Grant Information
| Knowledge Area | Subject of Investigation | Field of Science | Percent |
|---|---|---|---|
| 201 - Plant Genome, Genetics, and Genetic Mechanisms | 1213 - Walnut | 1040 - Molecular biology | 20% |
| 201 - Plant Genome, Genetics, and Genetic Mechanisms | 4099 - Microorganisms, general/other | 1040 - Molecular biology | 20% |
| 201 - Plant Genome, Genetics, and Genetic Mechanisms | 1119 - Deciduous tree fruits, general/other | 1040 - Molecular biology | 10% |
| 201 - Plant Genome, Genetics, and Genetic Mechanisms | 1139 - Grapes, general/other | 1040 - Molecular biology | 10% |
| 201 - Plant Genome, Genetics, and Genetic Mechanisms | 1212 - Almond | 1040 - Molecular biology | 10% |
| 201 - Plant Genome, Genetics, and Genetic Mechanisms | 1469 - Solanaceous and related crops, general/other (for potato use 1310) | 1040 - Molecular biology | 10% |
| 201 - Plant Genome, Genetics, and Genetic Mechanisms | 1640 - Alfalfa | 1040 - Molecular biology | 10% |
| 201 - Plant Genome, Genetics, and Genetic Mechanisms | 999 - Citrus, general/other | 1040 - Molecular biology | 10% |
Horticultural products a significant part of California's economy and vitality is critically influenced by both genetic traits and their interactions with environmental factors. Dissecting these traits at a molecular level provides a better understanding of the molecular mechanisms that determine how these plants adapt to various environmental factors enabling them to maintain the productivity and quality of their products. Understanding the molecular basis of fruit and nut quality traits will lead to the identification of biomarkers that can be used to breed new varieties or be used for improving the management of quality parameters in the field. To investigate disease or pest resistant traits, the complex interactions of the host-pathogen/pest will be analyzed using molecular/genomic tools to identify specific traits in the host or pathogen genomes that could be used to develop therapeutics that will provide disease/pest resistance. These therapeutics will be delivered by engineered rootstocks and that can be used to protect orchards and vineyards from pests and disease causing agents. The outcome of this research is the identification and deployment of specific traits that improve the productivity, quality while decreasing the susceptibility to environmental factors like disease and pests that would benefit the growers and consumers of horticultural products in California and elsewhere.
The principle goal of this research is to define quality and productivity traits in tree fruit and nut crops. The objectives are to investigate, discover and validate the relationship between genes or networks of genes and their products that regulate productivity and/or fruit 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 fruit/nut quality.Goal: To understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops.
The goal to understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops will be accomplished using the following methods.Objective 1: Investigate fruit/nut productivity and quality characteristics next generation DNA sequencing technologies to provide a deep profile of the transcriptome using RNAseq methods, high resolution proteomics and metabolomics. We will employ bioinformatics tools to integrate data across platforms and to identify key genes and pathways that can then serve as biomarkers. This information will be validated using plant transformation and via the expression of RNAi to create functional knockouts or via overexpression to discover and 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 breeding program to enable seedling based selection for new scion 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: Develop therapies that confer disease and or pest resistance. This will be accomplished by dissecting the complex host pathogen interaction by RNAseq to identify host transcripts and proteomics to identify host and pathogen proteins. Bioinformatic analysis will be conducted to understand the key components of this interaction and to identify novel genetic information, RNAi or protein-based. The new genetic information can be used to develop therapeutics against pests and disease causing organisms. These therapeutics can be delivered by engineered rootstocks developed via Agrobacterium-mediated plant transformation and selection methods that can be propagated, tested in the greenhouse and under field conditions to validate the disease or pest resistance. These rootstocks can be grafted to conventional scion varieties and used to protect orchards and vineyards from pests and disease causing agents. The genetic information developed can also be used to develop better 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 solution.Objective 3: Improving plant protein production and utilization will be accomplished using transient Agrobacterium-mediated plant transformation. This transient expression will be accomplished in tobacco plants. Plant virus vectors will be used to stimulate the expression of proteins. The structure of the proteins will be analyzed to improve their secretion into the apoplastic space so that they can be easily purified. Also the structure of the glycosyl residues that are attached to the surface of the secreted proteins will be modified by creating variants of the tobacco plant so that they lack the specific glycosyl transferase enzymes to modify the structure of the secreted proteins. The proteins will also be modified to add tags that will improve the ability to purify the expressed proteins.
