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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(s)
- Intro
- File Formatting
- Enter trial information
- Trial Linkage
- Fix missing accessions problem
- Fix missing seedlots problem
- Try submitting trial again
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This workflow will guide you through uploading a new trial or trials into the database
A field trial represents plots in the field where each plot has a globally unique plot_name, a sequential plot_number that is unique in the trial (e.g. 101, 102, 103 for three separate plots), and an accession_name representing the genotype being tested in that plot. In cases where a cross/family is being evaluated (e.g. F1 hybrid, backcrossing), a cross_unique_id or a family_name can be used instead of an accession_name. Each plot can belong to different blocks (block_number) and reps (rep_number) depending on the experimental design you are using (e.g. complete block vs augmented design). Each plot can have a row_number and col_number indicating the relative position of the plot in the field.
If a specific accession is a check or control, you can indicate the plots that that accession is planted in as controls using is_a_control.
You can provide the specific seedlot_name planted in each plot, along with the number of seeds (num_seed_per_plot) and/or the weight (g) of seed (weight_gram_seed_per_plot) that were used.
A trial can represent a yield trial, a phenotyping trial, a crossing block, a greenhouse, a nursery, etc.
A plot can have many plants, which the database can track as separate entities, allowing you to record plant level observations and information.
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File format information
Single trial spreadsheet
File format information
Multiple trial spreadsheet
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Enter information about the experiment and upload your trial layout
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Is your trial linked with other field trials, genotyping plates, or crossing experiments in the database? If you are unsure, you can skip this. This information can be added from the trial detail page after the trial is saved.
If you go on to collect tissue samples for creating a 96 well plate for genotyping, when adding the genotyping plate (96 well plate layout) to the database you can use plot names or plant names or tissue sample names from this field trial. By doing so, we can create linkage between this field trial and the genotyping plate.
If you go on to perform crosses on this field trial, each cross can be linked to specific female and male plots. When you upload these crosses we can then automatically link this field trial to the crossing experiment in the database.
Check this box to ignore any possible warning messages and save the trial to the database.
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Fixing the missing accession(s) problem
- Accessions tested in your trial must exist in the database prior to adding your trial. The reason for this is that an accession can be tested in many trials 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.
Trial Upload Error Messages
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Fixing the missing seedlot(s) problem
- Seedlots tested in your experimental trial must exist in the database prior to adding your trial. The reason for this is that a seedlot can be tested in many trials and therefore exists as a separate entity 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.
Trial Upload Error Messages
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Submit your trial 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 trial is now in the database
The trial file was uploaded successfully
- You may want to proceed to the trial detail page for the trial you just created.
- You can print barcodes for the plots or plants or tissue samples in this trial.
- You an add phenotypes for the plots or plants in this trial now.
Finished! Your trial is now in the database
The trial file was uploaded successfully
- You may want to proceed to the trial detail page for the trial you just created.
- You can print barcodes for the plots or plants or tissue samples in this trial.
- You an add phenotypes for the plots or plants in this trial now.
Upload Template Information
Stock type being evaluated in this trial: accession Stock type being evaluated in this trial: accession |
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 | entry_number |
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,entry_number
Stock type being evaluated in this trial: cross unique id Stock type being evaluated in this trial: cross unique id |
The first row (header) must contain the following:
plot_name | cross_unique_id | 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 | entry_number |
plot_name,cross_unique_id,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,entry_number
Stock type being evaluated in this trial: family name Stock type being evaluated in this trial: family name |
The first row (header) must contain the following:
plot_name | family_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 | entry_number |
plot_name,family_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,entry_number
- accession_name or cross_unique_id or family_name (must exist in the database. This is the accession or cross unique id or family name 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)
- plot_name (must be unique across entire database. If not provided in the file, it will be automatically generated as
{trial_name}-PLOT_{plot_number}
.) - is_a_control (type 1 in this field if the plot is a control, otherwise leave blank. generally you will have accessions/cross unique ids/family names that are controls, so you should indicate the plots of those accessions/cross unique ids/family names 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 should 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 should 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)
- entry_number (a trial-level entry number assigned to the stock. 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.)
Only the required fields are necessary to include in the upload template. You may add any additional optional fields. The fields can be in any order.
