Plant Biology Commons^™

Does The Fungal Pathogen (Botryosphaeria Dothidea) Exceed The Dehydration Tolerance Of Its Chaparral Host?, Cristian M. Garcia

Seaver College Research And Scholarly Achievement Symposium

We tested the hypothesis that an opportunistic endophytic fungus Botryosphaeria dothidea that frequently infects and causes dieback in several different species of chaparral shrubs in the Santa Monica Mountains continues to elongate and grow in host tissues at dehydration levels that exceed host survival. This was done by collecting several large branches from the field from three dominant species of co-occurring chaparral shrubs, Malosma laurina, Ceanothus spinosus, and Ceanothus megacarpus. We allowed branches to dehydrate at increasing lengths of time, from a few days to one week, in an air-conditioned laboratory, then sealed in plastic bags to allow tissuewater equilibration, …

2018 Barley Variety Fact Sheets For Western Australia, Blakely Paynter, Georgia Trainor, Raj Malik, Jeremy Curry, Sanjiv Gupta, Sarah Collins, Daniel Huberli, Harmohinder Dhammu, Geoff Thomas, Ben Biddulph

Bulletins 4000 -

This bulletin is designed as a reference to help determine which barley variety to grow in your region. It provides market feedback, relative grain yield comparisons, disease ratings, agronomic information and herbicide tolerance ratings for all malt barley varieties segregated in Western Australia (WA) and selected feed varieties.

The decision whether to grow barley with a malt or feed classification depends on five main factors:

(1) Premium paid for different varieties when segregated.

(2) Relative grain yield of malt and feed grade barley varieties.

(3) Differences in input costs due to their agronomic and disease characteristics.

(4) Likelihood that grain …

Mac3a And Mac3b, Two Core Subunits Of The Mos4-Associated Complex, Positively Influence Mirna Biogenesis, Shengjun Li, Kan Liu, Bangjun Zhou, Mu Li, Shuxin Zhang, Lirong Zeng, Chi Zhang, Bin Yu

Center for Plant Science Innovation: Faculty Publications

MAC3A and MAC3B are conserved U-box containing proteins in eukaryotes. They are subunits of the MOS4-associated complex (MAC) that plays essential roles in plant immunity and development in Arabidopsis. However, their functional mechanisms remain elusive. Here we show that Arabidopsis thaliana MAC3A and MAC3B act redundantly in microRNA (miRNA) biogenesis. Lack of both MAC3A and MAC3B in the mac3b mac3b double mutant reduces the accumulation of miRNAs, causing elevated transcript levels of miRNA targets. mac3a mac3b also decreases the levels of primary miRNA transcripts (pri-miRNAs). However, MAC3A and MAC3B do not affect the promoter activity of genes encoding miRNAs ( …

Evaluation Of Bacillus Strains For Plant Growth Promotion And Predictability Of Efficacy By In Vitro Physiological Traits, Rufus J. Akinrinlola, Gary Y. Yuen, Rhae A. Drijber, Anthony O. Adesemoye

Department of Plant Pathology: Faculty Publications

Bacilli are commonly used as plant growth-promoting agents but can be limited in effectiveness to certain crop and soil environments. The objectives of this study were to (1) identify Bacillus strains that can be consistent in promoting the growth of corn, wheat, and soybean and (2) determine whether physiological traits expressed in vitro can be predictive of growth promotion efficacy/consistency and be used for selecting effective strains. Twelve Bacillus strains isolated from wheat rhizospheres were evaluated in greenhouse pot tests with nonsterile soil for their effects on the growth of corn, soybean, and wheat. The strains also were assessed in …

Field Evaluation Of Commercially Available Small Unmanned Aircraft Crop Spray Systems, Wayne Woldt, D. Martin, M. Latheef, Greg Kruger, Robert J. Wright, Justin Mcmechan, Christopher A. Proctor, Tamra Jackson-Ziems

Department of Plant Pathology: Faculty Publications

Agricultural research and development on small unmanned aircraft systems (UAS) has been directed toward UAS enabled sensing to detect features of interest. While compelling, there is an immediate need to increase the breadth and depth of UAS-based research, to move beyond sensing, and explore active intervention in agricultural production systems. This paper is focused on the concept of crop protection through ultra-precise, unmanned aerial application systems, and seeks to initiate research discussion in this important area of opportunity. Toward this end, two different, commercially available, small Unmanned Aerial Application Systems (sUAAS - defined as less than 55 lbs. maximum take-off …

