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New to the database?
What are you interested in? For General Help
Upload an experimental field trial into the database that you have saved on your computer in Excel
Design a completely new experimental field trial in the database
Catalog your available seed inventory into the database
Upload phenotypic data into the database that you have saved on your computer in Excel
Plan tissue sampling
Upload crosses and crossing information into the database
Print barcode labels for my experiment (for your plots or plants or tissue samples in the field, or for your 96 well plate and tissue samples)
Analyze phenotypic performance across trials
Prepare a 96 or 384 well plate for a genotyping experiment
Upload VCF genotypic data
Tissue Sampling
- Intro
- Sampling Level
- Select a field trial
- Plant Entries
- Create Tissue Sample Entries
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This workflow will guide you through tissue sampling an experiment
Tissue samples collected from the field are linked to a single plant, which is in turn linked to a single plot.
Many tissue samples can be created for each plant.
Each tissue sample has a globally unique name.
A unique tissue sample is present in each well of a genotyping plate (96 or 384 well plates).
The tissue sample in a 96 well plate can originate from another tissue sample name, plant name, plot name, or accession name.
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Accession Level: The sample is not from a field trial entity and only the accession name is known.
At which level do you plan to keep track of your sampling?
Plot Level: Each plot in the field has a unique identifier, ideally with a barcode label.
Plant Level: Each plant in the field has a unique identifier, ideally with a barcode label.
Tissue Sample Level: Each tissue sample collected from the field has a unique identifier, ideally with a barcode label.
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Select a field trial
Field trial is not relevant for the type of tissue sampling you selected. Go to next step.
Select Trial name Description Breeding program Folder Year Location Trial type Design Planting Date Harvest Date Download
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Plant entries in your field trial
Plant entries not relevant for the type of tissue sampling you selected. Go to next step.
Plant entries exist for this trial. Go to next step.
Please create plant entries for this trial.
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Create tissue sample entries for this trial
Field trial tissue sample entries not relevant for the type of tissue sampling you selected. Go to next step.
Tissue sample entries exist for this trial. Go to next step.
Complete! You have all the entities you need to conduct your sampling.
- All of the entities that you want to sample are saved in the database and available to use!
- You can print barcodes for the entities you intend to sample on. These barcodes can be attached to your collection vials/containers to assist during sampling.
- After you have finished sampling, you can use these entities as source material for a genotyping plate (96 or 384 well plate). Click the button below to create a genotyping plate now, if you will create a 96 or 384 well plate.
- The Android Coordinate application can help you create 96 or 384 well plates. Alternatively you can create your plate layout in Excel and upload it.
Complete! You have all the entities you need to conduct your sampling.
- All of the entities that you want to sample are saved in the database and available to use!
- You can print barcodes for the entities you intend to sample on. These barcodes can be attached to your collection vials/containers to assist during sampling.
- After you have finished sampling, you can use these entities as source material for a genotyping plate (96 or 384 well plate). Click the button below to create a genotyping plate now, if you will create a 96 or 384 well plate.
- The Android Coordinate application can help you create 96 or 384 well plates. Alternatively you can create your plate layout in Excel and upload it.
Workflow for seedlot inventory
I have new seedlots that need to be added into the database.
I conducted an inventory (in weight(g)) and want to update the database to reflect the current state of the inventory.
Upload Existing Trial
Upload Template Information
(.xlsx format not supported)
Header:
The first row (header) must contain the following:
plot_name | accession_name | plot_number | block_number | is_a_control | rep_number | range_number | row_number | col_number | seedlot_name | num_seed_per_plot | weight_gram_seed_per_plot |
plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number,seedlot_name,num_seed_per_plot,weight_gram_seed_per_plot
Required fields:- plot_name (must be unique across entire database. this is often a concatenation of the trial name, the accession name, and the plot number.)
- accession_name (must exist in the database. this is the accession being tested in the plot.)
- plot_number (a sequential number for the plot in the field (e.g. 1001, 1002, 2001, 2002). these numbers should be unique for the trial.)
- block_number (a design parameter indicating which block the plot is in)
- is_a_control (type 1 in this field if the plot is a control, otherwise leave blank. generally you will have accessions that are controls, so you shuold indicate the plots that that accession is in as a control.)
- rep_number (replicate number, numeric)
- range_number (range number. often synonymous with col_number, numeric)
- row_number (row number. if the field is a grid, this represents the y coordinate, numeric, required for field map generation. the top left plot shuold be row 1, column 1)
- col_number (column number. if the field is a grid, this represents the x coordinate. sometimes called range_number, numeric, required for field map generation. the top left plot shuold be row 1, column 1)
- seedlot_name (the seedlot from where the planted seed originated. must exist in the database)
- num_seed_per_plot (number seeds per plot. seed is transferred from seedlot mentioned in seedlot_name. numeric)
- weight_gram_seed_per_plot (weight in gram of seeds in plot. seed is transferred from seedlot mentioned in seedlot name. numeric)
- treatment columns (additional column(s) that specify the name of a treatment (e.g. inoculated, drought, etc). the value for each plot should be 1 if the treatment was applied or empty.)
