CarrotOmics Status Report
Organisms
Currently 1,920 organisms from 406 genera in 8 families in the Apiales taxonomic order are present in CarrotOmics.
They can be viewed at the organism search page.
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, unless the number is greater than 100. For these organisms, view accessions using the germplasm search page.
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, unless the number is greater than 100. For these organisms, view accessions using the germplasm search page.
Germplasm and BioSamples
| Accessions | Collection Name | Collection Abbreviation |
|---|---|---|
| 1,071 | CarrotOmics | CarrotOmics |
| 5,945 | GRIN | GRIN Accession |
| 74 | GRIN-Global-CA | GRIN-Global-CA Accession |
| 5 | Indian Agricultural Research Institute | IARI |
| 3 | INTA | INTA |
| 497 | Leibniz Institute of Plant Genetics and Crop Plant Research | DEU146 |
| 9 | MSUGermplasmRelease | MSU Germplasm |
| 24 | University of Wisconsin - Madison | UW-Madison |
| 50 | USDAGermplasmRelease | USDA Germplasm |
| 292 | VCDNA27 | VCDNA27 |
| 10 | WARF | WARF |
| 1,545 | Warwick Crop Centre – Genetic Resources Unit | GBR006 |
| 2,901 | "BioSample" accessions | |
| 12,426 | Total |
View more information about the collections collection search page.
Geolocation data or origin country is loaded when available.
NCBI Data
Currently 2,900 NCBI biosamples, 224 projects, and 15 assemblies from the Apiales have been loaded into CarrotOmics.
Biosamples can be searched using the biosample search page, and biosample pages have links to Sequence Read Archive (SRA) accessions when those exist.
Phenotypic Data
Observations of the following phenotypes are currently available in CarrotOmics.
This list consists of 121 quantitative traits, 54 qualitative traits, 100 QTL, and 16 Mendelian trait loci
There are 62,108 phenotypic observations (4,051 counting replications) from 17,223 samples representing 204 different species or subspecies.
| Observations | Trait |
|---|---|
| 2,334 | alternaria dauci disease resistance |
| 1,148 | Canopy Coverage 100 DAS |
| 1,961 | Canopy Coverage 50 DAS |
| 675 | Canopy Coverage 80 DAS |
| 1,763 | Canopy Height 100 DAS |
| 1,369 | Canopy Height 40 DAS |
| 3,263 | Canopy Height 80 DAS |
| 1,287 | Canopy height at harvest |
| 2,055 | CarrotOmics Flowering Habit |
| 190 | Early Seedling Cell Membrane Stability Control |
| 190 | Early Seedling Cell Membrane Stability Control Standard Error |
| 190 | Early Seedling Cell Membrane Stability Stress |
| 190 | Early Seedling Cell Membrane Stability Stress Standard Error |
| 190 | Early Seedling Relative Cell Injury |
| 190 | Early Seedling Relative Cell Injury Rank |
| 663 | GRIN ANTHER COLOR |
| 10 | GRIN ANTHOCYANIN ROOT COLOR |
| 535 | GRIN ANTHOCYANINS IN THE PETALS |
| 729 | GRIN ANTHOCYANINS ON THE STEM |
| 253 | GRIN BARBS AT TIPS OF SPINES |
| 303 | GRIN BLADE SHAPE OF BASAL LEAF |
| 270 | GRIN BRACT LENGTH |
| 254 | GRIN BRACT LOBE PAIRS |
| 270 | GRIN BRACT WIDTH |
| 4 | GRIN COMMENT |
| 420 | GRIN Core Color |
| 13 | GRIN Core Size 1 |
| 44 | GRIN Core Size 2 |
