supplemental data for manuscript Genome wide association studies and transcriptome changes during acclimation
Leafy spurge (Euphorbia esula L.) is a noxious perennial weed that produces underground adventitious buds, which are crucial for generating new vegetative shoots following periods of freezing temperatures or exposure to various control... more
Leafy spurge (Euphorbia esula L.) is a noxious perennial weed that produces underground adventitious buds, which are crucial for generating new vegetative shoots following periods of freezing temperatures or exposure to various control measures. It is also capable of flow-ering and producing seeds, but requires vernalization in some cases. DORMANCY ASSO-CIATED MADS-BOX (DAM) genes have been proposed to play a direct role in the transition to winter-induced dormancy and maintenance through regulation of the FLOWERING LOCUS T (FT) gene, which also is likely involved in the vernalization process. To explore the regulation of FT and DAM during dormancy transitions in leafy spurge, the transcript ac-cumulation of two previously cloned DAM splice variants and two different previously cloned FT genes was characterized. Under long-photoperiods (16 h light), both DAM and FT tran-scripts accumulate in a diurnal manner. Tissue specific expression patterns indicated the tissues with high DAM ex...
Winter canola generally produces greater yields than spring canola. However, its range is limited due to its inability to withstand the harsh winter conditions that occur in many northern regions of the U.S.A. To identify loci associated... more
Winter canola generally produces greater yields than spring canola. However, its range is limited due to its inability to withstand the harsh winter conditions that occur in many northern regions of the U.S.A. To identify loci associated with freezing tolerance in canola, we conducted a genome-wide association study (GWAS) using a genotyped diversity panel containing 399 accessions consisting primarily of winter canola. One-month-old greenhouse grown plants were subsequently cold-acclimated for two months in an environmental growth chamber prior to phenotyping for freezing survival using a visual damage scale and chlorophyll fluorescence (Fv/Fo). There was reasonable correlation observed between visual damage and chlorophyll fluorescence ratings among the top associated loci; the results indicated that some loci contributed to both freezing damage/tolerance and photosynthetic efficiency. The resulting numerical values for phenotypes were used for association analyses with the identi...
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Winter canola generally produces greater yields than spring canola. However, its range is limited due to its inability to withstand the harsh winter conditions that occur in many northern regions of the U.S.A. To identify loci associated... more
Winter canola generally produces greater yields than spring canola. However, its range is limited due to its inability to withstand the harsh winter conditions that occur in many northern regions of the U.S.A. To identify loci associated with freezing tolerance in canola, we conducted a genome-wide association study (GWAS) using a genotyped diversity panel containing 399 accessions consisting primarily of winter canola. One-month-old greenhouse grown plants were subsequently cold-acclimated for two months in an environmental growth chamber prior to phenotyping for freezing survival using a visual damage scale and chlorophyll fluorescence (Fv/Fo). There was reasonable correlation observed between visual damage and chlorophyll fluorescence ratings among the top associated loci; the results indicated that some loci contributed to both freezing damage/tolerance and photosynthetic efficiency. The resulting numerical values for phenotypes were used for association analyses with the identi...
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Spring-type canola produces significantly smaller and less vigorous roots than winter type at later growth stages. To identify the gene-regulatory networks and cross talks among phytohormones that may be responsible for the difference... more
Spring-type canola produces significantly smaller and less vigorous roots than winter type at later growth stages. To identify the gene-regulatory networks and cross talks among phytohormones that may be responsible for the difference between the root system of the two growth types, we analyzed transcriptomes from the root samples collected at two time points, 30 and 60 days. Out of 169,646 transcripts that were analyzed, 582 and 555 transcripts were found to be significantly differentially expressed between spring and winter types at 30 and 60 days, respectively. Several auxin-responsive genes were significantly differentially expressed between spring and winter types at both time points, but no distinct pattern of differential regulation was observed in either of the growth types. Type-A and type-B ARABIDOPSIS RESPONSE REGULATOR (ARR) genes, and gene sets involved in cytokinin signaling pathway, were upregulated in the spring types at 60 days. This would be consistent with higher cytokinin activity, which is known to inhibit root growth, in spring type root system at the later growth stage. In addition, several gibberellin-responsive and gibberellin-signaling gene sets were also upregulated only in spring types at 60 days. We observed an elongated root system with fewer root branches in spring type compared to winter type at 60 days in this study, which is consistent with a role of gibberellin in root growth and development. Extensive gene expression data generated in this research will further assist in understanding the natural variation of root system in canola growth habits.
