Integrative bioinformatics for linking genomics to phenomics (a Netherlands-Pakistan collaboration)

Linking genetic variation to plant traits such as yield, resistance, taste, shape, color etc. lies at the core of fundamental and applied plant science. It is now feasible to measure genotypes of thousands of accessions and varieties and the same is happening for traits: phenomics facilities such as the Netherlands Plant Eco-phenotyping Centre currently being set up in Wageningen allow researchers to easily capture growth, shape, yield etc. of large collections of plants, in carefully controlled environments. Statistical genetics can link genetic to phenotypic variation, but fails when confronted with complex traits depending on combinations of variants. This is becoming a bottleneck in plant breeding, when developing new crops with combinations of multigenic traits to improve yield under increasingly adverse conditions, but also limits the utility of high-throughput phenotyping in fundamental plant studies. In this project, we will develop computational methods to link genomics to phenomics by exploiting the wealth of prior knowledge on genes and their products (transcripts and proteins), their interactions (pathways and metabolism) and functions (processes) amassed over the past decades. This will not only help to explain inferred links in biological terms, but also to group and prioritize variants underlying complex traits, with applications in plant breeding.