SeedUSoon is designed around the core concept of “plant lines,” whose definition is very similar to the one used by many plant science researchers when referring to the series of successive generations derived from particular plants. A “Plant line” is defined by a set of unique traits (mutations or transgenes, named “Genetic features” in SeedUSoon; Figures 1A,B) in a biological context (species and ecotype). All plants and seeds arising from selfcrosses or backcrosses are still considered part of the same “Plant line,” so that under a single “Plant line” entry, the user can record as many seeds or plants as desired. The precise genotyping (such as the heterozygous/homozygous state of each mutation, or the segregation pattern of seed batches) can be recorded for each individual plant or seed batch entry.

However, if crosses are performed with plants carrying other types or mutations or with plants from another ecotype, the genetic properties of the resulting line will significantly differ from the original plant. For this reason, the progeny of these types of crossings must be entered as a new “Plant line” entry. Similarly, if a previously mutagenized plant line is subjected to a secondary mutagenesis or transgenesis, the resulting progeny will constitute a new “Plant line.”

A “Plant line” datasheet is organized in five different parts (Figure 1A). The line name and general information associated with this line are displayed in the upper left area, including the plant species and ecotype, its origin and the existence of any MTA protecting the material (“General information” fields, Figures 1A,C, Supplementary Figure 1). In the center of the screen, a table presents blue or green boxes containing the names of all individual mutations or transgenes (i.e., “Genetic features”; Figures 1A–C) along with their origin (in which “from…” indicates the original plant line containing this mutation). The content of each box can be expanded in order to access the individual properties of each “Genetic feature” (“Genetic features fields,” Supplementary Figure 1). If no green or blue box appears inside this table, the genotype of the corresponding plant line is considered to be WT. At the upper right corner, the parental lineage and the mutagenesis/genetic history of the opened plant line datasheet is represented by a tree.

Finally, two tables for plants (Figures 1A,C, left) and seed batches (Figures 1A,C, right) are located in the lower part of the datasheet. Generations of plants and seeds can be recorded at any time, including the skipping of generations, which allows users to avoid a strict “generation workflow.” The user enters the generation stage and can record for each plant the precise genotyping of each “Genetic feature” listed in the upper table (or the segregation profile for each seed batch). Consequently, by using a “Plant line” as the entry point, the user can access all recorded generations of seeds or plants that share the same overall genetic background.

By organizing the datasheet into five parts (general information, genetic features, tree, the plants table, and the seed batches table), users can focus on the core properties of each line (genetic context and history, ecotype, etc.) before searching through all available seeds or plants corresponding to these criteria. The software also allows users to decide whether they want to track all successive generations of a plant line, or to only record a subset of particularly valuable seed batches.

During the development of our software, the ability to compare the behavior and properties of successive seed generations in a single table was a recurring request from researchers that we spoke with. One reason for this is that epigenetic phenomena can affect the behavior of descendants of seemingly identical plants, in particular through DNA methylation (Mlotshwa et al., 2010; Diez et al., 2014). A table comparing the properties of distinct generations can thus be instrumental in identifying the appearance or loss of specific phenotypes, or the progressive silencing of T-DNA expression. Similarly, the lack of a link between phenotype and desired mutations might suggest the presence of an unknown off-target mutation (frequent with CRISPR/Cas9 or EMS mutagenesis).

When performing T-DNA transformation for specific purposes (such as RNAi silencing or expression of GFP-protein fusions), it is convenient to visualize all available independent transformants at once (along with their descendants). In this case, a software user often prefers to record all independent transformants within a single “Plant line” rather than as separate “plant lines.” Properly speaking, the independent transformants do not share the exact same genetic properties. The T-DNA insertion sites are variable in these lines, and have a putative impact on the properties of the resulting plants (Kohli et al., 2006). Nevertheless, comparing all independent transformants within a single plant line can be advantageous for tracking the outcome of a T-DNA transformation; this approach can also quickly identify undesirable effects, such as construct silencing, patchy expression, etc. With SeedUSoon, laboratories can decide if they want to record independent plant line datasheets for each insertion or use a single datasheet for all independent transgene insertion events, since T-DNA insertion sites can be defined in two locations within the datasheet: either in the transgene sequence section in the “Genetic feature” table (Figure 1A), or for each of the individual plants recorded in the lower table (i.e., different insertion sites can be recorded in the plant table specifically for each plant entry; Figures 1A,C-a,b). Finally, seed batches can be linked to these individual plants.