Target Audience
The scientific community interested in agricultural research and innovation, the industry and growers of fruit and nut crops in California and elsewhere.
Changes / Problems
Nothing Reported
Training & Professional Development
We are actively training graduate and undergraduate students, post-doctoral researchers and professional researchers that participate in our research programs. We have also been involved in training visiting researcher, scientists and scholars who have chosen to visit the lab and to carry out research activities being conducted for this project. The research conducted on the project informs my teaching mission so this helps many undergraduates and graduate students who take the classes that I teach.
Dissemination Streams
All of our research is funded by fruit, nut and grapevine industries, so this allows us to interact with various grower groups and to communicate our results directly to the grower communities. We have a very strong publication record both peered reviewed and publication with limited distribution. For this particular project we have about 124 publications 46 being peer reviewed and 78 being reports and proceedings in the limited distribution category. The publications have a good impact value as can be judged on Google Scholar since 2015, the 5 years covered in this report I have 4851 citations with an h-index of 34 and an i10-index of 114.
Next Reporting Steps
Nothing Reported
Target Audience
The scientific community interested in agricultural research and innovation, the industry and growers of fruit and nut crops in California and elsewhere.
Changes / Problems
Nothing Reported
Training & Professional Development
Ongoing projects in the lab provide and active resourcefor the training of graduate, undergraduate students, post-doctoral researchers and professional researchers. We have also been involved in training visiting researcher, scientists and scholars who have chosen to visit the lab and to carry out research activities being conducted for this project. The research conducted on the project informs my teaching mission so this helps many undergraduates and graduate students who take the classes that I teach.
Dissemination Streams
All of the research conducted in my laboratory is funded by fruit, nut and grapevine industries, so this allows us to interact with various grower groups and to communicate our results directly to the grower communities. We have a very strong publication record both peered reviewed and publications with limited distribution. For this particular project year, we have about 25 publications 10 being peer reviewed and 15 being reports and proceedings in the limited distribution category.
Next Reporting Steps
We expect to continue to vigerously investigate the three objectives we described above to achieve the goals of this project which is to understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops. We are realizing this goal by pursuing three objectives simultaneously and have funded projects that provide us the resources to achieve this goal. Specifically, my laboratory connects genes to phenotypic traits that regulate productivity of fruit tree crops. We categorize genes by analyzing their encoded functional products, mRNA, small RNA, proteins and/or metabolites that contribute to the genetic basis of phenotypic traits. Outcomes of this effort include discovery of novel genes, development of diagnostic tools and deployment of therapeutic strategies. <br><br>
<br>What was accomplished under these goals? The overall goal of this project is to understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops. We are realizing this goal by pursuing three objectives. Objective 1: Investigate fruit/nut productivity and quality characteristics and develop trait specific biomarkers. Resilience a key attribute by which organisms can better adapt to adverse conditions and environments that greatly influences the expression of both productivity and quality traits. Osmoregulation is a source of resilience, where organisms are able to accumulate solutes like proline, glycine betaine or sorbitol that maintains macromolecular structure and function in an adverse condition. We dissected the biosynthesis sorbitol a known osmoregulatory molecule in the woody Rosaceae. We cloned the committed step in sorbitol biosynthesis in apple, examined plants that over expressed this gene, and found that sorbitol was involved in the symplastic movement of boron. Subsequently, we created functional knockouts where the same gene was suppressed via RNAi in apple plants/trees where we could connect the down regulation of sorbitol and the alterations in many quality traits in apple fruit like the regulation of sugar metabolism, starch and maleic acid. Apple trees suppressed for sorbitol biosynthesis substantially alter their global profile of genes that respond to stress. Sorbitol regulates stamen development and pollen tube growth via a MYB transcription factor. It also modulates fungal resistance to Alternaria alternata by regulating the expression of the NLR16 gene. The sequencing of the walnut genome is providing an unprecedented view into the `genomics of resilience', with the identification and functional analysis of antioxidant phenolic pathways that provide resilience to disease and pests. A large family of glycosyl transferases (GTs) was identified especially the one responsible for the synthesis hydrolysable tannins (HTs) building on our earlier discovery of the enzyme responsible for the synthesis of gallic acid a key intermediate in the biosynthesis of HTs. We were able to identify a second PPO gene (JrPPO2) and show that both are localized in the lumen of the thylakoid membranes of the plastid they have distinct