Design New Trial
Add Field Management Factor to Design
Add Field Management Factor to Design
Partially Replicated Design Usage Help
Background:
Partially replicated designs have some treatments that are unreplicated and rely on replicated treatments to make the trial analysable. The design were described in Cullis et al. (2006). It is recommended that at least 20% of the experimental units are occupied by replicated treatments. The aim of these experiments is usually to select promising treatments from a set of replicated and unreplicated test treatments, with check and quality standard treatments providing the necessary replication overall to give a valid experiment. DiGGer (Coombes, 2002) was used to implement this design. DiGGer is a flexible tool for creating experimental designs that are efficient for specified blocking and correlation patterns. DiGGer package (http://www.austatgen.org/files/software/downloads) is an add-on for the statistical computing language and environment R (R Development Core Team, 2009).
Design Parameters:
The parameters will consider a sample partially replicated design trial with 200 unreplicated accessions, 119 accessions replicated 4 times, 26 rows in design, 26 columns in design, bock sequence of 13 by 2 (13, 2) i.e 2 blocks with each having 13 rows; sub-block sequence of block of 13 by 1 (13, 1) i.e 1 sub-block with each having 13 rows in each block.
- List of Unreplicated Accession
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- You're expected to provide the list of unreplicated accessions in this selectbox. E.g. is a list of 200 accessions.
- List of Replicated Accession
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- List of replicated accessions should be provided in this selectbox. E.g. is a list of 119 accessions.
- Number of rows in design
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- Provide the number of rows you want to have in the design. E.g. 26 number of rows.
- Number of Columns in Design
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- Provide the number of columns you want to have in the design. E.g. 26 number of columns.
- Number of Times Replicated Accessions are Replicated
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- Provide the number of times you want the replicated accessions to be replicated. E.g. 4
- Block Sequence
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- The block sequence should reflect the blocking structure of your design. E.g. (13, 2), meaning the design has 2 blocks and each block has 13 rows.
- Sub-block Sequence
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- The sub-block sequence should reflect the sub-blocking structure of your design. E.g. (13, 1), meaning the design has 1 sub-block (column) and each sub-block has 13 rows.
NOTE:
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- The product of the number of rows and columns in the design should equal the total number of plots.
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- The sum of the unreplicated accessions and the replicated accessions (given the number of times it was replicated) should equal the total number of plots.
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Upload Genotypes
Upload VCF Template Information
VCF is a tab separated format
Header:
The first row (header) must contain the following fields, followed by all genotyped sample names:
#CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | Sample names... |
- #CHROM (chromosome: An identifier from the reference genome pointing to a contig in the assembly file (cf. the ##assembly line in the header). All entries for a specific CHROM should form a contiguous block within the VCF file. The colon symbol (:) must be absent from all chromosome names to avoid parsing errors when dealing with breakends. (String, no white-space permitted, Required))
- POS (position: The reference position, with the 1st base having position 1. Positions are sorted numerically, in increasing order, within each reference sequence CHROM. It is permitted to have multiple records with the same POS. Telomeres are indicated by using positions 0 or N+1, where N is the length of the corresponding chromosome or contig. (Integer, Required) )
- ID ( identifier: Semi-colon separated list of unique identifiers where available. If this is a dbSNP variant it is encouraged to use the rs number(s). No identifier should be present in more than one data record. If there is no identifier available, then the missing value should be used. (String, no white-space or semi-colons permitted) )
- REF (reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted. The value in the POS field refers to the position of the first base in the String. For simple insertions and deletions in which either the REF or one of the ALT alleles would otherwise be null/empty, the REF and ALT Strings must include the base before the event (which must be reflected in the POS field), unless the event occurs at position 1 on the contig in which case it must include the base after the event; this padding base is not required (although it is permitted) for e.g. complex substitutions or other events where all alleles have at least one base represented in their Strings. If any of the ALT alleles is a symbolic allele then the padding base is required and POS denotes the coordinate of the base preceding the polymorphism. Tools processing VCF files are not required to preserve case in the allele Strings. (String, Required) )
- ALT (alternate base(s): Comma separated list of alternate non-reference alleles. These alleles do not have to be called in any of the samples. Options are base Strings made up of the bases A,C,G,T,N,*, (case insensitive) or a breakend replacement string as described in the section on breakends. The '*' allele is reserved to indicate that the allele is missing due to a upstream deletion. If there are no alternative alleles, then the missing value should be used. Tools processing VCF files are not required to preserve case in the allele String, except for IDs, which are case sensitive. (String; no whitespace, commas, or angle-brackets are permitted in the ID String itself) )
