CarrotOmics Status Report

Data Overview

See the Data Overview for counts of various types of data present in CarrotOmics that are updated weekly.

The numbers in this report are obtained from the database and are always current and up-to-date.

Organisms

Currently 1,919 organisms from 406 genera in 8 families in the Apiales taxonomic order are present in CarrotOmics. They are listed here

Both GRIN taxon and NCBI taxon identifier numbers are present as Cross References when available.

Organism pages list all available germplasm accessions and breeding stocks as well as biomaterial references.

Germplasm and BioSamples

Currently, accessions or stocks from the following germplasm collections have been loaded:

  • 1,061 from "A collection for any germplasm referenced in CarrotOmics but not available in any other public database" (CarrotOmics)
  • 74 from "Canadian national genebank information system" (GRIN-Global-CA)
  • 497 from "Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Germany" (DEU146)
  • 5 from "Indian Agriculture Research Institute (IARI)" (Indian Agricultural Research Institute)
  • 3 from "Instituto Nacional de Tecnología Agropecuaria" (INTA)
  • 9 from "Michigan State University Germplasm Releases" (MSUGermplasmRelease)
  • 50 from "United States Department of Agriculture Germplasm Releases" (USDAGermplasmRelease)
  • 24 from "University of Wisconsin - Madison Carrot, Onion, and Table Beet Breeding and Genetics Program" (University of Wisconsin - Madison)
  • 5,945 from "USDA-ARS Germplasm Resources Information Network (GRIN)" (GRIN)
  • 292 from "Vegetable Cultivar Descriptions for North America - Lists 1-27 Combined" (VCDNA27)
  • 1,545 from "Warwick Genetic Resources Unit, United Kingdom" (GBR006)
  • 10 from "Wisconsin Alumni Research Foundation" (WARF)
  • 2,899 "BioSample" accessions

These 12,414 germplasm accessions and biosamples represent 1,039 different Apiales species or subspecies from 5 families

These collections are described in more detail here

Geolocation data or origin country is loaded when available

NCBI Data

Currently 2,898 NCBI biosamples, 222 projects, and 15 assemblies from the Apiales have been loaded into CarrotOmics

Biosamples can be searched using Tripal Megasearch or using Germplasm and BioSample Search, and biosample pages have links to Sequence Read Archive (SRA) accessions when those exist

Phenotypic Data

Phenotypic traits are searchable using Quantitative Trait Search, Qualitative Trait Search, or Tripal MegaSearch

