Gramene and SorghumBase Teams Present a Workshop, Talks and Posters at the ASPB 2023 Conference

The American Society of Plant Biologists (ASPB) held its much anticipated annual Plant Biology Conference in Savannah, Georgia from August 5 – 9, 2023. With a staggering attendance of over 1,200 plant enthusiasts, including researchers, students and industry professionals, the event as usual proved to be a vibrant platform for the exchange of ideas, insights, and advancements in plant biology. The conference featured an impressive array of  over 600 posters and over 200 engaging talks, fostering discussions from plant development, gene editing, abiotic stress interactions, artificial intelligence to soil microbial dynamics in space, the disease susceptibility of tomatoes on the international space station and artificial photosynthesis for the production of food during space flight. In addition, there were very interesting and interactive workshops covering topics from the plant bioinformatics resources and integrating plant scientists spotlights in the classroom to self advocacy. 

Sunita Kumari, a senior scientist at the Ware Lab of Cold Spring Harbor Laboratory (CSHL), organized the workshop “Plant Bioinformatics Resources for FAIR Agricultural Data Discovery and Reuse” at Plant Biology 2023, which featured six speakers covering the following topics: AgBioData Consortium (Annarita Marrano), BreedBase (Christine Nyaga), Bio-Analytic Resources for Plant Biology (Asher Pasha),   The Arabidopsis Information Resource (TAIR) (Sabarinath Subramaniam), Gramene (Sunita Kumari), and SorghumBase (Nick Gladman). All speakers also participated in a panel discussion.  During the Bioinformatics workshop, Sunita Kumari spotlighted the Gramene Knowledge Base, a meticulously curated open-source data hub designed for comparative functional genomics in both crops and model plant species. This invaluable resource embraces the FAIR data principles and encompasses 128 reference genomes along with specialized crop-specific pangenome sites dedicated to maize, rice, grapevine, and sorghum.

Nick Gladman, USDA scientist and member of the Ware Lab at CSHL, shared insights during the Bioinformatics workshop through his talk titled “SorghumBase: Public Genetic and Genomic Database for the Sorghum Community.” SorghumBase, a USDA-ARS funded resource, serves as a comprehensive hub for curated multi-omic and genetic datasets, facilitating collaborative efforts within the sorghum research community. The platform not only centralizes scientific publications, genome sequences, genetic variation, gene annotations and comparative analyses, but also fosters community engagement through adherence to FAIR practices, development of genetic markers and provision of weekly updates on publications, conferences and events, ultimately bolstering genomics-assisted breeding initiatives.

Janeen Braynen, also from CSHL, presented a talk titled “Regulatory Networks Governing Nitrogen Use Efficiency (NUE) in Maize and Sorghum,” in which the delicate balance of nitrogen availability in crop production and its consequences for plant growth and the environment were thoroughly examined. The discussion introduced a pioneering study that intricately explored the genetic foundations of nitrogen use efficiency using an advanced yeast one-hybrid gene regulatory network . This investigation unveils enduring interactions shared between maize and sorghum, imparting invaluable perspectives for the improvement of agricultural sustainability and refined nitrogen management tactics.

In addition to talks, seven posters were presented by members of the Ware Lab. Nick Gladman presented a poster on SorghumBase and a poster on the GRAS family of transcription factors in sorghum and other monocots, and Janeen Braynen presented a poster on Gramene, and a poster on NUE in maize and sorghum. In addition, Audrey Fahey’s poster was on the use of DAP-seq in studies of transcription factors, while Sunita Kumari’s posters concerned genome-wide transcriptomic analysis of iron and zinc, stressed poplar and sorghum, and the AgBioData Consortium poster titled, “FAIRification of agricultural data through standardization of practices and protocols across agricultural databases.”


Bioinformatics workshop at ASPB Plant Biology 2023 discussing the FAIR principle of data management. Presenters from left to right : Nicholas Gladman, Ph.D – Sorghumbase. USDA-ARS (CSHL), Christine Nyaga – Breedbase (Boyce Thompson Institute, Cornell University), Sunita Kumari, Ph.D – Gramene. (CSHL), Annarita Marrano – AgBioData Consortium (Phoenix Bioinformatics), Sabarinath Subramaniam, Ph.D – TAIR. (Phoenix Bioinformatics), Asher Pasha – BAR (University of Toronto). Photo credited by Janeen Braynen, Ph.D. (Postdoc CSHL).


A quite informative and resourceful talk given by Sunita Kumari, Ph.D, a senior scientist at CSHL on Gramene, a bioinformatics platform for comparative and functional genomics for plant species. Photo credited by Janeen Braynen, Ph.D. (Postdoc CSHL).


Excellent and informative talk by Nicholas Gladman, Ph.D, USDA at CSHL on Sorghumbase, a comprehensive online resource and database dedicated to the plant species Sorghum bicolor. Photo credited by Janeen Braynen, Ph.D. (Postdoc CSHL).


Informative talk by Janeen Braynen, Ph.D. at CSHL on Gene Regulatory Networks Governing Nitrogen Use Efficiency in Plants. Photo credited by Sunita Kumari, Ph.D.


Ware Lab members, Senior Scientist – Sunita Kumari, Ph.D., Postdoc – Janeen Braynen, Ph.D., and Research Technician – Audrey Fahey enjoying the ferry ride at Savannah, Georgia. Photo credited by Sunita Kumari, Ph.D.