Research Interests: Plant Biology and Biology
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Information concerning genes and signals regulating cold acclimation processes in plants is abundant; however, less is known about genes and signals regulating the deacclimation process. A population of primarily winter B. napus varieties... more
Information concerning genes and signals regulating cold acclimation processes in plants is abundant; however, less is known about genes and signals regulating the deacclimation process. A population of primarily winter B. napus varieties was used to conduct a genome-wide association study and to compare the transcriptomes from two winter B. napus varieties showing time-dependent differences in response to cold acclimation and deacclimation treatments. These studies helped to identify loci, candidate genes, and signaling processes impacting deacclimation in B. napus. GWAS identified polymorphisms at five different loci associated with freezing tolerance following deacclimation. Local linkage decay rates near these polymorphisms identified 38 possible candidate genes. Several of these genes have been reported as differentially regulated by cold stress in arabidopsis (Arabidopsis thaliana), including a calcium-binding EF-hand family protein (encoded by BnaCnng10250D) that was also dif...
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Supplementary material 3 from: Augustinus BA, Lommen STE, Fogliatto S, Vidotto F, Smith T, Horvath D, Bonini M, Gentili RF, Citterio S, Müller-Schärer H, Schaffner U (2020) In-season leaf damage by a biocontrol agent explains reproductive output of an invasive plant species. NeoBiota 55: 117-146....more
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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... more
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 589,23...
Research Interests: Weed Science and Biology
Earlier studies on the source of signals controlling correlative inhibition of root buds (underground adventitious buds located on the lateral roots) in Euphorbia esula indicated that either growing meristems (apical or axillary buds) or... more
Earlier studies on the source of signals controlling correlative inhibition of root buds (underground adventitious buds located on the lateral roots) in Euphorbia esula indicated that either growing meristems (apical or axillary buds) or fully expanded leaves could prevent root buds from breaking quiescence. An investigation of the production and transport requirements of the leaf-derived signal is described. As few as three leaves remaining on budless stems greatly reduced the growth of (but not the number of growing) root buds. Also, light and CO2 fixation were necessary for the leaf effects on root bud growth, but not necessary for correlative inhibition imposed by growing axillary buds. Treatment of plants with Ametryn induced root bud growth on budless plants but not on plants with intact axillary buds. The polar auxin transport inhibitor N-1-naphthylphthalamic acid prevented transmission or the signal from growing axillary buds, but it had only a minor effect on the transmissi...
Research Interests: Photosynthesis, Weed Science, Biology, Growth, Light, and 4 moreSignals, Translocation, Dormancy, and Gibberellins
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Winter dormancy is an important biological feature for tea plant to survive cold winters, and it also affects the economic output of tea plant, one of the few woody plants in the world whose leaves are harvested and one of the few... more
Winter dormancy is an important biological feature for tea plant to survive cold winters, and it also affects the economic output of tea plant, one of the few woody plants in the world whose leaves are harvested and one of the few non-conifer evergreen species with characterized dormancies. To discover the bud dormancy regulation mechanism of tea plant in winter, we analyzed the global gene expression profiles of axillary buds at the paradormancy, endodormancy, ecodormancy, and bud flush stages by RNA-Seq analysis. In total, 16,125 differentially expressed genes (DEGs) were identified among the different measured conditions. Gene set enrichment analysis was performed on the DEGs identified from each dormancy transition. Enriched gene ontology terms, gene sets and transcription factors were mainly associated with epigenetic mechanisms, phytohormone signaling pathways, and callose-related cellular communication regulation. Furthermore, differentially expressed transcription factors as...
