Colleen Doherty

A major challenge for humankind is to feed the increasing human population in a sustainable manner. According to UN??????????????????s development programme extreme hunger and malnutrition is a major barrier to development in many countries: 795 million people are estimated to be chronically undernourished as of 2014, often as a direct consequence of environmental degradation, drought and loss of biodiversity. The Sustainable Development Goals (SDGs) aim to end hunger and malnutrition by 2030. Improved agricultural productivity is a critical part of achieving the SDG goal 2, Zero Hunger. Currently more than one third of crop yields are lost due to abiotic and biotic stress factors, such as drought, salinity, pests and disease. To minimize this yield gap and to simultaneously reduce the environmental impact of current agricultural practices, future crop production needs to be achieved on sub-optimal soils with reduced input of fertilizers and pesticides (???????????????more with less??????????????????). These challenges have increased the awareness of the importance of the plant microbiome for improved agricultural practices. Plants are colonized by an astounding number of microorganisms that can have profound effects on seed germination, seedling vigour, plant growth and development, nutrition, diseases and productivity. Thus, the plants can be viewed as holobionts that benefits from its microbiome in terms of specific functions and traits. In return, plants transfer a substantial part of their photosynthetically fixed carbon directly into symbionts and into their immediate surroundings thereby supporting the microbial community and influencing its composition and activities. For the vast majority of plant-associated microorganisms, however, there is little knowledge of their specific impact on crop growth and crop resilience and the mechanisms underlying microbiome-plant interactions. Hence, a critical step in developing new microbiome-assisted approaches to quantitatively and predictably improve crop resilience management strategies is deciphering the hyperdiverse plant microbiome. In particular, we need to identify keystone microorganisms and mechanisms involved in plant growth promotion and protection against biotic and abiotic stresses. To that end, systems-based analyses combined with deep-learning and modelling are essential to decode the taxonomic diversity and functional potential of plant microbiomes. The overall aim of this multidisciplinary research program is to develop a scalable system-based strategy to harness the functional potential of plant microbiomes for improving crop resilience. More specifically, we will focus on experimental analyses and modelling of the phyllosphere microbiome of wheat (Triticum aestivum), one of the most important cereal food crops worldwide. The phyllosphere microbiome is defined here as the collective microbial communities inhabiting both the leaf surface as well as the internal leaf tissue. We will zoom in on the microbiome of flag leaves of wheat, as the flag leaf is a major determinant (up to 45%) of wheat yield. To do this, we combine renowned academic expertise in microbiology, chemistry, DNA and RNA sequencing, bioinformatics, machine-learning and modelling with company support in plant breeding and agronomy to deliver novel approaches and technologies.

Several carbon capture mechanisms have emerged in plant systems that provide unique advantages to plants depending on their environment. For example, while most plants use a C3 photosynthesis mechanism, C4 and CAM carbon capture mechanisms can increase water use efficiency or temperature tolerance. These advantages have been well-characterized in the atmospheric CO2 levels on Earth, but in enclosed human habitats such as those needed for long-term space flight, CO2 levels far exceed that of Earth???s atmosphere. Altered CO2 levels affect nutritional content and water use efficiency, but this research has used CO2 levels below that on enclosed human habitats. This proposed work would examine how high CO2 levels affect the plant physiology and nutritional content of edible microgreens that use different photosynthetic mechanisms: C3, C4, and CAM. We will monitor physiological characteristics and the nutritional profile across different CO2 levels for these microgreen species with C3, C4, and CAM photosynthesis. The combined effects of altered CO2 levels and other spaceflight relevant stresses such as water availability will be examined to understand if these different photosynthetic mechanisms can provide advantages to enhance plant productivity in space environments. These results would provide important baseline information on plant nutrition and performance that is needed for planning long-term space missions and thus would address the following objectives of the solicitation and NASA program goals: Decadal Survey- Priority 3: A systematic suite of plant biology experiments to elucidate mechanisms by which plants respond and adapt to spaceflight, and to facilitate their eventual use in Bioregenerative Life Support Systems; PB-1 How does gravity affect plant growth, development & metabolism (e.g. photosynthesis, reproduction, lignin formation, plant defense mechanisms) and PB-3 How can horticultural approaches for sustained production of edible crops in space be both improved and implemented (especially as related to water and nutrient provision in the root zone)?

The purpose of this project is to develop a handheld Mueller matrix polarimeter that can be deployed to measure leaves in transmission. Leaves from different corn varieties will be quantified using both this handheld unit and our laboratory unit (an imaging Mueller Matrix polarimeter). These data will be compared to ground truth from e.g., enzymatic, colorimetric, 1D-NMR, and Mass-spectrometry based analyses, to correlate polarimetry measurements to metabolic concentration. Additionally, we will investigate polarization in reflection using a hyperspectral imaging polarimeter to quantify polarization??????????????????s ability to correct for bidirectional reflectance effects from canopy level measurements.

Co-PI Nielsen will be responsible for overseeing all experimental design and computational components of this project. This includes QTL analyses, RNA-Seq data QC and processing, eQTL analyses, cross-species eQTL analyses, and network analysis. Nielsen will mentor the Ph.D. student selected for this project; this student will be selected from students in the NCSU Bioinformatics Graduate program. Under Nielsen??????????????????s supervision, the student will perform most of the analyses required for this project. Nielsen will also co-mentor the students involved with the summer internship program with St. Augustine??????????????????s. Dr. Doherty will serve as Co-I for the plant stress response, molecular, and biochemical analysis and validation of candidate regulatory interactions. Specifically, Dr. Doherty will oversee in: Aim 1: The phenotyping of the plant-response traits, monitoring general growth parameters and physiology related sensitivity due to WNT and nematode presence. Aim 2: Extraction of RNA, preparation and sequencing of the libraries for the RNA samples. QC will be performed on all samples prior to sequencing. Dr. Doherty will oversee library construction in her lab and will coordinate getting the samples sequenced. Aim 4: In this objective Dr. Doherty will oversee the validation of the predicted mechanisms. Again, the Doherty lab will be responsible for extracting RNA and preparing libraries from the for RNA-seq or generating constructs and IP-ing for ChIP-Seq. Once prepared and checked for quality, Dr. Doherty will coordinate sequencing of the libraries, will retrieve and store the data and will process the resulting data and evaluate the success of the predictions and the targets identified. The Doherty lab will assist with evaluating the success of the approach and interpreting the candidate targets.

Identification and testing of promoters for crops. Using our motif identification method Identify cis-regulatory regions and test their functionality.