Works (132)

Updated: April 3rd, 2024 19:09

2023 article

Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'

Chen, S., Yu, Y., Wang, X., Wang, S., Zhang, T., Zhou, Y., … Chen, S. (2023, February 27). MOLECULAR ECOLOGY RESOURCES.

author keywords: allele; allopolyploid; genome; Populus alba 'Berolinensis'; salinity stress; triploid
MeSH headings : Triploidy; Populus / genetics; Plant Breeding; Diploidy; Chromosomes
TL;DR: This study focused on the allelic genomic interactions in P. alba ‘Berolinensis’ and generated a high‐quality chromosome‐level genome assembly consisting of 19 allelic chromosomes, and found that some stress‐related genes such as RD22 and LEA7 exhibited sequence differences between different haploid genomes. (via Semantic Scholar)
Source: Web Of Science
Added: March 27, 2023

2023 journal article

Multiplex CRISPR editing of wood for sustainable fiber production

SCIENCE, 381(6654), 216-+.

By: D. Sulis n, X. Jiang n, C. Yang n, B. Marques n, M. Matthews n, Z. Miller n, K. Lan n, C. Cofre-Vega n ...

TL;DR: This work demonstrates that genome editing can be harnessed for breeding more efficient trees, which will provide timely opportunities for sustainable forestry and a more efficient bioeconomy. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 9, 2023

2023 journal article

Overexpression of a gibberellin 20-oxidase gene in poplar xylem led to an increase in the size of nanocellulose fibrils and improved paper properties

CARBOHYDRATE POLYMERS, 314.

By: X. Peng*, B. Tong*, J. Lee*, K. Wang*, X. Yu*, X. Huang*, J. Wen*, M. Makarem* ...

author keywords: Nanocellulose microfibril; Poplar; Gibberellin; Pulp
MeSH headings : Gibberellins; Xylem / genetics; Xylem / metabolism; Mixed Function Oxygenases / metabolism; Wood / metabolism; Cellulose / chemistry; Arabidopsis / genetics; Arabidopsis / metabolism; Populus / genetics; Populus / metabolism
Source: Web Of Science
Added: May 30, 2023

2022 journal article

Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change

FRONTIERS IN PLANT SCIENCE, 13.

By: X. Li*, K. Cai*, Z. Han*, S. Zhang*, A. Sun*, Y. Xie, R. Han*, R. Guo* ...

author keywords: Acer pseudosieboldianum; PacBio SMRT; HiFi; genome assembly; Hi-C; TCPs
TL;DR: A gene-to-metabolite correlation network is constructed and key genes and metabolites that might be involved in anthocyanin biosynthesis pathways during leaf color change and leaf morphology regulation of A. pseudosieboldianum are identified. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: April 18, 2022

2022 journal article

Genome-wide identification of the AlkB homologs gene family, PagALKBH9B and PagALKBH10B regulated salt stress response in Populus

FRONTIERS IN PLANT SCIENCE, 13.

By: Y. Zhao*, Q. Guo*, S. Cao*, Y. Tian*, K. Han*, Y. Sun*, J. Li*, Q. Yang* ...

author keywords: AlkB homologs; poplar 84K; m(6)A RNA methylation; demethylase; salt
TL;DR: This research revealed comprehensive information about the PagALKBH gene family and their roles in growth and development and responsing to salt stress of poplar. (via Semantic Scholar)
Source: Web Of Science
Added: October 31, 2022

2022 journal article

Morphological and Comparative Transcriptome Analysis of Three Species of Five-Needle Pines: Insights Into Phenotypic Evolution and Phylogeny

FRONTIERS IN PLANT SCIENCE, 13.

By: X. Li*, K. Cai*, Q. Zhao*, H. Li*, X. Wang*, M. Tigabu*, R. Sederoff n, W. Ma*, X. Zhao*

author keywords: five-needle pines; Pinus koraiensis; Pinus sibirica; Pinus pumila; transcriptome sequencing; SSRs; Pinus phylogeny
Source: Web Of Science
Added: March 7, 2022

2022 journal article

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

GIGASCIENCE, 11.

By: X. Li*, K. Cai*, Q. Zhang*, X. Pei*, S. Chen*, L. Jiang*, Z. Han*, M. Zhao* ...

author keywords: Juglans mandshurica; PacBio SMART; Hi-C; HiFi; genome assembly; comparative genomics; juglone; lipid
MeSH headings : Chromosomes; Genome; Juglans / genetics; Lipids; Naphthoquinones
TL;DR: Combining the high-quality genome, transcriptome, and metabolomics data, a gene-to-metabolite network was constructed and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. (via Semantic Scholar)
Source: Web Of Science
Added: September 19, 2022

2022 article

The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion

Wang, H., Lu, Y., Zhang, T., Liu, Z., Cao, L., Chang, Q., … Zheng, Z. (2022, December 10). PLANT PHYSIOLOGY, Vol. 12.

By: H. Wang*, Y. Lu*, T. Zhang*, Z. Liu*, L. Cao*, Q. Chang*, Y. Liu*, X. Lu* ...

MeSH headings : Phenotype; Sapindaceae / genetics; Magnoliopsida / genetics; DNA Transposable Elements / genetics; Flowers / genetics; Gene Expression Regulation, Plant
TL;DR: This work found a candidate C-class gene, AGAMOUS1 (XsAG1), through BSA sequencing and genetics analysis with a LONG INTERSPERSED NUCLEAR ELEMENTS 1 (LINE1) transposable element fragment inserted into its second intron that caused a loss-of-C-function and therefore the double-flower phenotype in yellowhorn. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: February 20, 2023

2022 article

The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence

Huang, X., Wang, W., Gong, T., Wickell, D., Kuo, L.-Y., Zhang, X., … Li, Q. (2022, May 9). NATURE PLANTS.

MeSH headings : Animals; Atelinae / genetics; Ferns / genetics; Genome, Plant; Phylogeny; Spiders / genetics
TL;DR: The genome of the flying spider-monkey tree fern and investigations on stem formation and secondary metabolite biosynthesis promote the understanding of fern evolution and arborescence, facilitating the protection and utilization of this endangered species. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: May 23, 2022

2022 article

Ubiquitinated DA1 negatively regulates vascular cambium activity through modulating the stability of WOX4 in Populus

Tang, X., Wang, C., Chai, G., Wang, D., Xu, H., Liu, Y., … Zhou, G. (2022, June 15). PLANT CELL.

By: X. Tang*, C. Wang*, G. Chai*, D. Wang*, H. Xu*, Y. Liu*, G. He*, S. Liu* ...

MeSH headings : Cambium; Gene Regulatory Networks; Populus; Transcription Factors; Ubiquitins; Wood; Xylem
TL;DR: A cambial regulatory protein complex, PagDA1-PagWOX4, is identified as a potential target for wood biomass improvement by identifying the ubiquitin receptor Pagda1 in hybrid poplar as a negative regulator of wood formation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: July 5, 2022

2021 journal article

A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 168–182.

By: M. Matthews*, J. Wang n, R. Sederoff n, V. Chiang n & C. Williams n

author keywords: Lignin biosynthesis; Multiscale modeling; Cross-regulatory influences; Random forests
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 20, 2021

2021 review

An Overview of the Practices and Management Methods for Enhancing Seed Production in Conifer Plantations for Commercial Use

[Review of ]. HORTICULTURAE, 7(8).

author keywords: conifers; flowering; seed production; pollination; phytohormones; tree management; nutrient fertilization
TL;DR: The review revealed that flowering and seed yields in conifers are affected by a variety of factors, such as pollen, temperature, light, water availability, nutrients, etc., and a number of management techniques, including topping off, pruning, fertilization, hormone treatment, supplementary pollination, etc. has been developed for improving cone yields. (via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: September 7, 2021

2021 journal article

BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAl5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar

FRONTIERS IN PLANT SCIENCE, 12.

By: Q. Wang*, X. Dai*, H. Pang*, Y. Cheng*, X. Huang*, H. Li*, X. Yan*, F. Lu* ...

author keywords: lignin; BEL1-like homeodomain protein; transcription factor; yeast one hybrid
TL;DR: It is proposed that BLH6a is a negative regulator of CAld5H2, which acts through combinatorial regulation of multiple TFs for sinapyl alcohol (S monolignol) biosynthesis in poplar. (via Semantic Scholar)
Source: Web Of Science
Added: July 19, 2021

2021 article

BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAld5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar (vol 12,& nbsp;695223, 2021)

Wang, Q., Dai, X., Pang, H., Cheng, Y., Huang, X., Li, H., … Li, Q. (2021, September 9). BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAld5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar (vol 12,& nbsp;695223, 2021). FRONTIERS IN PLANT SCIENCE, Vol. 12.

By: Q. Wang*, X. Dai*, H. Pang*, Y. Cheng*, X. Huang*, H. Li*, X. Yan*, F. Lu* ...

author keywords: lignin; BEL1-like homeodomain protein; transcription factor; yeast one hybrid
TL;DR: This research presents a novel probabilistic procedure that allows for direct measurement of the response of the immune system to earthquake-triggered landsliding. (via Semantic Scholar)
Source: Web Of Science
Added: November 29, 2021

2021 journal article

Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa

FRONTIERS IN PLANT SCIENCE, 12.

By: C. Lin n, Y. Sun*, J. Song n, H. Chen n, R. Shi n, C. Yang n, J. Liu n, S. Tunlaya-Anukit n ...

author keywords: protein interaction; monolignol biosynthesis; wood formation; Populus trichocarpa; BiFC; metabolic flux
TL;DR: It is proposed that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: November 8, 2021

2021 article

Epigenetic modification associated with climate regulates betulin biosynthesis in birch

Wang, J., Chen, B., Ali, S., Zhang, T., Wang, Y., Zhang, H., … Zhang, Q. (2021, December 4). JOURNAL OF FORESTRY RESEARCH, Vol. 12.

By: J. Wang*, B. Chen*, S. Ali*, T. Zhang*, Y. Wang*, H. Zhang*, L. Wang*, Y. Zhang* ...

author keywords: Epigenetics; DNA methylation; Betulin; bHLH9 transcription factor; Hormesis; Climate change; Secondary metabolite
TL;DR: The role of environmental signals to induce epigenetic changes that result in betulin production is highlighted, possibly helping to develop resilient plants to combat ongoing climate change and enhance secondary metabolite production. (via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: December 13, 2021

2021 review

MYB-Mediated Regulation of Anthocyanin Biosynthesis

[Review of ]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 22(6).

author keywords: MYB; transcription factor; anthocyanin; positive regulation; negative regulation; environment; MBW complexes
MeSH headings : Anthocyanins / biosynthesis; Gene Expression Regulation, Plant; Gene Regulatory Networks; Phylogeny; Plant Proteins / chemistry; Plant Proteins / metabolism; Transcription Factors / chemistry; Transcription Factors / metabolism
TL;DR: Some prospects for MYB-TF to modulate the comprehensive regulation of anthocyanins are put forward to provide a more relevant basis for further research in this field, and to guide the directed genetic modification of anthcyanins for the improvement of crops for food quality, nutrition and human health. (via Semantic Scholar)
Source: Web Of Science
Added: May 24, 2021

2021 journal article

Molecular and Metabolic Insights into Anthocyanin Biosynthesis for Leaf Color Change in Chokecherry (Padus virginiana)

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 22(19).

By: X. Li*, Y. Li*, M. Zhao*, Y. Hu*, F. Meng*, X. Song*, M. Tigabu*, V. Chiang n ...

author keywords: Padus virginiana; leaf color; anthocyanin biosynthesis; transcriptomics; metabolomic
MeSH headings : Anthocyanins / biosynthesis; Biosynthetic Pathways; Chlorophyll / biosynthesis; Color; Computational Biology / methods; Gene Expression Profiling; Gene Expression Regulation, Plant; Metabolome; Metabolomics / methods; Pigmentation / genetics; Plant Leaves / genetics; Plant Leaves / metabolism; Prunus / physiology; Transcriptome
TL;DR: In PRL, the expression of the genes encoding for UGFT and BZ1 enzymes was substantially higher than in leaves of other colors and may be related with the purple-red color change, which may facilitate genetic modification or selection for further improvement in ornamental qualities of P. virginiana. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: October 26, 2021

2021 journal article

Qu-2, a robust poplar suspension cell line for molecular biology

JOURNAL OF FORESTRY RESEARCH, 32(2), 733–740.

By: C. Liu*, K. Li*, M. Wang*, E. Fan*, C. Yang*, J. Wang*, P. Fu*, X. Ge* ...

Contributors: C. Liu*, K. Li*, M. Wang*, E. Fan*, C. Yang*, J. Wang*, P. Fu*, X. Ge* ...

author keywords: Qu-2 cell line; Suspension cell; Poplar; Protoplast isolation; Transient transformation
TL;DR: A hormone autotrophic poplar suspension cell line from a hybrid of Populus alba × P. berolinensis ‘Yinzhong’, named Qu-2, which has the great potential to be an excellent model cell line in tree molecular biological research, ranging from physiology to gene function. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: January 4, 2021

2021 article

Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus

Li, H., Dai, X., Huang, X., Xu, M., Wang, Q., Yan, X., … Li, Q. (2021, October 4). JOURNAL OF INTEGRATIVE PLANT BIOLOGY.

By: H. Li*, X. Dai*, X. Huang*, M. Xu*, Q. Wang*, X. Yan*, R. Sederoff n, Q. Li*

author keywords: differentiating trajectory; differentiating xylem; marker genes; Populus alba x Populus glandulosa; single-cell RNA-seq; wood formation
MeSH headings : Cell Differentiation; Cell Wall / metabolism; Gene Expression Profiling; Genome, Plant; Populus / cytology; Populus / genetics; Populus / metabolism; Sequence Analysis, RNA; Single-Cell Analysis; Xylem / cytology
TL;DR: This study generates a high resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation. (via Semantic Scholar)
Source: Web Of Science
Added: October 12, 2021

2020 review

Microbial Interactions Within Multiple-Strain Biological Control Agents Impact Soil-Borne Plant Disease

[Review of ]. FRONTIERS IN MICROBIOLOGY, 11.

By: B. Niu*, W. Wang*, Z. Yuan*, R. Sederoff n, H. Sederoff n, V. Chiang n, R. Borriss*

Contributors: B. Niu*, W. Wang*, Z. Yuan*, R. Sederoff n, H. Sederoff n, V. Chiang n, R. Borriss*

author keywords: microbial interaction; biological control agents; soil-borne disease; consortia; microbiome and community
TL;DR: The current state of the use of single strain and multi-strain biological control consortia in the management of soil-borne diseases and potential mechanisms used by microbial components to improve the disease suppressing efficacy are summarized. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: November 16, 2020

2019 journal article

CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa

NEW PHYTOLOGIST, 222(1), 244–260.

By: X. Yan*, J. Liu n, H. Kim*, B. Liu*, X. Huang*, Z. Yang n, Y. Lin*, H. Chen n ...

Contributors: X. Yan*, J. Liu n, H. Kim*, B. Liu*, X. Huang*, Z. Yang n, Y. Lin*, H. Chen n ...

author keywords: co-immunoprecipitation; enzyme activity; monolignol biosynthetic pathway; nuclear magnetic resonance (NMR); Populus trichocarpa; stem-differentiating xylem protein
MeSH headings : Aldehyde Oxidoreductases / genetics; Aldehyde Oxidoreductases / metabolism; Down-Regulation / genetics; Gene Expression Regulation, Plant; Lignin / metabolism; Magnetic Resonance Spectroscopy; Plant Proteins / genetics; Plant Proteins / metabolism; Plants, Genetically Modified; Populus / genetics; Populus / metabolism; RNA Interference; Recombinant Proteins / metabolism; Xylem / metabolism
TL;DR: Evidence is provided for the formation of PtrCAD1/PtrCCR2 protein complexes in monolignol biosynthesis in planta, and biomolecular fluorescence complementation and pull-down/co-immunoprecipitation experiments supported a hypothesis of P Tr trichocarpa heterodimer formation. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 17, 2018

2019 article

Editorial: Forest Genomics and Biotechnology

Allona, I., Kirst, M., Boerjan, W., Strauss, S., & Sederoff, R. (2019, October 11). FRONTIERS IN PLANT SCIENCE, Vol. 10.

By: I. Allona*, M. Kirst*, W. Boerjan*, S. Strauss* & R. Sederoff n

author keywords: tree; forest plantation; conifers; angiosperms; wood
TL;DR: This paper presents a meta-modelling procedure called “Smart Gene Counting” that allows for apples to be counted as “plants” rather than “ apples” in theiary systems. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Source: Web Of Science
Added: December 9, 2019

2019 review

Enzyme-Enzyme Interactions in Monolignol Biosynthesis

[Review of ]. FRONTIERS IN PLANT SCIENCE, 9.

By: J. Wang n, B. Liu*, Y. Sun*, V. Chiang n & R. Sederoff n

Contributors: J. Wang n, B. Liu*, Y. Sun*, V. Chiang n & R. Sederoff n

author keywords: monolignol biosynthesis; protein-protein interaction; lignin; enzyme kinetics; BiFC; co-immunoprecipitation
TL;DR: Support for interactions comes from new studies of enzyme activity, co-immunoprecipitation, chemical crosslinking, bimolecular fluorescence complementation, yeast 2-hybrid functional screening, and cell type–specific gene expression based on light amplification by stimulated emission of radiation capture microdissection. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: January 28, 2019

2018 journal article

Assessing the impact of the 4CL enzyme complex on the robustness of monolignol biosynthesis using metabolic pathway analysis

PLOS ONE, 13(3), e0193896.

By: P. Naik n, J. Wang n, R. Sederoff n, V. Chiang n, C. Williams n & J. Ducoste n

Contributors: P. Naik n, J. Wang n, R. Sederoff n, V. Chiang n, C. Williams n & J. Ducoste n

Ed(s): D. Cullen

MeSH headings : Biosynthetic Pathways; Homeostasis; Lignin / biosynthesis; Metabolic Networks and Pathways; Monte Carlo Method; Plant Proteins / metabolism; Populus / enzymology; Populus / metabolism
TL;DR: Results from robustness and stability analyses suggest that the monolignol biosynthetic pathway is resilient to mild perturbations in the presence of the Ptr4CL3-Ptr4CL5 complex, which increased the stability of the pathway by 22%. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2018 journal article

Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis

Nature Communications, 9(1), 1579.

By: J. Wang n, M. Matthews n, C. Williams n, R. Shi n, C. Yang n, S. Tunlaya-Anukit n, H. Chen n, Q. Li* ...

Contributors: J. Wang n, M. Matthews n, C. Williams n, R. Shi n, C. Yang n, S. Tunlaya-Anukit n, H. Chen n, Q. Li* ...

MeSH headings : Gene Expression Regulation, Plant; Lignin / biosynthesis; Lignin / genetics; Plants, Genetically Modified / genetics; Populus / genetics; Populus / metabolism; Transcriptome / genetics; Trees / genetics; Trees / metabolism; Wood / chemistry; Wood / physiology; Xylem / metabolism
TL;DR: A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels and may lead to greater understanding of other pathways for improved growth and adaptation. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2017 journal article

Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(45), E9722–E9729.

By: Y. Lin n, H. Chen n, Q. Li*, W. Li n, J. Wang n, R. Shi n, S. Tunlaya-Anukit n, P. Shuai n ...

Contributors: Y. Lin n, H. Chen n, Q. Li*, W. Li n, J. Wang n, R. Shi n, S. Tunlaya-Anukit n, P. Shuai n ...

author keywords: reciprocal cross-regulation; NAC transcription factors; alternative splicing; wood formation; Populus trichocarpa
MeSH headings : Alternative Splicing; Cell Wall / genetics; Cell Wall / metabolism; Cloning, Molecular; DNA, Plant; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks; Genes, Plant; Homeostasis; Multigene Family; Nuclear Proteins; Plant Leaves / genetics; Plant Leaves / metabolism; Plant Proteins / genetics; Plant Proteins / metabolism; Plant Shoots / genetics; Plant Shoots / metabolism; Populus / genetics; Populus / metabolism; Recombinant Proteins / genetics; Transcription Factors / genetics; Transcription Factors / metabolism; Transcriptional Activation / genetics; Transcriptome; Wood / genetics; Wood / growth & development; Xylem / genetics; Xylem / growth & development
TL;DR: The results indicate that the splice variants from the PtrVND6 and PtrSND1 family may exert reciprocal cross-regulation for complete transcriptional regulation of these two families in wood formation, suggesting a general mechanism among NAC domain proteins and likely other transcription factors. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa

PLANTA, 245(5), 927–938.

By: R. Shi n, J. Wang n, Y. Lin n, Q. Li*, Y. Sun*, H. Chen n, R. Sederoff n, V. Chiang*

Contributors: R. Shi n, J. Wang n, Y. Lin n, Q. Li*, Y. Sun*, H. Chen n, R. Sederoff n, V. Chiang*

author keywords: Wood formation; Transcriptome; Fiber cells; Vessel elements; Cell wall biosynthesis; Co-expression network
MeSH headings : Cell Wall / metabolism; Cellulose / metabolism; Cluster Analysis; Gene Expression Regulation, Plant; Lignin / metabolism; Molecular Sequence Annotation; Organ Specificity; Phloem / genetics; Phloem / growth & development; Plant Leaves / genetics; Plant Leaves / growth & development; Plant Proteins / genetics; Populus / genetics; Populus / growth & development; Sequence Analysis, RNA; Transcription Factors / genetics; Transcriptome; Wood / genetics; Wood / growth & development; Xylem / genetics; Xylem / growth & development
TL;DR: The co-expression networks revealed here suggest a well-structured transcriptional homeostasis for cell wall component biosynthesis during wood formation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

A cell wall-bound anionic peroxidase, PtrPO21, is involved in lignin polymerization in Populus trichocarpa

Tree Genetics & Genomes, 12(2).

By: C. Lin n, Q. Li*, S. Tunlaya-Anukit*, R. Shi n, Y. Sun*, J. Wang n, J. Liu n, P. Loziuk n ...

Contributors: C. Lin n, Q. Li*, S. Tunlaya-Anukit*, R. Shi n, Y. Sun*, J. Wang n, J. Liu n, P. Loziuk n ...

author keywords: Lignin polymerization; Populus trichocarpa; Lignin peroxidase; LC-MS/MS; Lignin systems biology
TL;DR: Differentially expressed gene (DEG) analysis of PtrPO21 downregulated transgenics identified a significant overexpression of PtPrx35, suggesting a compensatory effect within the peroxidase family. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, Crossref, NC State University Libraries
Added: August 6, 2018

2015 journal article

4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid: Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa

MOLECULAR PLANT, 8(1), 176–187.

By: C. Lin n, J. Wang n, Q. Li*, H. Chen n, J. Liu n, P. Loziuk n, J. Song n, C. Williams n ...

Contributors: C. Lin n, J. Wang n, Q. Li*, H. Chen n, J. Liu n, P. Loziuk n, J. Song n, C. Williams n ...

author keywords: monolignol biosynthesis; Populus trichocarpa; metabolic flux; reaction and inhibition kinetics; LC-MS/MS; 4-coumaroyl and caffeoyl shikimic acids
MeSH headings : Acyl Coenzyme A / metabolism; Coenzyme A Ligases / metabolism; Coumaric Acids / metabolism; Coumaric Acids / pharmacology; Hydroxylation / drug effects; Plant Proteins / metabolism; Populus / drug effects; Populus / enzymology; Populus / metabolism; Propionates; Shikimic Acid / pharmacology
TL;DR: 4-coumaroyl and caffeoyl shikimic acids are inhibitors of Ptr4CL3 and Ptr 4CL5, which can reduce lignin content in a number of plant species and play significant regulatory roles when these inhibitors accumulate. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2015 journal article

Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa

JOURNAL OF PROTEOME RESEARCH, 14(10), 4158–4168.

By: P. Loziuk n, J. Parker n, W. Li n, C. Lin n, J. Wang n, Q. Li*, R. Sederoff n, V. Chiang n, D. Muddiman n

Contributors: P. Loziuk n, J. Parker n, W. Li n, C. Lin n, J. Wang n, Q. Li*, R. Sederoff n, V. Chiang n, D. Muddiman n

author keywords: shotgun discovery proteomics; absolute quantification; PC-IDMS; cellulose biosynthesis; transcription factor; targeted mass spectrometiry; SRM
MeSH headings : Carbohydrate Metabolism; Cellulose / biosynthesis; Cellulose / genetics; Chromatography, Liquid; Gene Expression Regulation, Plant; Molecular Sequence Annotation; Plant Proteins / genetics; Plant Proteins / isolation & purification; Plant Proteins / metabolism; Populus / genetics; Populus / metabolism; Proteome / genetics; Proteome / isolation & purification; Proteome / metabolism; Proteomics; Tandem Mass Spectrometry; Transcription Factors / genetics; Transcription Factors / isolation & purification; Transcription Factors / metabolism; Wood / chemistry; Wood / metabolism; Xylem / genetics; Xylem / metabolism
TL;DR: The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins. (via Semantic Scholar)
UN Sustainable Development Goal Categories
9. Industry, Innovation and Infrastructure (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2015 journal article

Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis

Proceedings of the National Academy of Sciences, 112(27), 8481–8486.

By: J. Wang n, L. Chuang n, P. Loziuk n, H. Chen n, Y. Lin n, R. Shi n, G. Qu*, D. Muddiman n, R. Sederoff n, V. Chiang n

Contributors: J. Wang n, L. Chuang n, P. Loziuk n, H. Chen n, Y. Lin n, R. Shi n, G. Qu*, D. Muddiman n, R. Sederoff n, V. Chiang n

author keywords: AldOMT; COMT; lignin; phosphoproteomics; phosphoregulation
MeSH headings : Acrolein / analogs & derivatives; Acrolein / metabolism; Amino Acid Sequence; Binding Sites / genetics; Biocatalysis; Catechols / metabolism; Chromatography, Liquid; Electrophoresis, Polyacrylamide Gel; Green Fluorescent Proteins / genetics; Green Fluorescent Proteins / metabolism; Isoenzymes / genetics; Isoenzymes / metabolism; Lignin / biosynthesis; Methyltransferases / genetics; Methyltransferases / metabolism; Microscopy, Confocal; Molecular Sequence Data; Mutation; Phosphoproteins / metabolism; Phosphorylation; Plant Proteins / genetics; Plant Proteins / metabolism; Populus / enzymology; Populus / genetics; Populus / metabolism; Proteomics / methods; Protoplasts / enzymology; Protoplasts / metabolism; Sequence Homology, Amino Acid; Tandem Mass Spectrometry
TL;DR: It is shown that reversible monophosphorylation at Ser123 or Ser125 acts as an on/off switch for the activity of 5-hydroxyconiferaldehyde O-methyltransferase 2 (PtrAldOMT2), an enzyme central to monolignol biosynthesis for lignification in stem-differentiating xylem of Populus trichocarpa. (via Semantic Scholar)
Sources: Web Of Science, ORCID, Crossref, NC State University Libraries
Added: August 6, 2018

2015 article

Populus trichocarpa

AGROBACTERIUM PROTOCOLS, VOLUME 2, THIRD EDITION, Vol. 1224, pp. 357–363.

By: Q. Li*, T. Yeh*, C. Yang*, J. Song*, Z. Chen*, R. Sederoff*, V. Chiang*

author keywords: Agrobacterium tumefaciens; Genetic transformation; Populus trichocarpa; Transgenic trees
MeSH headings : Agrobacterium tumefaciens / genetics; Agrobacterium tumefaciens / growth & development; Coculture Techniques; Genetic Engineering / methods; Plant Roots / growth & development; Plant Shoots / growth & development; Populus / genetics; Populus / growth & development; Populus / physiology; Regeneration; Transformation, Genetic
TL;DR: A modified step-by-step protocol for Agrobacterium-mediated transformation of stem explants is described here and the health of the tissue explants and the time of cocultivation are among the critical steps in the protocol for successful transformation. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2014 journal article

A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue

NATURE PROTOCOLS, 9(9), 2180–2193.

By: W. Li n, Y. Lin n, Q. Li n, R. Shi n, C. Lin n, H. Chen n, L. Chuang n, G. Qu*, R. Sederoff n, V. Chiang n

MeSH headings : Base Sequence; Chromatin Immunoprecipitation / methods; DNA / metabolism; DNA Fragmentation; Histones / metabolism; Immunoprecipitation; Molecular Sequence Data; Populus / cytology; Populus / metabolism; Sequence Analysis, DNA; Transcription Factors / metabolism; Wood / cytology; Xylem / genetics; Xylem / metabolism
TL;DR: This protocol is the only working ChIP system for wood-forming tissue and uses stem-differentiating xylem to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2014 journal article

A simple improved-throughput xylem protoplast system for studying wood formation

NATURE PROTOCOLS, 9(9), 2194–2205.

By: Y. Lin n, W. Li n, H. Chen n, Q. Li n, Y. Sun*, R. Shi n, C. Lin n, J. Wang n ...

Contributors: Y. Lin n, W. Li n, H. Chen n, Q. Li n, Y. Sun*, R. Shi n, C. Lin n, J. Wang n ...

MeSH headings : Cell Wall / metabolism; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Green Fluorescent Proteins; Populus / cytology; Populus / growth & development; Protoplasts / metabolism; Transfection / methods; Wood / cytology; Wood / growth & development; Xylem / chemistry
TL;DR: A protocol for the isolation and transfection of protoplasts from wood-forming tissue, the stem-differentiating xylem (SDX), in the model woody plant Populus trichocarpa is presented. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

GENOME BIOLOGY, 15(3).

By: D. Neale*, J. Wegrzyn*, K. Stevens*, A. Zimin*, D. Puiu*, M. Crepeau*, C. Cardeno*, M. Koriabine ...

MeSH headings : Contig Mapping / methods; DNA, Plant / genetics; Genome, Plant; Haploidy; Pinus taeda / genetics; Sequence Analysis, DNA / methods
TL;DR: A novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology is developed, demonstrating a novel approach to sequencing the large and complex genomes of this important group of plants. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2014 journal article

Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry

ANALYST, 139(21), 5439–5450.

By: P. Loziuk n, R. Sederoff n, V. Chiang n & D. Muddiman n

MeSH headings : Chromatography, Liquid; Isotopes / chemistry; Proteins / analysis; Tandem Mass Spectrometry / methods
TL;DR: It is suggested that evaluation of the absolute ion abundance for any given transition is necessary in order to effectively implement RA thresholds, and these RA values should be assessed as close as possible to the time at which data is collected for quantification. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2014 journal article

Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling

The Plant Cell, 26(3), 876–893.

By: H. Chen n, J. Song n, J. Wang n, Y. Lin n, J. Ducoste n, C. Shuford n, J. Liu n, Q. Li n ...

Contributors: H. Chen n, J. Song n, J. Wang n, Y. Lin n, J. Ducoste n, C. Shuford n, J. Liu n, Q. Li n ...

MeSH headings : Coenzyme A Ligases / genetics; Coenzyme A Ligases / metabolism; Coumaric Acids / metabolism; Immunoprecipitation; Lignin / biosynthesis; Mass Spectrometry; Models, Biological; Populus / metabolism; Propionates; RNA, Messenger / genetics; Substrate Specificity; Systems Biology
TL;DR: This work shows that 4CL, an enzyme in monolignol biosynthesis, is found as a heterotetrameric complex of two isoforms in Populus trichocarpa, where the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterosymmetric protein complex. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2013 article

GENOMICS A spruce sequence

Sederoff, R. (2013, May 30). NATURE, Vol. 497, pp. 569–570.

By: R. Sederoff n

MeSH headings : Evolution, Molecular; Genome, Plant / genetics; Picea / genetics
TL;DR: Comparative sequencing of five further gymnosperm genomes suggests that transposable element diversity is shared among extant conifers. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2013 journal article

High-level gene expression in differentiating xylem of tobacco driven by a 2.0 kb Poplar COMT2 promoter and a 4 x 35S enhancer

PLANT BIOTECHNOLOGY, 30(2), 191–198.

By: E. Liu n, S. Peng, Q. Li n, Y. Sun*, V. Chiang n & R. Sederoff n

author keywords: PtrCOMT2 promoter; xylem-specific; 4 x 35S enhancer; woody plants; genetic engineering
TL;DR: While expression of some of the enhancer-plus-promoter constructs increased expression, there was a loss of specificity in the PtrCOMT2 promoter. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2013 journal article

Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes

PLANT PHYSIOLOGY, 161(3), 1501–1516.

By: H. Chen n, J. Song n, C. Williams n, C. Shuford n, J. Liu n, J. Wang n, Q. Li n, R. Shi n ...

Contributors: H. Chen n, J. Song n, C. Williams n, C. Shuford n, J. Liu n, J. Wang n, Q. Li n, R. Shi n ...

MeSH headings : Allosteric Regulation / drug effects; Binding Sites; Biosynthetic Pathways / drug effects; Blotting, Western; Caffeic Acids / pharmacology; Coenzyme A / metabolism; Coenzyme A Ligases / antagonists & inhibitors; Coenzyme A Ligases / metabolism; Computer Simulation; Coumaric Acids / chemistry; Coumaric Acids / metabolism; Coumaric Acids / pharmacology; Kinetics; Lignin / biosynthesis; Lignin / chemistry; Phenylpropionates / metabolism; Phosphoproteins / metabolism; Phosphorylation / drug effects; Plant Extracts; Populus / drug effects; Populus / enzymology; Propionates; Proteomics; Recombinant Fusion Proteins / metabolism; Sequence Homology, Amino Acid; Substrate Specificity / drug effects; Xylem / drug effects; Xylem / metabolism
TL;DR: Evidence is presented of two monolignol 4CLs, Ptr4CL3 and P tr4CL5, in Populus trichocarpa that act to mitigate the inhibition by caffeic acid to maintain a proper ligation flux and coenzyme A flux with novel specificity. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2013 journal article

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

Proceedings of the National Academy of Sciences, 110(26), 10848–10853.

By: S. Lu*, Q. Li n, H. Wei*, M. Chang*, S. Tunlaya-Anukit n, H. Kim*, J. Liu n, J. Song* ...

MeSH headings : Base Sequence; Down-Regulation / genetics; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Laccase / antagonists & inhibitors; Laccase / genetics; Lignin / antagonists & inhibitors; Lignin / chemistry; Lignin / metabolism; MicroRNAs / genetics; MicroRNAs / metabolism; Phylogeny; Plant Proteins / genetics; Populus / enzymology; Populus / genetics; RNA, Plant / genetics; RNA, Plant / metabolism
TL;DR: A hierarchical genetic regulatory network (GRN) built by a bottom-up graphic Gaussian model algorithm provides additional support for a role of ptr-miR397a as a negative regulator of laccases for lignin biosynthesis in wood formation. (via Semantic Scholar)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2013 journal article

Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa

Planta, 238(3), 487–497.

By: R. Shi n, C. Shuford n, J. Wang n, Y. Sun n, Z. Yang n, H. Chen n, S. Tunlaya-Anukit n, Q. Li n ...

Contributors: R. Shi n, C. Shuford n, J. Wang n, Y. Sun n, Z. Yang n, H. Chen n, S. Tunlaya-Anukit n, Q. Li n ...

MeSH headings : Gene Expression Regulation, Plant / physiology; Mass Spectrometry; Phenylalanine Ammonia-Lyase / metabolism; Populus / enzymology; Populus / metabolism
TL;DR: A greater functional significance of subgroup A PtrPALs for stem wood formation is indicated, and the role of gene post-transcriptional regulation is highlighted. (via Semantic Scholar)
Sources: NC State University Libraries, ORCID, NC State University Libraries
Added: August 6, 2018

2013 journal article

SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

PLANT CELL, 25(11), 4324–4341.

MeSH headings : Algorithms; Cell Wall / genetics; Chromatin Immunoprecipitation; Gene Expression Regulation, Plant; Gene Ontology; Gene Regulatory Networks; High-Throughput Nucleotide Sequencing; Models, Genetic; Plant Proteins / genetics; Plant Proteins / metabolism; Plants, Genetically Modified; Polymerase Chain Reaction / methods; Populus / genetics; Populus / metabolism; Protoplasts; Reproducibility of Results; Transcription Factors / genetics; Transcription Factors / metabolism; Transfection; Wood / genetics; Wood / metabolism; Xylem / cytology; Xylem / genetics
TL;DR: A genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)–directed hierarchical gene regulatory networks (hGRNs) in wood formation is developed and may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2013 journal article

The Amborella Genome and the Evolution of Flowering Plants

Science, 342(6165), 1456–1457.

By: V. Albert, W. Barbazuk*, C. dePamphilis*, J. Der, J. Leebens-Mack, H. Ma*, J. Palmer, S. Rounsley ...

Contributors: C. DePamphilis*, J. Palmer, S. Rounsley, D. Sankoff, S. Schuster*, J. Ammiraju*, W. Barbazuk*, S. Chamala ...

MeSH headings : Conservation of Natural Resources; Contig Mapping; Evolution, Molecular; Flowers / genetics; Gene Duplication; Genetic Variation; Genome, Plant; Metagenomics / statistics & numerical data; Molecular Sequence Annotation; Multigene Family; New Caledonia; Phylogeny; Sequence Analysis, DNA; Tracheophyta / classification; Tracheophyta / genetics; Tracheophyta / growth & development
TL;DR: Genome structure and phylogenomic analyses indicate that the ancestral Angiosperm was a polyploid with a large constellation of both novel and ancient genes that survived to play key roles in angiosperm biology. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2013 journal article

Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments

JOURNAL OF PROTEOME RESEARCH, 12(12), 5820–5829.

By: P. Loziuk n, J. Wang n, Q. Li n, R. Sederoff n, V. Chiang n & D. Muddiman n

Contributors: P. Loziuk n, J. Wang n, Q. Li n, R. Sederoff n, V. Chiang n & D. Muddiman n

author keywords: design of experiments; proteolytic digestion; LC-MS/MS; Populus trichocarpa
MeSH headings : Amino Acid Sequence; Animals; Cattle; Chromatography, Liquid / standards; Factor Analysis, Statistical; Hydrogen-Ion Concentration; Isotope Labeling; Molecular Sequence Annotation; Molecular Sequence Data; Peptide Fragments / chemistry; Peptide Fragments / isolation & purification; Plant Proteins / chemistry; Plant Proteins / isolation & purification; Populus / chemistry; Protein Stability; Proteolysis; Proteomics / methods; Proteomics / standards; Research Design; Swine; Tandem Mass Spectrometry / standards; Trypsin / chemistry; Xylem / chemistry
TL;DR: The tryptic digest optimization described here has eliminated this previously observed peptide decay as well as provided a greater understanding and standardization for a common but critical sample treatment used across the field of proteomics. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2012 journal article

A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities

PLANTA, 236(3), 879–885.

By: J. Liu n, R. Shi n, Q. Li n, R. Sederoff n & V. Chiang n

author keywords: Monolignols; Enzyme activity; Populus trichocarpa; Pinus taeda; Angiosperm; Gymnosperm
MeSH headings : Biosynthetic Pathways; Chromatography, High Pressure Liquid; Enzyme Assays; Lignin / biosynthesis; Methyltransferases / metabolism; Mixed Function Oxygenases / metabolism; Oxidoreductases / metabolism; Pinus taeda / enzymology; Plant Proteins / analysis; Plant Stems / enzymology; Populus / enzymology; Substrate Specificity; Xylem / enzymology
TL;DR: This work developed a method using a total protein extract (soluble and microsomal) for the comprehensive and simultaneous analysis of these ten enzyme activities in a single target tissue, stem differentiating xylem (SDX) of Populustrichocarpa. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2012 journal article

A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)

Tree Genetics & Genomes, 9(2), 557–571.

By: T. Kubisiak*, C. Nelson*, M. Staton*, T. Zhebentyayeva*, C. Smith n, B. Olukolu*, G. Fang*, F. Hebard* ...

author keywords: Fagaceae; Castanea spp.; Chestnut; Genetic map; Comparative genomics; Disease resistance
TL;DR: A highly informative genetic map was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Sources: Web Of Science, Crossref
Added: August 6, 2018

2012 journal article

Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry

Journal of Proteome Research, 11(6), 3390–3404.

By: C. Shuford n, Q. Li n, Y. Sun n, H. Chen n, J. Wang n, R. Shi n, R. Sederoff n, V. Chiang n, D. Muddiman n

Contributors: C. Shuford n, Q. Li n, Y. Sun n, H. Chen n, J. Wang n, R. Shi n, R. Sederoff n, V. Chiang n, D. Muddiman n

author keywords: quantification; isotope dilution mass spectrometry; selected reaction monitoring; filter-aided sample preparation; monolignol biosynthesis
MeSH headings : Amino Acid Sequence; Biosynthetic Pathways; Isotope Labeling; Molecular Sequence Data; Plant Proteins / chemistry; Plant Proteins / metabolism; Populus / enzymology; Proteome / chemistry; Proteome / metabolism; Reference Standards; Spectrometry, Mass, Electrospray Ionization / standards; Xylem / enzymology
TL;DR: This represents the most comprehensive assay for quantification of proteins regulating monolignol biosynthesis and will lead to a better understanding of lignin formation at a systems level. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, Crossref, NC State University Libraries
Added: August 6, 2018

2012 journal article

Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis

PLANTA, 236(3), 795–808.

By: J. Wang n, C. Shuford n, Q. Li n, J. Song n, Y. Lin n, Y. Sun n, H. Chen n, C. Williams n ...

Contributors: J. Wang n, C. Shuford n, Q. Li n, J. Song n, Y. Lin n, Y. Sun n, H. Chen n, C. Williams n ...

author keywords: Lignin; Syringyl lignin; Angiosperm; Kinetics; Subcellular localization
MeSH headings : Cloning, Molecular; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Plant; Hydroxylation; Kinetics; Lignin / analysis; Lignin / biosynthesis; Mixed Function Oxygenases / metabolism; Plants, Genetically Modified; Populus / metabolism; Xylem / enzymology; Yeasts / metabolism
TL;DR: The combination of genetic analysis, absolute protein quantitation-based enzyme kinetics, homologous CPR specificity, SNP characterization, and ER localization provides a more rigorous basis for a comprehensive systems understanding of 5-hydroxylation in lignin biosynthesis. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2012 journal article

MicroRNAs in trees

PLANT MOLECULAR BIOLOGY, 80(1), 37–53.

By: Y. Sun n, R. Shi n, X. Zhang n, V. Chiang n & R. Sederoff n

author keywords: MicroRNA; Woody plant; Gene regulation; Plant development; Plant stress response; Artificial microRNA
MeSH headings : Gene Expression Regulation, Plant; MicroRNAs / genetics; MicroRNAs / metabolism; Models, Genetic; Phylogeny; Plants, Genetically Modified / genetics; Plants, Genetically Modified / metabolism; RNA, Messenger / genetics; RNA, Messenger / metabolism; RNA, Plant / genetics; RNA, Plant / metabolism; Trees / classification; Trees / genetics; Trees / metabolism
TL;DR: The purpose of this review is to summarize the current status of information on mi RNAs in trees and to guide future studies on the role of miRNAs in the biology of woody perennials and to illustrate their utility in directed genetic modification of trees. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2012 journal article

Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109(36), 14699–14704.

By: Q. Li n, Y. Lin n, Y. Sun n, J. Song n, H. Chen n, X. Zhang*, R. Sederoff n, V. Chiang n

MeSH headings : Blotting, Western; Cloning, Molecular; DNA Primers / genetics; Dimerization; Electrophoresis, Polyacrylamide Gel; Gene Regulatory Networks / genetics; Homeostasis / physiology; Models, Biological; Plasmids / genetics; Populus / genetics; Protein Isoforms / genetics; Protein Transport; Real-Time Polymerase Chain Reaction; Transcription Factors / genetics
TL;DR: A stem-differentiating xylem (SDX)-specific alternative SND1 splice variant, PtrSND1-A2IR, that acts as a dominant negative of S ND1 transcriptional network genes in Populus trichocarpa is discovered and may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2011 journal article

Membrane protein complexes catalyze both 4-and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108(52), 21253–21258.

