 kb

Additional file 5: of Identification of recombination events in outbred species with next-generation sequencing data

Excel Sheets CS-B35–2, CS-C25–3, CS-C3–2, CS-C32–2, CS-C5–3, CS-3-12, CS-3-14, CS-3-15, CS-3-16 and CS-3-18 Crossover tracts on each chromosome of the maternal P. simonii that were identified in each progeny. Excel Sheet S7 Summary of the crossover numbers on the male chromosomes that were identified in each progeny. Excel Sheet S8 Summary of the crossover events on the male chromosomes that were identified within a short haplotype block region. (XLSX 58 kb

Additional file 4: of Identification of recombination events in outbred species with next-generation sequencing data

Excel Sheets CD-B35–2, CD-C25–3, CD-C3–2, CD-C32–2, CD-C5–3, CD-3-12, CD-3-14, CD-3-15, CD-3-16 and CD-3-18 Crossover tracts on each chromosome of the maternal P. deltoides that were identified in each progeny. Excel Sheet S5 Summary of the crossover numbers on the female chromosomes that were identified in each progeny. Excel Sheet S6 Summary of the crossover events on the female chromosomes that were identified within a short haplotype block region. (XLSX 72 kb

Additional file 2: of Identification of recombination events in outbred species with next-generation sequencing data

Excel Sheets RD-B35–2, RD-C25–3, RD-C3–2, RD-C32–2, RD-C5–3, RD-3-12, RD-3-14, RD-3-15, RD-3-16 and RD-3-18 Distribution of the number of recombination events over fragment length, which occurred in the meiosis of the female P. deltoides and were identified in each of the 10 progeny. Excel Sheet S1 Distribution of the average number of recombination events over fragment length, which occurred in the meiosis of the female P. deltoides and were identified in the 10 progeny. Excel Sheet S2 Summary of the number and the total length of haplotype blocks in which the maternal recombination events were identified in each progeny. (XLSX 29 kb

Additional file 3: of Identification of recombination events in outbred species with next-generation sequencing data

Excel Sheets RS-B35–2, RS-C25–3, RS-C3–2, RS-C32–2, RS-C5–3, RS-3-12, RS-3-14, RS-3-15, RS-3-16 and RS-3-18 Distribution of the number of recombination events over fragment length, which occurred in the meiosis of the male P. simonii and were identified in each of the 10 progeny. Excel Sheet S3 Distribution of the average number of recombination events over fragment length, which occurred in the meiosis of the male P. simonii and were identified in the 10 progeny. Excel Sheet S4 Summary of the number and the total length of haplotype blocks in which the paternal recombination events were identified in each progeny. (XLSX 29 kb

Additional file 5: Figure S13. of MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species

Richards’ growth curves of the 12 QTLs underlying the tree height of Populus, fitted with their genotype values (dot) over time estimated from the multivariate CIM method. The red is for the genotype QQ and the blue for Qq. (PDF 375 kb

Additional file 4: Figure S1. of MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species

Biological process GO category for the genes within the region of QTL Q1D1. Figure S2. Biological process GO category for the genes within the region of QTL Q2D1. Figure S3. Biological process GO category for the genes within the region of QTL Q3D1. Figure S4. Biological process GO category for the genes within the region of QTL Q1D2. Figure S5. Biological process GO category for the genes within the region of QTL Q2D2. Figure S6. Biological process GO category for the genes within the region of QTL Q3D2. Figure S7. Biological process GO category for the genes within the region of QTL QD5. Figure S8. Biological process GO category for the genes within the region of QTL QD9. Figure S9. Biological process GO category for the genes within the region of QTL Q1D14. Figure S10. Biological process GO category for the genes within the region of QTL Q2D14. Figure S11. Biological process GO category for the genes within the region of QTL QS7. Figure S12. Biological process GO category for the genes within the region of QTL QS9. (DOCX 642 kb

Additional file 6: Figure S14. of MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species

Plots of the mean cross-validated error against the log of parameter lambda for the female (a) and male (b) SNP datasets. Table S8. SNPs identified to be associated with Populus height by the LASSO method using the two SNP datasets from each parental linkage map. (DOCX 61 kb

Additional file 3: of MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species

Excel Sheets from Q1D1 to QS9. (XLSX 97 kb

Additional file 2: Table S1. of MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species

Average of parameter estimates with the standard deviation in bracket under different sample sizes when the QTL segregation type is QQ × Qq, based on 1000 simulation replicates. Table S2. Average of parameter estimates with the standard deviation in bracket under different sample sizes when the QTL segregation type is Qq × Qq, based on 1000 simulation replicates. Table S3. Average of parameter estimates with the standard deviation in bracket under different sample sizes when the QTL segregation type is Q1Q2 × Q3Q4, based on 1000 simulation replicates. Table S4. Average of parameter estimates with the standard deviation in bracket under different sample sizes when the QTL segregation type is Qq × QQ, based on 1000 simulation replicates. Table S5. Average of parameter estimates with the standard deviation in bracket under different sample sizes when the QTL segregation type is Qq × qQ, based on 1000 simulation replicates. Table S6. Summary on average estimates of QTL heritabilities (%) with the standard deviation in brackets under different time points (T1-T8) and different sample sizes based on 1000 simulation replicates. Table S7. The average estimate of the residual covariance matrix with standard deviations in brackets when the sample size is 300 and the QTL segregation type is Qq × qQ, based on 1000 simulation replicates. (DOCX 42 kb