Development Of Ifox-Hunting As A Functional Genomic Tool And Demonstration Of Its Use To Identify Early Senescence-Related Genes In The Polyploid Brassica Napus, Juan Ling, Renjie Li, Chinedu Charles Nwafor, Junluo Cheng, Maoteng Li, Qing Xi, Jian Wu, Lu Gan, Qingyong Yang, Chao Liu, Ming Chen, Yongming Zhou, Edgar B. Cahoon, Chunyu Zhang

Center for Plant Science Innovation: Faculty Publications

Functional genomic studies of many polyploid crops, including rapeseed (Brassica napus), are constrained by limited tool sets. Here we report development of a gain-of-function platform, termed ‘iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting’, for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway-compatible plant gene expression vector containing a methoxyfenozide-inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B. napus seeds and subsequent Agrobacterium-mediated transformation of Arabidopsis. The inducible promoter of this vector enabled identification of genes upon induction that are otherwise lethal when constitutively overexpressed and …

Conventional And Hyperspectral Time-Series Imaging Of Maize Lines Widely Used In Field Trials, Zhikai Liang, Piyush Pandey, Vincent Stoerger, Yuhang Xu, Yumou Qiu, Yufeng Ge, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Background: Maize (Zea mays ssp. mays) is 1 of 3 crops, along with rice and wheat, responsible for more than one-half of all calories consumed around the world. Increasing the yield and stress tolerance of these crops is essential to meet the growing need for food. The cost and speed of plant phenotyping are currently the largest constraints on plant breeding efforts. Datasets linking new types of high-throughput phenotyping data collected from plants to the performance of the same genotypes under agronomic conditions across a wide range of environments are essential for developing new statistical approaches and computer …

Single-Molecule Sequencing And Optical Mapping Yields An Improved Genome Of Woodland Strawberry (Fragaria Vesca) With Chromosome-Scale Contiguity, Patrick P. Edger, Robert Vanburen, Marivi Colle, Thomas J. Poorten, Ching Man Wai, Chad E. Niederhuth, Elizabeth I. Alger, Shujun Ou, Charlotte B. Acharya, Jie Wang, Pete Callow, Michael R. Mckain, Jinghua Shi, Chad Collier, Zhiyong Xiong, Jeffrey P. Mower, Janet P. Slovin, Timo Hytonen, Ning Jiang, Kevin L. Childs, Steven J. Knapp

Center for Plant Science Innovation: Faculty Publications

Background: Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings: Here we utilized a robust, cost-effective approach to produce high-quality reference genomes.We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ~7.9 million base pairs (Mb), representing a ~300-fold improvement of the previous version. The vast majority (>99.8%) …

Identification Of Bottlenecks In The Accumulation Of Cyclic Fatty Acids In Camelina Seed Oil, Xiao-Hong Yu, Rebecca E. Cahoon, Patrick J. Horn, Hai Shi, Richa R. Prakash, Yuanheng Cai, Maegan Hearney, Kent D. Chapman, Edgar B. Cahoon, Jorg Schwender, John Shanklin

Center for Plant Science Innovation: Faculty Publications

Modified fatty acids (mFA) have diverse uses; for example, cyclopropane fatty acids (CPA) are feedstocks for producing coatings, lubricants, plastics and cosmetics. The expression of mFA-producing enzymes in crop and model plants generally results in lower levels of mFA accumulation than in their natural-occurring source plants. Thus, to further our understanding of metabolic bottlenecks that limit mFA accumulation, we generated transgenic Camelina sativa lines co-expressing Escherichia coli cyclopropane synthase (EcCPS) and Sterculia foetida lysophosphatidic acid acyltransferase (SfLPAT). In contrast to transgenic CPA-accumulating Arabidopsis, CPA accumulation in camelina caused only minor changes in seed weight, germination rate, oil accumulation and seedling …

Integrating Phylogenetic And Network Approaches To Study Gene Family Evolution: The Case Of The Agamous Family Of Floral Genes, Daniel Santana De Carvalho, James C. Schnable, Ana Maria R. Almeida

