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
Prepare a 96 or 384 well plate for a genotyping experiment
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
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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Add Genotyping Trial
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)
- ncbi_taxonomy_id (NCBI taxonomy identifier)
- dna_person (the name of the person who prepared the well)
- notes (any additional notes on the well)
- tissue_type (free-text for what type of tissue is present in 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 trial submission form. e.g. NextGenCassava)
- plate_name (the unique name for the individual plate. called "Plate ID" in genotyping trial 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.)
- dna_person (the name of the person who plated the individual sample. can be any name.)
- notes (any additional notes on the well)
- tissue_type (free-text for what type of tissue is present in the well)
- extraction (free-text for the extraction method e.g. CTAB)
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.)
- description (information about why this seedlot is being added)
- box_name (the box name that the seed is located in. can be any name.)
Upload Template Information For Harvested Seedlots
(.xlsx format not supported)
Header:
The first row (header) must contain the following:
seedlot_name | cross_name | operator_name | amount | weight(g) | description | box_name |
- seedlot_name (must be unique)
- cross_name (must exist in the database. a cross_name 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.)
- description (information about why this seedlot is being added)
- box_name (the box name that the seed is located in. can be any name.)
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
- File Formatting
- Crossing trial
- Upload your crosses
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What are crosses?
- Crosses represent any pollination that occurs.
- Crosses can be of different types (biparental, self, open, 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)
- 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.
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Make sure your crosses are formatted in the right format
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Select a crossing trial
Crossing trials are for grouping crosses together. The grouping is most often done for geographic reasons, such as a group of crosses done in the same field trial. This grouping can be used to encapsulate 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 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:
The first row (header) must contain the following:
cross_name | cross_type | female_parent | male_parent | female_plot | male_plot | Tag Number | Pollination Date | Number of Bags | Number of Flowers | Number of Fruits | Number of Seeds |
- cross_name (must not conflict with an existing cross name)
- cross_type (must be one of the following: biparental, self, open, bulk, bulk_self, bulk_open, or doubled_haploid)
- female_parent (must exist in the database)
- male_parent (required in the header, but value may be left blank for most cross types. Must be specified for biparental and bulk crosses. When specified, must exist in the database)
- female_plot (required in the header, but value may be left blank. When specified, plot name must exist in the database)
- male_plot (required in the header, but value may be left blank. When specified, plot name must exist in the database)
- Tag Number
- Pollination Date
- Number of Bags
- Number of Flowers
- Number of Fruits
- Number of Seeds
Add New Cross
- Intro
- Crossing trial
- Enter cross information
- Enter parentage information
- Track exact cross parents
- Additional cross info
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What is a cross?
- The Cross Tool can track any pollinations in a breeding program.
- Each cross has a globally unique cross name.
- Supported cross types are: biparental, self, open, 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.
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Select a crossing trial
Crossing trials are for grouping crosses together. The grouping is most often done for geographic reasons, such as a group of crosses done in the same field trial. This grouping can be used to encapsulate 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 cross
Cross type information
Descriptions of cross typesRequired:
-
Enter basic information about the cross
(optional)
(optional)
-
If you choose to record exact cross parents, you can do so.
-
If you know more information about the cross, you can add it
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).
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 Trial
- Intro
- Add a crossing trial
-
What are crossing trials?
Crossing trials group crosses. The grouping can reflect crosses done in the same field trial or crosses in a breeding program in a given year. 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 trial
Finished! Your crossing trial is now in the database
Crossing trial was added successfully
- You may want to proceed to the crossing trial detail page you just created.
- You can add or upload crosses into your crossing trial as they become available.
- You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).
Finished! Your crossing trial is now in the database
Crossing trial was added successfully
- You may want to proceed to the crossing trial detail page you just created.
- You can add or upload crosses into your crossing trial 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...]
Cassavabase Mirror at IITA (Nigeria)
Cassava Descriptors
HTPG project
Intertek sample form and tutorial
For all questions about Cassava (phenotyping, genotyping, population genetics) subscribe to the cassava-discussion@cassavabase.org mailing list!
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Cassavabase adheres to the Toronto Agreement on prepublication data release.
All data deposited on cassavabase 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 cassavabase 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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