- QUAL (quality: Phred-scaled quality score for the assertion made in ALT. i.e. -10log10 prob(call in ALT is wrong). If ALT is '.' (no variant) then this is -10log10 prob(variant), and if ALT is not '.' this is -10log10 prob(no variant). If unknown, the missing value should be specified. (Numeric) )
- FILTER (filter status: PASS if this position has passed all filters, i.e. a call is made at this position. Otherwise, if the site has not passed all filters, a semicolon-separated list of codes for filters that fail. e.g. "q10;s50" might indicate that at this site the quality is below 10 and the number of samples with data is below 50% of the total number of samples. "0" is reserved and should not be used as a filter String. If filters have not been applied, then this field should be set to the missing value. (String, no white-space or semi-colons permitted) )
- INFO (additional information: (String, no white-space, semi-colons, or equals-signs permitted; commas are permitted only as delimiters for lists of values) INFO fields are encoded as a semicolon-separated series of short keys with optional values in the format: key=data[,data]. Arbitrary keys are permitted, although the following sub-fields are reserved (albeit optional):
- AA : ancestral allele
- AC : allele count in genotypes, for each ALT allele, in the same order as listed
- AF : allele frequency for each ALT allele in the same order as listed: use this when estimated from primary data, not called genotypes
- AN : total number of alleles in called genotypes
- BQ : RMS base quality at this position
- CIGAR : cigar string describing how to align an alternate allele to the reference allele
- DB : dbSNP membership
- DP : combined depth across samples, e.g. DP=154
- END : end position of the variant described in this record (for use with symbolic alleles)
- H2 : membership in hapmap2
- H3 : membership in hapmap3
- MQ : RMS mapping quality, e.g. MQ=52
- MQ0 : Number of MAPQ == 0 reads covering this record
- NS : Number of samples with data
- SB : strand bias at this position
- SOMATIC : indicates that the record is a somatic mutation, for cancer genomics
- VALIDATED : validated by follow-up experiment
- 1000G : membership in 1000 Genomes
- FORMAT (A format field is given specifying the data types and order (colon-separated alphanumeric String). This is followed by one field per sample, with the colon-separated data in this field corresponding to the types specified in the format. The first sub-field must always be the genotype (GT) if it is present. There are no required sub-fields. As with the INFO field, there are several common, reserved keywords that are standards across the community:
- GT : genotype, encoded as allele values separated by either of / or |. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1, 1 | 0, or 1/2, etc. For haploid calls, e.g. on Y, male nonpseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, '.' should be specified for each missing allele in the GT field (for example './.' for a diploid genotype and '.' for haploid genotype). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes):
- / : genotype unphased
- | : genotype phased
- DP : read depth at this position for this sample (Integer)
- FT : sample genotype filter indicating if this genotype was "called" (similar in concept to the FILTER field). Again, use PASS to indicate that all filters have been passed, a semi-colon separated list of codes for filters that fail, or '.' to indicate that filters have not been applied. These values should be described in the metainformation in the same way as FILTERs (String, no white-space or semi-colons permitted)
- GL : genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields. In presence of the GT field the same ploidy is expected and the canonical order is used; without GT field, diploidy is assumed. If A is the allele in REF and B,C,... are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc. For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Floats)
- GLE : genotype likelihoods of heterogeneous ploidy, used in presence of uncertain copy number. For example: GLE=0:-75.22,1:-223.42,0/0:-323.03,1/0:-99.29,1/1:-802.53 (String)
- PL : the phred-scaled genotype likelihoods rounded to the closest integer (and otherwise defined precisely as the GL field) (Integers)
- GP : the phred-scaled genotype posterior probabilities (and otherwise defined precisely as the GL field); intended to store imputed genotype probabilities (Floats)
- GQ : conditional genotype quality, encoded as a phred quality -10log10 p(genotype call is wrong, conditioned on the site's being variant) (Integer)
- HQ : haplotype qualities, two comma separated phred qualities (Integers)
- PS : phase set. A phase set is defined as a set of phased genotypes to which this genotype belongs. Phased genotypes for an individual that are on the same chromosome and have the same PS value are in the same phased set. A phase set specifies multi-marker haplotypes for the phased genotypes in the set. All phased genotypes that do not contain a PS subfield are assumed to belong to the same phased set. If the genotype in the GT field is unphased, the corresponding PS field is ignored. The recommended convention is to use the position of the first variant in the set as the PS identifier (although this is not required). (Non-negative 32-bit Integer)
- PQ : phasing quality, the phred-scaled probability that alleles are ordered incorrectly in a heterozygote (against all other members in the phase set). We note that we have not yet included the specific measure for precisely defining "phasing quality"; our intention for now is simply to reserve the PQ tag for future use as a measure of phasing quality. (Integer)
