David Horvath - Academia.edu (original) (raw)
Papers by David Horvath
supplemental data for manuscript Genome wide association studies and transcriptome changes during... more 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 adventiti... 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...
Agronomy
Winter canola generally produces greater yields than spring canola. However, its range is limited... 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...
Agronomy, 2021
Winter canola generally produces greater yields than spring canola. However, its range is limited... 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...
Journal of Plant Biology
Spring-type canola produces significantly smaller and less vigorous roots than winter type at lat... 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.
International Journal of Molecular Sciences
Information concerning genes and signals regulating cold acclimation processes in plants is abund... 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...
Weed Science
Leafy spurge (Euphorbia esula L.) is an invasive perennial weed infesting range and recreational ... 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...
Weed Science
Earlier studies on the source of signals controlling correlative inhibition of root buds (undergr... 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...
Frontiers in Plant Science
Frontiers in plant science, 2017
Winter dormancy is an important biological feature for tea plant to survive cold winters, and it ... 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...
Plant molecular biology, 2017
Leafy spurge (Euphorbia esula L.) is an herbaceous perennial weed that maintains its perennial gr... 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...
Frontiers in plant science, 2015
To survive winter, many perennial plants become endodormant, a state of suspended growth maintain... 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...
supplemental data for manuscript Genome wide association studies and transcriptome changes during... more 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 adventiti... 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...
Agronomy
Winter canola generally produces greater yields than spring canola. However, its range is limited... 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...
Agronomy, 2021
Winter canola generally produces greater yields than spring canola. However, its range is limited... 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...
Journal of Plant Biology
Spring-type canola produces significantly smaller and less vigorous roots than winter type at lat... 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.
International Journal of Molecular Sciences
Information concerning genes and signals regulating cold acclimation processes in plants is abund... 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...
Weed Science
Leafy spurge (Euphorbia esula L.) is an invasive perennial weed infesting range and recreational ... 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...
Weed Science
Earlier studies on the source of signals controlling correlative inhibition of root buds (undergr... 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...
Frontiers in Plant Science
Frontiers in plant science, 2017
Winter dormancy is an important biological feature for tea plant to survive cold winters, and it ... 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...
Plant molecular biology, 2017
Leafy spurge (Euphorbia esula L.) is an herbaceous perennial weed that maintains its perennial gr... 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...
Frontiers in plant science, 2015
To survive winter, many perennial plants become endodormant, a state of suspended growth maintain... 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...