Additional file 1 of Comparative transcriptome analysis reveals candidate gene for flowering time QTL HvHeading in barley

Supplementary Material 1: Table S1. The list of SNP markers in the HvHeading QTL interval according to barley 9k iSelect array, and the corresponding positions in reference genomes Morex IBSC v2 and Morex v3. Table S2. Primers description for genotyping of Ppd-H1, Vrn-H1 and Vrn-H3 in parental lines of spring barley MAGIC population. Table S3. Genotyping of Ppd-H1 locus using SNP markers for founders of spring barley MAGIC population and spring barley MAGIC DH lines 1–4 and 1–20. Table S4. Genotyping of Vrn-H1 locus using SNP markers for founders of spring barley MAGIC population and spring barley MAGIC DH lines 1–4 and 1–20. Table S5. Genotyping of Vrn-H3 locus using SNP markers for founders of spring barley MAGIC population and spring barley MAGIC DH lines 1–4 and 1–20. Table S6. Parental haplotype blocks for loci harboring HvHeading interval, Ppd-H1, Vrn-H1 and Vrn-H3 genes in spring barley MAGIC DH lines 1–4 and 1–20, and the allele corresponding to each gene. Table S7. Transcription expression in HvHeading QTL interval in apex tissue based on alignment of RNA-seq data to Morex IBSC v2 reference genome, and normalized using RPKM approach for DH lines 1–4 and 1–20 in three time-points; 11, 19, and 33 days after germination. Table S8. Transcription expression in HvHeading QTL interval in leaf tissue based on alignment of RNA-seq data to Morex IBSC v2 reference genome, and normalized using RPKM approach for DH lines 1–4 and 1–20 in three time-points 11, 19, and 33 days after germination. Table S9. Differentially expressed genes in the HvHeading interval (1 H chromosome) based on Morex IBSC v2 reference genome comparing barley MAGIC DH-line 1–20 to DH-line 1–4 for three time-points 11, 19, and 33 days after sowing (DAS). Table S10. Overview of the SNPs and InDels found in the expressed transcripts within the HvHeading interval (1 H chromosome) in barley MAGIC DH-line 1–20 to DH-line 1–4 including all tissues and time-points. Table S11. Differential gene expression analysis for HORVU1Hr1G067820, HORVU0Hr1G001120 and their cumulative reads based on alignment to Morex IBSC v2 reference genome, comparing barley MAGIC DH-line 1–20 to DH-line 1–4 for three time-points 11, 19, and 33 days after sowing (DAS). Table S12. Transcription expression in HvHeading QTL interval in apex tissue based on alignment of RNA-seq data to Morex v3 reference genome, and normalized using RPKM approach for DH lines 1–4 and 1–20 in three time-points; 11, 19, and 33 days after germination. Table S13. Transcription expression in HvHeading QTL interval in leaf tissue based on alignment of RNA-seq data to Morex v3 reference genome, and normalized using RPKM approach for DH lines 1–4 and 1–20 in three time-points; 11, 19, and 33 days after germination.