Upload Template Information
Multiple Trial Designs:
Header:
The first row (header) must contain the following, which is an expansion of the single trial design header:
trial_name | breeding_program | location | year | transplanting_date | design_type | description | trial_type | plot_width | plot_length | field_size | planting_date | harvest_date | 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 | entry_number |
trial_name,breeding_program,location,year,transplanting_date,design_type,description,trial_type,plot_width,plot_length,field_size,planting_date,harvest_date,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,entry_number
Required fields:- trial_name (Must be unique across entire database. It is often a concatenation of the year, transplanting_date, purpose, unique number, and location.)
- breeding_program (The name of breeding program that managed the trial, must exist in the database.)
- location (The name or abbreviation of the location where the trial was held, must exist in the database.)
- year (The year the trial was held.)
- design_type (The shorthand for the design type, must exist in the database. Possible values include CRD (Completely Randomized Design), RCBD (Randomized Complete Block Design), RRC (Resolvable Row-Column), DRRC (Doubly-Resolvable Row-Column), ARC (Augmented Row-Column), Alpha (Alpha Lattice Design), Lattice (Lattice Design), Augmented (Augmented Design), MAD (Modified Augmented Design), greenhouse (undesigned Nursery/Greenhouse), splitplot (Split Plot), p-rep (Partially Replicated), Westcott (Westcott Design))
- description (Additional text with any other relevant information about the trial.)
- accession_name (The accession being tested in the plot, must exist in the database.)
- 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.)
- plot_name (Must be unique across entire database. If not provided in the file, it will be automatically generated as
{trial_name}-PLOT_{plot_number}
) - trial_type (The name of the trial type, must exist in the database. Possible values include Seedling Nursery, phenotyping_trial, Advanced Yield Trial, Preliminary Yield Trial, Uniform Yield Trial, Variety Release Trial, Clonal Evaluation, genetic_gain_trial, storage_trial, heterosis_trial, health_status_trial, grafting_trial, Screen House, Seed Multiplication, crossing_block_trial, Specialty Trial)
- plot_width (plot width in meters)
- plot_length (plot length in meters)
- field_size (field size in hectares)
- planting_date (Date of Planting in YYYY-MM-DD format)
- transplanting_date(The transplanting_date of the trial was conducted. Date in YYYY-MM-DD format))
- harvest_date (Date of Harvest in YYYY-MM-DD format)
- is_a_control (type 1 in this field if the plot is a control, otherwise 0 or leave blank. generally you will have accessions that are controls, so you should indicate the plots that that accession is in as a control.)
- rep_number (replicate number, must be numeric)
- range_number (range number. often synonymous with col_number, must be 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)
- entry_number (a trial-level entry number assigned to the stock. 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 if not applied.)
Only the required fields are necessary to include in the upload template. You may add any additional optional fields. The fields can be in any order.
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 VCF Template Information
VCF is a tab separated format. If your VCF is very large (greater than 10GB), please consider converting it to an HDF5 (.h5) file using Tassel, and uploading the HDF5 formatted file instead.
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 | Optional: additional marker info can be included. Please see below. |
- Quality
- Filter
- Info
- Format
- Sequence
Upload Tassel HDF5 Template Information
Please use HDF5 (.h5) formatted files that work with Tassel
Uploading an HDF5 file is important when the size of the VCF grows greater than 10GB
Upload SSR Marker Info Template Information
Header:
The first row (header) must contain the following fields:
marker_name | forward_primer | reverse_primer | annealing_temperature | product_sizes | sequence_motif | sequence_source | linkage_group |
- marker_name
- forward_primer
- reverse_primer
- annealing_temperature
- product_sizes
- sequence_motif
- sequence_source
- linkage_group
Upload SSR Marker Info Error
Success
SSR marker info was saved successfully. You can now proceed with SSR genotyping data upload.
Upload SSR Protocol (Marker Info)
Upload SSR Data Template Information
Example of SSR Data Spreadsheet:
sample_name | s01 | s01 | s01 | s02 | s02 | s02 |
139 | 170 | 194 | 203 | 229 | 290 | |
sample_A | 1 | 0 | 0 | 0 | 1 | 1 |
sample_B | 0 | 0 | 0 | 1 | 0 | 0 |
sample_C | 0 | 1 | 1 | 0 | 1 | 0 |
- s01 and s02 are marker names.
- 139, 170, 194 are product sizes generated by marker s01 and 203,229,290 are product sizes generated by marker s02.