differences in their active site architecture and expression pattern in different tissues. It appears that JrPPO1 is a recent duplication and appears as walnuts were domesticated. Building on earlier work where we showed that JrPPO1 was responsible for making melanin from tyrosine and in functional walnut knockouts for JrPPO1, loose this ability under stress tyrosine flows to make tyramine causing cell death, indicate that PPOs are part of the resilience network. Objective 2: Develop therapies that confer disease and or pest resistance. Here we have focused on understanding and building on innate immunity resources specifically RNA-mediated interference (RNAi) which is part of the damage associated molecular pattern (DAMP) system and antimicrobial peptides an inbuilt innate immunity (a resilient system) to target and clear pathogens. We targeted bacterial crown gall disease successfully have successfully field tested resistant walnut rootstocks validated their resistance under field conditions and are now developing a similar approach for grapevine and almond. We have successfully extended this strategy to combat nematodes and are currently developing and testing an RNAi strategy against Phythophthora for walnut and almond rootstocks. We have successfully field-tested the efficacy of transgenic rootstocks expressing a pear polygalacturonase inhibitory protein (PGIP) against Pierce's Disease. Protecting the degradation of the pectin surface delays/prevents PD development by limiting pathogen movement and spread. Success against PD was also achieved in the field by targeting the pathogen surface via an engineered innate immune defense mediated by a chimeric antimicrobial protein (CAP). A range of tools were developed to design novel CAP proteins. Using the PDB database were able to identify, test and validate novel alpha helical AMP peptide domains present in existing plant proteins and used these to successfully design plant based CAP therapeutics. A general principle holds, that `disease is the exception rather than the rule', which would indicate that sensitivity or a lack of resilience can lead to disease. We have shown this to be the case using a multi omic (transcriptome, proteome and metabolome) analysis approach to dissect various plant pathogen interactions to arrive at this conclusion. Some common themes are inability to deal with oxidative/photoxidative/anoxic and/or energy stress, down regulation of immune response or an inappropriate immune response, key features of Xylella-grapevine interaction. In the case of Huanglongbing (HLB) - citrus disease interaction we observe alterations in source-sink regulation with starch accumulation, altered hormone cross talk, modulation of antioxidant pathways. Spraying plants with small molecules to reverse some of these pathways was successful in restoring health. Analyzing tolerant cultivars highlighted the role of detoxification pathways to increase tolerance to HLB. We are analyzing common virulence factors secreted by Xylella/grapevine and Xanthomonas/walnut aided by pathogen genome sequences and analyzing alterations in disease response when the pathogen are mutated for the expression of the common virulence factors. Apart from using this information to understand disease mechanism we have been investigating, the information generated from our host-pathogen analysis to develop unique diagnostic approaches and tools to enable early disease detection. Objective 3: Improving plant protein production and utilization. DNA is the ultimate as a resilient molecule, it is pretty indestructible and Proteobacterial resilience for the last billions of years of their evolution has been largely based on their ability to take up DNA molecules from the environment via natural transformation to repair their genomes adapting to new environments. I began my scientific career studying the natural transformation process using alpha proteobacteria as an experimental system to study genetics. We pioneered the transformation of woody plants using the alpha proteobacteria Agrobacterium. A landmark in this effort was our report on the transformation of walnut somatic embryos and the regeneration of transgenic plants that showed the pathway to transform and to obtain transgenic plants for many recalcitrant plant species. We have also spent a considerable effort using plant transformation as a means to develop a resilient and sustainable plant cell-based manufacturing system, an application of plant transformation. Here we are developing and improving plant transformation systems and expressing novel proteins, like butrylcholinesterase in its tetrameric form an antidote against nerve gas. Successfully expressed and purified from the plant cell cultures an anthrax decoy protein an antidote against the anthrax toxin. The efficacy of the anthrax antidote has been evaluated as has the structure and function relationship to the modification of the N-linked glycosylation structure. We are also developing and deploying novel plant transformation systems to enable the genome editing of plants. In summary, we have been able to decipher agriculturally significant phenotypic traits and to define the underlying molecular genetic and biochemical mechanisms that regulate their expression for many of the traits explained above. Specifically, my laboratory connects genes to phenotypic traits by analyzing their encoded functional products, mRNA, small RNA, proteins and/or metabolites that contribute to the genetic basis of productivity and quality of fruit tree crops. <br><br><b>Publications</b><br>
Target Audience
The scientific community interested in agricultural research and innovation, the industry and growers of fruit and nut crops in California and elsewhere.
