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Scholarly Works (10 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2012)

Aphids cause extensive economic losses to cultivated crops worldwide. Their success as pests is in part due to their complex life cycle, wide host range, and the ability of a female aphid to contain not only the developing embryos of her daughters, but also those of her grand-daughters which develop within her daughters. The latter results in build up of immense populations very quickly. Resistant plants represent an environmental friendly approach to combat aphid pests. Better understanding of plant-aphid interaction will contribute to engineering durable plant resistance. In tomato (Solanum lycopersicum), the Mi-1 gene confers resistance to potato aphid (Macrosiphum euphorbiae), root-knot nematode (RKN) (Meloidogyne sp.), whitefly (Bemisia tabaci), and tomato psyllid (Bactericera cockerelli). This incompatible tomato interaction with RKN is characterized by hypersensitive response and vast transcriptional reprogramming, including differential regulation of transcription factors (TFs). Using gene knock-down approach in Chapter one, a role for SlWRKY70 TF was identified in Mi-1-mediated tomato resistance against potato aphid and RKN. Gene expression analysis showed that the regulation of this TF by Salicylic acid and Jasmonic acid hormones is conserved between tomato and Arabidopsis thaliana. The study of SlWRKY70 revealed that there is no consistent nomenclature for plant WRKY TF family. For this reason a phylogenetic analysis was conducted using sequences from 15 plant species. Chapter two presents the analysis and the established orthologous relationship of WRKY TFs among these plant species. Consequently, this analysis allowed the design of a systemic nomenclature for the WRKY TF family to include the inferred orthology relationships. Chapters three and four pursued another approach to understand plant-aphid interactions. These chapters focused on identifying the aphid effectors and putative lineage-specific set of genes through sequencing the aphid and its salivary gland transcriptomes. In Chapter three sequencing and annotation of the potato aphid transcriptome enabled us to conduct comparative sequence analysis with three other aphid species, as well as seven additional species of insects from different clades and a planktonic crustacean. This analysis identified a set of aphid-specific genes, which may contribute to aphid's unconventional biology. The transcripts of a subset of these aphid-specific genes were expressed in the salivary glands suggesting that they are involved in aphid-host interactions. To study this interaction in more detail, the potato aphid salivary gland transcriptome was sequenced in Chapter four. This enabled identification of secreted proteins based on prediction of secretion signal peptides. In planta functional characterization of eight of these putative aphid secreted proteins identified roles for two, Me10 and Me23, in altering tomato responses to the aphid's advantage.

  • 12 supplemental files
Cover page: Tomato-Potato Aphid Interactions: Insights into Plant Defense and the Aphid Pest
  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2016)
The survival and reproduction of plants depend on their ability to cope with a wide range of daily and seasonal environmental fluctuations during their life cycle. Phytohormones are plant growth regulators that are involved in almost every aspect of growth and development as well as plant adaptation to myriad abiotic and biotic conditions. The circadian clock, an endogenous and cell-autonomous biological timekeeper that produces rhythmic outputs with close to 24-h rhythms, provides an adaptive advantage by synchronizing plant physiological and metabolic processes to the external environment. The circadian clock regulates phytohormone biosynthesis and signaling pathways to generate daily rhythms in hormone activity that fine-tune a range of plant processes, enhancing adaptation to local conditions. This review explores our current understanding of the interplay between the circadian clock and hormone signaling pathways.
    Cover page: Circadian regulation of hormone signaling and plant physiology
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2023)
    Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We found the expected transcriptome signatures of phototropin-mediated phototropism in sunflower stems bending towards monochromatic blue light. Surprisingly, the expression patterns of these phototropism-regulated genes are quite different in heliotropic plants. Most genes rapidly induced during phototropism display only minor differences in expression across solar tracking stems. However, some genes that are both rapidly induced during phototropism and are implicated in growth responses to foliar shade are rapidly induced on the west sides of stems at the onset of heliotropism, suggesting a possible role for red light photoreceptors in solar tracking. To test the involvement of different photoreceptor signaling pathways in heliotropism, we modulated the light environment of plants initiating solar tracking. We found that depletion of either red and far-red light or blue light did not hinder the initiation or maintenance of heliotropism in the field. Together, our results suggest that the transcriptional regulation of heliotropism is distinct from phototropin-mediated phototropism and likely involves inputs from multiple light signaling pathways.
      Cover page: Multiple light signaling pathways control solar tracking in sunflowers.