Center for Plant Science Innovation: Faculty Publications

The study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations …

Functional Modeling Of Plant Growth Dynamics, Y. Xu, Y. Qiu, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Recent advances in automated plant phenotyping have enabled the collection of time series measurements from the same plants of a wide range of traits at different developmental time scales. The availability of time series phenotypic datasets has increased interest in statistical approaches for comparing patterns of change among different plant genotypes and different treatment conditions. Two widely used methods of modeling growth with time are pointwise analysis of variance (ANOVA) and parametric sigmoidal curve fitting. Pointwise ANOVA yields discontinuous growth curves, which do not reflect the true dynamics of growth patterns in plants. In contrast, fitting a parametric model to …

Gipc Glcnac Glycosyltransferase, Toshiki Ishikawa, Lin Fang, Emilie A. Rennie, Julien Sechet, Jingwei Yan, Beibei Jing, William Moore, Edgar B. Cahoon, Henrik V. Scheller, Maki Kawai-Yamada, Jenny C. Mortimer

Center for Plant Science Innovation: Faculty Publications

Glycosylinositol phosphorylceramides (GIPCs), which have a ceramide core linked to a glycan headgroup of varying structure, are the major sphingolipids in the plant plasma membrane. Recently, we identified the major biosynthetic genes for GIPC glycosylation in Arabidopsis thaliana, and demonstrated that the glycan headgroup is essential for plant viability. However, the function of GIPCs and the significance of their structural variation are poorly understood. Here, we characterized the Arabidopsis glycosyltransferase GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) and showed that it is responsible for the glycosylation of a subgroup of GIPCs found in seeds and pollen that contain N-acetylglucosamine (GlcNAc) and glucosamine …

Sma1, A Homolog Of The Splicing Factor Prp28, Has A Multifaceted Role In Mirna Biogenesis In Arabidopsis, Shengjun Li, Ran Xu, Aixia Li, Kan Liu, Liqing Gu, Mu Li, Hairui Zhang, Yueying Zhang, Shangshang Zhuang, Quanhui Wang, Gang Gao, Na Li, Chi Zhang, Yunhai Li, Bin Yu

Center for Plant Science Innovation: Faculty Publications

MicroRNAs (miRNAs) are a class of small non-coding RNAs that repress gene expression. In plants, the RNase III enzyme Dicer-like (DCL1) processes primary miRNAs (pri-miRNAs) into miRNAs. Here, we show that SMALL1 (SMA1), a homolog of the DEADbox pre-mRNA splicing factor Prp28, plays essential roles in miRNA biogenesis in Arabidopsis. A hypomorphic sma1-1 mutation causes growth defects and reduces miRNA accumulation correlated with increased target transcript levels. SMA1 interacts with the DCL1 complex and positively influences primiRNA processing. Moreover, SMA1 binds the promoter region of genes encoding pri-miRNAs (MIRs) and is required for MIR transcription. Furthermore, SMA1 also …

Generation And Evaluation Of Modified Opaque-2 Popcorn Suggests A Route To Quality Protein Popcorn, Ying Ren, Abou Yobi, Leandra Marshall, Ruthie Angelovici, Oscar Rodriguez, David R. Holding

Center for Plant Science Innovation: Faculty Publications

Introducing traits from dent corn to popcorn is challenging because it is difficult to recover adequate popping characteristics. QPM (Quality Protein Maize) is a dent corn variety carrying the opaque-2 (o2) mutation, specifying increased amounts of normally limiting essential amino acids, and modifier genes which restore the wild type vitreous kernel phenotype. In this study, we introgressed o2 and selected for endosperm modification using vitreousness and high 27-kD gamma zein content. In this way, we recovered high-lysine, fully poppable Quality Protein Popcorn (QPP). BC₂F₄ individuals with vitreous kernels were confirmed to be o2 mutants by …

Molecular Tools Enabling Pennycress (Thlaspi Arvense) As A Model Plant And Oilseed Cash Cover Crop, Michaela Mcginn, Winthrop B. Phippen, Ratan Chopra, Sunil Bansal, Brice A. Jarvis, Mary E. Phippen, Kevin M. Dorn, Maliheh Esfahanian, Tara J. Nazarenus, Edgar B. Cahoon, Timothy P. Durrett, M. David Marks, John C. Sedbrook

Center for Plant Science Innovation: Faculty Publications

Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run-off on otherwise barren farmland. We demonstrate that pennycress can serve as a user-friendly model system akin to Arabidopsis that is well-suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring-type Spring 32-10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter-type pennycress, as well as predominantly a one-to-one correspondence with Arabidopsis genes, …

