Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Plant Sciences
Non Technical Summary
This project supports the mission of the Agricultural Experiment Station by addressing the Hatch Act area(s) of: plant and animal production, protection, and health; sustainable agriculture; molecular biology; and biotechnology.Horticultural products harvested from orchard and vineyard crops contribute significantly to California's and as a consequence the US's agricultural economy. This economic value is inextricably linked to the sustainability of genetic adaptations that encode and/or that regulate productivity and quality traits of these crops. Since all of these crops are vegetatively propagated there is a wide cultivar and rootstock based variation in the composition and distribution of specific genetic attributes that regulate productivity and quality of these crops. This project uses genomics based tools to functionally map and dissect different cultivar specific adaptations that provide resilience to support productivity and improve quality. Natural adaptations that contribute to resilience will be dissected to better understand sources of sensitivity or vulnerability to diseases, pests, and different sorts of environmental stressors. Productivity and quality traits of orchard and vineyard crops will be explored as a means to address this problem for growers, producers and consumers of these crops. Our approach is to dissect agriculturally significant phenotypic traits to decipher sources of genetic resilience and/or sensitivity using the genome as a lens to reveal the underlying molecular biology, and/or biochemical mechanisms that are sources of resilience. Outcomes of this effort include discovery of novel traits, therapies, treatments and the development of diagnostic tools leading to the development of strategies to repair, restore and transform quality and productivity traits that would benefit both the growers and consumers of these crops.
Animal Health Component
80%
Research Effort Categories
Basic
20%
Applied
80%
Developmental
(N/A)
Goals / Objectives
The principle goal of this research is to define quality and productivity traits in orchard and vineyard crops. The objectives are to investigate, discover and validate the relationship between genes or networks of genes and their products that regulate productivity and quality traits. The outcome of this research will be increased trait specific strategic information and the development of unique therapies and diagnostic tools to improve the breeding of new varieties of scion and rootstocks and for the management of orchard and vineyard health to sustain crop productivity and product quality.Goal: Is to enhance the resilience of productivity and quality traits of orchard and vineyard crops.Objective 1: Functional genomic analysis to define sources of resilience that enhance productivity and quality traitsObjective 2: Functional metagenomics analysis of productivity and quality traits to identify sources of resilienceObjective 3: Functional validation and deployment strategies to enhance the resilience of quality traits.
Project Methods
The goal is to enhance the resilience of productivity and quality traits in orchard and vineyard crops using the following methods.Objective 1: To investigate and to define sources of resilience that enhance productivity and quality traits we will use next generation DNA sequencing technologies to provide a deep profile of the transcriptome using RNAseq to discover sources of resilience and then employ high resolution proteomics and metabolomics to corroborate the information. We will employ bioinformatics tools to integrate data across platforms to create a knowledgebase that will be used to identify key genes and pathways that provide resilience. This information will be validated using plant transformation and via the expression of RNAi to create functional knockouts or using genome editing tools to validate the relationship between genes within specific gene networks that influence productivity/quality traits. The major products of this research is the development of new genetic information that can be used to develop DNA or protein-based biomarkers that can be used in a genome editing-based breeding program to enable somatic embryo-based selection for new scion and/or rootstock varieties with improved productivity or enhanced quality. The biomarkers can also be used to develop and validate management strategies to better manage productivity and quality.?Objective 2: To improve productivity in response to disease and pests we will be dissecting the complex host pathogen interaction using a variety of tools, RNAseq to identify host transcripts and then use proteomics and metabolomics to corroborate the information leading to the identification of specific host defense responses and pathogen virulence proteins. Bioinformatics analysis will be conducted to understand the key components of this interaction and to identify novel genetic targets. Specific pathogen genes will be knocked out to validate novel genes in plants that provide resilience to disease and pests. The new genetic information can be used to develop therapeutics against pests and disease causing organisms. Therapeutics that provide disease and pest resistance can be delivered by engineered rootstocks developed via Agrobacterium-mediated plant transformation. These rootstocks can be used to protect orchards and vineyards from pests and disease causing agents by grafting to conventional scion varieties. The genetic information developed can be used to deploy improved pest and disease management strategies by identifying specific chemicals or peptides that can be used to inhibit the interaction of a target gene/protein networks and thus limit the pest/pathogen interaction without requiring a genetic intervention.Objective 3: To enhance the resilience of quality traits we will use programmable cell and tissue culture systems. To analyze and simulate a variety of health promoting quality traits present in nuts we will use somatic embryo stem cells that can be reprogrammed using stable/transient Agrobacterium-mediated transformation to deliver new proteins or pathways as a means to analyze nut quality traits. These programmable somatic embryo cultures can be engineered to synthesize of new proteins, enzymes, pathways leading to the accumulation of specific health promoting metabolites. The structure of the proteins can be analyzed to improve their function and expression. Somatic embryos will be used to study subcellular protein/pathway localization the secretion of proteins and products into the apoplastic space so that they can be easily purified or extracted. Since the somatic embryos are edible, they can be amplified to do feeding studies to further validate health enhancing quality attributes.