David P. Horvath

Regulation of Arabidopsis thaliana L. (Heyn) cor78 in response to low temperature.

Changes in gene expression occur during cold acclimation in a variety of plants including Arabidopsis thaliana L. (Heyn). Here we examine the cold-regulated expression of A. thaliana cor78. The results of gene-fusion experiments confirm the finding of Yamaguchi-Shinozaki and Shinozaki ([1993] Mol Gen Genet 236: 331–340) that the 5[prime] region of cor78 has cis-acting regulatory elements that can impart cold-regulated gene expression. Further, histochemical staining experiments indicated that this cold-regulatory element(s) was active at low temperature throughout much of the plant including leaves, stems, roots, flower petals, filaments, and sepals. Time-course experiments indicated that the activity of the cor78 promoter in cold-acclimated plants was down-regulated quickly in response to noninducing temperatures and that the half-life of the cor78 transcripts was only about 40 min at normal growth temperature. Fusion of the entire transcribed region of cor78 to the cauliflower mosaic virus 35S promoter resulted in a chimeric gene that was constitutively expressed and displayed little if any posttranscriptional regulation in response to low temperature.

Molecular Analysis of Signals Controlling Dormancy and Growth in Underground Adventitious Buds of Leafy Spurge

Dormancy and subsequent regrowth of adventitious buds is a critical physiological process for many perennial plants. We have used the expression of hormone and cell cycle-responsive genes as markers to follow this process in leafy spurge (Euphorbia esula). In conjunction with earlier studies, we show that loss of mature leaves results in decreased sugar levels and increased gibberellin perception in underground adventitious buds. Gibberellin is sufficient for induction of S phase-specific but not M phase-specific gene expression. Loss of both apical and axillary buds or inhibition of polar auxin transport did not result in induction of S phase- or M phase-specific gene expression. Loss of polar auxin transport was necessary for continuation of the cell cycle and further bud development if the S phase was previously initiated.

Changes in the Transcriptome of Dry Leafy Spurge (Euphorbia esula) Seeds Imbibed at a Constant and Alternating Temperature

Abstract Leafy spurge seeds are responsive to alternating temperature rather than constant temperature for germination. Transcriptome changes of dry leafy spurge seeds and seeds imbibed for 1 and 3 d at 20 C constant (C) and 20 ∶ 30 C alternating (A) temperature were determined by microarray analysis to examine temperature responsiveness. Principal component analysis revealed differences in the transcriptome of imbibed seeds based on the temperature regime. Computational methods in bioinformatics parsed the data into overrepresented AraCyc pathways and gene regulation subnetworks providing biological context to temperature responses. After 1 d of imbibition, the degradation of starch and sucrose leading to anaerobic respiration were common pathways at both temperature regimes. Several overrepresented pathways unique to 1 d A were associated with generation of energy, reducing power, and carbon substrates; several of these pathways remained overrepresented and up-regulated at 3 d A. At 1 d C, pathways for the phytohormones jasmonic acid and brassinosteroids were uniquely overrepresented. There was little similarity in overrepresented pathways at 1 d C between leafy spurge and arabidopsis seeds, indicating species-specific effects upon imbibition of dry seeds. Overrepresented gene subnetworks at 1 d and 3 d at both temperature regimes related to signaling processes and stress responses. A major overrepresented subnetwork unique to 1 d C related to photomorphogenesis via the E3 ubiquitin ligase COP1. At 1 d A, major overrepresented subnetworks involved circadian rhythm via LHY and TOC1 proteins and expression of stress-related genes such as DREB1A, which is subject to circadian regulation. Collectively, substantial differences were observed in the transcriptome of leafy spurge seeds imbibed under conditions that affect the capacity to germinate. Nomenclature: Mouse-ear cress, Arabidopsis thaliana (L.) Heynh.; leafy spurge, Euphorbia esula L. (EPHES).

