On the last day of a five-day conference, I normally feel exhausted and have limited mental bandwidth to process scientific information. To my surprise, the Plenary Symposium V at the Plant Biology Worldwide Summit was an eye-opening and thought-inspiring session that used science to reflect and celebrate the visions and passions of an extraordinary science leader – Mary E. Clutter (1930 – 2019).

Mary famously liked to make predictions. Co-organizers Machi Dilworth and Joe Ecker

For generations of plant scientists, it is not an overstatement to say that Mary changed their careers. Her leadership at the National Science Foundation enabled plant biology to reach multiple milestones, including the international collaborative Arabidopsis Genome Project and the Plant Genome Research Program, and supported programs to advance the status of women and underrepresented minorities in science.

Symposium organizer Joe Ecker talked about his interactions with Mary and how the interactions shaped his career. For example, Mary once asked him, “Where are the genes?” after the Arabidopsis genome was sequenced, which led to a series of functional genomic and epigenetic studies.

The other symposium organizer Machi Dilworth elucidated how the four selected speakers represented Mary’s visions and passions. Although the first speaker Natalie Clark and Mary probably never met, “Mary was instrumental in establishing and expanding the research grant program (NIFA) at USDA,” which has sponsored Natalie’s postdoctoral training. The second speaker Zachary Lippman “exemplifies the new generation of scientists that Mary envisioned;” scientists who work across disciplines and span fundamental and translational research. Mary had tremendous passions in science, and people who worked with her often heard her ask: “What about the science?” The third speaker Maria Harrison was among the researchers whose research Mary was personally interested in. Lastly, throughout Mary’s long career, she often sought advice from scientists, and the fourth speaker Chris Somerville was one whom Mary frequently queried.

Natalie M. Clark – Gene regulatory network implementation

Large-scale omics studies further our understanding of biological processes, but analyzing such data often requires statistical and computational expertise. Natalie Clark showed the disparity of network outcomes when using different processing criteria and provided experimental examples of genes selected by the algorithm she developed. 

Gene regulatory networks are “the structure that illustrates the relationships between the genes in your biological systems.” Common relationships include protein-protein interactions and transcription factor-target interactions. Most gene regulatory networks use transcriptomic data to predict the relationships, but it is common to see weak correlation between transcripts and protein abundance. Furthermore, Natalie showed two sets of predicted gene regulatory networks using either transcripts or protein abundance as the basis for processing; only 11% of the predicted networks overlapped, prompting the need to develop algorithms to identify complex networks.

Low network overlaps between three sets of predictions based on different processing criteria (transcript, protein, and phosphosite abundance)

Natalie developed a computational pipeline to infer gene regulatory networks from omics data, which is called Spatiotemporal Clustering and Inference of Omics Networks (SCION). SCION detects characteristic network motifs and identifies key genes of interest. She has used SCION to identify the BRON gene in Arabidopsis brassinosteroid signaling and BX9 in maize northern corn leaf blight resistance. 

Bioinformatic computation to predict key genes and generate hypotheses will be essential for understanding our biological systems. SCION was developed with the goal of increasing accessibility to researchers who don’t have much experience in programming languages. It is worth trying it out.

Zachary Lippman – Fine tuning trait variations

Crop domestication and improvement rely on incremental, fine-tuned trait modification. Zachary Lippman demonstrated that trait variation could be tuned by mixing and matching naturally-occurring and engineered mutations as well as targeting and modifying cis-regulatory regions.

Flower architecture directly impacts crop yield, especially in fruit crops. Zach dissected shoot meristem maturation and flower architecture in the Solanaceae family (tomato) and found that the dosage of MADS-box transcription factors was negatively correlated with the number of flower branches. Naturally occurring loss-of-function mutations in two MADS-box transcription factors (J2 and EJ2; belong to the Arabidopsis SEP4 clade) were isolated based on increased flower branches in tomato mutants. However, the extremely branched flower structure (resembling cauliflowers) was only achieved when combined with a third, CRISPR/Cas9 engineered mutation in LIN (another transcription factor belongs to the SEP4 clade). Combination between naturally-occurring and engineered mutations not only allows titration of the traits but also facilitates investigation of epistasis of genes.

Weak alleles with mutations in the protein coding regions have provided valuable assets for fine-tuning desired traits. To ultimately control traits quantitatively, Zach argued that mutations in cis-regulatory regions would be a powerful tool. He showed examples of using global promoter mutagenesis and “CRISPR micro-bashing” to generate mutations in the cis-regulatory region of CLV3, which is an important gene in tomato domestication (regarding locule number and fruit size). Incremental phenotypic changes were detected in the series of generated mutants and the phenotypic impacts of the sub-regions were mapped. Moreover, the impacts of these sub-regions can be combined, showing additive or synergistic effects as well as displaying tissue-specific functions.