- EC : comma separated list of expected alternate allele counts for each alternate allele in the same order as listed in the ALT field (typically used in association analyses) (Integers)
- MQ : RMS mapping quality, similar to the version in the INFO field. (Integer)
If any of the fields is missing, it is replaced with the missing value. For example if the FORMAT is GT:GQ:DP:HQ then 0 | 0 : . : 23 : 23, 34 indicates that GQ is missing. Trailing fields can be dropped (with the exception of the GT field, which should always be present if specified in the FORMAT field). )
The exact format of each INFO sub-field should be specified in the meta-information (as described above). Example for an INFO field: DP=154;MQ=52;H2. Keys without corresponding values are allowed in order to indicate group membership (e.g. H2 indicates the SNP is found in HapMap 2). It is not necessary to list all the properties that a site does. )
Upload Intertek Template Information
Please use CSV formatted files
For Intertek SNP Result Grid File:
The header must be:
SampleName.LabID | All Marker Names In Separate Columns (e.g. marker name = S12_7926132) |
The SampleName.LabID column should contain the sample name (exported_tissue_sample_name or accession_name) and it must exist in the database already
For Intertek SNP Information File:The header must be:
IntertekSNPID | CustomerSNPID | Reference | Alternate | Chromosome | Position | Quality | Filter | Info | Format |
Add Genotyping Plate
Upload Template Information
File must be Excel file (.xls)
(.xlsx format not supported)
Header:
The first row (header) must contain the following:
date | sample_id | well_A01 | row | column | source_observation_unit_name | ncbi_taxonomy_id | dna_person | notes | tissue_type | extraction | concentration | volume | is_blank |
- date (should be YYYY-MM-DD)
- sample_id (the unique identifier for the sample in the well)
- well_A01 (the position of the sample in the plate)
- row (the row position of the sample in the plate e.g. A)
- column (the column position of the sample in the plate e.g. 10)
- source_observation_unit_name (must exist in the database. the identifier of the origin material. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name. For blank wells, you can write BLANK here and place a 1 in the is_blank column also.)
- tissue_type (must be either leaf, root, or stem)
- ncbi_taxonomy_id (NCBI taxonomy identifier)
- dna_person (the name of the person who prepared the well)
- notes (any additional notes on the well)
- extraction (free-text for the extraction method e.g. CTAB)
- concentration (concentration in ng/ul)
- volume (volume in ul)
- is_blank (indicates if well is blank. write 1 if blank, otherwise leave empty.)
Upload Template Information
File must be a CSV file (.csv)
(Excel format not supported)
Header:
The first row (header) must contain the following:
date | plate_id | plate_name | sample_id | well_A01 | well_01A | tissue_id | dna_person | notes | tissue_type | extraction |
- date (should be YYYY-MM-DD)
- plate_id (an identifier for a grouping of plates. called "Genotyping Project Name" in genotyping plate submission form. e.g. NextGenCassava)
- plate_name (the unique name for the individual plate. called "Plate ID" in genotyping plate submission form. e.g. 18DNA00001)
- sample_id (the unique identifier for the sample in the well. e.g. 18DNA00001_A01)
- well_A01 (the position of the sample in the plate in this format A01)
- well_01A (the position of the sample in the plate in this format 01A)
- tissue_id (the identifier of the origin material. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name. this can also say 'BLANK' to indicate a blank well.)
- dna_person (the name of the person who plated the individual sample. can be any name.)
- tissue_type (must be either leaf, root, or stem)
- notes (any additional notes on the well)
- extraction (free-text for the extraction method e.g. CTAB)
Upload Template Information
File must be a CSV file (.csv)
(Excel format not supported)
Header:
Note that tissue type will be set to 'leaf' if you use this upload type, since tissue type is not provided in the upload and tissue type is required for DaRT. The first row (header) must contain the following:
Value | Column | Row | Identification | Person | Date |
- Value (the identifier of the origin material. e.g. 2018MyPlant0001. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name. This can also say 'exclude' to indicate a BLANK)
- Column (the column position of the sample e.g. 10)
- Row (the row position of the sample e.g. A)
- Identification (free text)
- Person (the name of the person who plated the individual sample. can be any name.)
- Date (should be YYYY-MM-DD)
Upload Seedlot Inventory
- Intro
- File format
- Upload inventory
- Fix missing seedlots problem
- Try submitting inventory again
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What is a seedlot inventory?
- Seedlots represent physical seed in packets.
- This seed can be from crosses or for named accessions.
- Seedlots can have a specific location, box, weight(g), and count.
- Seedlots can belong to breeding programs and organizations.
- Seedlots can be used in trials (e.g. they were planted in a plot) and they can be harvested from a plot or plant (e.g. a cross was performed and seeds were collected.)
- A seedlot inventory consists of giving a location and current weight(g) to your seedlots. The seedlot name is the unique identifier for each seedlot and so should be encoded in a barcode on each seedlot packet.
- You can use the "Seed Inventory" Android Application to scan seedlot barcodes and record weight. If you prefer you can create your own CSV file and upload that, if you do not want to use the Seed Inventory Application. For info about the format of the file to upload, go to the next tab.