| 89 | GRIN Crown width |
| 103 | GRIN DAYS STEM ELONGATION TO FLOWER |
| 103 | GRIN DAYS TO END OF FLOWERING |
| 103 | GRIN DAYS TO HARVEST |
| 103 | GRIN DAYS TO MATURITY |
| 103 | GRIN DAYS TO START OF FLOWERING |
| 103 | GRIN DAYS TO STEM ELONGATION |
| 103 | GRIN ESSENTIAL OIL CONTENT IN % |
| 103 | GRIN FATTY ACID CONTENT IN % |
| 383 | GRIN Flesh Color |
| 22 | GRIN Flower Color |
| 103 | GRIN FLOWERING RANGE |
| 257 | GRIN FLOWER RAY NUMBER |
| 358 | GRIN Foliage Color |
| 304 | GRIN Foliage Texture |
| 89 | GRIN Growth habit |
| 253 | GRIN HAIRS AT BASE OF PRIMARY SPINE |
| 89 | GRIN Height |
| 6,480 | GRIN HUNDRED SEED WEIGHT |
| 35 | GRIN HYPOCOTYL PIGMENTATION |
| 428 | GRIN INSERTION ANGLE BASAL LEAF |
| 302 | GRIN INVOLUCRAL BRACT POSITION |
| 76 | GRIN Keeping quality |
| 89 | GRIN Leaf color |
| 89 | GRIN Leafiness |
| 399 | GRIN LEAF PUBESCENCE |
| 394 | GRIN LEAF TYPE |
| 103 | GRIN LENGTH OF LONGEST BASAL LEAF |
| 255 | GRIN LENGTH OF SECONDARY RIB SPINES |
| 297 | GRIN Life Cycle |
| 361 | GRIN MATURE LEAF LENGTH |
| 361 | GRIN MATURE LEAF WIDTH |
| 361 | GRIN MATURE PETIOLE LENGTH |
| 359 | GRIN MATURE PETIOLE THICKNESS |
| 22 | GRIN MAXIMUM CORE SIZE |
| 16 | GRIN Maximum Secondary Root |
| 22 | GRIN MAXIMUM STORAGE ROOT LENGTH |
| 22 | GRIN MAXIMUM STORAGE ROOT WEIGHT |
| 22 | GRIN MEAN CORE SIZE |
| 22 | GRIN MEAN STORAGE ROOT LENGTH |
| 22 | GRIN MEAN STORAGE ROOT WEIGHT |
| 22 | GRIN MINIMUM CORE SIZE |
| 110 | GRIN Minimum Secondary Root |
| 22 | GRIN MINIMUM STORAGE ROOT LENGTH |
| 22 | GRIN MINIMUM STORAGE ROOT WEIGHT |
| 22 | GRIN NATURE OF STORAGE ORGAN |
| 256 | GRIN NO. OF SPINES ON SECONDARY RIB |
| 103 | GRIN NUMBER OF BASAL LEAVES |
| 271 | GRIN NUMBER OF BRACT POINTS |
| 89 | GRIN Number of petioles |
| 103 | GRIN NUMBER OF UMBELS |
| 358 | GRIN PEDUNCLE PUBESCENCE |
| 103 | GRIN PERCENTAGE OF SPLIT FRUIT/ WT |
| 139 | GRIN Percent Bolt 1st Year |
| 323 | GRIN PETAL COLOR |
| 269 | GRIN PETAL LENGTH CENTRAL |
| 269 | GRIN PETAL LENGTH PERIPHERAL |
| 88 | GRIN Petiole color |
| 89 | GRIN Petiole diameter |
| 499 | GRIN PETIOLE HAIRINESS |
| 89 | GRIN Petiole length |
| 483 | GRIN PETIOLE SHAPE |
| 87 | GRIN Petiole type |
| 412 | GRIN PIGMENTED CENTRAL UMBEL |
| 335 | GRIN PIGMENTED CENTRAL UMBEL COLOR |
| 272 | GRIN PLANT HEIGHT |
| 103 | GRIN PLANT HEIGHT IN CM |
| 89 | GRIN Plant vigor |
| 89 | GRIN Plant width |
| 103 | GRIN PLANT YIELD, GRAMS OF SEEDS |
| 270 | GRIN PRIMARY UMBEL DIAMETER |
| 271 | GRIN PRIMARY UMBEL FLOWER HEIGHT |
| 260 | GRIN Root Diameter 1 |
| 283 | GRIN Root Diameter 2 |
| 12 | GRIN ROOT GREENING |
| 260 | GRIN Root Length 1 |
| 284 | GRIN Root Length 2 |
| 22 | GRIN ROOT PHLOEM CAROTENOID COLOR |
| 530 | GRIN Root Shape |
| 28 | GRIN ROOT SKIN PIGMENTATION / COLOR |
| 238 | GRIN Root Weight 1 |
| 256 | GRIN Root Weight 2 |
| 40 | GRIN ROOT XYLEM CAROTENOID COLOR |
| 50 | GRIN Secondary Root Surface 1 |
| 28 | GRIN Secondary Root Surface 2 |
| 268 | GRIN SECONDARY UMBEL DIAMETER |
| 261 | GRIN SEED LENGTH |
| 4 | GRIN Seedling Vigor 1 |
| 7 | GRIN Seedling Vigor 2 |
| 261 | GRIN SEED WIDTH |
