Studying the interactions between plants, microbes and the environment

Welcome to the BART LAB website

The 21st century is a transformative time to be a geneticist with an affinity for agriculture because modern molecular biology tools can be readily applied to genetically intractable organisms. We develop a lot of tools and work hard to make them accessible to the larger research community. Cassava Atlas is a tool that lets users query global gene expression patterns across 11 distinct cassava tissues and organs. The youtube video highlights some of our other fun tools. Don't forget to turn up the volume!


In the Bart Lab, we combine genetics, molecular and computational biology and phenomics to further understand the complex interactions between hosts microbes and the environment. With funding from the Bill and Melinda Gates Foundation, The Department of Energy (DOE), The USDA, Cotton Incorporated and the Donald Danforth Plant Science Center, we are pursuing research on all sides of the disease triangle as follows: 

HOST
On the host side, we are working to identify resistance genes for use in crop improvement. A major limitation facing this type of crop improvement is the slow and laborious nature of traditional breeding. Next-generation sequencing technologies can be applied rapidly to any organism and can increase the speed at which genetic loci are identified. The majority of identified resistance genes contain nucleotide binding site and leucine rich repeat domains. We are working to develop computational methods of using genomics data to identify candidate resistance genes. These candidates will be validated through transient assays and then used directly for crop improvement.  In addition, future research will aim to tease out the molecular mechanisms governing resistance gene function.

PATHOGEN
One the pathogen side, our research is aimed at identifying conserved components of the microbial arsenal, as resistance genes generally target proteins involved in pathogen virulence. Targeting the most highly conserved virulence components with resistance strategies will lead to durable resistance in the field. Here again we can apply next generation sequencing to rapidly construct draft genomes for hundreds of bacterial isolates. Genes involved in virulence are computationally predicted and used as molecular probes for cognate resistance genes. A sub-class of bacterial virulence determinants known as type three effectors (T3Es) are secreted directly into the plant cell via the type three secretion system. Many T3Es contain eukaryotic domains that allow them to function inside the host cell. Transcription activator-like (TAL) effectors, for example, are able to bind promoter elements and direct transcription of host genes. TAL effectors have received attention recently for their potential in genome editing. Research in the Bart lab aims to understand the molecular function of these effectors as well as to characterize their respective roles in overall virulence.

ENVIRONMENT
Many bacterial diseases require humid climates to establish infection. A long term goal is to understand the impact of environmental changes on the interaction between pathogens and their hosts. Examples of important environmental changes include modulations in temperature, humidity, and light quality throughout the growing season or as a result of global climate change, new cultivar introduction, chemical inputs and seasonal variation. To aid our efforts to understand the role of the environment in observed disease, we are developing a number of sensitive phenotyping platforms for quantitatively measuring pathogen spread and symptom development over time.


Ongoing Funded projects:

DOE - SORGHUM MICROBIOME PROJECT
Bacteria play vital roles in our day-to-day lives that we are only just now beginning to understand and appreciate. That said, if our understanding of the importance of our own microbiome is in its infancy, then our understanding of the beneficial relationships between crop plants and microbes is near nonexistent . In recent years, sorghum has come to the forefront as an important, understudied crop variety  due its flexible growing requirements and many end-uses including forage and silage feed stocks (grain sorghum), lignocellulosic biomass production (energy sorghum), and sugar production (sweet sorghum). The goal of this DOE-funded project is to establish a foundational understanding of plant, microbial, and environmental interactions. In doing so, we will be cataloging and testing the importance of the sorghum microbiome in order to understand the role that microbes play in growing healthy plants. The information gain from this project will ultimately be applied to strategies designed to enhance growth and sustainability of sorghum through improved genetic and microbial adaptations to water and nutrient limited environments.


COTTON INC. - COTTON BACTERIAL BLIGHT

Cotton Bacterial Blight (CBB) is a worldwide disease that is re-emerging in the Southern United States.  The proteobacterium Xanthomonas citri pv. malvacearum (Xcm) triggers the disease by injecting type three effector proteins into plant cells. These proteins work in a variety of ways to inhibit the plant immune responses and promote susceptibility. One type of effector, the transcription activator-like (TAL) effector, promotes susceptibility by binding to and upregulating susceptibility genes. This project aims to characterize the genetic, transcriptional, and translational diversity among cotton cultivar-pathovar pairs that leads to variation in disease severity. Eventually we will use this information to develop cotton varieties that are resistant to CBB using CRISPR/Cas9 technologies and/or traditional breeding.


GATES FOUNDATION - TARGETED GENOME METHYLATION IN CASSAVA

The recent advent of genome editing technologies such as those based on ZNF, TALENs and CRISPR/Cas9 are revolutionizing biotechnology. In addition, recent work by several labs has demonstrated the ability to direct DNA methylation to specific places within plant genomes, the effect of which can silence genes in the methylated region. In collaboration with Steve Jacobsen at UCLA and Jim Carrington at the DDPSC, we are working to adapt this technology to cassava. Immediate targets include genes involved in susceptibility to bacterial and viral disease of cassava. If successful, we will achieve novel strategies for controlling these devastating diseases.


DOE - UNDERSTANDING THE EFFECT OF ALTERED CELL WALL AND SUGAR CONTENT ON SORGHUM-ASSOCIATED PATHOGENIC BACTERIA

High-biomass-yielding crops may harbor modifications to cell walls, which are a major barrier to pathogen entry, and to the tissue distribution of sugars, which are the pathogen’s food source; hence they are likely to present previously unseen challenges for disease resistance. Xanthomonas is a known pathogen of sorghum (Sorghum bicolor (L.) Moench), though the incidence and impact of the disease has historically been low. We are working to establish the sorghum – Xanthomonas pathosystem as a model for deducing how latent microbial pathogens might exploit key biofuel crop traits. Our approach will be to quantitatively model the disease triangle that describes sorghum, pathogenic bacteria, and the environment. Field and laboratory experiments will be combined to determine bacterial susceptibility of genetically diverse sorghum genotypes that differ in cell wall and sugar composition. Standard plant pathology techniques combined with powerful phenomics approaches will provide a holistic view of this pathosystem within variable environments. Further, transcriptomics will be employed to elucidate mechanisms used by bacterial pathogens to induce sorghum susceptibility. Microbial pathogens are known to manipulate the sugar and cell wall characteristics of their hosts. Consequently, these characteristics will be analyzed during pathogen invasion. This research will reveal the mechanisms underlying tolerance to pathogens that must be maintained during biofuel trait optimization. The proposed research will yield a detailed understanding of the impact of bioenergy relevant traits on pathogen susceptibility. This is a necessary first step towards the development of novel routes for disease control that can be deployed in parallel with targeted alterations to sugar and cell wall composition during bioenergy crop improvement and breeding efforts.