- sample_A, sample_B, sample_C are accession names.
- "1" indicates the presence of PCR product.
- "0" indicates the absence of PCR product.
Upload KASP data Template Information
Please use csv formatted files
For KASP Marker Information File:
The header must be:
MarkerName | Xallele | Yallele | Chromosome | Position | Optional: additional marker info can be included. Please see below. |
Optional columns: You can include additional marker information by selecting one or more column headers listed below. Please add the selected column(s) after "Position" column.
- Quality
- Filter
- Info
- Format
- Sequence
- FacilityMarkerName: if you are uploading genotyping data by using facility marker names, please include these names in the KASP marker information file using "FacilityMarkerName" header
For KASP Result File:
Note: If your genotyping facility assigned facility marker names and facility sample names for the genotyping data generated, you have an option to directly use these facility names for uploading. After uploaded into database, the genotyping data will be automatically linked to the original marker names and sample names.
If you are uploading genotyping data using your marker names and sample names, the header must be:
MarkerName | SampleName | SNPcall | Xvalue | Yvalue |
- MarkerName: Must exist in the marker information file. If you are uploading genotyping data using previously stored protocol, marker names must exist in the selected protocol.
- SampleName: Must exist in the database as uniquenames.
- SNPcall: Allele separated by ":" (for example A:G).
- Xvalue: raw data of X.
- Yvalue: raw data of Y.
If you are uploading genotyping data using facility marker names and facility sample names, the header must be:
FacilityMarkerName | FacilitySampleName | SNPcall | Xvalue | Yvalue |
- FacilityMarkerName: Must exist in the marker information file.
- FacilitySampleName: Must exist in the database. You can create a link between each sample name and facility sample name by including facility sample name during uploading genotyping plates
- SNPcall: Allele separated by ":" (for example A:G).
- Xvalue: raw data of X.
- Yvalue: raw data of Y.
Add Genotyping Plate
- Intro
- Genotyping Project
- Basic Plate Info
- Well Info
- Trial Linkage
- Confirm
-
This workflow will guide you through adding a genotyping plate in the database
Genotyping plates represent 96 or 384 well plates.
Each plate has a globally unique Plate ID.
Each well in the plate has a globally unique tissue sample ID.
The "contents" of each well can be either a tissue sample, plant name, plot name, or accession name. This "source" name must be in the database already. This is useful if you provide a field trial entity (such as a plot or plant or tissue sample name), so that phenotypes and genotypes can be directly compared.
If you choose to submit your genotyping plate to a genotyping facility (Cornell IGD, Intertek, BGI, etc) we can generate the files they require for you. Please be aware of their requirements, such as blank well positions and concentrations.
In addition to sample ID, you have an option to include facility identifier for each well.
-
Select a genotyping project
Genotyping projects are for grouping genotyping plates and/or genotyping data together. Genotyping Project should match Vendor Project if you have one.
-
Provide info about your plate
-
Provide information about the wells in your plate
You want to upload an existing plate layout
File format information
Spreadsheet format
You want to upload a Coordinate Android Application file.
File format information
Spreadsheet format
You want to upload a Custom Android Application file.
File format information
Spreadsheet format
You want to design a completely new plate.
- Select a list for the source material going into each well. Your list should be a one to one pairing to each well e.g. if you want to fill 95 wells you should supply a list of 95 elements.
- Note: From the most desirable to least desirable source observation unit you can choose: tissue samples, plants, plots, or accessions
[loading...]
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Is your genotyping plate linked with field trials in the database? This information can also be added from the genotyping plate detail page once the trial is saved in the database.
If you provided us with information about where the tissue sample in each well originated (e.g. it came from a plot name or plant name or tissue sample name in a field trial), we will automatically create linkage between the field trial(s) and this genotyping plate.
-
Finalize and submit your genotyping plate
Automatic submission to the Genotyping Facility currently not working. You can submit it from the Genotyping Plate's detail page or download the information from the Genotyping Plate's detail page and submit it yourself after clicking Submit
Complete! Your genotyping plate was saved in the database.
The genotyping plate was saved successfully
- You may want to proceed to the genotyping plate detail page for the trial you just created.
- You can print barcodes for the plate and tissue samples.
Complete! Your genotyping plate was saved in the database.
