Cascadilla: A new tool for crop breeders to efficiently manage huge volumes of genomic data

Date:06-12-2017


To assist crop breeders to use huge volumes of genomic data effectively in breeding programs and significantly increase genetic gain in key crop performance traits, the Genomic Open-source Breeding Informatics Initiative (GOBII) released its first production version of a new tool ‘Cascadilla’. A team from Cornell University and ICRISAT developed the tool.

‘Cascadilla’ comes with improved loader and extractor user interface with improved workflow, usability and file transfer to extract genotype data by samples, markers and datasets. Earlier, GOBII had also launched breeders’ tools such as ‘Flapjack’ for Marker Assisted Backcrossing (MABC) and ‘Ped Ver’ for pedigree verification.

In his keynote address, Dr David Bergvinson, Director General, ICRISAT, highlighted the importance and timely intervention of the GOBII project. He said that the intersection of biological and computer science is where innovation is going to be the richest in several decades.

“I believe GOBII is an example, where we bring together information technologists, data scientists, breeders and all supporting disciplines in an effort to unlock the genetic diversity of crops. Currently, only 1% of genetic resources are utilized,” he said. “Climate change is happening faster than most people actually appreciate, so we need to work with urgency to unlock the genetic diversity to address the challenge,” he added. Emphasizing the importance of behavioral change, he said, “Technology and structures are only 30% of the challenge, the biggest challenge will be the behavior change to use these tools and platforms.”

Dr Rajeev Varshney, Research Program Director – Genetic Gains, ICRISAT, said that the intended key contributions of GOBII to CGIAR breeding success include removing barriers to breeding innovation by having robust systems for handling high-dimension genomic data, efficient decision support tools and enabling scientists to focus their time on strategy development and execution. He said that the CGIAR’s Excellence in Breeding (EiB) Platform has been envisioned as a model for cross-institutional collaboration and for streamlining the use of genomic information to accelerate breeding progress in multiple crops. The aim, he said, is to make science and technology breakthroughs relevant to crop improvement communities serving the resource-poor worldwide.

‘Cascadilla’ was launched at ICRISAT headquarters onMay 26. A team from Cornell University and ICRISAT worked together from 22-26 May for on-site deployment of ‘Cascadilla’. The team included Dr Yanxin Star Gao, Mr Yaw Nti-Addae and Mr Kevin Palis from Cornell University and Drs Himabindu Kudapa, Manish Roorkiwal, Abhishek Rathore, Santosh Deshpande, Ms Anu Chitikineni, Mr Prasad Bajaj, Ms Roma Rani Das, Mr S Sivasubramani, Mr Anilkumar V and Mr Chaitanya Sarma from ICRISAT.

The workshop was attended by around 34 participants including breeders from ICRISAT, CIMMYT and IRRI.