Lycophyte Plastid Genomics: Extreme Variation In Gc, Gene And Intron Content And Multiple Inversions Between A Direct And Inverted Orientation Of The Rrna Repeat, Jeffrey P. Mower, Peng-Fei Ma, Felix Grewe, Alex Taylor, Todd P. Michael, Robert Vanburen, Yin-Long Qiu

Center for Plant Science Innovation: Faculty Publications

Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences. Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes. Lycopodiaceae plastomes have remained largely unchanged compared with the common ancestor of land plants, whereas plastome evolution in Isoetes and especially Selaginella is highly dynamic. Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynthetic land plant. Uniquely, the canonical inverted repeat was converted into a direct repeat (DR) …

The Role Of Type Iii Effectors From Xanthomonas Axonopodis Pv. Manihotis In Virulence And Suppression Of Plant Immunity, Cesar Augusto Medina, Paola Andrea Reyes, Cesar Augusto Trujillo, Juan Luis Gonzalez, David Alejandro Bejarano, Nathaly Andrea Montenegro, Jonathan M. Jacobs, Anna Joe, Silvia Restrepo, James R. Alfano, Adriana Bernal

Center for Plant Science Innovation: Faculty Publications

Xanthomonas axonopodis pv. manihotis (Xam) causes cassava bacterial blight, the most important bacterial disease of cassava. Xam, like other Xanthomonas species, requires type III effectors (T3Es) for maximal virulence. Xam strain CIO151 possesses 17 predicted T3Es belonging to the Xanthomonas outer protein (Xop) class. This work aimed to characterize nine Xop effectors present in Xam CIO151 for their role in virulence and modulation of plant immunity. Our findings demonstrate the importance of XopZ, XopX, XopAO1 and AvrBs2 for full virulence, as well as a redundant function in virulence between XopN and XopQ in susceptible cassava plants. We tested their role …

Xanthomonas Oryzae Pv. Oryzae Tale Proteins Recruit Ostfiiaγ1 To Compensate For The Absence Of Ostfiiaγ5 In Bacterial Blight In Rice, Wenxiu Ma, Lifang Zou, Zhiyuan Ji, Xiameng Xu, Zhengyin Xu, Yangyang Yang, James R. Alfano

Center for Plant Science Innovation: Faculty Publications

Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight (BB) of rice, uses transcription activator-like effectors (TALEs) to interact with the basal transcription factor gamma subunit OsTFIIAγ5 (Xa5) and activates the transcription of host genes. However, how OsTFIIAγ1, the other OsTFIIAγ protein, functions in the presence of TALEs remains unclear. In this study, we show that OsTFIIAγ1 plays a compensatory role in the absence of Xa5. The expression of OsTFIIAγ1, which is activated by TALE PthXo7, increases the expression of host genes targeted by avirulent and virulent TALEs. Defective OsTFIIAγ1 rice lines show reduced expression of the TALE-targeted …

Characterization Of Neofabraea Actinidiae And N. Brasiliensis As Causal Agents Of Apple Bull’S-Eye Rot In Southern Brazil, Amauri Bogo, Carla C. Comparin, Rosa M. Valdebenito Sanhueza, Patricia Ritschel, Ricardo T. Casa, Fábio N. Silva, Sydney E. Everhart

Department of Plant Pathology: Faculty Publications

The causal agents of apple bull’s-eye rot in southern Brazil have recently been described as Neofabraea actinidiae and N. brasiliensis. Isolates of both species were evaluated for response of mycelial growth index (MGI) to different temperatures, enzyme production, mycelial growth inhibition and effective concentrations (EC₅₀ and EC₁₀₀) of the fungicides triflumizole, pyrimethanil and thiophanate methyl, as well as aggressiveness on fruits of ‘Fuji’ hybrid and ‘Pink Lady’. There was significantly lower mycelium growth in N. brasiliensis compared with N. actinidiae at all temperatures tested. Neither species grew at 3 and 32°C. There were minor differences in …

Elucidating The Role Of Highly Homologous Nicotiana Benthamiana Ubiquitin E2 Gene Family Members In Plant Immunity Through An Improved Virus‑Induced Gene Silencing Approach, Bangjun Zhou, Lirong Zeng

