B-G.53: Prioritizing non-coding variants to discover mutations governing agronomic traits in plants
During the development of agriculture over centuries, humans have selected plants with advantageous agronomic traits. This process has led to genomic diversification between varieties within a species. A striking example is Brassica oleracea, a highly diversified species that includes cabbages, cauliflowers, and broccoli.
Association studies often highlight cis-regulatory regions as targets of selection. However, identifying causal mutations remains a major challenge, as genomic regions associated with a trait can harbor thousands of variants in strong linkage disequilibrium.
To address this challenge, we developed a tool dedicated to prioritizing non-coding variants (NCVs) with potential regulatory functions. This tool is based on a framework originally developed for human disease studies and distinguishes likely functional variants from non-functional ones by leveraging transcription factor binding sites (TFBS) and modules of TFBS that show higher-than-expected phylogenetic conservation.
As a case study, we applied this tool to curd formation in cauliflower, a trait known to result from deregulation of the floral development gene regulatory network. Using kmer variants from several accessions of B. oleracea, we first performed an association study that highlighted both coding and non-coding regions. We are now using our tool to specifically prioritize NCVs potentially involved in curd formation.
These results with our current knowledge of transcription factors and the gene regulatory network underlying floral development will allow us to identify candidate causal mutations responsible for cauliflower head formation, which can then be experimentally validated. Beyond this example, our tool provides a general framework to identify causal NCVs associated with other agronomic traits.
Co-authors: Romain Blanc-Mathieu, Francois Parcy
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