Mutations or transgenes present in the genome of a “Plant line” are recorded as unique “Genetic Features,” and listed in the corresponding table of the plant line datasheet (Figure 1A). There are two distinct feature categories, “Transgenesis” and “Endogenous gene mutagenesis,” with the latter one corresponding to point mutations, nucleic deletions and insertions affecting an endogenous genomic sequence that does not involve the insertion of a transgene (T-DNA or transposon).

The “Transgenesis” feature must be selected for T-DNA or transposon mutagenesis (Clough and Bent, 1998; Greco et al., 2001; Gomez et al., 2009), and corresponding mutations will appear in green in the features table (Figure 1B). “Endogenous gene mutagenesis” corresponds to mutations in endogenous genes with no transgene insertion, such as EMS, gamma irradiation, or natural variants (Kim et al., 2006; Svistoonoff et al., 2007; Fauser et al., 2014). These will appear in blue in the features table (Figure 1B). In the case of CRISPR, TALEN, or ZFN mutagenesis, the plant line will contain both a “Transgenesis” box in green (i.e., the T-DNA containing the mutagenic machinery) and an “Endogenous gene mutagenesis” box in blue [i.e., the targeted endogenous gene loci (Fauser et al., 2014)].

The blue/green color code allows the user to quickly recognize the “Transgenesis” from “Endogenous gene mutagenesis” features. Plants potentially containing transgenes (i.e., GMOs) can thus be immediately distinguished from all other mutation categories (Figure 1A).

Each feature category will call for a specific set of information fields that are ready to be completed by the user (Supplementary Figure 1). In particular, a single sequence can be recorded for “Endogenous mutagenesis” (the mutated genomic locus), whereas a “Transgenesis” feature can record the transgene sequence (in the “Genetic features” properties) as well as several independent genomic insertion sites (in the plant table entries; Figure 1A).

Scrolling the mouse pointer over most fields or icons activates pop-ups that provide more information to the user about the purpose of these functions (Figure 2). In some cases, pop-ups will recommend reading the “Our lab” document mentioned in the previous section, to ensure that users will follow the specific rules that have been decided for their laboratory.

A search engine is located at the bottom of the user interface (Figures 1C-g and 2), which can provide access to all “Plant lines” present in the database (by clicking on “Show all lines”), or only a subset of lines when “Search lines by criteria” is selected (Figure 2). The first field (“Gene, Line, Genetic feature”) can be used to search a keyword throughout all plant line names, gene names and genetic features recorded in the database. Alternatively, users can select more restrictive query criteria by completing the fields specifically associated with the 4 individual sub-parts of a plant line datasheet. These fields can be among the general properties of the line, genetic feature properties, and plant or seed batch properties (including seed batch name or ID, person involved, etc.; Figures 1A and 2; Supplementary Figure 1).

When there is some uncertainty regarding the exact spelling of a query, a “%” symbol can be included at the beginning or end of the word (Figure 2). This will identify any lines containing the searched criteria, including any number of characters appearing before or after the searched word (i.e., “%” = any number of characters).

Clicking on the name of a plant line in the search engine result table will open the corresponding datasheet (Figure 1C-h).

There are four possible ways to create a new line in SeedUSoon: through the generation of a “New record,” crossing, secondary mutagenesis or by import. A button corresponding to each mode is located at the upper left corner of the user interface (Figure 1C-k).

Following the creation of a “Plant line,” it is possible to record the corresponding seed batches or individual plants in two dedicated tables (Figures 1A,C-b,c and 7A,B). These tables can contain any generation of seed batches or plants sharing the same ecotype and set of mutations (i.e., “Genetic features”), including descendants of self-crossed or back-crossed plants. For each plant or seed batch entry, the user can specify their specific genotype or segregation profile (heterozygous/homozygous, single/multiple transgene insertions, resistance or mutation segregation ratio).