Department of Plant Pathology: Faculty Publications

Background: Virus-induced gene silencing (VIGS) has been used in many plant species as an attractive post transcriptional gene silencing (PTGS) method for studying gene function either individually or at large-scale in a high-throughput manner. However, the specificity and efficiency for knocking down members of a highly homologous gene family have remained to date a significant challenge in VIGS due to silencing of off-targets. Results: Here we present an improved method for the selection and evaluation of gene fragments used for VIGS to specifically and efficiently knock down members of a highly homologous gene family. Using this method, we knocked down …

The Tomato U-Box Type E3 Ligase Pub13 Acts With Group Iii Ubiquitin E2 Enzymes To Modulate Fls2-Mediated Immune Signaling, Bangjun Zhou, Lirong Zeng

Department of Plant Pathology: Faculty Publications

In Arabidopsis and rice, the ubiquitin ligase PUB13-mediated protein degradation plays a significant role in plant pattern-triggered immunity (PTI) and flowering time control. The Arabidopsis PUB13 has been shown to attenuate the pattern recognition receptor FLS2-mediated immune signaling by ubiquitinating FLS2 and consequently promoting its degradation by the 26S proteasome. Nevertheless, the cognate ubiquitin-conjugating enzymes (E2) with which PUB13 acts to modulate FLS2-mediated PTI are unknown. To address this question, we investigate here the tomato (Solanum lycopersicum) homolog of PUB13, SlPUB13 by utilizing the recently characterized complete set of tomato E2s. Of the 13 groups of tomato E2s, …

Proteomic Analysis Of Ubiquitinated Proteins In Rice (Oryza Sativa) After Treatment With Pathogen-Associated Molecular Pattern (Pamp) Elicitors, Xiao-Lin Chen, Xin Xie, Liye Wu, Caiyun Liu, Lirong Zeng, Xueping Zhou, Feng Luo, Guo-Liang Wang, Wende Liu

Department of Plant Pathology: Faculty Publications

Reversible protein ubiquitination plays essential roles in regulating cellular processes. Although many reports have described the functions of ubiquitination in plant defense responses, few have focused on global changes in the ubiquitome. To better understand the regulatory roles of ubiquitination in rice pattern-triggered immunity (PTI), we investigated the ubiquitome of rice seedlings after treatment with two pathogen-associated molecular patterns, the fungal-derived chitin or the bacterialderived flg22, using label-free quantitative proteomics. In chitin-treated samples, 144 and 167 lysine-ubiquitination sites in 121 and 162 proteins showed increased and decreased ubiquitination, respectively. In flg22-treated samples, 151 and 179 lysine-ubiquitination sites in 118 and …

Mac3a And Mac3b, Two Core Subunits Of The Mos4-Associated Complex, Positively Influence Mirna Biogenesis, Shengjun Li, Kan Liu, Bangjun Zhou, Mu Li, Shuxin Zhang, Lirong Zeng, Chi Zhang, Bin Yu

Center for Plant Science Innovation: Faculty Publications

MAC3A and MAC3B are conserved U-box containing proteins in eukaryotes. They are subunits of the MOS4-associated complex (MAC) that plays essential roles in plant immunity and development in Arabidopsis. However, their functional mechanisms remain elusive. Here we show that Arabidopsis thaliana MAC3A and MAC3B act redundantly in microRNA (miRNA) biogenesis. Lack of both MAC3A and MAC3B in the mac3b mac3b double mutant reduces the accumulation of miRNAs, causing elevated transcript levels of miRNA targets. mac3a mac3b also decreases the levels of primary miRNA transcripts (pri-miRNAs). However, MAC3A and MAC3B do not affect the promoter activity of genes encoding miRNAs ( …

Tomato Spotted Wilt Virus Nss Protein Supports Infection And Systemic Movement Of A Potyvirus And Is A Symptom Determinant, Hernan Garcia-Ruiz, Sergio M. Gabriel Peralta, Patricia A. Harte-Maxwell

Department of Plant Pathology: Faculty Publications

Plant viruses are inducers and targets of antiviral RNA silencing. To condition susceptibility, most plant viruses encode silencing suppressor proteins that interfere with antiviral RNA silencing. The NSs protein is an RNA silencing suppressor in orthotospoviruses, such as the tomato spotted wilt virus (TSWV). The mechanism of RNA silencing suppression by NSs and its role in virus infection and movement are poorly understood. Here, we cloned and tagged TSWV NSs and expressed it from a GFP-tagged turnip mosaic virus (TuMV-GFP) carrying either a wild-type or suppressor-deficient (AS9) helper component proteinase (HC-Pro). When expressed in cis, NSs restored pathogenicity and promoted …