Mutations in the CLV3 cis-regulatory regions correlate with tomato fruit size and locule numbers.

Maria Harrison – Symbiosis between plant roots and arbuscular mycorrhizae

Plants and fungi have coexisted on earth for over one billion years, and some of them have found symbiotic relationships to boost their success. About 72% of flowering plants have symbiotic associations with arbuscular mycorrhizal fungi. The symbiosis has evolved together for over 400 million years and facilitates nutrient exchanges: plants provide carbon source (lipids and sugars) for fungi whereas fungi supply plants with phosphorus and nitrogen. The fungal structures, arbuscules, reside in plant roots and can occupy a large portion of a root cell; consequently and/or preemptively, plants reprogram themselves to accommodate the fungal existence. Maria examined the symbiosis from the host plant genomes and physiology of the fungal structure arbuscules.

Arbuscular mycorrhizae reside in the roots of Medicago truncatula.

Comparing 50 plant genomes of hosts (represent by Medicago truncatula) and non-hosts of arbuscular mycorrhiza fungi, Maria has found 138 plant genes that only exist in host plant genomes. Previous genetic screenings have identified 15 of the genes to be related to the symbiosis. Maria tested another 9 genes and found 8 of them were important for the symbiosis, validating the approach to identify crucial plant genes for the symbiosis. The FaTM gene was given as an example. FaTM encodes a plastid-localized acyl-acyl carrier protein (ACP) thioesterase, which cleaves the 16:0-ACP and generates the 16:0 fatty acids. In the Medicago fatm mutant, fungal arbuscules can form but quickly die off inside of root cells. On the other hand, genomes of arbuscular mycorrhiza lack fatty acid synthase genes but have the genes that encode enzymes to modify or extend fatty acid chain lengths, both of which suggest that the symbiosis relies on the lipid supplies by host plants.

The interface between host plant root cells and fungal arbuscules is carefully maintained, and the composition of the interconnected matrix is really similar to plant primary cell walls. Electron microscopy coupled with tomography was used to study the ultrastructure of the plant-fungus interface. Surprisingly, the periarbuscular space (between fungal cell wall and periarbuscular membrane) was filled with many membrane-bound vesicles. Maria proposed that these vesicles could facilitate lipid transport from host plants to fungi.

Chris Somerville – “What would I do if I were to start my career again”

After a long successful academic career, Chris now works in Open Philanthropy where he identifies and supports scientific research through grant funding. Reflecting on his own career along with his experience in philanthropy, he suggested some research directions in plant biology with great societal impacts.

Before starting his academic career, he and his partner stayed in Paris for several months to contemplate research directions. Growing population, climate change, and resource depletion; the questions they identified at the time are still very much challenging today. Besides the obvious directions (e.g., developing stress-tolerant crops), he pointed out some pressing issues that are worth researching.

Protect boreal forest: Climate change has not only threatened global food production but also devastated the largest ecosystem on the planet – boreal forest, which is killed by over-populated bark beetles. Prolonged cold days are the natural way of controlling bark beetle populations. Because of climate change and the decreasing number of cold days, it is critical to find ways to re-establish and protect boreal forest.

Increase yields of cash crops: According to GiveDirectly, the most effective way to combat poverty is to give cash directly to people living in poverty. Therefore, improving yields of cash crops would have a profound impact on welfare. For example, projected climate change impact may decrease coffee yield by 80%, and this would be a huge burden on people who are already in crisis.

Improve crop nutrition: Despite being the second most abundant element in the Earth’s crust, plants inefficiently uptake iron, and consequently iron deficiency affect hundreds of million people. Research to improve crop nutrition is needed, especially in crops that are consumed in developing countries. Chris mentioned that sorghum and millet had the highest potential beneficial effects in productivity investment, so he encouraged researchers to consider factors outside of research. The African Orphan Crops Consortium was brought up by Kent Bradford in the chat box for their work in “applying new breeding methods to improve the productivity of crops that are widely utilized but not fully domesticated,” which would be a good resource for selecting crops to study.

Expand plant properties for plant-based meat research: The rise of plant-based meat, egg, cheese, etc. increases the demand for alternative plant properties to provide taste elements and protein sources. With the benefits of low carbon footprint and no animal cruelty concern, plant-based meat market is expected to grow. Plant research will be crucial for lowering the cost of production and therefore increase accessibility. 

Chris concluded his talk by recommending a strategy to include both model systems and crops in research plans. Last but not least, having collaborators who have local knowledge of how specific crops are consumed and utilized is important and mutually beneficial.

Chris laid out a strategy to combine basic and applied research.

Let the legacy continue

For me, this plenary symposium exemplifies the profound impacts of a leader who had clear visions and worked tirelessly to fulfill them. Mary Clutter changed the world. It is now our responsibilities to continue the legacy in advancing plant science with genuine passions and caring for the world.