The Buckler Lab hosted a hackathon in February 2020 to develop a Practical Haplotype Graph (PHG) for wheat to be used by wheat breeding programs. Funded by the Bill and Melinda Gates Foundation as part of an effort to develop methods for genotyping a variety of crops, the hackathon was led by Buckler Lab Project Manager, Cinta Romay; programmers Zack Miller, Peter Bradbury, Terry Casstevens, and Lynn Johnson; and postdoc Brandon Monier.
The team of wheat genetic experts who participated included Umesh Rosyara from the International Maize and Wheat Improvement Center (CIMMYT); Kansas State University Plant Pathology faculty Katherine Jordan and Jesse Poland; post-docs Liangliang Gao and Sandesh Shrestha; and visiting faculty member Moses Nyine. USDA contributors included research geneticists Jean-Luc Jannink, Brian Ward and Jason Fiedler; as well as IT specialist Clay Birkett.
During the week-long event, the team made great progress toward constructing a breeding PHG for wheat and overcoming the speed and memory difficulties generated by its large genome size, which is approximately six times larger than maize and humans. Additionally, promising results suggest it can be a useful tool to combine knowledge from historical data (90K chip, GBS, etc.) with the new, less-expensive genotyping methods enabled by recent technological developments. In summary, building a wheat PHG proved to be a great stress test for the PHG pipelines and presented opportunities for developing new strategies for data management that could be very useful across multiple crops.