On June 22nd to 26th, the American Society of Plant Biologists (ASPB) 2024 conference in Honolulu celebrated its 100 years of advancing plant science and creating an international plant science community. The meeting covered the most recent developments in plant science and brought together over 1400 leading scientists,researchers and students, over 20 exhibitors, 16 workshops and over 883 posters, with an emphasis on machine learning/AI, regenerative agriculture, and climate change, as well as single cell expression, multi-Omics data.
Dr. Sunita Kumari, a senior scientist at the Cold Spring Harbor Laboratory organized the AgBioData workshop titled, “Plant Bioinformatics Resources for FAIR Agricultural Data Discovery and Reuse.” The workshop was presented by 8 members of the AgBioData Consortium (www.agbiodata.org), which comprises over 44 Genetic, Genomic and Breeding (GGB) databases and more than 200 scientists, fostering collaborations and open discussions about the common practices, challenges and solutions to big data agricultural research. During the workshop, Dr. Kumari provided an overview on our homegrown online open resource, “Gramene Plants,” on comparative functional genomics in plants. Starting from collaborations of Gramene with various groups including Ensembl Plants, Plant Reactome, EBI Expression Atlas, eFP Seq browser with BioAnalytical Resource (BAR) from University of Toronto, CLIM Tools on the development of genomic resources, Gramene team is heavily engaged with several AgBioData working groups in biocuration efforts to have robust standards and best practices to the agriculture community. Sharon Wei, also from the Ware Lab, gave a talk, “SorghumBase 2024: Building Partnerships and Integrating Genetic Knowledge for the Sorghum Community,” updating the community with the progress on the database and showcasing the FAIR elements in SorghumBase. Over 60 attendees participated in the workshop.
Each of the 5 days of the Plant Biology Meeting started with an interesting plenary session. Plenary speaker Shin-Han Shiu, a professor from Michigan State University, talked about “Opportunities and Challenges in Connecting Genotype to Phenotype Using Computational Models.” In his talk, he emphasized the importance of explainable AI (XAI), demonstrated the feasibility of phenotype prediction using only transcriptome or methylome data instead of the genome and introduced an important feature measurement score, SHAP (SHapley Additive Explanation). His team demonstrated that 1) at the genome level, the same SNP can have different (even opposite) effects on the same trait, such as flowering time, for different accessions; 2) some transcripts, like SOC1, have opposite effects on flowering time at different expression levels (potentially due to genetic interaction); and 3) the same pattern applies to methylation levels, where the effect on flowering time could be opposite at different methylation levels (e.g., FLC mCG). He then called for better data and better models, emphasizing the importance of data quality and diversity, in addition to mere quantity, and cautioned against data leakage and mistaking association for causation. He concluded by pointing out that data generation and hypothesis generation are no longer the primary challenges, but large-scale experimental validation remains a significant hurdle in the foreseeable future.
Ángel Ferrero-Serrano, an Assistant Research Professor in the Assmann Lab at Pennsylvania State University, introduced Oryza CLIMtool, a set of interactive web-based databases of the environment × genome associations and correlations between the local environment and a large pool of curated Oryza genotypes. He used the rice dwarf gene as a use case to demonstrate the application of this tool. Wayne Parrott, a professor from the University of Georgia, talked about plantGene and the concept of social license. Using the controversy over golden rice and GMO as examples, he pointed out the necessity of building and nurturing trust between scientists and society. Vipula Shukla, Senior Program Officer at the Bill & Melinda Gates Foundation, gave a talk titled, “From Science to Solutions: Translating Plant Biology Research into Real World Impact.”
Highlights from the concurrent symposiums included “Gene Editing and Molecular Breeding,” chaired by former Ware Lab member, Dr. Yinping Jiao, now an Assistant Professor at Texas Tech University. In this symposium, Dr. Jiao talked about “Functional genomics enabled by the large scale sequence indexed sorghum mutant population,” a project in collaboration with the Ware Lab and Sorghumbase. Rahul Singh, a postdoc from the University Of Pennsylvania, gave a 2 min talk on “Orally delivered marker-free lettuce leaves produced CTB-proinsulin regulates blood sugar levels similar to natural insulin.” Kavin Cope, Scientist II from Bayer Crop Science, chaired the symposium, “Promoting sustainable food systems of the future: Industrial to Indigenous perspectives on regenerative agriculture.” Koon-Hui Wang (professor from the Univ. of Hawaii at Manoa) presented, “Prescription of Soil Health for Farmers in Hawaii: perspective from nematodes,” in which she ranked sorghum as the 2nd ground covering crop for tropical areas. A very interesting talk from Vena Adae Romero Briones, VP, First Nations Development Institute, titled, “Re-orientation,” presented her analysis and comparison between indigenous agriculture and present agriculture, offered insights and opportunities to re-frame agricultural issues and how we conceptualize local food systems and solutions.
); Asher Pasha – BAR (University of Toronto); Dr. Lukas Muller (Cornell University); Annarita Marrano (Phoenix Binf); Dr. Leonore Reiser (Phoenix Binf); Sharon Wei (CSHL). Photo credit Ware Lab.