Gene Space and Transcriptome Assemblies of Leafy Spurge (Euphorbia esula) Identify Promoter Sequences, Repetitive Elements, High-Quality Markers, and a Full-Length Chloroplast Genome

Abstract Leafy spurge (Euphorbia esula L.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects with E. esula have helped develop it as a model for studying many aspects of perennial plant development and response to abiotic stress. However, the lack of an assembled genome for E. esula has limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome for E. esula would enhance our understanding of signaling processes controlling plant development and responses to environmental stress and provide a better understanding of genetic factors impacting weediness traits, evolution, and herbicide resistance. A comprehensive transcriptome database would also assist in analyzing future RNA-seq studies and is needed to annotate and assess genomic sequence assemblies. Here, we assembled and annotated 56,234 unigenes from an assembly of 589,235 RNA-seq-derived contigs and a previously published Sanger-sequenced expressed sequence tag collection. The resulting data indicate that we now have sequence for >90% of the expressed E. esula proteincoding genes. We also assembled the gene space of E. esula by using a limited coverage (18X) genomic sequence database. In this study, the programs Velvet and Trinity produced the best gene-space assemblies based on representation of expressed and conserved eukaryotic genes. The results indicate that E. esula contains as much as 23% repetitive sequences, of which 11% are unique. Our sequence data were also sufficient for assembling a full chloroplast and partial mitochondrial genome. Further, marker analysis identified more than 150,000 high-quality variants in our E. esula L-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results, E. esula appears to have limited heterozygosity. This study provides a blueprint for low-cost genomic assemblies in weed species and new resources for identifying conserved and novel promoter regions among coordinately expressed genes of E. esula.

Omics in Weed Science: A Perspective from Genomics, Transcriptomics, and Metabolomics Approaches

Abstract Modern high-throughput molecular and analytical tools offer exciting opportunities to gain a mechanistic understanding of unique traits of weeds. During the past decade, tremendous progress has been made within the weed science discipline using genomic techniques to gain deeper insights into weedy traits such as invasiveness, hybridization, and herbicide resistance. Though the adoption of newer “omics” techniques such as proteomics, metabolomics, and physionomics has been slow, applications of these omics platforms to study plants, especially agriculturally important crops and weeds, have been increasing over the years. In weed science, these platforms are now used more frequently to understand mechanisms of herbicide resistance, weed resistance evolution, and crop–weed interactions. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding weedy traits. Although these techniques can provide robust insights about the molecular functioning of plants, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. Therefore, it is desirable to integrate the different omics technologies to give a better understanding of molecular functioning of biological systems. This multidimensional integrated approach can therefore offer new avenues for better understanding of questions of interest to weed scientists. This review offers a retrospective and prospective examination of omics platforms employed to investigate weed physiology and novel approaches and new technologies that can provide holistic and knowledge-based weed management strategies for future.

Microarray Analysis of the Semicompatible, Pathogenic Response and Recovery of Leafy Spurge (Euphorbia esula) Inoculated with the Cassava Bacterial Blight Pathogen Xanthomonas axonopodis pv. manihotis

Abstract Infection by Xanthomonas axonopodis pv. manihotis (Xam) of the perennial rangeland weed leafy spurge was tested to see whether Xam might serve a potential biological control agent for this invasive weed. Although leafy spurge was susceptible to Xam infection, it recovered within 21 d after inoculation (DAI). Microarray resources available for leafy spurge allowed us to follow the physiological and signaling pathways that were altered as leafy spurge was infected and then recovered from Xam infection. The first physiological effect of Xam infection was a down-regulation of photosynthetic processes within 1 DAI. By 7 DAI, numerous processes associated with well-documented pathogenesis responses of plants were observed. Although some pathogenesis responses were still detectable at 21 DAI, other processes associated with meristem development were noted. Ontological analysis of potential signaling systems indicated jasmonic acid plays a significant role in the recovery processes. Nomenclature: Leafy spurge, Euphorbia esula L. EPHES.

Dormancy Induction and Release in Buds and Seeds

Dormancy is a complex trait in both buds and seeds, which is an important mechanism for survival during the life cycle of plants. Over the years, a vast wealth of information has been generated on how environmental and developmental signals impact dormancy in buds and seeds. At the molecular level, these studies have identified many factors including light (photoperiod), temperature (cold), hormones, circadian clock, and epigenetic regulation that control dormancy-associated genes regulating induction and release of dormancy in buds and seeds. Due to intrinsic differences between buds and seeds across a multitude of plant species, it should not be surprising that similar and dissimilar signals may control different phases of dormancy. This review focuses on the main similarities in gene expression and molecular mechanisms involved in bud and seed dormancy and release. A model perennial weed, leafy spurge, is presented as an example to compare commonalities in gene expression and molecular mechanisms during bud and seed dormancy and release. The study indicated that the physiological state of dormant imbibed, but growth competent seeds (21d C) are more analogous to paradormant buds than that of ecodormant buds. In addition, common molecular mechanisms associated with dormancy transitions in buds and seeds involved processes associated with abscisic acid- and auxin-signaling and transport, cell cycle, and AP2/ERF transcription factors or their up-stream regulators.