
Daniel Runcie
Assistant Professor of Plant Sciences, UC Davis
Executive Committee Member, Lead of Molecular Breeding Cluster
Daniel Runcie's lab research delves into understanding the intricate interplay between environmental factors and genetic disparities among plant varieties, shaping their performance. Employing gene expression assays across both controlled laboratory settings and real-world field conditions, he and his team unveil the pivotal molecular pathways dictating phenotypic variations among genotypes. They also craft sophisticated statistical methodologies to distill insights from vast datasets. With a core focus on enhancing predictions of crop performance, deciphering the forces molding the evolutionary trajectories of natural plant populations, and pinpointing pivotal systems constraining plant adaptability in the face of climate change, Daniel and his team wield an arsenal of tools, including statistics, quantitative genetics, gene network and ecophysiological models, bioinformatics, and laboratory experiments. The bulk of their projects revolves around gene expression analysis, aimed at unraveling molecular variations within specific gene networks and establishing connections between gene expression traits and variations in plant development or physiology.
Project Involvement

Developing an AI-Enabled Toolkit for Routine Integration of Quality Traits into Molecular Breeding Strategies

Developing an AI-Enabled Toolkit for Routine Integration of Quality Traits into Molecular Breeding Strategies

AI-Enabled and Compound-Driven Toolkit for Molecular Breeding, Nutritional Quality, Aroma, Flavor and Health Traits
AIFS Publications
- Journal Article ⏐ Computers and Electronics in Agriculture 2022Journal Article ⏐ Comput. Electron. Agric. 2022
Special Report: AI Institute for Next Generation Food Systems (AIFS)
Tagkopoulos, Ilias,Steve Brown,Xin Liu,Qing Zhao,Tarek I Zohdi,Mason Earles,Nitin Nitin,Daniel Runcie,Danielle G Lemay,Aaron Smith,Pamela Ronald,Hao Feng,and Gabriel YoutseyDOI: 10.1016/j.compag.2022.106819 - Journal Article ⏐ Genome Biology 2021Journal Article ⏐ Genome Biol. 2021
MegaLMM: Mega-scale Linear Mixed Models for Genomic Predictions with Thousands of Traits
DOI: 10.1186/s13059-021-02416-w - Journal Article ⏐ bioRxiv 2024Journal Article ⏐ bioRxiv 2024
Why Is Usefulness Rarely Useful
DOI: 10.1101/2024.04.12.589314