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Leafy spurge (Euphorbia esula L.) is an herbaceous perennial weed that maintains its perennial growth habit through generation of underground adventitious buds (UABs) on the crown and lateral roots. These UABs undergo seasonal phases of... more
Leafy spurge (Euphorbia esula L.) is an herbaceous perennial weed that maintains its perennial growth habit through generation of underground adventitious buds (UABs) on the crown and lateral roots. These UABs undergo seasonal phases of dormancy under natural conditions, namely para-, endo-, and ecodormancy in summer, fall, and winter, respectively. These dormancy phases can also be induced in growth chambers by manipulating photoperiod and temperature. In this study, UABs induced into the three phases of dormancy under controlled conditions were used to compare changes in phytohormone and transcriptome profiles. Results indicated that relatively high levels of ABA, the ABA metabolite PA, and IAA were found in paradormant buds. When UABs transitioned from para- to endodormancy, ABA and PA levels decreased, whereas IAA levels were maintained. Additionally, transcript profiles associated with regulation of soluble sugars and ethylene activities were also increased during para- to endo...
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To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant... more
To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found that 1,362 (3.1%) were differentially expressed among the three dormancy states, and 429 (1.0%) were differentially expressed during only one of the two dormancy transitions (FDR p-value < 0.05). Of all differentially expressed genes, 69% were down-regulated from paradormancy to endodormancy, which was expected given the lower metabolic activity associated with endodormancy. Dormancy transitions were accompanied by changes in genes associated with DNA methylation (via RNA-directed DNA methylation) and histone modifications (via Polycomb Repressive Complex 2), confirming and extending knowledge of chromatin...
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Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy... more
Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which...
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Insect diapause (dormancy) synchronizes an insect's life cycle to seasonal changes in the abiotic and biotic resources required for development and reproduction. Transcription analysis of diapause to post‐diapause quiescent transition... more
Insect diapause (dormancy) synchronizes an insect's life cycle to seasonal changes in the abiotic and biotic resources required for development and reproduction. Transcription analysis of diapause to post‐diapause quiescent transition in the alfalfa leafcutting bee Megachile rotundata Fabricius identifies 643 post‐diapause up‐regulated gene transcripts and 242 post‐diapause down‐regulated transcripts. The log2 fold change in gene expression levels ranges from −5 to 7. Transcripts from several pivotal diapause‐related processes, including chromatin remodelling, cellular signalling pathways, microRNA processing, anaerobic glycolysis, cell cycle arrest and neuroendocrine control, are identified as being differentially expressed during the diapause to post‐diapause transition. In conjunction with studies from other insect species, the data indicate that there are several common mechanisms of diapause control and maintenance.
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Recent studies have brought into question the mechanisms through which weeds cause reduced crop yield. In modern agricultural systems, it is rare that nutrients, light, or even water are limiting- yet weed presence still causes... more
Recent studies have brought into question the mechanisms through which weeds cause reduced crop yield. In modern agricultural systems, it is rare that nutrients, light, or even water are limiting- yet weed presence still causes significant yield loss. Thus, understanding how weeds are sensed by crop plants and the physiological and developmental processes that are negatively affected by weed presence could provide new insights needed to develop novel weed resistance in crops. In order to gain an enhanced understanding of crop- weed interactions, we have undertaken a transcriptomics approach to identify weed-responsive genes in soybean and corn under field conditions. Over multiple years, with multiple reps per treatment, young leaf material was collected in weed- free or weed infested plots from soybean at the V3 stage of growth, and corn at the V4 stage of growth. RNA was extracted from the leaf and subjected to RNAseq or microarray/qRT-PCR analysis. Numerous weed-responsive genes ...
Switchgrass flag leaves can be expected to be a source of carbon to the plant, and its senescence is likely to impact the remobilization of nutrients from the shoots to the rhizomes. However, many genes have not been assigned a function... more
Switchgrass flag leaves can be expected to be a source of carbon to the plant, and its senescence is likely to impact the remobilization of nutrients from the shoots to the rhizomes. However, many genes have not been assigned a function in specific stages of leaf development. Here, we characterized gene expression in flag leaves over their development. By merging changes in leaf chlorophyll and the expression of genes for chlorophyll biosynthesis and degradation, a four-phase molecular roadmap for switchgrass flag leaf ontogeny was developed. Genes associated with early leaf development were up-regulated in phase 1. Phase 2 leaves had increased expression of genes for chlorophyll biosynthesis and those needed for full leaf function. Phase 3 coincided with the most active phase for leaf C and N assimilation. Phase 4 was associated with the onset of senescence, as observed by declining leaf chlorophyll content, a significant up-regulation in transcripts coding for enzymes involved wit...
