10.1534/g3.117.043067 Supplementary File S1.xlsx

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Description:

List of Supplementary Tables

Table S1: Filtered SNP polymorphisms in the 74146 carrot population, in a, h, b format, for Joinmap input.

Table S2: Primers used for fine mapping, sequencing DCAR_026175, and cleaved amplified polymorphic sequence (CAPs) marker production.

Table S3: Plant materials used for resequencing.

Table S4: Transcriptome mapping statistics for each technical replicate of Y₂Y₂ (yellow) and y₂y₂ (orange) carrots of population 74146. Orange and yellow highlighting indicates orange and yellow root samples, respectively. Within the sample name a "r" indicates a technical replicate that was re-run on the Illumina sequencer and the number after the dot indicates time point one or time point two. Samples without a NCBI BioSample accession number were not used in downstream analyses. See the erratum excel file for a version of this table with corrected NCBI biosample accession numbers.

Table S5. Pearson correlation between RNASeq samples. High correlations are in red and low correlations are in green. Sample names correspond to those in Supplementary Table 4.

Table S6. Pearson correlation, after correction, between RNASeq samples. High correlations are in red and low correlations are in green. Sample names correspond to those in Supplementary Table 4.

Table S7: Phenotypic information for root color in population 74146. Samples not used in downstream analyses were not assigned an NCBI BioSample number.

Table S8. Distribution of GBS markers across the nine carrot chromosomes in family 74146.

Table S9. GLM output for the beta-carotene trait. P-values are in bold.

Table S10. Distribution of filtered SNPs across the nine carrot linkage groups in family 74146.

Table S11. Position of filtered SNPs across the nine carrot linkage groups in family 74146. Chromosomes 1 through 9 correspond to NCBI accessions CM004278 through CM004286.

Table S12: Summary annotation of predicted genes located in the genomic region associated with carotenoid accumulation in the 74146 population. Cells highlighted in yellow represent predicted genes differentially expressed between yellow and orange samples at time point one, cells in blue are differentially expressed at time point two and those in orange are differentially expressed at both time points.

Table S13: Top two Blastp hits, in SwissProt and trEMBL for the 72 candidate genes in the Y₂ region.

Table S14. Carotenoid HPLC data for samples used in the RNA-sequencing analysis. Orange biological and technical replicates are highlighted with orange and yellow replicates are shown in yellow. Dash one (-1) or two (-2) indicates time point one or time point two.

Table S15. Number of differentially expressed genes (DEGs) detected in the whole carrot genome for each pairwise comparison between Orange (O) and Yellow (Y) at time point one and time point two.

Table S16. Gene annotations (ID) of DEGs detected in the whole carrot genome for each pairwise comparison between Orange (O) and Yellow (Y) at time point one and time point two.

Table S17. Number of DEGs detected in the isoprenoid pathway and Y₂ QTL region in the carrot genome for each pairwise comparison between Orange (O) and Yellow (Y) at time point one and time point two.

Table S18. Annotation of DEGs detected in the isoprenoid pathway and Y₂ QTL region in the carrot genome for each pairwise comparison between Orange (O) and Yellow (Y) at time point one and time point two. Samples highlighted in blue are differentially expressed at one time point, between yellow and orange samples, while samples in yellow are differentailly expressed at both time points.

Table S19. Number of common DEGs detected in the carrot genome, isoprenoid pathway and Y₂ QTL region for each pairwise comparison between Orange (O) and Yellow (Y) carrots at time point one and time point two.

Table S20. Annotation of DEGs detected in the Y₂ QTL and isoprenoid pathway between Orange (O) and Yellow (Y) at both time points.

Table S21. Plant introductions used in CAPs marker analysis.

References:

The following records refer to this file:


Journal Article	Fine Mapping, Transcriptome Analysis, and Marker Development for Y₂, the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.).

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