SeedUSoon: A New Software Program to Improve Seed Stock Management and Plant Line Exchanges between Research Laboratories

Abstract

Plant research is supported by an ever-growing collection of mutant or transgenic lines. In the past, a typical basic research laboratory would focus on only a few plant lines that were carefully isolated from collections of lines containing random mutations. The subsequent technological breakthrough in high-throughput sequencing, combined with novel and highly efficient mutagenesis techniques (including site-directed mutagenesis), has led to a recent exponential growth in plant line collections used by individual researchers. Tracking the generation and genetic properties of these genetic resources is thus becoming increasingly challenging for researchers. Another difficulty for researchers is controlling the use of seeds protected by a Material Transfer Agreement, as often only the original recipient of the seeds is aware of the existence of such documents. This situation can thus lead to difficult legal situations. Simultaneously, various institutions and the general public now demand more information about the use of genetically modified organisms (GMOs). In response, researchers are seeking new database solutions to address the triple challenge of research competition, legal constraints, and institutional/public demands. To help plant biology laboratories organize, describe, store, trace, and distribute their seeds, we have developed the new program SeedUSoon, with simplicity in mind. This software contains data management functions that allow the separate tracking of distinct mutations, even in successive crossings or mutagenesis. SeedUSoon reflects the biotechnological diversity of mutations and transgenes contained in any specific line, and the history of their inheritance. It can facilitate GMO certification procedures by distinguishing mutations on the basis of the presence/absence of a transgene, and by recording the technology used for their generation. Its interface can be customized to match the context and rules of any laboratory. In addition, SeedUSoon includes functions to help the laboratory protect intellectual property, export data, and facilitate seed exchange between laboratories. The SeedUSoon program, which is customizable to match individual practices and preferences, provides a powerful toolkit to plant laboratories searching for innovative approaches in laboratory management.

Keywords: MTA; database; genealogy; genetics; plant; seed; software.

FIGURE 1

User mode interface. (A) General organization of a plant line datasheet. (B) The two categories of genetic features (transgenesis/endogenous gene mutagenesis) with examples of corresponding applications. (C) Detailed user mode organization; a: genetic features table, b: plant table, c: seed batches table, d: access to the customized laboratory guidelines, e: access to the user mode, f: access to the administrative mode, g: search engine, h: plant line datasheet, i: general information, j: genealogy tree, k: access to plant line generation wizards (new, crossing, mutagenesis, and import), l: addition of new genetic features, m,n: lock buttons, o,p: export buttons.

FIGURE 2

Search engine interface. Key words can be entered in a generic field (“Gene/Line/Genetic feature” field) or in specific sub-categories to narrow the search. A “%” symbol can be included to replace any number of characters in the query. Including a “_” indicates the presence of a single missing unknown character in the query. Adding a “$” before “_” or “%” in the query field will allow the user to search for items containing the characters “_” or “%,” bypassing the use of these symbols as replacements of any characters in the query.

FIGURE 3

Principle steps in the new plant line wizard. A new plant line can be recorded de novo following these successive steps. One or several “Genetic features” can be included during the creation process. The resulting “tree” shows that this line does not depend on any parental lines present in the database (no parental lines indicated in the tree). The icons at the bottom provide access to the number of descendants from the plant line, and to an export function of the graphical representation.

FIGURE 4

Simulated crossing of two lines using the “cross” wizard. A new plant line can be created using the simulated crossing between two parental lines present in the database. This line will inherit all genetic features from the parents. It is possible to add an extra genetic feature during the crossing process for the specific case of pollen mutagenesis, where crossings are combined with additional mutagenesis. The resulting “genealogical tree” reflects the relationship between the parental and resulting plant lines. A plant line protected by an Material Transfer Agreement (MTA) is indicated in red. The icons at the bottom provide access to the number of descendants from the plant line, and to an export function of the graphical representation.

FIGURE 5

Creation of a line using the “MUTAG” wizard in order to apply a secondary mutagenesis to an existing plant line. A new plant line can be created by secondary mutagenesis (addition of a genetic feature) to a parental line already present in the database. The new line will inherit all genetic features from this parental line, and combine it to the new genetic feature. The resulting “genealogical tree” reflects the relationship between the parental and resulting plant lines. The icons at the bottom provide access to the number of descendants from the plant line, and to an export function of the graphical representation.

FIGURE 6

Wizards for plant line export/import between SeedUSoon databases. (A) Batch export of plant lines through the result of the search engine (without seed batches attached). (B) Single export of a plant line with attached seed batches (from a plant line datasheet). (C) Plant line import from a .json file into a SeedUSoon database.

FIGURE 7

Two tables for recording biological material corresponding to a plant line. Samples are separated into two tables: plants (A) and seed batches (B). In the example shown here, the researcher decided to record different T1 plants derived from a T-DNA transformation within a single plant line datasheet. The number of insertion sites and location/sequences of independent insertions can be stored separately for each plant. Only the major fields are shown in the columns; detailed information and attached files can be accessed by clicking on the eye icon. It is possible to link the mother plants to their seed batches. The “Copy” button permits fast duplication of plant or seed batch data.

FIGURE 8

Administrative mode and database configuration. (A) The administrative interface is organized in eight tabs: SeedUSoon users (selected here), Persons, species, Ecotypes, Mutation methods, Method references, Strains and Resistances. (B) Persons tab, displaying how many lines or experiments are associated with specific names corresponding to laboratory members. (C) Database configuration panel.