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The genetic improvement of trees is a slow process in comparison to that of annual crops. Tree breeding though is important, given the ever increasing demand for wood and wood products. It is the aim of this paper to show that the... more
The genetic improvement of trees is a slow process in comparison to that of annual crops. Tree breeding though is important, given the ever increasing demand for wood and wood products. It is the aim of this paper to show that the classical genetic improvement of trees by breeding and selection can be assisted and accelerated by the application of molecular biology tools that have been developed over the last decade. First, it is now possible to develop a set of diagnostic markers that predict the characteristics of new hybrids soon after they have germinated, thus long before the traits are displayed. Second, genetic engineering allows the modification or addition of a given trait that would be difficult or impossible to obtain by conventional breeding. Case studies in both fields, with respect to disease resistance and wood quality, are presented.
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Lignin is the main factor limiting the enzymatic conversion of lignocellulosic biomass into fermentable sugars. To reduce the recalcitrance engendered by the lignin polymer, the coumarin scopoletin was incorporated into the lignin polymer... more
Lignin is the main factor limiting the enzymatic conversion of lignocellulosic biomass into fermentable sugars. To reduce the recalcitrance engendered by the lignin polymer, the coumarin scopoletin was incorporated into the lignin polymer through the simultaneous expression ofFERULOYL-CoA 6′-HYDROXYLASE 1(F6′H1) andCOUMARIN SYNTHASE(COSY) in lignifying cells inArabidopsis. The transgenic lines overproduced scopoletin and incorporated it into the lignin polymer, without adversely affecting plant growth. About 3.3% of the lignin units in the transgenic lines were derived from scopoletin, thereby exceeding the levels of the traditionalp-hydroxyphenyl units. Saccharification efficiency of alkali-pretreated scopoletin-overproducing lines was 40% higher than for wild type.
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Arabidopsis (Arabidopsis thaliana) transfer DNA (T-DNA) insertion collections are popular resources for fundamental plant research. Cinnamoyl-CoA reductase 1 (CCR1) catalyzes an essential step in the biosynthesis of the cell wall polymer... more
Arabidopsis (Arabidopsis thaliana) transfer DNA (T-DNA) insertion collections are popular resources for fundamental plant research. Cinnamoyl-CoA reductase 1 (CCR1) catalyzes an essential step in the biosynthesis of the cell wall polymer lignin. Accordingly, the intronic T-DNA insertion mutant ccr1-6 has reduced lignin levels and shows a stunted growth phenotype. Here, we report restoration of the ccr1-6 mutant phenotype and CCR1 expression levels after a genetic cross with a UDP-glucosyltransferase 72e1 (ugt72e1),-e2,-e3 T-DNA mutant. We discovered that the phenotypic recovery was not dependent on the UGT72E family loss of function but due to an epigenetic phenomenon called trans T-DNA suppression. Via trans T-DNA suppression, the gene function of an intronic T-DNA mutant was restored after the introduction of an additional T-DNA sharing identical sequences, leading to heterochromatinization and splicing out of the T-DNA–containing intron. Consequently, the suppressed ccr1-6 allele...
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International audienceThe seasonal cycle of growth and dormancy is a distinct character of perennial plants and represents one of the most basic adaptations of trees to their environment. The recurrent transitions of meristems into and... more
International audienceThe seasonal cycle of growth and dormancy is a distinct character of perennial plants and represents one of the most basic adaptations of trees to their environment. The recurrent transitions of meristems into and out of dormancy are of primary significance to plant productivity and survival. These transitions are tightly linked to the yearly dates of bud flush and bud set that in turn delimit the growth season. ln poplar, perception of a short-day signal leads to apical bud set and dormancy induction. Because bud set is of prime importance in determining season length in a changing environment, we dissected this developmental program at the phenotypical, genetical and molecular levels. Taking advantage of the poplar genome sequence, we integrate candidate genes obtained in large-scale gene expression studies with information of QTLs determined in three poplar pedigrees. Expressional candidate genes were identified in the apex/bud during short-day-induced bud s...