| 103 | GRIN SHAPE OF THE FRUIT |
| 401 | GRIN Skin Color |
| 258 | GRIN SPINE CONFLUENCY |
| 253 | GRIN SPINE CURVATURE |
| 41 | GRIN Split petioles |
| 266 | GRIN STAMEN LENGTH |
| 268 | GRIN STEM DIAMETER |
| 269 | GRIN STIPULE WIDTH |
| 22 | GRIN STORAGE ROOT DIAMETER |
| 24 | GRIN STORAGE ROOT SHAPE |
| 33 | GRIN STORAGE ROOT SURFACE |
| 24 | GRIN STORAGE ROOT TIP SHAPE |
| 91 | GRIN STYLE LENGTH |
| 91 | GRIN STYLOPODIUM LENGTH |
| 91 | GRIN STYLOPODIUM WIDTH |
| 500 | GRIN UMBEL SHAPE - FULL BLOOM |
| 321 | GRIN UMBEL SHAPE - MATURE SEED |
| 88 | GRIN Uniformity |
| 103 | GRIN WEIGHT OF 1000 FRUITS IN GRAMS |
| 91 | GRIN WIDTH SEC RIB SPINE CONFLUENCE |
| 396 | Harsh flavor at harvest |
| 587 | HUNDRED SEED WEIGHT |
| 190 | Late Seedling Cell Membrane Stability Control |
| 190 | Late Seedling Cell Membrane Stability Control Standard Error |
| 190 | Late Seedling Cell Membrane Stability Stress |
| 190 | Late Seedling Cell Membrane Stability Stress Standard Error |
| 190 | Late Seedling Relative Cell Injury |
| 190 | Late Seedling Relative Cell Injury Rank |
| 253 | Mean absolute decrease (AD) in percent seed germination after 10 days due to -0.58 MPa PEG-6000 solution drought stress |
| 294 | Mean absolute decrease in percent seed germination after 18 days due to 150 mM NaCl solution salt stress |
| 293 | Mean absolute decrease in percent seed germination after 18 days due to 35 ºC heat stress |
| 253 | Mean drought tolerance index (DTI) for percent seed germination after 10 days due to -0.58 MPa PEG-6000 solution drought stress |
| 293 | Mean heat tolerance index (HTI) for percent seed germination after 18 days due to 35 ºC heat stress |
| 294 | Mean inhibition index for percent seed germination after 18 days due to 150 mM NaCl solution salt stress |
| 293 | Mean inhibition index for percent seed germination after 18 days due to 35 ºC heat stress |
| 253 | Mean inhibition index (II) for percent seed germination after 10 days due to -0.58 MPa PEG-6000 solution drought stress |
| 253 | Mean percent seed germination after 10 days with -0.58 MPa PEG-6000 solution drought stress |
| 253 | Mean percent seed germination after 10 days without abiotic stress |
| 294 | Mean percent seed germination after 18 days with 150 mM NaCl solution salt stress |
| 293 | Mean percent seed germination after 18 days with 35 ºC heat stress |
| 587 | Mean percent seed germination after 18 days without abiotic stress |
| 294 | Mean salt tolerance index (STI) for percent seed germination after 18 days due to 150 mM NaCl solution salt stress |
| 4,039 | Percent Emergence 20 DAS |
| 1,874 | Percent Flowering 100 DAS |
| 978 | Percent Flowering 60 DAS |
| 253 | 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 | Rank of mean heat tolerance index (HTI) for percent seed germination after 18 days due to 35 ºC heat stress |
| 294 | Rank of mean salt tolerance index (STI) for percent seed germination after 18 days due to 150 mM NaCl solution salt stress |
| 253 | Relative drought tolerance (RDT) for percent seed germination after 10 days due to -0.58 MPa PEG-6000 solution drought stress |