- For more info about the "Seed Inventory" Android Application go to Seed Inventory.
- It is also possible to manually enter a transaction by going to the seedlot detail page and clicking "Add New Transaction".
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Make sure you are collecting seedlot inventory in the following format
The "Seed Inventory" Android Application will export this same exact format by default.
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Select your file and upload seedlot inventory
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Fixing the missing seedlot(s) problem
- Seedlots must exist in the database prior to updating or adding inventory. The reason for this is that the inventory does not give information about the content (a named accession or a cross name) and this information is required for a seedlot to exist in the database. We also want to be careful about adding new seedlots into the database because we do not want data to be incorrectly linked to duplicates.
- When adding seedlots into the database, you can upload an Excel file or you can add seedlots one at a time.
Seedlot Inventory Upload Error Messages
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Submit your inventory again. You should have corrected all errors by now, but if not please take a look at the errors in the red box below. You can continue to modify your file and then click Upload until it works.
There exist these problems in your file:
Finished! Your seedlot inventory is in the database
The seedlot inventory file was uploaded successfully
- You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just updated.
- You can print barcodes for the seedlots.
Finished! Your seedlot inventory is in the database
The seedlot inventory file was uploaded successfully
- You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just updated.
- You can print barcodes for the seedlots.
Upload Template Information
(Excel .xls and .xlsx format not supported)
Header:
The first row (header) should contain the following:
box_id | seed_id | inventory_date | inventory_person | weight_gram |
- box_id (the name of the box that the seedlot is in. also called box_name.)
- seed_id (unique identifier for the seedlot. must exist in the database. also called seedlot_name)
- inventory_date (a timestamp for when the seedlot was inventoried)
- inventory_person (the name of the person doing the inventory. can be any name. also called operator_name)
- weight_gram (the weight in grams of the seedlot)
Upload Seedlots
- Intro
- What seedlots do you have?
- File format
- Upload seedlots
- Fix errors in file
- Try submitting seedlots again
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What are seedlots?
- Seedlots represent physical seed in packets.
- This seed can be from crosses or for named accessions.
- Seedlots can have a specific location, box, weight(g), and count.
- Seedlots can belong to breeding programs and organizations.
- Seedlots can be used in trials (e.g. they were planted in a plot) and they can be harvested from a plot or plant (e.g. a cross was performed and seeds were collected.)
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Seedlots fall into two categories
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Make sure your file matches the correct file format
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Provide basic information about the seedlots and upload your file
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Fix all errors in your file
- Accessions must exist in the database prior to adding seedlots of them. The reason for this is that an accession can be exist in many seedlots and therefore exists as a separate entity in the database. We also want to be careful about adding new accessions into the database because we do not want incorrectly duplicated data.
- When adding accessions into the database, you can use either a list of accessions or an Excel file.
- Crosses must exist in the database before adding your seed lots. The reason for this is that a cross can produce many seed lots and so the cross must exists as a separate entity in the database. We also want to be careful about adding new crosses into the database because we do not want data to be incorrectly linked to duplicates.
- When adding crosses into the database, you can upload an Excel file or you can add seedlots one at a time.
Seedlot Upload Error Messages
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Submit your seedlots again. You should have corrected all errors by now, but if not please take a look at the errors in the red box below. You can continue to modify your file and then click Upload until it works.
There exist these problems in your file:
Finished! Your seedlots are now in the database
The seedlot file was uploaded successfully
- You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just created.
- You can print barcodes for the seedlots.
Finished! Your seedlots are now in the database
The seedlot file was uploaded successfully
- You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just created.
- You can print barcodes for the seedlots.
Upload Template Information For Named Accessions
(.xlsx format not supported)
Header:
The first row (header) must contain the following:
seedlot_name | accession_name | operator_name | amount | weight(g) | description | box_name |
- seedlot_name (must be unique)
- accession_name (must exist in the database. the accession_name is the unique identifier for the named genotype)
- operator_name (the name of the person who oversaw the inventory process. can be any name.)
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amount (number of seeds in seedlot. can be provided in conjunction with weight(g). must provide a value for amount or weight(g) or both.)
AND/OR
weight(g) (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight(g) or both.) - box_name (the box name that the seed is located in. can be any name.)
- description (information about why this seedlot is being added)
Upload Template Information For Harvested Seedlots
(.xlsx format not supported)
Header:
The first row (header) must contain the following:
seedlot_name | cross_unique_id | operator_name | amount | weight(g) | description | box_name |
- seedlot_name (must be unique)
- cross_unique_id (must exist in the database. a cross_unique_id can represent a cross between accessions e.g. AxB, but a cross can also represent a cross between specific plots in the field if you have this information)
- operator_name (the name of the person who oversaw the inventory process. can be any name.)
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amount (number of seeds in seedlot. can be provided in conjunction with weight(g). must provide a value for amount or weight(g) or both.)
AND/OR
weight(g) (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight(g) or both.) - box_name (the box name that the seed is located in. can be any name.)