Changes / Problems
Nothing Reported
Training & Professional Development
We are actively training graduate and undergraduate students, post-doctoral researchers and professional researchers that participate in our research programs. We have also been involved in training visiting researcher, scientists and scholars who have chosen to visit the lab and to carry out research activities being conducted for this project. The research conducted on the project informs my teaching mission so this helps many undergraduates and graduate students who take the classes that I teach.
Dissemination Streams
All of our research is funded by fruit, nut and grapevine industries, so this allows us to interact with various grower groups and to communicate our results directly to the grower communities. We have a very strong publication record both peered reviewed and publication with limited distribution. For this particular project year, we have about 25 publications 7 being peer reviewed and 18 being reports and proceedings in the limited distribution category.
Next Reporting Steps
We expect to continue to investigate the three objectives we described above to investigate the goal of this project which is to understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops. We are realizing this goal by pursuing three objectives simultaneously and have funded projects that provide us the resources to achieve this goal. Specifically, my laboratory connects genes to phenotypic traits that regulate productivity of fruit tree crops. We categorize genes by analyzing their encoded functional products, mRNA, small RNA, proteins and/or metabolites that contribute to the genetic basis of phenotypic traits. Outcomes of this effort include discovery of novel genes, development of diagnostic tools and deployment of therapeutic strategies. <br><br>
<br>What was accomplished under these goals? The overall goal of this project is to understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops. We are realizing this goal by pursuing three objectives. Objective 1: Investigate fruit/nut productivity and quality characteristics and develop trait specific biomarkers. A key attribute of walnuts is the color of the seedcoat/pellicle. We have examined in 5 different varieties the type of pigments that accumulate and to correlate these to the accumulation of specific proteins and mRNA. Collectively these products of gene activity serve to pathways involved in the synthesis of nonstructural phenols. These compounds play a significant role in nut quality and in conferring disease and pest resistance and we are dissecting the pathways along these 3 lines. For quality we are focusing on the genes associated with the coloration of walnut pellicles a key quality trait for walnuts. We were also able to examine the role of sorbitol in apple where we have been investigating the effects of knocking sown the activity of S6PDH an enzyme unique to apple that converts glucose 6 phosphate to sorbitol. We found that decreased sorbitol production led to changes in how pathogens are perceived by the plant and disease progresses in leaf and fruit tissues. Objective 2: Develop therapies that confer disease and or pest resistance. We are gaining a deeper understanding of the development of Pierce's disease in grapevine especially how the gpevine responses. We have analyzed infected leaves using RNAseq, proteomics and metabolomics and these tree unique datasets correlate well complimenting the disease pathways. The pathogen virulence factors cause a photoxidative stress to occur in the plant which leads to all of the observed symptoms. There is also a down regulation of the immune response and likely accelerates the disease process and stimulates bacterial growth in the xylem.identified two secreted virulence factors of Xylella that are intimately involved in the disease. We have competed a bioinformatics analysis where we have found that 7 secreted virulence factors are conserved in Xanthomonadeaceae including LesA and chorismate mutase (CM). We have created mutants of LesA and CM and are examining the role that LesA and CM plays in walnut blight disease development as these genes are highly conserved in Xanthomonas arboricola pv juglandis. We have done further analysis of data available to further dissect the plant responses to HLB and were able to show the role played by detoxification pathway enzymes that may be responsible to increase the tolerance of citrus to HLB disease. The RNAseq analysis also revealed overarching relationships between response to disease and those associated to the general stress response that further highlighted this important response in plants. Objective 3: Improving plant protein production and utilization. We are investigating using plant tissues as a protein production platform for the synthesis and production of bio medically and agriculturally important proteins. The focus of these efforts is to improve and enhance