Intermolecular Rna Recombination Occurs At Different Frequencies In Alternate Forms Of Brome Mosaic Virus Rna Replication Compartments, Hernan Garcia-Ruiz, Arturo Diaz, Paul Ahlquist

Department of Plant Pathology: Faculty Publications

Positive-strand RNA viruses replicate their genomes in membrane-bound replication compartments. Brome mosaic virus (BMV) replicates in vesicular invaginations of the endoplasmic reticulum membrane. BMV has served as a productive model system to study processes like virus-host interactions, RNA replication and recombination. Here we present multiple lines of evidence showing that the structure of the viral RNA replication compartments plays a fundamental role and that recruitment of parental RNAs to a common replication compartment is a limiting step in intermolecular RNA recombination. We show that a previously defined requirement for an RNA recruitment element on both parental RNAs is not to …

Metagenomic Analysis Of Viruses Associated With Maize Lethal Necrosis In Kenya, Mwathi Jane Wamaitha, Deepti Nigam, Solomon Maina, Francesca Stomeo, Anne Wangai, Joyce Njoki Njuguna, Timothy A. Holton, Bramwel W. Wanjala, Mark Wamalwa, Tanui Lucas, Appolinaire Djikeng, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

Background: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. Methods: We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples …

Susceptibility Genes To Plant Viruses, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

Plant viruses use cellular factors and resources to replicate and move. Plants respond to viral infection by several mechanisms, including innate immunity, autophagy, and gene silencing, that viruses must evade or suppress. Thus, the establishment of infection is genetically determined by the availability of host factors necessary for virus replication and movement and by the balance between plant defense and viral suppression of defense responses. Host factors may have antiviral or proviral activities. Proviral factors condition susceptibility to viruses by participating in processes essential to the virus. Here, we review current advances in the identification and characterization of host factors …

Profile Of Genetically Modified Plants Authorized In Mexico, Mayra Teresa Garcia Ruiz, Aaron N. Knapp, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

Mexico is a center of origin for several economically important plants including maize, cotton, and cocoa. Maize represents more than a food crop, has been declared a biological, cultural, agricultural and economic patrimony, and is linked to the national identity of Mexicans. In this review, we describe the historic and current use of genetically modified plants in Mexico and factors that contributed to the development of the biosafety regulation. We developed a database containing all permit applications received by the government to release genetically modified plants. A temporal and geographical analysis identified the plant species that have been authorized for …

Pushing The Resolution Limit By Correcting The Ewald Sphere Effect In Single-Particle Cryo-Em Reconstructions, Dongjie Zhu, Xiangxi Wang, Qianglin Fang, James L. Van Etten, Michael G. Rossmann, Zihe Rao, Xinzheng Zhang

Department of Plant Pathology: Faculty Publications

The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a reconstruction. Here we estimate the attainable resolution and report a “block-based” reconstruction method for extending the resolution limit. We find the Ewald sphere effect limits the resolution of large objects, especially large viruses. After processing two real datasets of large viruses, we show that our procedure can extend the resolution for both datasets and can accommodate the flexibility associated with large protein complexes.

Genome-Wide Analysis Of Genes Encoding Core Components Of The Ubiquitin System In Soybean (Glycine Max) Reveals A Potential Role For Ubiquitination In Host Immunity Against Soybean Cyst Nematode, Chunyu Zhang, Li Song, Mani Kant Choudhary, Bangjun Zhou, Guangchao Sun, Kyle C. Broderick, Loren Giesler, Lirong Zeng

Department of Plant Pathology: Faculty Publications

Background: Ubiquitination is a major post-translational protein modification that regulates essentially all cellular and physiological pathways in eukaryotes. The ubiquitination process typically involves three distinct classes of enzymes, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3). To date, a comprehensive identification and analysis of core components comprising of the whole soybean (Glycine max) ubiquitin system (UBS) has not been reported.

Results: We performed a systematic, genome-wide analysis of genes that encode core members of the soybean UBS in this study. A total of 1431 genes were identified with high confidence to encode putative soybean UBS components, …