The genotyping plate was saved successfully
- You may want to proceed to the genotyping plate detail page for the trial you just created.
- You can print barcodes for the plate and tissue samples.
Upload Template Information
File must be Excel file (.xls or .xlsx)
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 |
Required fields:
- 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 e.q. A10)
- 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, stem, seed, fruit or tuber)
- 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.)
- facility_identifier (if you would like to include facility identifiers in your genotyping plate layout, you can add facility identifiers in the last column with the header "facility_identifier")
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 |
Required fields:
- 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)
- facility_identifier (if you would like to include facility identifiers in your genotyping plate layout, you can add facility identifiers in the last column with the header "facility_identifier")
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 |
Required fields:
- 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)
- Facility Identifier (if you would like to include facility identifiers in your genotyping plate layout, you can add facility identifiers in the last column with the header "Facility Identifier")
Upload Seedlot Inventory
- Intro
- File format
- Upload inventory
- Fix missing seedlots problem
- Try submitting inventory again
-
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 "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 Inventory Application. For info about the format of the file to upload, go to the next tab.
- It is also possible to manually enter a transaction by going to the seedlot detail page and clicking "Add New Transaction".
-
Make sure you are collecting seedlot inventory in the following format
The "Seed Inventory" Android Application will export this same exact format by default.
-
Select your file and upload seedlot inventory
-
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
-
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
-
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_gram, 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.)
-
Seedlots fall into two categories
-
Make sure your file matches the correct file format
-
Provide basic information about the seedlots and upload your file
-
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
-
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
The first row (header) should contain the following:
seedlot_name | accession_name | operator_name | amount | weight_gram | description | box_name | quality | source |
- 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.)
-
amount (number of seeds in seedlot. can be provided in conjunction with weight_gram. must provide a value for amount or weight_gram or both.)
AND/OR
weight_gram (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight_gram 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)
- quality (status of the seedlot, for example "ok", "moldy", "insect damage" etc.
- source (an alternate source, such as a plot, subplot, or plant identifier from which the seed was collected)
Seedlots may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).
Optional columns may be left out, if not used in your data.
Upload Template Information For Harvested Seedlots
The first row (header) should contain the following:
seedlot_name | cross_unique_id | operator_name | amount | weight_gram | description | box_name | quality |
- 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.)
-
amount (number of seeds in seedlot. can be provided in conjunction with weight_gram. must provide a value for amount or weight_gram or both.)
AND/OR
weight_gram (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight_gram 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)
- quality (brief description of quality, e.g., "ok", "moldy", "insect damage", etc)
Seedlots may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).
Optional columns may be left out, if not used in your data.
Create New Seedlot
Add Accessions
File format information
|
Accessions may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).
Optional columns may be left out, if not used in your data.
Upload Accessions Template Information
The first row (header) should contain the following:
accession_name | species_name | population_name | organization_name | synonym | PUI | accession number | acquisition date | biological status of accession code | country of origin | donor | donor PUI | donor institute | genome_structure | institute code | institute name | introgression_backcross_parent | introgression_chromosome | introgression_end_position_bp | introgression_map_version | introgression_parent | introgression_start_position_bp | location_code | ncbi_taxonomy_id | notes | organization | ploidy_level | released_variety_name | seed source | state | transgenic | type of germplasm storage code | variety |
- The following fields can take comma-separated values to indicate there are several values for the accession: organization_name, synonym , PUI, accession number, acquisition date, biological status of accession code, country of origin, donor, donor PUI, donor institute, genome_structure, institute code, institute name, introgression_backcross_parent, introgression_chromosome, introgression_end_position_bp, introgression_map_version, introgression_parent, introgression_start_position_bp, location_code, ncbi_taxonomy_id, notes, organization, ploidy_level, released_variety_name, seed source, state, transgenic, type of germplasm storage code, variety
- 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_name (the name(s) of the organization(s) which use this accession e.g. NARO,IITA)
- synonym (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. e.g. accession_synonym1,accession_synonym001)
- PUI (no definition available)
- accession number (no definition available)
- acquisition date (no definition available)
- biological status of accession code (no definition available)
- country of origin (no definition available)
- donor (no definition available)
- donor PUI (no definition available)
- donor institute (no definition available)
- genome_structure (no definition available)
- institute code (no definition available)
- institute name (no definition available)
- introgression_backcross_parent (no definition available)
- introgression_chromosome (no definition available)
- introgression_end_position_bp (no definition available)
- introgression_map_version (no definition available)
- introgression_parent (no definition available)
- introgression_start_position_bp (no definition available)
- location_code (no definition available)
- ncbi_taxonomy_id (no definition available)
- notes (no definition available)
- organization (no definition available)
- ploidy_level (no definition available)
- released_variety_name (no definition available)
- seed source (no definition available)
- state (no definition available)
- transgenic (no definition available)
- type of germplasm storage code (no definition available)
- variety (no definition available)
Accessions may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).