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Leafy spurge (Euphorbia esula L.) is a herbaceous perennial weed and dormancy in both buds and seeds is an important survival mechanism. Bud dormancy in leafy spurge exhibits three well-defined phases of para-, endo- and ecodormancy;... more
Leafy spurge (Euphorbia esula L.) is a herbaceous perennial weed and dormancy in both buds and seeds is an important survival mechanism. Bud dormancy in leafy spurge exhibits three well-defined phases of para-, endo- and ecodormancy; however, seed dormancy for leafy spurge is classified as physiological dormancy that requires after-ripening and alternating temperature for maximal germination. Overlaps in transcriptome profiles between different phases of bud and seed dormancy have not been determined. Thus, we compared various phases of dormancy between seeds and buds to identify common genes and molecular processes, which should provide new insights about common regulators of dormancy. Cluster analysis of expression profiles for 201 selected genes indicated bud and seed samples clustered separately. Direct comparisons between buds and seeds are additionally complicated since seeds incubated at a constant temperature of 20°C for 21 days (21d C) could be considered paradormant (Para)...
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Vegetative shoot growth from underground adventitious buds of leafy spurge is critical for survival of this invasive perennial weed after episodes of severe abiotic stress. To determine the impact that dehydration-stress has on molecular... more
Vegetative shoot growth from underground adventitious buds of leafy spurge is critical for survival of this invasive perennial weed after episodes of severe abiotic stress. To determine the impact that dehydration-stress has on molecular mechanisms associated with vegetative reproduction of leafy spurge, greenhouse plants were exposed to mild- (3-day), intermediate- (7-day), severe- (14-day) and extended- (21-day) dehydration treatments. Aerial tissues of treated plants were then decapitated and soil was rehydrated to determine the growth potential of underground adventitious buds. Compared to well-watered plants, mild-dehydration accelerated new vegetative shoot growth, whereas intermediate- through extended-dehydration treatments both delayed and reduced shoot growth. Results of vegetative regrowth further confirmed that 14 days of dehydration induced a full-state of endodormancy in crown buds, which was correlated with a significant (P < 0.05) change in abundance of 2,124 tran...
Research Interests: Genetics, Plant Biology, Biology, Plant Molecular Biology, Medicine, and 10 morePlant Growth Regulators, Dehydration, Time Factors, Euphorbia, PLANT PROTEINS, Biochemistry and cell biology, Gene expression profiling, Plant Leaves, reverse transcriptase polymerase chain reaction, and Stress Physiological
Weeds reduce yield in soybeans (Glycine max) through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. RNASeq data were collected... more
Weeds reduce yield in soybeans (Glycine max) through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. RNASeq data were collected from six biological samples of soybeans growing with or without weeds. Weed species and the methods to maintain weed-free controls varied between years to mitigate treatment effects, and to allow detection of general soybean weed responses. Soybean plants were not visibly nutrient- or water-stressed. We identified 55 consistently downregulated genes in weedy plots. Many of the downregulated genes were heat shock genes. Fourteen genes were consistently upregulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the upregulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. The relationship of thi...
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ABSTRACT
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Page 1. Chapter 4 Bud Dormancy and Growth D. Horvath 4.1 Introduction Buds are the primary shoot-producing meristematic organs for dicotyledonous plants, and thus play the key role in growth, reproduction, and architecture. ...
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Research Interests: Genomics and Weed Science
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... 5.1). The early preformed leaves may provide the florigenic signal required for the axillary buds of the late-formed leaves to differentiate into floral organs (Yuceer et al. 2003). ... 2006; Kobayashi et al. 1999; Mohamed 2006).... more
... 5.1). The early preformed leaves may provide the florigenic signal required for the axillary buds of the late-formed leaves to differentiate into floral organs (Yuceer et al. 2003). ... 2006; Kobayashi et al. 1999; Mohamed 2006). Interestingly, whereas wild-type Populus spp. ...