transient expression using an Agrobacterium-mediated process. Transient expression systems are clearly the future for large-scale bio manufacture of proteins in plants. We have been working on two therapeutic proteins an anthrax decoy protein that can block the toxicity of Anthrax toxin and were able to show large scale production of this protein and to examine the biophysical characteristics of the secreted protein. The other protein that we have been working with is butrylcholine esterase a protein that is used to block the tocic effect of nerve gas agents. These proteins are bio scavengers that bind very tightly to the toxic components. These proteins are secreted and therefore the glycosyl residues on these proteins are key for their activity and is a subject that we are actively investigating. In summary, we have been able to decipher agriculturally significant phenotypic traits and to define the underlying molecular genetic and biochemical mechanisms that regulate their expression for many of the traits explained above. Specifically, my laboratory connects genes to phenotypic traits that regulate productivity of fruit tree crops. We categorize genes by analyzing their encoded functional products, mRNA, small RNA, proteins and/or metabolites that contribute to the genetic basis of phenotypic traits. Outcomes of this effort include discovery of novel genes, development of diagnostic tools and deployment of therapeutic strategies. <br><br><b>Publications</b><br>
Target Audience
The scientific community interested in agricultural research and innovation, the industry and growers of fruit and nut crops in California and elsewhere.
Changes / Problems
Nothing Reported
Training & Professional Development
We are actively training graduate and undergraduate students, post-doctoral researchers and professional researchers that participate in our research programs. We have also been involved in training visiting researcher, scientists and scholars who have chosen to visit the lab and to carry out research activities being conducted for this project. The research conducted on the project informs my teaching mission so this helps many undergraduates and graduate students who take the classes that I teach
Dissemination Streams
All of our research is funded by fruit, nut and grapevine industries, so this allows us to interact with various grower groups and to communicate our results directly to the grower communities. We have a very strong publication record both peered reviewed and publication with limited distribution. For this particular project year, we have about 18 publications 6 being peer reviewed and 18 being reports and proceedings in the limited distribution category.
Next Reporting Steps
We expect to continue to investigate the three objectives we described above to investigate the goal of this project which is to understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops. We are realizing this goal by pursuing three objectives simultaneously and have funded projects that provide us the resources to achieve this goal. Specifically, my laboratory connects genes to phenotypic traits that regulate productivity of fruit tree crops. We categorize genes by analyzing their encoded functional products, mRNA, small RNA, proteins and/or metabolites that contribute to the genetic basis of phenotypic traits. Outcomes of this effort include discovery of novel genes, development of diagnostic tools and deployment of therapeutic strategies. <br><br>
<br>What was accomplished under these goals? The overall goal of this project is to understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops. We are realizing this goal by pursuing three objectives. Objective 1: Investigate fruit/nut productivity and quality characteristics and develop trait specific biomarkers. Our ability to identify traits that determine productivity and quality at the molecular level is to use RNA as a means to identify the gene space and correlate that with the genome sequence. I this period we have examined the role of plant hormones in modulating stress gene networks, specifically as it relates to brassinosteroids. We have also been investigating movement of proteins across the graft union and we were able to examine that using a fluorescent protein dsRED. We were also able to examine the role of sorbitol in apple where we have been investigating the effects of knocking sown the activity of S6PDH an enzyme unique to apple that converts glucose 6 phosphate to sorbitol. We found that decreased sorbitol production led to reproductive problems with abnormal stamen development and reduced pollen growth. This study further showed the importance of sorbitol metabolism in apple as it relates to plant productivity. For quality, we are focusing on the genes associated with the coloration of walnut pellicles a key quality trait for walnuts and have conducted metabolomics analysis and transcriptome analysis to devine the pathways