Additional file 8 of Intricate genetic variation networks control the adventitious root growth angle in apple

Additional file 8: Table S1 The phenotype data for the adventitious root growth angle (RGA) of leafy cuttings of hybrids derived from ‘Baleng Crab (BC)’ (Malus robusta) × ‘M9’ (M. pumila) in 2016 and 2017. Table S2 Summary of the results of bulked segregant analysis by next generation genomic sequencing (BSA-seq) of extreme bulks of small and large adventitious RGAs using hybrids derived from ‘BC’ × ‘M9’. Table S3 Summary of BSA-seq detected QTLs for apple adventitious RGA before and after narrowing by changing slide window sizes. Table S4 Twenty-four stem tissue samples for RNA sequencing (RNA-seq) taken from leafy cuttings of hybrids derived from ‘BC’ × ‘M9’. Table S5 Summary of the sequencing reads and reads mapped with RNA-seq. Table S6 Sample correlation analysis of three biological replicates with RNA-seq. Table S7 KEGG pathway analysis of DEGs (ko00500, ko00592, ko00900, and ko04075) from RNA-seq results. Table S8 Co-expression network of RGA identified by AppleMDO in hybrids from ‘BC’ × ‘M9’. Table S9 Candidate genes for RGA screened by parental resequencing, BSA-seq, and RNA-seq in a hybrid population from ‘BC’ × ‘M9’. Table S10 Candidate gene mining from BSA-seq regions based on multiomics data. Table S11 Allelic variations of MdLAZY1, MdIAA1, MdDREB2A, MdHSFB3, MdNPR5, MdLBD41, and MdbHLH48. Table S12 Closely linked relationship between six diagnostic markers (SNP-1485/− 474 of MdLAZY1, SNP223 of MdIAA1, SNP-1228 of MdNPR5, SNP908 of MdLBD41, and Del360 of MdbHLH48) and Kompetitive Allele Specific PCR (KASP) markers (b13, G122, S1272, Z312, and S1288). Table S13 Joint genotype effects of markers linked to b13, SNP592, and G122 on RGA phenotype in hybrids from ‘BC’ × ‘M9’. Table S14 Joint genotype effects of markers linked to S1272, Z312, and S1288 on RGA phenotype in hybrids from ‘BC’ × ‘M9’. Table S15 Detailed data and primers for 26 allelic variations used for KASP in ‘BC’ and ‘M9’. Table S16 The genotypes of 26 markers in 266 F1 hybrids from ‘BC’ × ‘M9’. Table S17 The individual genotype effects of the 26 markers in 266 F1 hybrids from ‘BC’ × ‘M9’. Table S18 Primers used for experimental validation in this study.