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Reliable reference selection for the accurate quantification of gene expression under various experimental conditions is a crucial step in qRT-PCR normalization. To date, only a few housekeeping genes have been identified and used as... more
Reliable reference selection for the accurate quantification of gene expression under various experimental conditions is a crucial step in qRT-PCR normalization. To date, only a few housekeeping genes have been identified and used as reference genes in tea plant. The validity of those reference genes are not clear since their expression stabilities have not been rigorously examined. To identify more appropriate reference genes for qRT-PCR studies on tea plant, we examined the expression stability of 11 candidate reference genes from three different sources: the orthologs of Arabidopsis traditional reference genes and stably expressed genes identified from whole-genome GeneChip studies, together with three housekeeping gene commonly used in tea plant research. We evaluated the transcript levels of these genes in 94 experimental samples. The expression stabilities of these 11 genes were ranked using four different computation programs including geNorm, Normfinder, BestKeeper, and the ...
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Weed interference with crop growth is often attributed to water, nutrient, or light competition; however, specific physiological responses to these stresses are not well described. This study's objective was to compare growth, yield,... more
Weed interference with crop growth is often attributed to water, nutrient, or light competition; however, specific physiological responses to these stresses are not well described. This study's objective was to compare growth, yield, and gene expression responses of corn to nitrogen (N), low light (40% shade), and weed stresses. Corn vegetative parameters from V2 to V12 stages, yield parameters, and gene expression using transcriptome (2008) and quantitative polymerase chain reaction (qPCR) (2008/09) analyses at V8 were compared among the stresses and with nonstressed corn. N stress did not affect vegetative parameters, although grain yield was reduced by 40% compared with nonstressed plants. Shade, present until V2, reduced biomass and leaf area > 50% at V2, and recovering plants remained smaller than nonstressed plants at V12. However, grain yields of shade-stressed and nonstressed plants were similar, unless shade remained until V8. Weed stress reduced corn growth and yiel...
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Microarray analysis was used to identify changes in gene expression in velvetleaf that result from competition with corn. The plants were grown in field plots under adequate N (addition of 220 kg N ha−1) to minimize stress and sampled at... more
Microarray analysis was used to identify changes in gene expression in velvetleaf that result from competition with corn. The plants were grown in field plots under adequate N (addition of 220 kg N ha−1) to minimize stress and sampled at the V6 growth stage of corn (late June). Leaf area, dry weight, and N and P concentration were similar in velvetleaf plants grown alone or with corn. Competition, however, did influence velvetleaf gene expression. Genes involved in carbon utilization, photosynthesis, red light signaling, and cell division were preferentially expressed when velvetleaf was grown in competition with corn. A less clear picture of the physiological impact of growth in monoculture was provided by the data. However, several genes involved in secondary metabolism and a gene preferentially expressed in response to phosphate availability were induced. No differences were observed in genes responsive to water stress or sequestering/transporting micronutrients.
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... tslotta@comcast.net Jennifer M. Rothhouse North Dakota State University, Fargo, ND 58105 David P. Horvath Michael E. Foley US Department of Agriculture-Agricultural Research Service, Fargo, ND 58105-5674 Canada thistle ...
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Microarray analysis was used to follow changes in gene expression coinciding with seasonal changes in the dormancy status of crown buds of field-grown leafy spurge. Known cold-regulated genes were induced, and numerous gibberellic... more
Microarray analysis was used to follow changes in gene expression coinciding with seasonal changes in the dormancy status of crown buds of field-grown leafy spurge. Known cold-regulated genes were induced, and numerous gibberellic acid–responsive genes were down-regulated during the transition from paradormancy to endodormancy. Genes involved in photomorphogenesis were induced during endodormancy. Also, ethylene signaling responses were observed during ecodormancy rather than endodormancy. These results provide additional insights into the signals regulating expression of several genes previously associated with transition from paradormancy to growth in root buds.