Observations of the following phenotypes are currently available in CarrotOmics

  • 2,334 observations for "alternaria dauci disease resistance"
  • 1,287 observations for "Canopy height at harvest"
  • 190 observations for "Early Seedling Cell Membrane Stability Control"
  • 190 observations for "Early Seedling Cell Membrane Stability Control Standard Error"
  • 190 observations for "Early Seedling Cell Membrane Stability Stress"
  • 190 observations for "Early Seedling Cell Membrane Stability Stress Standard Error"
  • 190 observations for "Early Seedling Relative Cell Injury"
  • 190 observations for "Early Seedling Relative Cell Injury Rank"
  • 663 observations for "GRIN ANTHER COLOR"
  • 10 observations for "GRIN ANTHOCYANIN ROOT COLOR"
  • 535 observations for "GRIN ANTHOCYANINS IN THE PETALS"
  • 729 observations for "GRIN ANTHOCYANINS ON THE STEM"
  • 253 observations for "GRIN BARBS AT TIPS OF SPINES"
  • 303 observations for "GRIN BLADE SHAPE OF BASAL LEAF"
  • 270 observations for "GRIN BRACT LENGTH"
  • 254 observations for "GRIN BRACT LOBE PAIRS"
  • 270 observations for "GRIN BRACT WIDTH"
  • 4 observations for "GRIN COMMENT"
  • 420 observations for "GRIN Core Color"
  • 13 observations for "GRIN Core Size 1"
  • 44 observations for "GRIN Core Size 2"
  • 89 observations for "GRIN Crown width"
  • 103 observations for "GRIN DAYS STEM ELONGATION TO FLOWER"
  • 103 observations for "GRIN DAYS TO END OF FLOWERING"
  • 103 observations for "GRIN DAYS TO HARVEST"
  • 103 observations for "GRIN DAYS TO MATURITY"
  • 103 observations for "GRIN DAYS TO START OF FLOWERING"
  • 103 observations for "GRIN DAYS TO STEM ELONGATION"
  • 103 observations for "GRIN ESSENTIAL OIL CONTENT IN %"
  • 103 observations for "GRIN FATTY ACID CONTENT IN %"
  • 383 observations for "GRIN Flesh Color"
  • 22 observations for "GRIN Flower Color"
  • 103 observations for "GRIN FLOWERING RANGE"
  • 257 observations for "GRIN FLOWER RAY NUMBER"
  • 358 observations for "GRIN Foliage Color"
  • 304 observations for "GRIN Foliage Texture"
  • 89 observations for "GRIN Growth habit"
  • 253 observations for "GRIN HAIRS AT BASE OF PRIMARY SPINE"
  • 89 observations for "GRIN Height"
  • 6,480 observations for "GRIN HUNDRED SEED WEIGHT"
  • 35 observations for "GRIN HYPOCOTYL PIGMENTATION"
  • 428 observations for "GRIN INSERTION ANGLE BASAL LEAF"
  • 302 observations for "GRIN INVOLUCRAL BRACT POSITION"
  • 76 observations for "GRIN Keeping quality"
  • 89 observations for "GRIN Leaf color"
  • 89 observations for "GRIN Leafiness"
  • 399 observations for "GRIN LEAF PUBESCENCE"
  • 394 observations for "GRIN LEAF TYPE"
  • 103 observations for "GRIN LENGTH OF LONGEST BASAL LEAF"
  • 255 observations for "GRIN LENGTH OF SECONDARY RIB SPINES"
  • 297 observations for "GRIN Life Cycle"
  • 361 observations for "GRIN MATURE LEAF LENGTH"
  • 361 observations for "GRIN MATURE LEAF WIDTH"
  • 361 observations for "GRIN MATURE PETIOLE LENGTH"
  • 359 observations for "GRIN MATURE PETIOLE THICKNESS"
  • 22 observations for "GRIN MAXIMUM CORE SIZE"
  • 16 observations for "GRIN Maximum Secondary Root"
  • 22 observations for "GRIN MAXIMUM STORAGE ROOT LENGTH"
  • 22 observations for "GRIN MAXIMUM STORAGE ROOT WEIGHT"
  • 22 observations for "GRIN MEAN CORE SIZE"
  • 22 observations for "GRIN MEAN STORAGE ROOT LENGTH"
  • 22 observations for "GRIN MEAN STORAGE ROOT WEIGHT"
  • 22 observations for "GRIN MINIMUM CORE SIZE"
  • 110 observations for "GRIN Minimum Secondary Root"
  • 22 observations for "GRIN MINIMUM STORAGE ROOT LENGTH"
  • 22 observations for "GRIN MINIMUM STORAGE ROOT WEIGHT"
  • 22 observations for "GRIN NATURE OF STORAGE ORGAN"
  • 256 observations for "GRIN NO. OF SPINES ON SECONDARY RIB"
  • 103 observations for "GRIN NUMBER OF BASAL LEAVES"
  • 271 observations for "GRIN NUMBER OF BRACT POINTS"
  • 89 observations for "GRIN Number of petioles"
  • 103 observations for "GRIN NUMBER OF UMBELS"
  • 358 observations for "GRIN PEDUNCLE PUBESCENCE"
  • 103 observations for "GRIN PERCENTAGE OF SPLIT FRUIT/ WT"
  • 139 observations for "GRIN Percent Bolt 1st Year"
  • 323 observations for "GRIN PETAL COLOR"
  • 269 observations for "GRIN PETAL LENGTH CENTRAL"
  • 269 observations for "GRIN PETAL LENGTH PERIPHERAL"
  • 88 observations for "GRIN Petiole color"
  • 89 observations for "GRIN Petiole diameter"
  • 499 observations for "GRIN PETIOLE HAIRINESS"
  • 89 observations for "GRIN Petiole length"
  • 483 observations for "GRIN PETIOLE SHAPE"
  • 87 observations for "GRIN Petiole type"
  • 412 observations for "GRIN PIGMENTED CENTRAL UMBEL"
  • 335 observations for "GRIN PIGMENTED CENTRAL UMBEL COLOR"
  • 272 observations for "GRIN PLANT HEIGHT"
  • 103 observations for "GRIN PLANT HEIGHT IN CM"
  • 89 observations for "GRIN Plant vigor"
  • 89 observations for "GRIN Plant width"
  • 103 observations for "GRIN PLANT YIELD, GRAMS OF SEEDS"
  • 270 observations for "GRIN PRIMARY UMBEL DIAMETER"
  • 271 observations for "GRIN PRIMARY UMBEL FLOWER HEIGHT"
  • 260 observations for "GRIN Root Diameter 1"
  • 283 observations for "GRIN Root Diameter 2"
  • 12 observations for "GRIN ROOT GREENING"
  • 260 observations for "GRIN Root Length 1"
  • 284 observations for "GRIN Root Length 2"
  • 22 observations for "GRIN ROOT PHLOEM CAROTENOID COLOR"
