Transforming breeding through integrated data management and analysis

Date:11-02-2018


Together with the BCBC, GOBii, Cassavabase, and Cornell University, Boyce Thompson Institute(BTI) recently hosted a fall workshop titled “Transforming Breeding through Integrated Data Management and Analysis”. Attendees from around the globe gathered in Ithaca for a week-long intensive course featuring keynote speakers, workshops, and training sessions.

The workshop featured daily plenary keynote lectures by world renowned experts, hands-on training on the state-of-the-art systems and tools, and customer-driven consulting on strategy and applications. Broad range topics, including data management systems; tracking breeding activities and materials from fields, labs, to data management and analysis; genotyping technologies, vendors, bioinformatics analysis tools and pipelines, marker and genomic breeding applications, were taught. Among those from America, participants traveled to Ithaca, NY from nine other countries: Canada, Kenya, Peru, Nigeria, Côte d’Ivoire, Colombia, New Zealand, Lebanon, and Belgium.

“The goal of the workshop was to introduce the vision and road map of fully integrated data management and decision support, provide available open-source resources to our participants,” said Star Yanxin Gao, GOBii Breeding Informatics and Application Specialist and event organizer. “Also to empower them with strategy, vision, knowledge, and skills to advocate and adopt integrated data management and analysis when they return their institutes and companies. For those who attended, they want to learn the state-of-the-art resources in handling data management and analysis and stay connected with trainers and community for support.”

GOBii has previously given onsite workshops to existing clients. However, others who need genomic data management and decision support tools have reached out for consulting and training. NEXTGEN Cassava and BCBC are also located in BTI and have a wealth of knowledge to share. Organizers collated a list of external contacts and offered either an online workshop or to bring them to Ithaca for in-person training. After six months of planning, the first pilot joint workshop was held at BTI this October 8-12, with Excellence in Breeding (http://excellenceinbreeding.org/) Platform as one of the key sponsors to the workshop.”

“I will apply tools learned during the workshop in my daily work (analysis) including dissemination among students and technical staff,” said participant Ana Luisa Oliveira, a Molecular Breeder and Geneticist from the International Institute of Tropical Agriculture. “I’m very enthusiastic in apply them to my routine work.”

“I will share the links and information with my colleagues because this is important information and we need to build new capabilities,” said Elisa Salas a Field Breeder from CGIAR.

Participants and organizers left the week-long of learning feeling excited for next year, as this becomes an annual event.

“I am very proud to work with a great team of PIs, trainers, organizers, and a communication team at Cornell University and BTI who are the foundation of the success of this workshop,” said Gao. “I am truly energized and satisfied by the fantastic responses from the participants, and heartily committed for continued engagement and future workshop organization!”

The BCBC enables computational approaches, provides educational resources, and develops new methods in a collaborative framework to advance understanding of the complexity of plant life.

GOBii is a team of developers, molecular breeders, statisticians, bioinformaticists and breeders with a mission to build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding programs. Their work has the potential to transform breeding by connecting diverse data with precision breeding tools to advance yields and adaptation to local growing conditions, bringing global communities closer to a sustainable, reliable food supply.

Cassavabase (cassavabase.org) is the breeding database developed at the Mueller lab and supported by Next Generation Cassava Breeding project (NEXTGEN Cassava). NEXTGEN Cassava aims to significantly increase the rate of genetic improvement in cassava breeding and unlock the full potential of cassava, a staple crop central to food security and livelihoods across Africa. The project will implement and empirically test a new breeding method known as Genomic Selection that relies on statistical modeling to predict cassava performance before field-testing, and dramatically accelerates the breeding cycle