that lead to the accumulation of colored pigments in these tissues. Objective 2: Develop therapies that confer disease and or pest resistance. We have made very good progress gaining a deeper understanding of the development of Pierce's disease in grapevine. We identified two secreted virulence factors of Xylella that are intimately involved in the disease. LesA, which is one of these factors we show, is responsible for the symptoms observed for this disease both in grapevine and in citrus. PrtA the second protein is necessary for the biofilm form of the pathogen and may serve as an anti-virulence factor that we show that expression of this protein can reduce the symptoms in a non-host plant tobacco; we created grapevines that express these proteins and will soon begin testing this in the field and greenhouse. We are examining the role that LesA plays in walnut blight disease development as this gene is highly conserved in Xanthomonas arboricola pv juglandis. We have developed a walnut rootstock that is resistant to bacterial crown gall formation a significant disease of walnut that affects all rootstocks. The rootstock expresses RNAi against the tumor forming genes of Agrobacterium tumefaciens the causative agent of bacterial crown gall disease. We are characterizing a lead line that is completely resistant to tumor formation when infected with A.tumefaciens. We are developing regulatory data to deregulate this elite event. In citrus we have evaluated other products apart from the transcriptome have included the proteome and metabolome. Using proteomics we could more clearly define plant responses to HLB and were able to show the role played by detoxification pathway enzymes that may be responsible to increase the tolerance of citrus to HLB disease. The RNAseq analysis also revealed overarching relationships between response to disease and those associated to the general stress response that further highlighted this important response in plants. Objective 3: Improving plant protein production and utilization. We are investigating using plant tissues as a protein production platform for the synthesis and production of bio medically and agriculturally important proteins. The focus of these efforts is to improve and enhance transient expression using an Agrobacterium-mediated process. Transient expression systems are clearly the future for large-scale biomanufacture of proteins in plants. We have been working on two therapeutic proteins an anthrax decoy protein that can block the toxicity of Anthrax toxin and were able to show large scale production of this protein and to examine the biophysical characteristics of the secreted protein. The other protein that we have been working with is butrylcholine esterase a protein that is used to block the tocic effect of nerve gas agents. These proteins are bio scavengers that bind very tightly to the toxic components. These proteins are secreted and therefore the glycosyl residues on these proteins are key for their activity and is a subject that we are actively investigating. In summary, we have been able to decipher agriculturally significant phenotypic traits and to define the underlying molecular genetic and biochemical mechanisms that regulate their expression for many of the traits explained above. Specifically, my laboratory connects genes to phenotypic traits that regulate productivity of fruit tree crops. We categorize genes by analyzing their encoded functional products, mRNA, small RNA, proteins and/or metabolites that contribute to the genetic basis of phenotypic traits. Outcomes of this effort include discovery of novel genes, development of diagnostic tools and deployment of therapeutic strategies. <br><br><b>Publications</b><br>
Target Audience
The scientific community interested in agricultural research and innovation, the industry and growers of fruit and nut crops in California and elsewhere.
Changes / Problems
Nothing Reported
Training & Professional Development
We are actively training graduate and undergraduate students, post-doctoral researchers and professional researchers that participate in our research programs. We have also been involved in training visiting researcher, scientists and scholars who have chosen to visit the lab and to carry out research activities being conducted for this project. The research conducted on the project informs my teaching mission so this helps many undergraduates and graduate students who take the classes that I teach.
Dissemination Streams
All of our research is funded by fruit, nut and grapevine industries, so this allows us to interact with various grower groups and to communicate our results directly to the grower communities. We have a very strong publication record both peered reviewed and publication with limited distribution. For this particular project year, we have about 29 publications 13 being peer reviewed and 16 being reports and proceedings in the limited distribution category.