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Lignin content and its molecular structure influence various wood characteristics. In this study, the anatomical and physicochemical properties of wood derived from a naturally occurring mulberry mutant deficient in cinnamyl alcohol... more
Lignin content and its molecular structure influence various wood characteristics. In this study, the anatomical and physicochemical properties of wood derived from a naturally occurring mulberry mutant deficient in cinnamyl alcohol dehydrogenase (CAD), a key enzyme in lignin biosynthesis, were analyzed using conventional staining assays on stem sections, length and width measurements of xylem fiber cells, wood pulping and saccharification assays, and sugar compositional analysis of extractive-free wood powder. The present data indicate that the mutation in the CAD gene leads to improved wood delignification efficiency, increased pulp yield under alkaline pulping conditions, and enhanced saccharification efficiency following alkaline pretreatment. This study opens up new avenues for the multipurpose use of the mulberry CAD-deficient mutant as a raw material for biorefinery processes, in addition to its traditional use as a favored feed for silkworms.
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ABSTRACTLignin is a complex polymer precisely deposited in the cell wall of specialised plant cells, where it provides essential cellular functions. Plants coordinate timing, location, abundance and composition of lignin deposition in... more
ABSTRACTLignin is a complex polymer precisely deposited in the cell wall of specialised plant cells, where it provides essential cellular functions. Plants coordinate timing, location, abundance and composition of lignin deposition in response to endogenous and exogenous cues. In roots, a fine band of lignin, the Casparian strip encircles endodermal cells. This forms an extracellular barrier to solutes and water and plays a critical role in maintaining nutrient homeostasis. A signalling pathway senses the integrity of this diffusion barrier and can induce over-lignification to compensate for barrier defects. Here, we report that activation of this endodermal sensing mechanism triggers a transcriptional reprogramming strongly inducing the phenylpropanoid pathway and immune signaling. This leads to deposition of compensatory lignin that is chemically distinct from Casparian strip lignin. We also report that a complete loss of endodermal lignification drastically impacts mineral nutrie...
Research Interests: Chemistry, Reprogramming, Biology, Cell Biology, Lignin, and 3 moreCell Wall, Endodermis, and Phenylpropanoid
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Background Cassava whitefly outbreaks were initially reported in East and Central Africa cassava (Manihot esculenta Crantz) growing regions in the 1990’s and have now spread to other geographical locations, becoming a global pest severely... more
Background Cassava whitefly outbreaks were initially reported in East and Central Africa cassava (Manihot esculenta Crantz) growing regions in the 1990’s and have now spread to other geographical locations, becoming a global pest severely affecting farmers and smallholder income. Whiteflies impact plant yield via feeding and vectoring cassava mosaic and brown streak viruses, making roots unsuitable for food or trading. Deployment of virus resistant varieties has had little impact on whitefly populations and therefore development of whitefly resistant varieties is also necessary as part of integrated pest management strategies. Suitable sources of whitefly resistance exist in germplasm collections that require further characterization to facilitate and assist breeding programs. Results In the present work, a hierarchical metabolomics approach has been employed to investigate the underlying biochemical mechanisms associated with whitefly resistance by comparing two naturally occurring...
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BackgroundGiven its tolerance to stress and its richness in particular secondary metabolites, the tobacco tree, Nicotiana glauca, has been considered a promising biorefinery feedstock that would not be competitive with food and fodder... more
BackgroundGiven its tolerance to stress and its richness in particular secondary metabolites, the tobacco tree, Nicotiana glauca, has been considered a promising biorefinery feedstock that would not be competitive with food and fodder crops.ResultsHere we present a 3.5 Gbp draft sequence and annotation of the genome of N. glauca spanning 731,465 scaffold sequences, with an N50 size of approximately 92 kbases. Furthermore, we supply a comprehensive transcriptome and metabolome analysis of leaf development comprising multiple techniques and platforms.The genome sequence is predicted to cover nearly 80% of the estimated total genome size of N. glauca. With 73,799 genes predicted and a BUSCO score of 94.9%, we have assembled the majority of gene-rich regions successfully. RNA-Seq data revealed stage-and/or tissue-specific expression of genes, and we determined a general trend of a decrease of tricarboxylic acid cycle metabolites and an increase of terpenoids as well as some of their cor...
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Apoplastic events such as monolignol oxidation and lignin polymerization are difficult to study in intact trees. To investigate the role of apoplastic H2O2 in gymnosperm phenolic metabolism, an extracellular lignin-forming cell culture of... more
Apoplastic events such as monolignol oxidation and lignin polymerization are difficult to study in intact trees. To investigate the role of apoplastic H2O2 in gymnosperm phenolic metabolism, an extracellular lignin-forming cell culture of Norway spruce (Picea abies) was used as a research model. Scavenging of apoplastic H2O2 by KI repressed lignin formation, in line with peroxidases activating monolignols for lignin polymerization. Time course analyses coupled to candidate substrate product pair network propagation revealed differential accumulation of low-molecular-weight phenolics, including (glycosylated) oligolignols, (glycosylated) flavonoids and proanthocyanidins, in lignin-forming and H2O2-scavenging cultures, and supported that monolignols are oxidatively coupled not only in the cell wall, but also in the cytoplasm where they are coupled to other monolignols and proanthocyanidins. Dilignol glycoconjugates with reduced structures were found in the culture medium, suggesting t...
Research Interests: Biochemistry, Chemistry, Principal Component Analysis, Oxidative Stress, Medicine, and 15 moreSignal Transduction, Biological Sciences, Antioxidants, Plant Physiology, Lignin, Cultures, Gene Regulatory Networks, Hydrogen Peroxide, Phenols, Picea, Peroxidases, Picea abies, Extracellular Space, Gene expression profiling, and Apoplast
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Research Interests: Biochemistry, Genetics, Mass Spectrometry, Biology, Oxidative Stress, and 15 moreMagnetic Resonance Spectroscopy, Medicine, Lignans, Oxidoreductases, Lignin, Phenotype, Amino Acids, Phenolic Compounds, Lignification, Cysteine, Cell Wall, Biochemistry and cell biology, Immunoblotting, Molecular Sequence Data, and Phenylpropanoid
... Daayf Professor Victor AP de Freitas Dr. Claire Dufour Professor Gilles Comte Dr. Ismail El-Hadrami Dr. Maria Teresa Escribano ... João Laranjinha,Center for Neurosciences and Cell Biology and Faculty of Pharmacy, University of... more
... Daayf Professor Victor AP de Freitas Dr. Claire Dufour Professor Gilles Comte Dr. Ismail El-Hadrami Dr. Maria Teresa Escribano ... João Laranjinha,Center for Neurosciences and Cell Biology and Faculty of Pharmacy, University of Coimbra, Health Sciences Campus, Azinhaga ...
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SummaryLignin is a polymeric constituent of the cell wall that needs to be removed during the paper making process. Bi‐specific caffeic acid/5‐hydroxyferulic acid O‐methyltransferase (COMT) catalyses the O‐methylation of caffeic acid and... more
SummaryLignin is a polymeric constituent of the cell wall that needs to be removed during the paper making process. Bi‐specific caffeic acid/5‐hydroxyferulic acid O‐methyltransferase (COMT) catalyses the O‐methylation of caffeic acid and 5‐hydroxyferulic acid to ferulic acid and sinapic acid, respectively. These compounds are intermediates in the biosynthesis of the lignin precursors. Therefore, COMTs are potential target enzymes for reducing the amount, or modifying the composition, of lignin in plants. Different antisense and sense constructs have been expressed of a gene encoding a COMT from poplar (Populus trichocarpa x P. deltoides) in a P. tremula x P. alba clone under the control of the cauliflower mosaic virus 35S promoter. From all analysed transformants, four lines transformed with an antisense construct had a reduced COMT activity. Two showed a 50% reduction of COMT activity, which altered only slightly the monomeric composition. In the two other transformants, the COMT a...
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Cell separation is thought to involve degradation of pectin by several hydrolytic enzymes, particularly polygalacturonase (PG). Here, we characterize an activation tagging line with reduced growth and male sterility caused by increased... more
Cell separation is thought to involve degradation of pectin by several hydrolytic enzymes, particularly polygalacturonase (PG). Here, we characterize an activation tagging line with reduced growth and male sterility caused by increased expression of a PG encoded by QUARTET2 (QRT2). QRT2 is essential for pollen grain separation and is part of a small family of three closely related endo-PGs in the Arabidopsis thaliana proteome, including ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE1 (ADPG1) and ADPG2. Functional assays and complementation experiments confirm that ADPG1, ADPG2, and QRT2 are PGs. Genetic analysis demonstrates that ADPG1 and ADPG2 are essential for silique dehiscence. In addition, ADPG2 and QRT2 contribute to floral organ abscission, while all three genes contribute to anther dehiscence. Expression analysis is consistent with the observed mutant phenotypes. INDEHISCENT (IND) encodes a putative basic helix-loop-helix required for silique dehiscence, and we demonstrate t...
Research Interests: Genetics, Plant Biology, Biology, Medicine, Multidisciplinary, and 15 moreCell separation, Arabidopsis thaliana, Mutation, Abscission, Complementation, Flowers, Arabidopsis, Enzyme, Male Sterility, Genetic Analysis, Plant cell, Expression analysis, Biochemistry and cell biology, Jasmonic Acid, and Oxylipins
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Research Interests: Genetics, Gene Flow, Population Genetics, Forest Ecology And Management, Biology, and 15 moreEcology, Czech Republic, Genetic Diversity, Biological Sciences, Environmental Sciences, Population, Genetic Structure, Microsatellite, Keystone species, Natural Regeneration, Genetic variation, Clonal propagation, Genetic distance, microsatellite loci, and Drainage basin
Research Interests: Engineering, Forestry, Biotechnology, Biology, Medicine, and 15 moreGene expression, Functional Genomics, Genetic Engineering, Biological Sciences, Bacillus thuringiensis, Expressed Sequence Tags, Domestication, Genome, Ecosystem, Linkage Disequilibrium, Conservation of Natural Resources, Loblolly Pine, Environment, alleles, and LEAPS
The potential of whole genome duplication to increase plant biomass yield is well-known. In Arabidopsis tetraploids, an increase in biomass yield was accompanied by a reduction in lignin content and, as a result, a higher saccharification... more
The potential of whole genome duplication to increase plant biomass yield is well-known. In Arabidopsis tetraploids, an increase in biomass yield was accompanied by a reduction in lignin content and, as a result, a higher saccharification efficiency was achieved compared with diploid controls. Here, we evaluated whether the results obtained in Arabidopsis could be translated into poplar and whether the enhanced saccharification yield upon alkaline pretreatment of hairpin-downregulated CINNAMYL ALCOHOL DEHYDROGENASE1 (hpCAD) transgenic poplar could be further improved upon a whole genome duplication. Using a colchicine treatment, wild-type (WT) Populus tremula x P. alba cv. INRA 717-1B4, a commonly used model clone in tree biotechnology research, and hpCAD tetraploids were generated and grown in the greenhouse. In parallel, WT tetraploid poplars were grown in the field. In contrast to Arabidopsis, a whole genome duplication of poplar had a negative impact on the biomass yield of both...
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Hydroxycinnamoyl shikimates were reported in 2005 to be intermediates in monolignol biosynthesis. 3-Hydroxylation of p-coumarate, originally thought to occur via coumarate 3-hydroxylase (C3H) from p-coumaric acid or its CoA thioester, was... more
Hydroxycinnamoyl shikimates were reported in 2005 to be intermediates in monolignol biosynthesis. 3-Hydroxylation of p-coumarate, originally thought to occur via coumarate 3-hydroxylase (C3H) from p-coumaric acid or its CoA thioester, was revealed to be via the action of coumaroyl shikimate 3′-hydroxylase (C3′H) utilizing p-coumaroyl shikimate as the substrate, itself derived from p-coumaroyl-CoA via hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyltransferase (HCT). The same HCT was conjectured to convert the product, caffeoyl shikimate, to caffeoyl-CoA to continue on the pathway starting with its 3-O-methylation. At least in some plants, however, a more recently discovered caffeoyl shikimate esterase (CSE) enzyme hydrolyzes caffeoyl shikimate to caffeic acid from which it must again produce its CoA thioester to continue on the monolignol biosynthetic pathway. HCT and CSE are therefore monolignol biosynthetic pathway enzymes that have provided new opportunities to misregulate lignif...
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Higher plant morphogenesis has received renewed interest over the past few years. The improvement of molecular genetic approaches to generate tagged developmental mutants, for instance by T-DNA insertion, facilitated the isolation and... more
Higher plant morphogenesis has received renewed interest over the past few years. The improvement of molecular genetic approaches to generate tagged developmental mutants, for instance by T-DNA insertion, facilitated the isolation and characterization of the altered genes. Here we present recent progress on flower and root morphogenesis in the small crucifer Arabidopsis thaliana. The current model of Arabidopsis flower development is presented. We report on FLOWER1 (Fl1), which is a T-DNA-tagged ap2 allele. Our observations indicate that this Fl1 mutant has, besides the homeotic Ap2 phenotype, an aberrant seed coat, suggesting that this gene has also a function late in flower development. Furthermore, we present a brief summary about root development and focus on the super root (Sur) mutant, which is an ethyl methanesulfonate-induced mutant that produces excess lateral roots. Root explants of the Sur mutant, that do not develop further than the 4-leaf stage, can be induced to produc...
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Lignin causes lignocellulosic biomass recalcitrance to enzymatic hydrolysis. Engineered low-lignin plants have reduced recalcitrance but often exhibit yield penalties, offsetting their gains in fermentable sugar yield. Here,... more
Lignin causes lignocellulosic biomass recalcitrance to enzymatic hydrolysis. Engineered low-lignin plants have reduced recalcitrance but often exhibit yield penalties, offsetting their gains in fermentable sugar yield. Here, CRISPR/Cas9-generated CCR2(−/*) line 12 poplars have one knockout CCR2 allele while the other contains a 3-bp deletion, resulting in a 114I115A-to-114T conversion in the corresponding protein. Despite having 10% less lignin, CCR2(−/*) line 12 grows normally. On a plant basis, the saccharification efficiency of CCR2(−/*) line 12 is increased by 25–41%, depending on the pretreatment. Analysis of monoallelic CCR2 knockout lines shows that the reduced lignin amount in CCR2(−/*) line 12 is due to the combination of a null and the specific haploinsufficient CCR2 allele. Analysis of another CCR2(−/*) line shows that depending on the specific CCR2 amino-acid change, lignin amount and growth can be affected to different extents. Our findings open up new possibilities for...
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Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these... more
Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 × P. nigra cv. Ghoy and P. deltoides cv. S9-2 × P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%...
Research Interests: Genetics, Biology, Molecular Genetics, Medicine, DNA, and 15 morePopulus, Microsatellite, Trees, Genome, RAPD MARKERS, Genetic linkage analysis, Eucalyptus urophylla, Linkage Group, Genetic Polymorphism, Quantitative Trait Loci, Statistical models, Populus Deltoides, Genetic Markers, Linkage Analysis, and Genetic Linkage Map
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Tricin [5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-4H-chromen-4-one] is a flavone that has been found to be incorporated in grass lignin polymers via 4′–O–β coupling. Herein, we investigated the tricin-lignin structure using nuclear... more
Tricin [5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-4H-chromen-4-one] is a flavone that has been found to be incorporated in grass lignin polymers via 4′–O–β coupling. Herein, we investigated the tricin-lignin structure using nuclear magnetic resonance (NMR) methods by comparing the 1H–13C heteronuclear correlation (HSQC) NMR spectra of the isolated lignin with a series of dimeric and trimeric tricin-4′–O–β-ether model compounds. Results showed that the tricin moiety significantly affects the chemical shift of the Cβ/Hβ of 4′–O–β unit, producing peaks at around δC/δH 82.5–83.5/4.15–4.45, that differ from the Cβ/Hβ correlations from normal 4–O–β units formed solely by monolignols, and that have to date been unassigned.
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One of the most striking features occurring in the root-knot nematode Meloidogyne incognita induced galls is the reorganization of the vascular tissues. During the interaction of the model tree species Populus and M. incognita, a... more
One of the most striking features occurring in the root-knot nematode Meloidogyne incognita induced galls is the reorganization of the vascular tissues. During the interaction of the model tree species Populus and M. incognita, a pronounced xylem proliferation was previously described in mature galls. To better characterise changes in expression of genes possibly involved in the induction and the formation of the de novo developed vascular tissues occurring in poplar galls, a comparative transcript profiling of 21-day-old galls versus uninfected root of poplar was performed. Genes coding for transcription factors associated with procambium maintenance and vascular differentiation were shown to be differentially regulated, together with genes partaking in phytohormones biosynthesis and signalling. Specific signatures of transcripts associated to primary cell wall biosynthesis and remodelling, as well as secondary cell wall formation (cellulose, xylan and lignin) were revealed in the ...
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Significance In nature, plants and microbes process substantial amounts of aromatic carbon for lignin biosynthesis and breakdown, respectively. These natural processes have important implications in the pursuit of lignin valorization,... more
Significance In nature, plants and microbes process substantial amounts of aromatic carbon for lignin biosynthesis and breakdown, respectively. These natural processes have important implications in the pursuit of lignin valorization, which is crucial for a vibrant, global bioeconomy. In both plant and microbial systems, an open question remains regarding how lignin-related aromatic compounds are transported across compartmental membranes, either by active membrane transporters or via passive membrane crossing. In this study, we predict that passive transport processes in plants and bacteria for uncharged aromatic compounds are likely sufficient for lignin biosynthesis and catabolism, thus implying that membrane translocation rates are controlled by compound delivery and utilization rates and membrane concentration gradients.