CyVerse for Brassica: Performing Associative Transcriptomics by Integrating with Sequence and Phenotype Repositories

Associative Transcriptomics (AT) is a method that links a physical genome, via the transcriptome, to quantitative phenotypic information. For complex polyploid crops such as Brassica napus, AT can be used to facilitate the identification of SNP markers. However, there are certain problems in performing AT for the Brassica Community: 1) this process is often data-intensive, as it commonly relies on large-scale genotypic and phenotypic raw data, and not all research groups have the computational capacity to do such analysis; 2) many groups are still dependent on the expertise of a small number of researchers who are able to generate AT data. With the help of CyVerse UK (http://cyverseuk.org), we are developing a reproducible workflow to make AT analysis available to the UK Brassica Community and beyond. The aim is to integrate phenotyping data stored in the Brassica Information Portal (BIP) (https://bip.earlham.ac.uk/) and sequence data from sequence repositories to establish an AT analysis framework, powered by tools and resources available within CyVerse.

A Brassica researcher would first submit their genotypic and phenotypic raw data to the BIP and respective public repositories (e.g. the SRA/ENA sequence read archives). This ensures that their data will be stored in standardised formats and marked up with required metadata to enable reuse and subsequent comparison. With the data in place, the researcher will then be able to run AT analyses on CyVerse.

We will present the current state of the project to the CyVerse user and Brassica communities in order to receive additional input and feedback.