Tripal File

A set of 110,155 Single nucleotide polymorphisms derived from Genotyping-By-Sequencing of 65 taxa. Missing data have been imputed using Beagle v4.1

Supplemental Dataset S2. Growth of carrot wild relatives in fields in Bangladesh and Pakistan exposed to heat, drought, and salinity, and in the greenhouse. Para-salinity (Para-STI), -drought ((Para-DTI) and -heat (Para-HTI) tolerance index scores during field growth and HTI and STI during seed germination (Germ) in the lab (Bolton et al., 2019, Bolton and Simon, 2019) are included; and entries producing seed in the field are noted.

Variants derived from Genotyping-By-Sequencing of 65 taxa. This is the raw, unfiltered file from TASSEL-GBS, and contains 187,376 variants.

Variants derived from Genotyping-By-Sequencing of 65 taxa were filtered with vcftools to include only those markers with <0.50 missing data and a minor-allele frequency of >0.05. This provided a set of 110,155 Single nucleotide polymorphisms available for initial genomic analyses.

Each sample used in this analysis has experiment specific reference numbers. This file can be used to convert the reference number to a plant introduction or accession name.

This file resulted from combining genotyping data (by position) from the Resequencing data and GBS data in the two trials included in this experiment.

The genotypic data used in association analyses including variant name and the allele for each sample included in the analysis.

Has name and physical position of genetic variants used in association analysis.

This file contains the p-values for each SNP included in association analyses of carrot color, total carotenoids and alpha carotene content.

Authors' original version of figure 1 from the publication

This VCF file was generated using Genotyping-by-sequencing (GBS) to genotype the carrot F3 mapping population in this publication.

Fig. S1 Phenotypic means for carotenoids across each of the three environments tested. (a) β-carotene, (b) α-carotene, (c) lutein, (d) phytoene, (e) ζ-carotene, (f) total carotenoids, (g) the ratio of β-carotene to total carotenoids. Values are in μg/g DW except for β:total. CA2018: California 2018, CA2019: California 2019, and WIGH2018: Wisconsin Greenhouse 2018

Fig. S2 Linkage groups for the B493 X Z007 Population. The distribution of 1,668 markers is plotted according to their respective linkage group. The position of known carotenoid pathway genes is indicated in red relative to the closest marker in the linkage map. The…

Table S1: Genomic coordinates and predicted amino acid changes of SNPs identified within the Or CDS of the wild parent (Z007) relative to the reference genome (representative of cultivated carrots)

Table S2: Phenotypic means, standard deviations (SD), minimum, and maximum values for carotenoids by Or genotypic classes (A = Orc, B = Orw). Values are in µg/g except for beta-carotene : total.

Table S3: Phenotypic means, standard deviations (SD), minimum, and maximum values for carotenoids by environment

Table S4: Summary of the genetic linkage map in cM for the B493 X Z007 F3 Population

Table S5: Summary of the genetic linkage map in physical coordinates…

Brainard, Scott, 2021, "2016 diversity panel images", https://doi.org/10.7910/DVN/UYMLSY, Harvard Dataverse, V1

Straightened, deptipped binary masks of roots grown in WI in 2016

Brainard, Scott, 2021, "2018 diversity panel images", https://doi.org/10.7910/DVN/MD1EEQ, Harvard Dataverse, V1

Straightened, deptipped binary masks of roots grown in WI in 2018

Brainard, Scott, 2021, "2019 diversity panel images", https://doi.org/10.7910/DVN/RQG780, Harvard Dataverse, V1

Straightened, deptipped binary masks of roots grown in two replicates in CA in 2018-2019

Brainard, Scott, 2021, "Genotype and phenotype files used in GWAS", https://doi.org/10.7910/DVN/2JUUR0, Harvard Dataverse, V1, UNF:6:BIT8gLxI1YyseHCVMB2iFg== [fileUNF]

.csv files formatted according to the standards required by GWASpoly v2.07

Brainard, Scott, 2021, "VCF file containing SNP markers", https://doi.org/10.7910/DVN/4HCYWK, Harvard Dataverse, V2

Markers from PI Collection

Supplementary Tables 1–46.

Supplementary Figs 1–10 and Note.

List of Supplementary Tables

Expression data from merged technical replicates analysis. Expression data from is derived from the cufflinks "cds_exp.diff" file.

Phenotypic data from this publication. This is the mainlab chado loader file used to load the data into CarrotOmics.

Phenotypic data from this publication. This is the mainlab chado loader file used to load the data into CarrotOmics.

Phenotypic data from this publication. This is the mainlab chado loader file used to load the data into CarrotOmics.

Phenotypic data from this publication. This is the mainlab chado loader file used to load the data into CarrotOmics.

This file provides all accessions (plant introductions) evaluated, affiliated raw phenotype data for each year, and marginal means from shoot growth in Loarca et al., 2024a (doi: 10.3389/fpls.2024.1342512) and flowering habit in Loarca et al., 2024b (doi: 10.3389/fpls.2024.1342513). Phenotype data for all accessions were collected from Hancock Agricultural Research Station from 2016 - 2018. Seed viability-% and 100-seed weight (g) values for each accession were sourced from GRIN passport data and were generated at the North Central Regional Plant Introduction Station (NCRPIS) in Ames IA.

Additional file 1:

Table S1 – Individual genotype transcriptome assemblies. Summary of the number of contigs and singletons obtained for the B493, B493×QAL, B6274 and B7262 individual transcriptome assemblies using different assembly methods.

Table S2 – Combined transcriptome assemblies. Summary of the B493, B493×QAL, B6274, and B7262 combined transcriptome assemblies.

Table S4 – Transposable element superfamilies and families represented in ESTs.

Table S7 – Distribution of motif length in the SSR dataset.

Table S8 – Comparison of SNP validation rates using intron prediction.

Table S9 – Polymorphic SNPs tested in two mapping populations.…

ACE file from CAP3 assembly from the publication "De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity".

This file was not included in the publication, and was provided by the publication authors.

This fasta file contains 58,751 nucleotide sequences from "Additional file 2" from the publication "De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity"

Linkage map markers and information.