Implementing functional annotation into genome wide prediction and genome-wide association studies for plant breeding pipelines

Analyzing, translating, and applying big data is crucial for the advancement of crop improvement to realize the genetic gains necessary to achieve the economic, resiliency, and nutrition goals of the Global Food Security Strategy. Despite this, applications developed specifically for end-users at NARIs to incorporate genomics into breeding pipelines has been limited. Many NARIs are limited by data processing capacity, which can be overcome by using server-based applications, and training in the bioinformatics skills needed to analyze and apply the data resulting from new genotyping platforms.

In this project, early career researchers at CACCIA (Costa Rica) and CIWA (Senegal) work alongside ILCI’s software developers based at Cornell University to create an updated, server-based, BrAPI compatible and R-based version of TASSEL (TASSEL 6, rTASSEL) that incorporates genic allele activity data. These researchers will become proficient users of R while guiding ILCI programmers to the forms of application development needed for their programs. In doing so, CACCIA and CIWA are the forefront of innovation in research, technology, and software development that will drive agricultural productivity and transformation within their own countries. The approach has the dual aim of developing effective and applicable server- and R-based applications, while training early career scientists and establishing large data processing capacity at CACCIA and CIWA.

Project objectives include:

• Evaluate genic allele activity in the context of discovery and breeding for improved genomic prediction.
• Develop server-based tools for applied bioinformatics in NARIs breeding programs, including an updated version of TASSEL (TASSEL 6) compatible with BrAPI data and RStudio.
• Train early career scientists at CACCIA and CIWA in bioinformatics to apply genomic data sets to crop improvement plans.
• Create and teach a multilingual curriculum on R features of TASSEL 6 in the R environment to Centers of Innovation.