Boyce Thompson Institute for Plant Research (BTI) is partnering with CGIAR and its associate centers to create a shared database and bioinformatics platform to help breeders develop improved root, tuber and banana crops. This platform will enable RTB breeders to access and use massive amounts of genotypic and phenotypic data to develop new varieties with precisely targeted traits for disease resistance, higher yields and consumer acceptability.
Graham Thiele, RTB Program Director, visited Cornell last week, at the invitation of Hale Ann Tufan, project manager for the Next Generation Cassava Breeding project (NEXTGEN Cassava). During the visit he met with BTI project leader Lukas Mueller to learn about Mueller’s experience leading a BTI Bioinformatics group and several large genome sequencing projects. Mueller directs the SOL Genomics Network (SGN), an open-source website for genome data of Solanaceae species such as tomato, potato and pepper, and CassavaBase, a database for cassava breeding information. These databases are always expanding, since users can add genetic annotations, phenotypes, and genetic trait mapping data to the sites.
“I was excited to meet Lukas and see what he’s doing,” said Thiele. “There already is excellent collaboration going on and we want to build on this, giving it more coherence and clarity across the different crops and centers involved.” There are plans to adapt the Cassavabase database for other crops, including bananas, sweetpotatoes and yams, to create a suite of similar tools for these clonally propagated crops and increased scope for collaboration with RTB.
NEXTGEN Cassava is led by Cornell’s International Programs, with BTI providing database development, hosting and management; a similar project for sweetpotato also has recently been funded. Mueller said an expanded partnership with RTB would benefit all parties, since BTI could apply its database knowledge to more a broader array of crops, and environments while helping RTB create better breeding outcomes.
Thiele commented, “A lot of end user traits, especially relevant to quality, are not prioritized by breeding programs, yet these are often gender differentiated. We are exploring ways to capture these with Hale Tufan at NEXTGEN Cassava. We’d like to build synergies and collaborate across crops, creating a space to put the whole lot together.”
Though a formal RTB/BTI/Cornell partnership is still in talks, Thiele said that practical conversations are happening now around using Mueller’s work with SGN and Cassavabase to add value without raising costs and to improve collaboration among the CGIAR research centers: the International Potato Center (CIP) which leads the program, Bioversity International, the International Institute for Tropical Agriculture (IITA) and the International Center for Tropical Agriculture (CIAT).
“Databases are expensive,” said Mueller. “Shared databases reduce cost, but the larger field of application allows for adding features that wouldn’t otherwise be available.”
Post originally published on October 1st, 2014 on the Boyce Thompson Institute website