  • 530 observations for "GRIN Root Shape"
  • 28 observations for "GRIN ROOT SKIN PIGMENTATION / COLOR"
  • 238 observations for "GRIN Root Weight 1"
  • 256 observations for "GRIN Root Weight 2"
  • 40 observations for "GRIN ROOT XYLEM CAROTENOID COLOR"
  • 50 observations for "GRIN Secondary Root Surface 1"
  • 28 observations for "GRIN Secondary Root Surface 2"
  • 268 observations for "GRIN SECONDARY UMBEL DIAMETER"
  • 261 observations for "GRIN SEED LENGTH"
  • 4 observations for "GRIN Seedling Vigor 1"
  • 7 observations for "GRIN Seedling Vigor 2"
  • 261 observations for "GRIN SEED WIDTH"
  • 103 observations for "GRIN SHAPE OF THE FRUIT"
  • 401 observations for "GRIN Skin Color"
  • 258 observations for "GRIN SPINE CONFLUENCY"
  • 253 observations for "GRIN SPINE CURVATURE"
  • 41 observations for "GRIN Split petioles"
  • 266 observations for "GRIN STAMEN LENGTH"
  • 268 observations for "GRIN STEM DIAMETER"
  • 269 observations for "GRIN STIPULE WIDTH"
  • 22 observations for "GRIN STORAGE ROOT DIAMETER"
  • 24 observations for "GRIN STORAGE ROOT SHAPE"
  • 33 observations for "GRIN STORAGE ROOT SURFACE"
  • 24 observations for "GRIN STORAGE ROOT TIP SHAPE"
  • 91 observations for "GRIN STYLE LENGTH"
  • 91 observations for "GRIN STYLOPODIUM LENGTH"
  • 91 observations for "GRIN STYLOPODIUM WIDTH"
  • 500 observations for "GRIN UMBEL SHAPE - FULL BLOOM"
  • 321 observations for "GRIN UMBEL SHAPE - MATURE SEED"
  • 88 observations for "GRIN Uniformity"
  • 103 observations for "GRIN WEIGHT OF 1000 FRUITS IN GRAMS"
  • 91 observations for "GRIN WIDTH SEC RIB SPINE CONFLUENCE"
  • 396 observations for "Harsh flavor at harvest"
  • 587 observations for "HUNDRED SEED WEIGHT"
  • 190 observations for "Late Seedling Cell Membrane Stability Control"
  • 190 observations for "Late Seedling Cell Membrane Stability Control Standard Error"
  • 190 observations for "Late Seedling Cell Membrane Stability Stress"
  • 190 observations for "Late Seedling Cell Membrane Stability Stress Standard Error"
  • 190 observations for "Late Seedling Relative Cell Injury"
  • 190 observations for "Late Seedling Relative Cell Injury Rank"
  • 253 observations for "Mean absolute decrease (AD) in percent seed germination after 10 days due to -0.58 MPa PEG-6000 solution drought stress"
  • 294 observations for "Mean absolute decrease in percent seed germination after 18 days due to 150 mM NaCl solution salt stress"
  • 293 observations for "Mean absolute decrease in percent seed germination after 18 days due to 35 ºC heat stress"
  • 253 observations for "Mean drought tolerance index (DTI) for percent seed germination after 10 days due to -0.58 MPa PEG-6000 solution drought stress"
  • 293 observations for "Mean heat tolerance index (HTI) for percent seed germination after 18 days due to 35 ºC heat stress"
  • 294 observations for "Mean inhibition index for percent seed germination after 18 days due to 150 mM NaCl solution salt stress"
  • 293 observations for "Mean inhibition index for percent seed germination after 18 days due to 35 ºC heat stress"
  • 253 observations for "Mean inhibition index (II) for percent seed germination after 10 days due to -0.58 MPa PEG-6000 solution drought stress"
  • 253 observations for "Mean percent seed germination after 10 days with -0.58 MPa PEG-6000 solution drought stress"
  • 253 observations for "Mean percent seed germination after 10 days without abiotic stress"
  • 294 observations for "Mean percent seed germination after 18 days with 150 mM NaCl solution salt stress"
  • 293 observations for "Mean percent seed germination after 18 days with 35 ºC heat stress"
  • 587 observations for "Mean percent seed germination after 18 days without abiotic stress"
  • 294 observations for "Mean salt tolerance index (STI) for percent seed germination after 18 days due to 150 mM NaCl solution salt stress"
  • 253 observations for "Rank of mean drought tolerance index (DTI) for percent seed germination after 10 days due to -0.58 MPa PEG-6000 solution drought stress"
  • 293 observations for "Rank of mean heat tolerance index (HTI) for percent seed germination after 18 days due to 35 ºC heat stress"
  • 294 observations for "Rank of mean salt tolerance index (STI) for percent seed germination after 18 days due to 150 mM NaCl solution salt stress"
  • 253 observations for "Relative drought tolerance (RDT) for percent seed germination after 10 days due to -0.58 MPa PEG-6000 solution drought stress"
  • 293 observations for "Relative heat tolerance for percent seed germination after 18 days due to 35 ºC heat stress"
  • 294 observations for "Relative salt tolerance for percent seed germination after 18 days due to 150 mM NaCl solution salt stress"
  • 253 observations for "Standard error of percent seed germination after 10 days with -0.58 MPa PEG-6000 solution drought stress"
  • 253 observations for "Standard error of percent seed germination after 10 days without abiotic stress"
  • 294 observations for "Standard error of percent seed germination after 18 days with 150 mM NaCl solution salt stress"
  • 293 observations for "Standard error of percent seed germination after 18 days with 35 ºC heat stress"
  • 587 observations for "Standard error of percent seed germination after 18 days without abiotic stress"