- description (information about why this seedlot is being added)
Create New Seedlot
Upload Accessions Template Information
(.xlsx format not supported)
Header:
The first row (header) should contain the following:
accession_name | species_name | population_name | organization_name(s) | synonym(s) | location_code(s) | ploidy_level(s) | genome_structure(s) | variety(s) | donor(s) | donor_institute(s) | donor_PUI(s) | country_of_origin(s) | state(s) | institute_code(s) | institute_name(s) | biological_status_of_accession_code(s) | notes(s) | accession_number(s) | PUI(s) | seed_source(s) | type_of_germplasm_storage_code(s) | acquisition_date(s) | transgenic | introgression_parent | introgression_backcross_parent | introgression_map_version | introgression_chromosome | introgression_start_position_bp | introgression_end_position_bp |
- accession_name (must be unique)
- species_name (must exist in the database)
- population_name (a population is a grouping of accessions. if the population already exists in the database, the accession will be added into it, otherwise, the new population will be created.)
- organization_names (the name(s) of the organization(s) which use this accession. multiple organizations can be given with comma separation (e.g. NARO,IITA))
- synonyms (an accession can be known by many names including local popular names. a synonym name can be used instead of the accession_name throughout the database; because of this, synonyms must themselves be unique. multiple synonyms can be given with comma separation (e.g. accession_synonym1,accession_synonym001))
- location_code(s) (location code(s) for the accession. many can be uploaded at once in comma separated list)
- ploidy_level(s) (a number indicating the ploidy (e.g. 2 for diploid, 3 for triploid), numeric. many values can be uploaded as comma separated list.)
- genome_structure(s) (genome structure(s) for accession which take into account ploidy and ancestral genome info e.g. AAA, AB. many can be uploaded as comma separated list.)
- variety(s) (variety can be defined as a group of individuals or plants having similar traits that can be reproduced "true to type" from generation to generation. may be uploaded as comma separated list.)
- donor(s) (the accession_name of the donor accession. may be uploaded as comma separated list.)
- donor_institute(s) (the institute of the donor accession. may be uploaded as comma separated list.)
- donor_PUI(s) (the permanent unique identifier of the donor accession. may be uploaded as comma separated list.)
- country_of_origin(s) (the country of origin. may be uploaded as comma separated list.)
- state(s) (the state of origin. may be uploaded as comma separated list.)
- institute_code(s) (the institute code of origin. may be uploaded as comma separated list.)
- institute_name(s) (the institute name of origin. may be uploaded as comma separated list.)
- biological_status_of_accession_code(s) (code indicating the state of accession. may be uploaded as comma separated list.)
- notes(s) (free text for notes. may be uploaded as comma separated list.)
- accession_number(s) (accession number for accession from germplasm bank. may be uploaded as comma separated list.)
- PUI(s) (permanent unique identifier of the accession. may be uploaded as comma separated list.)
- seed_source(s) (origin of seed source. may be uploaded as comma separated list.)
- type_of_germplasm_storage_code(s) (code indicating the type of germplasm storage. may be uploaded as comma separated list.)
- acquisition_date(s) (date(s) of acquisition YYYYMMDD for accession. may be uploaded as comma separated list.)
- transgenic (indicates if accession is transgenic. Please indicate 1 if transgenic and empty if otherwise.)
- introgression_parent (if the accession you are adding has an introgression that originated from one of the parents, you can specify the parent here)
- introgression_backcross_parent (the backcross parent for introducing an introgression into the accession being added)
- introgression_map_version (the map version for identifying the start and stop position of the introgression. e.g. AGPv2)
- introgression_chromosome (the chromosome number that the introgression is on.)
- introgression_start_position_bp (the start position of the introgression in base pairs)
- introgression_start_position_bp (the end position of the introgression in base pairs)
Accessions to be Added
The following accessions are new and will be added to the database:
Fuzzy Matches
Found Accessions
Accessions Saved
Upload Crosses
- Intro
- Crossing experiment
- Upload your crosses
-
What are crosses?
- Crosses represent any pollination that occurs.
- Crosses can be of different types (biparental, self, open, sib, polycross, bulk, bulk_self, bulk_open, or doubled_haploid)
- Depending on the cross type, an individual cross can be defined as between two accessions (e.g. accession A is the female and accession B is the male in a biparental cross)
- For an open pollinated cross, the cross can be defined as between female accession A and male population P1 (populations in the database are only defined as groups of accessions), or between female accession A and unknown male parents
- An individual cross can be linked to the specific female plot or plant, as well as the specific male plot or plant.
- A cross can have a number of properties associated to it, such as number of flowers, pollination date, etc.
- A cross can produce seed, which goes into a seedlot.
- A cross can ultimately produce progeny, which then become named accessions in the database.
-
Select a crossing experiment for your crosses
Crossing experiments are for grouping crosses together. The grouping is most often done for crosses derived from the same field trial, the same year, or for crosses that have the same breeding objective.
