Applying systems biology approaches to understand plant immunity

I am particularly interested in the potato and how it interacts with pathogens. My group takes a systems biology approach which places individual components of responses to pathogens within the whole picture of what is happening in the plant to understand the mechanisms of response better. The questions which drive my research are: what are the mechanisms underlying pathogen responses in potato? How they are dependent on environmental factors? How do responses vary depending on variability of the pathogen?

Applying systems biology approaches to understand plant immunity

To understand these mechanisms of immunity in potato, we are collecting data which describes the disease processes going on in the cells at multiple molecular levels using genomics, transcriptomics and some proteomics and then integrating them into models. Using different network methodologies, we identify how the immune system is working in potato. Then we use genome editing tools to check and validate our modelling and see whether these are influencing the efficiency of the immune response.

To study specific genes within the biological system we have invested quite some time into utilization of CRISPR/Cas9 technology in our lab. We have been modifying normal genes – protein coding genes – and also the small RNA coding genes. What we are finding is that because the potato is a tetraploid, quite often, we don’t get mutations on all four copies of the gene that are in potato, but only on one or two, or sometimes three. Also, the mutations can be very diverse. Anyways, CRISPR/Cas9 technology enables us to develop mutations and understand the function of individual genes. We can sometimes even study dose dependent effects.

The challenges of CRISPR/Cas9 technology and systems biology

Whilst using CRISPR/Cas9 technology enables us to understand the genome in a way we have never been able to before, there are also limitations to this technology. The particular challenge in potato is working with tetraploid tissues with four alleles of each gene in the genome.

Another challenge we face is related to the pathogens we are working with. The most important viral pathogen in potato, PVY, does not interact with all the cells in the leaf at the same time. We have started using spatial analysis of responses and include it in our modelling to allow for this complexity. With a systems approach, we want to understand all the complexity of the dynamics of responses, but omics methods aren’t particularly scalable, and the enormity of complexity requires huge amounts of data and therefore requires innovative bioinformatic solutions. We have been advancing both biostatistics and machine learning approaches. We are also developing plants with genetically encoded sensors into our research, so that we would be able to monitor the responses in time with a very dense time series resolution required for modelling dynamics.

The future: integrating technologies to build food security

As I look to the future, I would like to see more integration of cell biology, molecular biology and systems biology and biostatistics, computer science and artificial intelligence to understand plant immunity and develop resilience in the potato and other crops.

At the Plant Genomics and Gene Editing Congress: Europe, I’ll be presenting on the opportunities and challenges associated with CRISPR/Cas9 technology particularly in potatoes, but also more broadly. I will also be expanding on the advantages and difficulties particular to a systems biology approach and how we are developing new methodologies to make multidimensional omics data biologically meaningful and further develop systems biology.

Kristina Gruden is Professor and Group Leader at the National Institute of Biology in Ljubljana, Slovenia.