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.

补充材料1：表S1。基于大麦9k iSelect基因分型芯片，HvHeading数量性状基因座（Quantitative Trait Locus, QTL）区间内的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记列表，及其在参考基因组Morex IBSC v2与Morex v3中的对应位置。
表S2。春大麦多亲本高级互交（Multi-parent Advanced Generation Intercross, MAGIC）群体亲本中Ppd-H1、Vrn-H1与Vrn-H3基因分型所用引物说明。
表S3。针对春大麦MAGIC群体创始亲本与春大麦MAGIC双单倍体（Double Haploid, DH）系1–4、1–20，采用SNP标记对Ppd-H1基因座进行分型的结果。
表S4。针对春大麦MAGIC群体创始亲本与春大麦MAGIC双单倍体（DH）系1–4、1–20，采用SNP标记对Vrn-H1基因座进行分型的结果。
表S5。针对春大麦MAGIC群体创始亲本与春大麦MAGIC双单倍体（DH）系1–4、1–20，采用SNP标记对Vrn-H3基因座进行分型的结果。
表S6。春大麦MAGIC双单倍体（DH）系1–4、1–20中，携带有HvHeading区间、Ppd-H1、Vrn-H1与Vrn-H3基因的基因座的亲本单倍型区块，以及各基因对应的等位基因信息。
表S7。将RNA-seq数据比对至Morex IBSC v2参考基因组后，采用每百万reads每千碱基转录本长度（Reads Per Kilobase per Million mapped reads, RPKM）法进行标准化的顶端组织中HvHeading QTL区间转录表达数据，涵盖春大麦MAGIC双单倍体（DH）系1–4、1–20在萌发后11、19、33天三个时间点的样本。
表S8。将RNA-seq数据比对至Morex IBSC v2参考基因组后，采用RPKM法进行标准化的叶片组织中HvHeading QTL区间转录表达数据，涵盖春大麦MAGIC双单倍体（DH）系1–4、1–20在萌发后11、19、33天三个时间点的样本。
表S9。基于Morex IBSC v2参考基因组，对比春大麦MAGIC双单倍体（DH）系1–20与1–4在播种后11、19、33天三个时间点的样本，得到的HvHeading区间（1H染色体）内的差异表达基因列表。
表S10。春大麦MAGIC双单倍体（DH）系1–20与1–4的HvHeading区间（1H染色体）内表达转录本中检出的单核苷酸多态性（SNP）与插入缺失（Insertion-Deletion, InDel）汇总，涵盖所有组织与时间点的样本。
表S11。将测序读数比对至Morex IBSC v2参考基因组后，针对基因HORVU1Hr1G067820、HORVU0Hr1G001120及其累计测序读数，对比春大麦MAGIC双单倍体（DH）系1–20与1–4在播种后11、19、33天三个时间点的样本开展的差异基因表达分析结果。
表S12。将RNA-seq数据比对至Morex v3参考基因组后，采用RPKM法进行标准化的顶端组织中HvHeading QTL区间转录表达数据，涵盖春大麦MAGIC双单倍体（DH）系1–4、1–20在萌发后11、19、33天三个时间点的样本。
表S13。将RNA-seq数据比对至Morex v3参考基因组后，采用RPKM法进行标准化的叶片组织中HvHeading QTL区间转录表达数据，涵盖春大麦MAGIC双单倍体（DH）系1–4、1–20在萌发后11、19、33天三个时间点的样本。