-
Enter basic information about the crosses and upload your file
Finished! Your crosses are now in the database
The crosses file was uploaded successfully
- You may want to proceed to the cross detail page(s) for the cross(es) you just created.
- You can print barcodes for the crosses.
- You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).
Finished! Your crosses are now in the database
The crosses file was uploaded successfully
- You may want to proceed to the cross detail page(s) for the cross(es) you just created.
- You can print barcodes for the crosses.
- You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).
Upload Crosses File Error
Template Information
(.xlsx format not supported)
Header:
To set up crosses in the database, please provide required information. The first row (header) must contain the following:
cross_unique_id | cross_combination | cross_type | female_parent | male_parent |
- cross_unique_id (must NOT exist in the database)
- cross_combination (required in the header, but value for cross combination (e.g. female accession/male accession) may be left blank)
- cross_type (must be one of the following: biparental, self, open, sib, polycross, bulk, bulk_self, bulk_open, or doubled_haploid)
- cross type descriptions:
- biparental: An individual plant pollinated by another individual plant.
- self: A self pollinated individual plant.
- open: An individual plant pollinated by a group of plants or open pollinated (pollen may be from a group with known or unknown members).
- sib: Mating between individuals that have at least one parent in common. Generally between two individuals within the same plot.
- polycross: Mating between individual female parent from a population and the corresponding male population.
- bulk: A group of plants (usually a related family) pollinated by an individual plant.
- bulk_self: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
- bulk_open: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (pollen may be from a group with known or unknown members).
- doubled_haploid: Plants derived from doubling the chromosome number of haploid tissue.
- female_parent (accession names or population names must exist as uniquenames in the database)
- male_parent (required in the header, but value may be left blank for most cross types. Must be specified for biparental, sib, polycross and bulk cross types. When specified, accession names or population names must exist as uniquenames in the database)
- After you establish cross unique ids in the database, you can add additional cross info (e.g. pollination date, total number of flowers pollinated, total number of fruits set) or progenies to the corresponding cross unique ids.
- Cross info and progenies can be uploaded via links in crossing experiment detail page or can be added directly in each cross detail page.
Template Information
(.xlsx format not supported)
Header:
To set up crosses in the database, please provide required information. The first row (header) must contain the following:
cross_unique_id | cross_combination | cross_type | female_parent | male_parent | female_plot | male_plot |
- cross_unique_id (must NOT exist in the database)
- cross_combination (required in the header, but value for cross combination (e.g. female accession/male accession) may be left blank)
- cross_type (must be one of the following: biparental, self, open, sib, polycross, bulk, bulk_self, bulk_open, or doubled_haploid)
- cross type descriptions:
- biparental: An individual plant pollinated by another individual plant.
- self: A self pollinated individual plant.
- open: An individual plant pollinated by a group of plants or open pollinated (pollen may be from a group with known or unknown members).
- sib: Mating between individuals that have at least one parent in common. Generally between two individuals within the same plot.
- polycross: Mating between individual female parent from a population and the corresponding male population.
- bulk: A group of plants (usually a related family) pollinated by an individual plant.
- bulk_self: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
- bulk_open: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (pollen may be from a group with known or unknown members).
- doubled_haploid: Plants derived from doubling the chromosome number of haploid tissue.
- female_parent (accession names must exist as uniquenames in the database)
- male_parent (required in the header, but value may be left blank for most cross types. Must be specified for biparental, sib, polycross and bulk cross types. When specified, accession or population names must exist as uniquenames in the database)
- female_plot (Plot names must exist in the database)
- male_plot (Plot names must exist in the database)
- After you establish cross unique ids in the database, you can add additional cross info (e.g. pollination date, total number of flowers pollinated, total number of fruits set) or progenies to the corresponding cross unique ids.
- Cross info and progenies can be uploaded via links in crossing experiment detail page or can be added directly in each cross detail page.
Template Information
(.xlsx format not supported)
Header:
To set up crosses in the database, please provide required information. The first row (header) must contain the following:
cross_unique_id | cross_combination | cross_type | female_parent | male_parent | female_plant | male_plant |
- cross_unique_id (must NOT exist in the database)
- cross_combination (required in the header, but value for cross combination (e.g. female accession/male accession) may be left blank)
- cross_type (must be one of the following: biparental, self, open, sib, polycross, bulk, bulk_self, bulk_open, or doubled_haploid)
- cross type descriptions:
- biparental: An individual plant pollinated by another individual plant.
- self: A self pollinated individual plant.
- open: An individual plant pollinated by a group of plants or open pollinated (pollen may be from a group with known or unknown members).
- sib: Mating between individuals that have at least one parent in common. Generally between two individuals within the same plot.
- polycross: Mating between individual female parent from a population and the corresponding male population.
- bulk: A group of plants (usually a related family) pollinated by an individual plant.