The “Plant” and “Seed batch” wizards can be activated by clicking on “Add a plant” or “Add a seed batch” located at the right corner above the plant and seed tables, respectively (Figures 7A,B). The only mandatory field here is the personal plant or seed batch identifier. All other information (generation, phenotyping, genotyping, harvest date, etc.) is optional (see Supplementary Figure 1 for the list of available fields) and can be completed later. Generation stages are entered by the user in the corresponding field, according to the recommendations of the customizable “Laboratory guidelines.” These guidelines can request the use of classical terms, such as T1, T2, F1, F3, as well as other terms such as “unknown” or “Tx” when receiving seeds from another laboratory, for example (see Supplementary Data Sheet 1). Although there is no requirement to track all successive generations, it is possible to associate specific plants with their progeny using the “S” (seed batch) function available for each plant table entry (Figure 7A). Reciprocally, mother plants from seed batches can be indicated when using the “Seed batch” wizard.

SeedUSoon will assign a unique ID number to each seed batch (in addition to the identifier entered by the user; Figure 7B, “ID” column). If a seed batch is deleted (for instance if no seeds are left), this ID number can never be reallocated to any other seed batch. Similarly, even if two seed batches possess the same personal identifier, they will have two unique ID numbers. This software-generated unique ID number therefore provides an easy and secure way to unambiguously distinguish seed batches. This feature can also be used to improve seed stock organization, if included in the label present on the seed stock tubes. SeedUSoon users can simply enter this ID number in the software search engine, and, with this information alone, directly access the corresponding seed batch and plant line information.

An additional field can only be activated for plants resulting from transgenesis, to permit the recording of the location and sequences of one of several insertion sites in individual plants. This facilitates the work of users who prefer to record a series of plants with independent T-DNA or transposon locations within the same table of a unique “Plant line,” rather than in separate “Plant lines” (an example of this application can be seen in Figure 7B).

A “Copy” button is located at the left of each table entry to accelerate the recording of similar seed batches or plants (Figures 7A,B). Its activation will open a wizard, and the user will only need to validate or edit the duplicated information. For seed batches, the software will allocate a unique ID number to the new entry.

Since phenotypical data are often influenced by plant or seed batches, phenotypical results can be individually recorded for each entry in the “Plant” and/or “Seed batch” tables of SeedUSoon (Figure 1C-b,c, Supplementary Figure 1). The user can type a short description of the phenotype in the corresponding wizard field (this text will appear in the table; see the plant example in Figure 1C-b). The user can also upload files describing detailed phenotyping results in the same section. Scrolling the mouse over the “phenotyping” section of the table will reveal the presence of the uploaded file.

Results of tissue-expression patterns (such as from GFP-fusion or reporter gene studies) can also be uploaded in this “phenotyping” section of the “Plant” and “Seed batch” tables.

Germination assays, genotyping and sequencing results can also be recorded or uploaded within individual seed or plant batches. The reference number and pages of the laboratory notebook can be indicated for each result section (phenotyping, germination assay, genotyping, etc.), along with the name of the person who conducted the experiment.

SeedUSoon includes a function to help protect the intellectual property of laboratories, especially related to MTA tracking. An MTA field is included in the plant lines “General information” panel (Figure 1C-i). The “MTA details” field allows users to record the recipient of the MTA, its location, or any particular recommendation. When exporting a line, the information regarding the presence of an MTA protecting the line is preserved. However, the “MTA details” field is left empty for confidential reasons.

SeedUSoon’s graphical “tree” representations of plant lines allow users to immediately identify a protected material. Any plant line protected by an MTA will be indicated in red (Figure 4), so that tracking its descendants will be straightforward, even long after obtaining and using the original seeds.

In the first tab (“SeedUSoon Users”), the administrator can create login accounts and define distinct levels of user’s rights (Figure 8A). SeedUSoon users will either be allowed to enter and modify data (“Writer” level), or will only be able to access the data without modifying them (“Reader” level). The final user level (“Administrator”) gives additional access to the administrative mode.

All tabs (aside from the one used to define “SeedUSoon users”) are dedicated to the customization of the user’s module (Figure 8B). This allows the administrator to specify the options available in the scroll-down menus presented to the users. The software comes with a set of pre-recorded options for each tab, which can easily be edited by the database manager. For each tab entry, the software will automatically verify and count lines, features or experiments containing the corresponding scroll-down menu option. This will help the manager visualize the relevance of certain fields, in order to only delete unused menu options.