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2023)
      Microbial symbionts range from mutualistic to commensal to antagonistic. While these roles are distinct in their outcome, they are also fluid in a changing environment. Here, we used the Lotus japonicus-Mesorhizobium japonicum symbiosis to investigate short-term and long-term shifts in population abundance using an effective, fast, and low-cost tracking methodology for M. japonicum. We use quantitative polymerase chain reaction (qPCR) to track previously generated signature-tagged M. japonicum mutants targeting the Tn5 transposon insertion and the flanking gene. We used a highly beneficial wild type and moderately beneficial and non-beneficial mutants of M. japonicum sp. nov. to demonstrate the specificity of these primers to estimate the relative abundance of each genotype within individual nodules and after serial transfers to new hosts. For the moderate and non-beneficial genotypes, qPCR allowed us to differentiate genotypes that are phenotypically indistinguishable and investigate host control with suboptimal symbionts. We consistently found the wild type increasing in the proportion of the population, but our data suggest a potential reproductive trade-off between the moderate and non-beneficial genotypes. The multi-generation framework we used, coupled with qPCR, can easily be scaled up to track dozens of M. japonicum mutants simultaneously. Moreover, these mutants can be used to explore M. japonicum genotype abundance in the presence of a complex soil community.
        Cover page: Evaluation of qPCR to Detect Shifts in Population Composition of the Rhizobial Symbiont Mesorhizobium japonicum during Serial in Planta Transfers.
        • Article
        • Peer Reviewed
        UC Riverside Previously Published Works (2015)
        Aphids deliver saliva into plants and acquire plant sap for their nourishment using a specialized mouthpart or stylets. Aphid saliva is of great importance because it contains effectors that are involved in modulating host defense and metabolism. Although profiling aphid salivary glands and identifying secreted proteins have been successfully used, success in direct profiling of aphid saliva have been limited due to scarcity of saliva collected in artificial diets. Here we present the use of a neurostimulant, resorcinol, for inducing aphid salivation. Saliva of potato aphids (Macrosiphum euphorbiae), maintained on tomato, was collected in resorcinol diet. Salivary proteins were identified using mass spectrometry and compared with the existing M. euphorbiae salivary proteome collected in water. Comparative analysis was also performed with existing salivary proteomes from additional aphid species. Most of the proteins identified in the resorcinol diet were also present in the water diet and represented proteins with a plethora of functions in addition to a large number of unknowns. About half of the salivary proteins were not predicted for secretion or had canonical secretion signal peptides. We also analyzed the phosphorylation states of M. euphorbiae salivary proteins and identified three known aphid effectors, Me_WB01635/Mp1, Me10/Mp58, and Me23 that carry phosphorylation marks. In addition to insect proteins, tomato host proteins were also identified in aphid saliva. Our results indicate that aphid saliva is complex and provides a rich resource for functional characterization of effectors.
          Cover page: Potato Aphid Salivary Proteome: Enhanced Salivation Using Resorcinol and Identification of Aphid Phosphoproteins
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2014)

          Aphids are sap-feeding plant pests and harbor the endosymbiont Buchnera aphidicola, which is essential for their fecundity and survival. During plant penetration and feeding, aphids secrete saliva that contains proteins predicted to alter plant defenses and metabolism. Plants recognize microbe-associated molecular patterns and induce pattern-triggered immunity (PTI). No aphid-associated molecular pattern has yet been identified. By mass spectrometry, we identified in saliva from potato aphids (Macrosiphum euphorbiae) 105 proteins, some of which originated from Buchnera, including the chaperonin GroEL. Because GroEL is a widely conserved bacterial protein with an essential function, we tested its role in PTI. Applying or infiltrating GroEL onto Arabidopsis (Arabidopsis thaliana) leaves induced oxidative burst and expression of PTI early marker genes. These GroEL-induced defense responses required the known coreceptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR KINASE 1. In addition, in transgenic Arabidopsis plants, inducible expression of groEL activated PTI marker gene expression. Moreover, Arabidopsis plants expressing groEL displayed reduced fecundity of the green peach aphid (Myzus persicae), indicating enhanced resistance against aphids. Furthermore, delivery of GroEL into tomato (Solanum lycopersicum) or Arabidopsis through Pseudomonas fluorescens, engineered to express the type III secretion system, also reduced potato aphid and green peach aphid fecundity, respectively. Collectively our data indicate that GroEL is a molecular pattern that triggers PTI.

            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2024)
            Many parts of the world face severe and prolonged drought conditions, stressing the sustainability of water resources and agriculture. Transitioning to water-efficient crops is one strategy that can help adapt to water scarcity. An emerging drought-tolerant crop of interest is chia (Salvia hispanica). Yet, no study has compared its large-scale water use dynamics to those of widely established crops across the globe. Here, we use satellite data over multiple years to assess the water use efficiency of chia, alfalfa, corn, and soybean globally. Results show that chia consumed 13-38% less water than alfalfa, corn, and soy and assimilated 14-20% more carbon per amount of water used. Substituting 10% of Southwest United States alfalfa cultivation with chia would save 184 million liters of water per growing season, equivalent to the annual water consumption of 1,300 households. Future research shall explore the economic, societal, and environmental ramifications of substituting alfalfa with chia in dry areas worldwide. These insights can guide decision-makers in promoting sustainable agriculture and water resource management.
              Cover page: Satellite observations indicate that chia uses less water than other crops in warm climates.