Optional columns may be left out, if not used in your data.
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
-
Introduction
- Crosses can be of different types (biparental, self, open, backcross, sib, polycross, bulk, bulk_open, bulk_self, doubled_haploid, or dihaploid_induction)
- 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).
- backcross: An individual plant pollinated by one of its parents. Cross Unique ID can be used as one of the parents.
- 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 (between a female population and a male accession).
- bulk_open: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (between a female population and a male population or unknown male parent).
- bulk_self: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
- doubled_haploid: Plants derived from doubling the chromosome number of haploid tissue.
- dihaploid_induction: Plants derived from reducing the chromosome set from tetraploid to diploid.
- An individual cross can be linked to a female plot or plant, as well as a 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
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 | cross_combination | cross_type | female_parent | male_parent | female_plot | male_plot |
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, backcross, bulk, bulk_open, bulk_self, doubled_haploid, dihaploid_induction)
- 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).
- backcross: An individual plant pollinated by one of its parents.
- 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 (between a female population and a male accession).
- bulk_open: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (between a female population and a male population or unknown male parent).
- bulk_self: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
- doubled_haploid: Plants derived from doubling the chromosome number of haploid tissue.
- dihaploid_induction: Plants derived from reducing the chromosome set from 4 to 2.
- female_parent: Accession names (for biparental, self, open, sib, polycross, doubled_haploid cross types) or population names (for bulk, bulk_self and bulk_open cross types) or cross unique ids (for backcross cross type) must exist as uniquenames in the database.
- male_parent: Required in the header, but value may be left blank for open cross type. Must be specified for biparental, sib, polycross, bulk, backcross, doubled_haploid and dihaploid_induction cross types. When specified, accession names or population names must exist as uniquenames in the database.
- 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.
- 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.
- female_parent: Female parent names must exist as uniquenames in the database, can be accession, plot, plant or population stock type.
- 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, male parent names must exist as uniquenames in the database, can be accession, plot, plant or population stock type.
- objective
- female_focus_trait
- male_focus_trait
- female_source_trial
- male_source_trial
- After cross unique ids are stored in the database, you can add field crossing data (e.g. pollination date, total number of flowers pollinated, total number of fruits set) or progenies to each cross unique id.
- Field crossing data 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
- 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, backcross, sib, polycross, bulk, bulk_self, bulk_open, doubled_haploid, or dihaploid_induction
- 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.
- For backcross cross type, cross unique id can be used as one of the parents.
- 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).
backcross: An individual plant pollinated by one of its parents.
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.
dihaploid induction: Plants derived from a chromosome reduction from tetraploid to diploid
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
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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)
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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).
Cassava (Manihot esculenta), a major staple crop, is the main source of calories for 500 million people across the globe. No other continent depends on cassava to feed as many people as does Africa. Cassava is indispensable to food security in Africa. It is a widely preferred and consumed staple, as well as a hardy crop that can be stored in the ground as a fall-back source of food that can save lives in times of famine. Despite the importance of cassava for food security on the African continent, it has received relatively little research and development attention compared to other staples such as wheat, rice and maize. The key to unlocking the full potential of cassava lies largely in bringing cassava breeding into the 21st century. [More...]
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Intertek sample form and tutorial
For all questions about Cassava (phenotyping, genotyping, population genetics) subscribe to the cassava-discussion@cassavabase.org mailing list!
Global Cassava Partnership (GCP)
Int'l Society for Tropical Root Crops (ISTRC)
Integrated Breeding Platform
CassavaCyc
RIKEN Cassava Database
Cassavabiotech.org (CAS, Shanghai, China)
Cassavagenome.org
GOBii project
Cassava Disease Net
Plant Village
Cassava in tropical Africa a reference manual
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