| 293 | Relative heat tolerance for percent seed germination after 18 days due to 35 ºC heat stress |
| 294 | Relative salt tolerance for percent seed germination after 18 days due to 150 mM NaCl solution salt stress |
| 253 | Standard error of percent seed germination after 10 days with -0.58 MPa PEG-6000 solution drought stress |
| 253 | Standard error of percent seed germination after 10 days without abiotic stress |
| 294 | Standard error of percent seed germination after 18 days with 150 mM NaCl solution salt stress |
| 293 | Standard error of percent seed germination after 18 days with 35 ºC heat stress |
| 587 | Standard error of percent seed germination after 18 days without abiotic stress |
| 4,039 | Stand Count 20 DAS |
| 4,051 | Total |
Images
Images are viewable from individual germplasm accession pages, or searchable using the image search page (not yet implemented).
The Current status of images loaded in CarrotOmics is
The Current status of images loaded in CarrotOmics is
| Count | Source |
|---|---|
| 11,369 | GRIN Image |
| 7 | INTA |
| 11,376 | Total |
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
The following types of downloadable files are available
| Count | File Type |
|---|---|
| 1 | ACE |
| 7 | comma-delimited text file |
| 9 | FASTA format |
| 1 | GenBank format |
| 3 | Gene expression profile |
| 22 | GFF3 |
| 1 | hapmap |
| 36 | Image |
| 171 | microsoft excel xlsx file |
| 1 | microsoft word doc file |
| 1 | microsoft word docx file |
| 9 | NCBI Data Download FTP Link |
| 38 | newick |
| 7 | portable document format |
| 3 | tab-delimited text file |
| 4 | URL |
| 10 | VCF |
| 324 | Total |
Publications
41,915 publications from both PubMed, the National Agricultural Library, and other sources matching selected search terms have been loaded into CarrotOmics, and are searchable through the publication search page.
Specialty publication types such as theses (1,941) and variety release notices (40) are also available.
Specialty publication types such as theses (1,941) and variety release notices (40) are also available.
Markers and Linkage Maps
73 genetic linkage maps are present in CarrotOmics.
11,209 genetic markers, 352 quantitative trait loci (QTL), and 17 heritable mendelian trait loci (MTL) have been loaded and can be viewed with the Tripal Map Viewer.
Maps are listed in the genetic map search page.
Search for genetic markers on the genetic marker search page. Search for QTL on the QTL search page. Search for MTL on the heritable phenotypic marker search page.
Search for genetic markers on the genetic marker search page. Search for QTL on the QTL search page. Search for MTL on the heritable phenotypic marker search page.
Genomes
Waiting on reimplementation of JBrowse and BLAST.
Resequencing, Variants
The following sets of variants are available. Analysis descriptions or publications are avaliable from the linked files.
Phylogenetic Trees
Currently 60 trees from 18 publications have been loaded in CarrotOmics.
View them on the tree search page.
View them on the tree search page.