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              • Peer Reviewed
              UC Riverside Previously Published Works (2014)
              MicroRNAs (miRNAs) suppress the transcriptional and post-transcriptional expression of genes in plants. Several miRNA families target genes encoding nucleotide-binding site-leucine-rich repeat (NB-LRR) plant innate immune receptors. The fungus Fusarium oxysporum f. sp. lycopersici causes vascular wilt disease in tomato. We explored a role for miRNAs in tomato defense against F. oxysporum using comparative miRNA profiling of susceptible (Moneymaker) and resistant (Motelle) tomato cultivars. slmiR482f and slmiR5300 were repressed during infection of Motelle with F. oxysporum. Two predicted mRNA targets each of slmiR482f and slmiR5300 exhibited increased expression in Motelle and the ability of these four targets to be regulated by the miRNAs was confirmed by co-expression in Nicotiana benthamiana. Silencing of the targets in the resistant Motelle cultivar revealed a role in fungal resistance for all four genes. All four targets encode proteins with full or partial nucleotide-binding (NB) domains. One slmiR5300 target corresponds to tm-2, a susceptible allele of the Tomato Mosaic Virus resistance gene, supporting functions in immunity to a fungal pathogen. The observation that none of the targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response. Taken together, our findings suggest that Moneymaker is highly susceptible because its potential resistance is insufficiently expressed due to the action of miRNAs.
                Cover page: MicroRNAs Suppress NB Domain Genes in Tomato That Confer Resistance to Fusarium oxysporumCreative Commons 'BY-NC-SA' version 4.0 license
                • Article
                • Peer Reviewed
                UC Riverside Previously Published Works (2018)
                The potato aphid, Macrosiphum euphorbiae, is an important agricultural pest that causes economic losses to potato and tomato production. To establish the transcriptome for this aphid, RNA-Seq libraries constructed from aphids maintained on tomato plants were used in Illumina sequencing generating 52.6 million 75-105 bp paired-end reads. The reads were assembled using Velvet/Oases software with SEED preprocessing resulting in 22,137 contigs with an N50 value of 2,003bp. After removal of contigs from tomato host origin, 20,254 contigs were annotated using BLASTx searches against the non-redundant protein database from the National Center for Biotechnology Information (NCBI) as well as IntereProScan. This identified matches for 74% of the potato aphid contigs. The highest ranking hits for over 12,700 contigs were against the related pea aphid, Acyrthosiphon pisum. Gene Ontology (GO) was used to classify the identified M. euphorbiae contigs into biological process, cellular component and molecular function. Among the contigs, sequences of microbial origin were identified. Sixty five contigs were from the aphid bacterial obligate endosymbiont Buchnera aphidicola origin and two contigs had amino acid similarities to viruses. The latter two were named Macrosiphum euphorbiae virus 2 (MeV-2) and Macrosiphum euphorbiae virus 3 (MeV-3). The highest sequence identity to MeV-2 had the Dysaphis plantaginea densovirus, while to MeV-3 is the Hubei sobemo-like virus 49. Characterization of MeV-2 and MeV-3 indicated that both are transmitted vertically from adult aphids to nymphs. MeV-2 peptides were detected in the aphid saliva and only MeV-2 and not MeV-3 nucleic acids were detected inside tomato leaves exposed to virus-infected aphids. However, MeV-2 nucleic acids did not persist in tomato leaf tissues, after clearing the plants from aphids, indicating that MeV-2 is likely an aphid virus.
                  Cover page: Sequence analysis of the potato aphid Macrosiphum euphorbiae transcriptome identified two new viruses
                  • Article
                  • Peer Reviewed
                  UC Riverside Previously Published Works (2010)
                  Abstract Background Recent genomic analyses of arthropod defense mechanisms suggest conservation of key elements underlying responses to pathogens, parasites and stresses. At the center of pathogen-induced immune responses are signaling pathways triggered by the recognition of fungal, bacterial and viral signatures. These pathways result in the production of response molecules, such as antimicrobial peptides and lysozymes, which degrade or destroy invaders. Using the recently sequenced genome of the pea aphid (Acyrthosiphon pisum), we conducted the first extensive annotation of the immune and stress gene repertoire of a hemipterous insect, which is phylogenetically distantly related to previously characterized insects models. Results Strikingly, pea aphids appear to be missing genes present in insect genomes characterized to date and thought critical for recognition, signaling and killing of microbes. In line with results of gene annotation, experimental analyses designed to characterize immune response through the isolation of RNA transcripts and proteins from immune-challenged pea aphids uncovered few immune-related products. Gene expression studies, however, indicated some expression of immune and stress-related genes. Conclusions The absence of genes suspected to be essential for the insect immune response suggests that the traditional view of insect immunity may not be as broadly applicable as once thought. The limitations of the aphid immune system may be representative of a broad range of insects, or may be aphid specific. We suggest that several aspects of the aphid life style, such as their association with microbial symbionts, could facilitate survival without strong immune protection.
                    Cover page: Immunity and other defenses in pea aphids, Acyrthosiphon pisum
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