CrossesAndPedigrees
Critical to plant breeding programs is the generation of new material through crossing experiments. To organize collection of data from crosses performed, Breedbase requires creation of a top-level crossing experiment; the crossing experiment is defined with a unique name, a breeding program, a location, a year, and a description. The individual crosses performed are then stored under the crossing experiment; individual crosses are defined by a unique cross name, a location, a crossing experiment, and a cross type. The cross type can be one of the following: biparental, self, open-pollinated, bulk, bulk selfed, bulk and open-pollinated, doubled haploid, polycross, reciprocal, or multicross. Depending on the type of cross performed, different requirements are needed; for example, in a biparental cross, information from both the male and female parent is required, whereas in an open-pollinated cross, information on only the female is required. In the case of an open-pollinated cross, a population name representing a group of male germplasm can be given as the male parent.
Breedbase tracks parental information from crosses in two ways. The first way is through the germplasm names of the female and male parents, allowing for simple ancestry tracking of AxB pedigrees for the progeny from a cross. Pedigrees will be further described in the following section; however, it is important to note that when a cross is created in Breedbase, the pedigree between progeny germplasm and parental germplasm is automatically created as well. This first form of parental tracking is applied in all cases when a cross is created in Breedbase. The second way is through the plot or plant names of the male and female parents. The plot or plant names of the parents are related to the field trial in which they are planted, as will be described in the following field trial section. This second form of tracking is more detailed; however, it is completely optional because of the difficulty in recording this information in many cases.
Recording information on the parental plots is possible with mobile data collection platforms. Of note are customized Open Data Kit (ODK) Android applications, such as BTract. With BTract, after scanning barcodes to track the precise male and female plots or plants involved in the pollination, the application assigns and prints a unique cross barcode label; through ODK data synchronization, the cross information can be uploaded into Breedbase. Another mobile Android application is the Intercross App, which can be used to scan parental barcodes and associate a unique cross name to the performed cross. The output from Intercross can be uploaded directly into Breedbase. In crossing experiments where evaluation of crosses is performed, Breedbase can store the following optional cross properties: pollination date, tag number, number of flowers, number of bags, number of fruits, and number of seeds. These cross properties are arbitrary and are not found in any controlled vocabulary for practical reasons. The cross properties are stored in a JSON encoded string where the key is one of the listed cross properties, or an entirely new property, and the value is the observed quantity; the JSON encoded string is stored in the stockprop table using the type name ‘crossing_metadata_json’ from the ‘stock_property’ controlled vocabulary. These properties are set in the configuration file for the Breedbase instance, allowing researchers flexibility in defining these terms.
Crosses can be created one at a time using an interactive interface on Breedbase or they can be uploaded in bulk using an Excel spreadsheet. The uploaded Excel file contains the unique cross name, the cross type, the parents involved, and optionally, values for the evaluated cross properties. Uploading of the spreadsheet has the added action of updating the evaluated cross properties for any existing crosses in the database. After a cross is saved in the database, progeny of the cross can be saved as new germplasm in the database, automatically creating pedigrees for the new germplasm. Progeny germplasm can be interactively created in Breedbase and have unique names templated from the cross name.
Crossing experiments are stored as an entry in the project table and are linked to their breeding program through a project_relationship entry with the type name ‘breeding_program_trial_relationship’ from the ‘project_relationship’ controlled vocabulary; the project entry is linked to entries in the projectprop table in an EAV model to store values for the year and location using type names from the ‘project_property’ controlled vocabulary. Individual cross entries are stored as entries in the stock table using the type name ‘cross’ from the ‘stock_type’ controlled vocabulary; this stock entry is linked to the crossing experiment project via entries in the nd_experiment_stock and nd_experiment_project tables, ultimately linked by an nd_experiment entry with the type name ‘cross_experiment’ from the ‘experiment_type’ controlled vocabulary. A cross is linked to the involved parental germplasm through entries in the stock_relationship table using the type names ‘female_parent’ and ‘male_parent’ from the ‘stock_relationship’ controlled vocabulary for the female and male parents, respectively. The stock_relationship entry linking the cross to the female germplasm parent also contains the cross type in the value field. In the case where plot or plant parental information is known, the cross is linked to the female and male plots using stock_relationship entries with the type names ‘female_plot_of’ and ‘male_plot_of’ from the ‘stock_relationship’ controlled vocabulary, respectively, and the cross is linked to the female and male plants using stock_relationship entries with the type names ‘female_plant_of’ and ‘male_plant_of’ from the ‘stock_relationship’ controlled vocabulary, respectively. Progeny germplasm are created as entries in the stock table using the type name ‘accession’ from the ‘stock_type’ controlled vocabulary. Progeny germplasm of the cross are linked to the female and male germplasm using stock_relationship entries with the type names ‘female_parent’ and ‘male_parent’ from the ‘stock_relationship’ controlled vocabulary; these two relationships constitute the pedigree as is described in the next section. Progeny germplasm are also linked to their cross using a stock_relationship entry with the type name ‘offspring_of’ from the ‘stock_relationship’ controlled vocabulary.
A pedigree in Breedbase is represented by relationships between germplasm stock table entries via the stock_relationship table. It is important to remember that all germplasm, whether they are progeny or parents in a pedigree, are stored in the same way as entries in the stock table with type name of ‘accession’ from the ‘stock_type’ controlled vocabulary. The pedigree stems from the relationships, such that a progeny germplasm is linked to its female and male germplasm parents through entries in the stock_relationship table with type names of ‘female_parent’ and ‘male_parent’ from the ‘stock_relationship’ controlled vocabulary, respectively.
The pedigree in Breedbase can be queried and transformed into a pedigree string of any format, such as Purdy. More interestingly, the pedigree can be displayed visually and interactively using the BrAPI-Pedigree-Viewer (https://github.com/solgenomics/BrAPI-Pedigree-Viewer) implemented in Breedbase. More information on Breeding API applications (BrAPPs) can be found in the section below.
Pedigrees can be created in Breedbase three ways. The first way is by uploading a simple Excel file that contains the progeny germplasm name, the female parent germplasm name, the cross type, and optionally, the male parent germplasm name. The cross type here can be bi-parental, open, or self, and the male parent can be a population name representing a group of male germplasm. This method is ideal for filling in pedigrees for a large amount of historic material. The second way is to add the male and female parent to a single germplasm progeny through an interactive interface on Breedbase; this method is ideal for correcting small issues in pedigrees and germplasm management. The third way is to create progeny from crosses, as was described in the previous crossing experiments section. The third method is preferred given that it provides the most descriptive information for the cross underlying the pedigree and potentially provides evaluation metrics for the cross through cross properties.