There are 38,944 phenotypic observations (43,710 counting replications) from 11,071 samples representing 204 different species or subspecies

Images

Images are viewable from individual germplasm accession pages, or searchable using Image Search
The Current status of images loaded in CarrotOmics is:

  • "GRIN Image": 11,369 images
  • "INTA": 7 images

Total = 11,376

Downloadable Files

Data files associated with content on CarrotOmics that are available for download can be searched on the File Search page
The following types of downloadable files are available:

  • "ACE": 1 file
  • "comma-delimited text file": 4 files
  • "FASTA format": 9 files
  • "GenBank format": 1 file
  • "Gene expression profile": 3 files
  • "GFF3": 22 files
  • "hapmap": 1 file
  • "Image": 36 files
  • "microsoft excel xlsx file": 170 files
  • "microsoft word doc file": 1 file
  • "microsoft word docx file": 1 file
  • "NCBI Data Download FTP Link": 9 files
  • "newick": 38 files
  • "portable document format": 6 files
  • "tab-delimited text file": 2 files
  • "URL": 2 files
  • "VCF": 8 files

Total = 314

Publications

Publications from both PubMed and the National Agricultural Library matching selected search terms have been loaded with the Tripal Publication Importer, and are searchable through either Publication Search or Tripal MegaSearch

37 Variety release notices were loaded with Chado bulk loaders

A small number of publications were entered manually or with the mainlab chado loader, including 1,940 theses.

Currently there are 37,308 publications in Carrotomics.

Markers and Linkage Maps

73 linkage maps are present in CarrotOmics, the oldest are the 1984 celery isozyme maps

11,209 markers, 352 Quantitative trait loci, and 17 Mendelian trait loci have been loaded and can be viewed using the Tripal MapViewer module, and QTL and MTL can be searched using QTL search or Tripal MegaSearch

6,641 marker to genome position correspondences have been loaded

Genomes

JBrowse is installed and loaded with the published carrot genome and the gene predictions from the genome paper (DCAR) as well as NCBI gene predictions (LOC)

Blast searches are functional

All JBrowse tracks link to a CarrotOmics analysis page which gives detailed information about the track

ToDo: Load additional tracks into JBrowse

ToDo: When it is published, load the new carrot genome

Resequencing, Variants

The following sets of variants are available. Analysis descriptions or publications are avaliable from the linked files:

ToDo: Make a list of other published data sets.

ToDo: Load other published data sets.

Expression

Expression data and p-values from the genome paper have been loaded, this is viewable from individual gene pages, or as a heatmap

ToDo: Make a list of other published expression data and load into CarrotOmics This has been started

Phylogenetic Trees

Currently, 60 trees from 18 publications have been loaded in CarrotOmics, view them here

ToDo: Load additional trees from TreeBASE

Search Functions

All search functions in the Search menu are functional, including Tripal MegaSearch.

Data Downloads

The Tripal File module is used to make data files accessible for download directly from the corresponding analysis, for example DCAR gene prediction analysis.

Other

ToDo: Home page, update sponsor logos and information