Understanding phenotypic variation of plants using the hologenomic framework within the The Plant Hologenome Group

There is still so much unknown about why plants of the same species can vary so much (their phenotype or functioning). This can have huge implications. For example, if this is susceptibility to disease, it could lead to some populations or crop varieties being decimated by a pathogen while others are relatively unaffected.

We know that many differences in the plant phenotype lie within the genome, but similarly, there a number of processes linked to the microbes that associate with plants. However, the genome and microbiome are rarely considered together, and neither has the interaction between the two. In The Plant Holobiome Group, we are interested in how the genome and microbiome interact to shape plant phenotypes, which we believe will help us better understand plant phenotypic variation than traditional methods (i.e. considering them alone).

In order to achieve this goal, we characterise the genome and microbiome using high-throughput sequencing methods. We profile the phenotype using transcriptomics, metabolomics or as morphological traits (such as yield or shoot:root ratio). We then integrate the multiple ‘omic datasets (genomic, transcriptomic, microbiomic, metabolomic) into comprehensive syntheses of plant functioning.

Projects

Maize genome-microbiome project

Plantago major holobiome project

Currently, we work on model plants (Zea mays, [maize]) and non-model plants (Plantago major [broadleaf plantain], Cinchona calisaya [the fever tree]). These approaches are ambitious, and therefore we generally focus on singular correlations initially (genome-microbiome or microbiome-plant chemistry) before building complexity into our models.