Breeding Information Management System Software

ISSUE: Marker-assisted breeding of crops in the Rosaceae family requires massive amounts of data, including:

• measurements of observed characteristics (phenotypes),
• genetic variation in the form of DNA sequences and their variants (genotypes),
• pedigrees connecting breeding germplasm individuals,
• DNA information describing associations between phenotypes and genotypes, and
• DNA information describing what form of each trait-influencing genomic region is carried by each breeding individual.

Managing all these data types and making them accessible to inform breeding and associated research decisions is a daunting task. Online tools that leverage the trillions of data points generated are needed. By performing both simple and complicated calculations and visualizations, users can efficiently and strategically manage the information for genetic improvement of rosaceous crops.

WHAT HAS BEEN DONE: Online, searchable data repositories and associated calculation and visualization tools to assist apple, cherry, peach, and strawberry breeding were developed and made available for public use on the Genome Database for Rosaceae portal (www.rosaceae.org).

IMPACT: U.S. rosaceous crop breeders and allied scientists can now efficiently upload, browse, search, and download genetic data and observed traits of crop varieties for apple, peach, cherry, and strawberry; generate input files to use in breeding pedigree software; visualize all of these data types from any web portal (even on smartphones); receive decision support for identifying efficient crosses and seedling selection schemes; and develop and validate their own genetic tests using the best available genomic knowledge about each crop. These breeding decision-support tools are increasing the efficiency, accuracy, and creativity and capability of breeding programs. These tools are:

• Trait Locus Warehouse – where all known genetic discoveries to date across each crop’s genome are compiled, visualized, and chosen for further consideration.
• Selection Target Identifier – where the most promising genetic discoveries are determined by associating socio-economic values to the trait level increase promised by each “trait locus”.
• Technology Portfolio – where regularly updated details about commercial service providers for genetic testing are made available to all breeding programs.
• Marker Converter – where breeders or supporting researchers use DNA sequences and other genomics data to design new genetic tests for valuable discoveries that are appropriate for a breeder’s genetic testing service provider.
• QTL Validator – where tools reside for characterizing the predictiveness of each new DNA for a specific breeder’s parents and families.
• Cross Assist – where breeders use all available genetic information to determine efficient cross combinations among their parent pool for target performance outcomes in the next generation.
• Seedling Select – where breeders model the costs and logistics of evaluating the genetic potential of thousands of young seedlings to identify when and how much to best integrate available genetic tests to save resources.

Training Future Plant Breeders

ISSUE: Plant breeders who can utilize DNA information will be more efficient in developing superior new varieties with improved fruit quality and greater productivity. Preparing future plant breeders who can integrate DNA-based knowledge and technology into their breeding programs, a process called Marker-Assisted Breeding (MAB), assures an exciting future for new cultivar development. Training of the next generation in appropriate application of state-of-the-art technologies leverages public and private investments in advanced genetics and genomics research for sustained breeding outcomes. Breeder education programs that include MAB will help meet industry needs for new breeders, in turn serving producers, packers, shippers, and sellers who will have new fruit varieties that meet their various needs and the preferences of consumers.

WHAT HAS BEEN DONE: RosBREED’s “demonstration” apple, cherry, peach, and strawberry breeders are each training one or more graduate students. These Breeding Trainees have gained knowledge, experience, and skills in setting breeding targets, accurately measuring fruit and plant characteristics, determining trait inheritance, designing and implementing genetic tests, evaluating alternative selection strategies, and managing breeding program logistics, personnel, budgets, and timelines. A coordinated team approach is used to provide a multi-disciplinary learning experience for these students.

IMPACT: As a result of RosBREED’s investment in the next generation of plant breeders:

• Four doctoral students have graduated and an additional two doctoral students will graduate in the next two years with skills, knowledge, and experience in MAB that would not have been provided without RosBREED funding, training opportunities, and collaborative networks among breeding programs and educational institutions.
• Four Master’s students have graduated and an additional one Master’s student will graduate in the next year with similar added skills, knowledge, and experience.
• These 11 students represent a doubling in the number of students trained in these programs in the last decade. Many of their graduate education opportunities would not have existed without RosBREED support, and all of their educational experiences were greatly enriched by learning opportunities in MAB provided through the RosBREED project.
• These students are prepared for the breeding jobs of the future. They have learned how to use new genetic tests to determine the best parents to combine in new crosses and to determine the best seedlings to advance through their programs. These applications reduce the costly and time-consuming need to plant , maintain for years, and thoroughly field test thousands of seedlings that are likely to have unacceptable fruit quality or growth characteristics. By using genetic tests to avoid the least promising parents and eliminate inferior seedlings early in this multi-year process, these students have learned how to focus breeding program resources where they are most likely to succeed.