- bulk_self: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
- bulk_open: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (pollen may be from a group with known or unknown members).
- doubled_haploid: Plants derived from doubling the chromosome number of haploid tissue.
- female_parent (accession names must exist as uniquenames in the database)
- male_parent (required in the header, but value may be left blank for most cross types. Must be specified for biparental, sib, polycross and bulk cross types. When specified, accession or population names must exist as uniquenames in the database)
- female_plant (Plant names must exist in the database)
- male_plant (Plant names must exist in the database)
- After you establish cross unique ids in the database, you can add additional cross info (e.g. pollination date, total number of flowers pollinated, total number of fruits set) or progenies to the corresponding cross unique ids.
- Cross info and progenies can be uploaded via links in crossing experiment detail page or can be added directly in each cross detail page.
Add New Cross
- Intro
- Crossing Experiment
- Enter cross information
- Enter parentage information
- Track exact cross parents
- Additional cross info
-
What is a cross?
- The Cross Tool can track any pollinations in a breeding program.
- Each cross has a globally unique cross id.
- Supported cross types are: biparental, self, open, sib, polycross, bulk, bulk_self, bulk_open, or doubled_haploid
- For an open pollinated cross, the cross can be defined as between female accession A and male population P1 (populations in the database are defined strictly as groups of accessions). If the male parent is not known, it can be left blank.
- An individual cross can be linked to the specific female plot or plant, as well as to the specific male plot or plant.
- A cross can have other data associated to it, such as number of flowers, pollination date, etc.
- Seed produced by a cross can be managed using a seedlot.
- Progenies from a cross can become named accessions in the database.
-
Select a crossing experiment
Crossing experiments are for grouping crosses together. The grouping is most often done for crosses derived from the same field trial, the same year, or for crosses that have the same breeding objective.
-
Enter basic information about the cross
Cross type information
Descriptions of cross types
-
Enter basic information about the cross
(optional)
(optional)
-
Optional: If you choose to record exact cross parents, you can do so.
-
If you would like to add auto-generated progeny names for this cross, you can add it here
Optional:
Finished! Your cross is now in the database
The cross was added successfully
- You may want to proceed to the cross detail page for the cross you just created.
- You can print barcodes for the cross.
- You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).
Finished! Your cross is now in the database
The cross was added successfully
- You may want to proceed to the cross detail page for the cross you just created.
- You can print barcodes for the cross.
- You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).
Template Information
Individual Crosses:
biparental: An individual plant pollinated by another individual plant.
self: A self pollinated individual plant.
open pollinated: An individual plant pollinated by a group of plants or open pollinated (pollen may be from a group with known or unknown members).
sib: Mating between individuals that have at least one parent in common. Generally between two individuals within the same plot.
bulk: A group of plants (usually a related family) pollinated by an individual plant.
bulk selfed: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
bulk and open pollinated: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (pollen may be from a group with known or unknown members).
doubled haploid: Plants derived from doubling the chromosome number of haploid tissue.
Group of Crosses:
polycross: Creates a group of open pollinated crosses. Each accession in the selected list becomes the female parent in an open cross, and all the members of the list grouped together form the male parent.
reciprocal: Creates a group of biparental crosses. Starting with a list of accessions, all possible biparental cross combinations are made between them.
multicross: Creates a group of biparental crosses. Starting with a list of maternal accessions and a list of paternal accessions, direct crosses are made in order.
Success
The cross or crosses were saved successfully.
Add New Crossing Experiment
- Intro
- Add a crossing experiment
-
What are crossing experiments?
Crossing experiments group crosses. The grouping can reflect crosses done in the same field trial, crosses in a breeding program in a given year, or crosses that have the same breeding objective. This grouping can be used to encapsulate all the crosses done in a crossing block field trial that you have saved in the database (e.g. in Manage Trials your crossing block will appear as a field trial with plots)
-
Enter basic information about the crossing experiment
Finished! Your crossing experiment is now in the database
Crossing experiment was added successfully
- You may want to proceed to the crossing experiment detail page you just created.
- You can add or upload crosses into your crossing experiment as they become available.
- You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).
Finished! Your crossing experiment is now in the database
Crossing experiment was added successfully
- You may want to proceed to the crossing experiment detail page you just created.
- You can add or upload crosses into your crossing experiment as they become available.
- You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).
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SweetPotatoBase adheres to the Toronto agreement on prepublication data release
All data deposited on SweetPotatoBase adheres to the Toronto Agreement on prepublication data release. To foster transparent and accessible data sharing culture, in accordance with the Toronto Agreement, all data deposited on SweetPotatoBase will be made public immediately. Data producers can provide information on the data they deposit, including planned analyses and publication timeline information, to indicate their publication intentions. Data users are expected to respect scientific etiquette and allow data producers the first global analyses of their data set, and should be aware that pre-publication data may not have been subject to full quality control and peer review, so caution must be applied when utilizing these data. More information is available on the data usage policy page.Featured Publication
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