Next Reporting Steps
We expect to continue to investigate the three objectives we described above to investigate the goal of this project which is to understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops. We are realizing this goal by pursuing three objectives simultaneously and have funded projects that provide us the resources to achieve this goal. Specifically, my laboratory connects genes to phenotypic traits that regulate productivity of fruit tree crops. We categorize genes by analyzing their encoded functional products, mRNA, small RNA, proteins and/or metabolites that contribute to the genetic basis of phenotypic traits. Outcomes of this effort include discovery of novel genes, development of diagnostic tools and deployment of therapeutic strategies. <br><br>
<br>What was accomplished under these goals? The overall goal of this project is to understand the relationship between genes and genetic phenotypes that define productivity and quality traits of fruit tree crops. We are realizing this goal by pursuing three objectives. Objective 1: Investigate fruit/nut productivity and quality characteristics and develop trait specific biomarkers. Our ability to identify traits that determine productivity and quality at the molecular level is to use RNA as a means to identify the gene space and correlate that with the genome sequence. I this period we were involved in describing the genome sequence of walnut focusing on the genes involved in the synthesis of nonstructural phenols. These compounds play a significant role in nut quality and in conferring disease and pest resistance and we are dissecting the pathways along these 3 lines. For quality we are focusing on the genes associated with the coloration of walnut pellicles a key quality trait for walnuts. In citrus we have evaluated other products apart from the transcriptome have included the proteome and metabolome. Using low mol weight volatile organic compounds we could develop profiles that reveal and that are predictive of plants infected with the CTV virus. Using proteomics we could more clearly define plant responses to HLB and were able to distinguish between tolerance and sensitive responses in citrus. The RNAseq analysis also revealed overarching relationships between response to disease and those associated to the general stress response that further highlighted this important response in plants. Objective 2: Develop therapies that confer disease and or pest resistance. We have made very good progress gaining a deeper understanding of the development of Pierce's disease in grapevine. We identified two secreted virulence factors of Xylella that are intimately involved in the disease. LesA which is one of these factors we show is responsible for the leaf scorch symptoms observed for this disease. This protein is an excellent diagnostic tool to detect the disease early. The other virulence factor appears to be an anti-virulence factor that we show that expression of this protein can reduce the symptoms in a non-host plant tobacco, we are now going to test this in grapevine. We are focusing on the role that LesA plays in disease development as it is highly conserved in Xanthomonas in Xylella. We have developed a walnut rootstock that is resistant to bacterial crown gall formation a significant disease of walnut that affects all rootstocks. The rootstock expresses RNAi against the tumor forming genes of Agrobacterium tumefaciens the causative agent of bacterial crown gall disease. We are characterizing a lead line that is completely resistant to tumor formation when infected with A.tumefaciens. We are developing regulatory data to deregulate this elite event. Objective 3: Improving plant protein production and utilization. We are investigating using plant tissues as a protein production platform for the synthesis and production of bio medically and agriculturally important proteins. The focus of these efforts is to improve and enhance transient expression using an Agrobacterium-mediated process. Transient expression systems are clearly the future for large-scale biomanufacture of proteins in plants. We have been working on two therapeutic proteins an anthrax decoy protein that can block the toxicity of Anthrax toxin. The other protein that we have been working with is butrylcholine esterase a protein that is used to block the tocic effect of nerve gas agents. These proteins are bio scavengers that bind very tightly to the toxic components. These proteins are secreted and therefore the glycosyl residues on these proteins are key for their activity and is a subject that we are actively investigating. In summary, we have been able to decipher agriculturally significant phenotypic traits and to define the underlying molecular genetic and biochemical mechanisms that regulate their expression for many of the traits explained above. Specifically, my laboratory connects genes to phenotypic traits that regulate productivity of fruit tree crops. We categorize genes by analyzing their encoded functional products, mRNA, small RNA, proteins and/or metabolites that contribute to the genetic basis of phenotypic traits. Outcomes of this effort include discovery of novel genes, development of diagnostic tools and deployment of therapeutic strategies. <br><br><b>Publications</b><br>