Additional file 4 of Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

Additional file 4: Supplementary Table S11. Sample correlation analysis of three biological replicates in RNA-seq. Supplementary Table S12. Differentially expressed genes (DEGs) detected by DESeq2 methods (FDR < 0.05, log2FC > 1 or log2FC < − 1,verticals represent normal genes. Up and down arrows represent up and down) in RNA-seq of salt. Supplementary Table S13. Differentially expressed genes (DEGs) detected by DESeq2 methods (FDR < 0.05, log2FC > 1 or log2FC < − 1, verticals represent normal genes. Up and down arrows represent up and down) in RNA-seq of alkali. Supplementary Table S14. Differentially expressed genes (DEGs) detected by DESeq2 methods (FDR < 0.05, log2FC > 1 or log2FC < − 1,verticals represent normal genes. Up and down arrows represent up and down) in RNA-seq of salt-alkali. Supplementary Table S15. Co-expression network identified by AppleMDO analysis tools in hybrids tolerant or sensitive to salt, alkali, and salt-alkali treatments in hybrids from Malus robusta Rehd. ‘Baleng Crab’ × M. pumila Mill. ‘M9’. Supplementary Table S16. Data for allelic variations of markers using for KASP assay in hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila). Supplementary Table S17. Estimates of marker genotype effects on salt, alkali, and salt-alkali injury indices in hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila). Supplementary Table S18. The marker genotypes, genomics predicted values (GPV), and observed phenotype values (OPV) of alkali injury index in 299 F1 hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila) . Supplementary Table S19. The marker genotypes, genomics predicted values (GPV), and observed phenotype values (OPV) of salt injury index in 285 F1 hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila). Supplementary Table S20. The marker genotypes, genomics predicted values (GPV), and observed phenotype values (OPV) of saline-alkali injury index in 194 F1 hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila)