Welcome to the Benfey Lab!

A central question in developmental biology is how cells progress from relatively undifferentiated stem cells to fully differentiated tissues. We address this question using the root of Arabidopsis as a tractable model. We take advantage of the root’s simple organization including a stem cell niche that gives rise to all the tissues in the root. Lack of cell movement means that each lineage represents a developmental time line, with the least differentiated cells being closest to the niche. Our work has identified the core molecular network required for the division and differentiation of a key stem cell population. Mathematical modeling of this network generated hypotheses as to how it functions. We are now experimentally testing those hypotheses as well as imaging network dynamics in real time. We have also identified key regulators of differentiation in this lineage.

A striking aspect of root development is the production of lateral roots, which form new stem cell niches from internal root tissues. We are interested in how new niches are positioned along the primary root and how they grow out to form the ramified structure known as root system architecture. We had previously shown that a periodic oscillation of gene expression at the root tip was critical for positioning lateral roots. We have identified a derivative of the carotenoid biosynthesis pathway that plays a key role in this process. In addition, we pioneered the use of gel-based and x-ray imaging to quantify root system architecture traits and developed image analysis software to identify quantitative trait loci (QTL) for root traits in rice and maize.

We strive to develop new technology and provide critical datasets to the community. We have generated comprehensive gene expression maps of the Arabidopsis root at cell type resolution and generated a high-resolution analysis of translation and DNA methylation. A major effort has been to develop or enhance imaging modalities including light sheet microscopy, fluorescence correlation spectroscopy and microfluidics for confocal imaging of living seedlings.


Dynamics of regulatory networks

The Lateral Root Clock

Understanding the genetic basis of root traits

Development of Enabling Technology