By: H. Chen*, Q. Li*, C. Shuford n, J. Liu, D. Muddiman n, R. Sederoff*, V. Chiang*

MeSH headings : Carboxylic Ester Hydrolases / chemistry; Carboxylic Ester Hydrolases / metabolism; Chromatography, Liquid; Coumaric Acids; DNA Primers / genetics; Hydroxylation; Immunoprecipitation; Kinetics; Lignin / biosynthesis; Mass Spectrometry; Membrane Proteins / chemistry; Membrane Proteins / metabolism; Microscopy, Confocal; Molecular Structure; Multiprotein Complexes / chemistry; Multiprotein Complexes / metabolism; Phenols; Phenylpropionates; Plasmids / genetics; Populus / metabolism; Propionates; Trans-Cinnamate 4-Monooxygenase / chemistry; Trans-Cinnamate 4-Monooxygenase / metabolism; Xylem / metabolism; Yeasts
TL;DR: Affinity purification-quantitative mass spectrometry, bimolecular fluorescence complementation, chemical cross-linking, and reciprocal coimmunoprecipitation provide further evidence for functional involvement of membrane protein complexes in monolignol biosynthesis. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2010 journal article

Arabidopsis thaliana as a model for gelatinous fiber formation

RUSSIAN JOURNAL OF PLANT PHYSIOLOGY, 57(3), 363–367.

author keywords: Arabidpsis thaliana; cambium; gelatinous fibers; gravity; reaction wood; tension wood
TL;DR: Repeated clipping of the emerging inflorescence stems of Arabidopsis thaliana augments wood formation in organs, including those inflorescent stems that are allowed to develop later, allowing the use of A.Thaliana for a molecular and genetic analysis of the mechanisms of tension wood formation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2010 journal article

Genomics of forest and ecosystem health in the Fagaceae: meeting report

TREE GENETICS & GENOMES, 6(5), 815–820.

By: A. Kremer*, R. Sederoff n & N. Wheeler n

author keywords: Fagaceae; Genomics
TL;DR: A summary of 35 keynote, invited and volunteer papers delivered at a recent international conference is provided, along with web links to PDFs of those presentations, for reviewing the rapidly expanding knowledge base on Fagaceae genomics. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2010 journal article

Lignin and Biomass: A Negative Correlation for Wood Formation and Lignin Content in Trees

PLANT PHYSIOLOGY, 154(2), 555–561.

Contributors: E. Novaes n, M. Kirst n, V. Chiang n, H. Winter-Sederoff & R. Sederoff n

MeSH headings : Biomass; Gene Expression Regulation, Plant; Lignin / biosynthesis; Lignin / chemistry; Transcription Factors / metabolism; Trees / genetics; Trees / growth & development; Trees / metabolism; Wood / genetics; Wood / growth & development; Wood / metabolism
TL;DR: Studies in populations of forest tree hybrids have shown a negative correlation of biomass growth and lignin content, implying that selection for biomass growth may be highly regulated. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Specific down-regulation of PAL genes by artificial microRNAs in Populus trichocarpa

PLANTA, 232(6), 1281–1288.

By: R. Shi n, C. Yang n, S. Lu n, R. Sederoff n & V. Chiang n

author keywords: Artificial microRNA; Phenylalanine ammonia-lyase; Populus trichocarpa transformation; Down-regulation; PolyA tailing-based real time RT-PCR; Quantitation
MeSH headings : Base Sequence; DNA Primers; Down-Regulation; Genes, Plant; MicroRNAs / physiology; Mutation; Populus / genetics; Reverse Transcriptase Polymerase Chain Reaction; Sequence Homology, Nucleic Acid
TL;DR: This paper describes the specific down-regulation of multiple genes in the phenylalanine ammonia-lyase (PAL) gene family of Populus trichocarpa using amiRNA sequences incorporated in a ptc-MIR408 miRNA-producing precursor, revealing differential regulation within the gene family. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2010 review

Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes

[Review of ]. PLANT AND CELL PHYSIOLOGY, 51(1), 144–163.

By: R. Shi n, Y. Sun n, Q. Li n, S. Heber n, R. Sederoff n & V. Chiang n

author keywords: Lignin systems biology; Monolignol biosynthesis; Populus trichocarpa; Promoter motifs; Transcript abundance; Xylem-specific expression
MeSH headings : Amino Acid Motifs / genetics; Biosynthetic Pathways / genetics; Enzymes / biosynthesis; Enzymes / genetics; Gene Expression Regulation, Enzymologic / physiology; Gene Expression Regulation, Plant / physiology; Genome, Plant / genetics; Lignin / biosynthesis; Lignin / genetics; Phloem / enzymology; Phloem / genetics; Plant Shoots / enzymology; Plant Shoots / genetics; Populus / genetics; Populus / metabolism; Promoter Regions, Genetic / genetics; RNA, Messenger / analysis; RNA, Messenger / genetics; RNA, Messenger / metabolism; RNA, Plant / analysis; RNA, Plant / genetics; RNA, Plant / metabolism; Transcription, Genetic / physiology; Xylem / enzymology; Xylem / genetics
TL;DR: The identified 23 genes that most probably encode monolignol biosynthesis enzymes during wood formation are identified and evidence suggesting functional redundancy at the transcript level for phenylalanine ammonia-lyase and cinnamate 4-hydroxylase is found. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2009 journal article

Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection

BMC PLANT BIOLOGY, 9.

By: A. Barakat*, D. DiLoreto*, Y. Zhang*, C. Smith n, K. Baier*, W. Powell*, N. Wheeler n, R. Sederoff n, J. Carlson*

MeSH headings : Ascomycota; DNA, Complementary / genetics; Expressed Sequence Tags; Fagaceae / genetics; Fagaceae / microbiology; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Library; Genes, Plant; Genomics; Plant Diseases / genetics; RNA, Plant / genetics; Sequence Analysis, DNA
TL;DR: This study sequenced the transcriptome from fungal infected and healthy stem tissues collected from blight-sensitive American chestnut and blight-resistant Chinese chestnut trees using ultra high throughput pyrosequencing to identify genes involved in resistance to Cryphonectria parasitica, resulting in the identification of a large set of cDNA unigenes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2009 review

Genomics of growth traits in forest trees

[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 12(2), 148–156.

MeSH headings : Genomics; Plants, Genetically Modified; Population Dynamics; Quantitative Trait Loci / genetics; Quantitative Trait, Heritable; Trees / genetics; Trees / growth & development
TL;DR: Genetics and genomics are unifying disciplines that will serve well to dissect the variables and mechanisms of tree growth and development. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2009 journal article

Role of genomics in the potential restoration of the American chestnut

TREE GENETICS & GENOMES, 5(1), 181–187.

By: N. Wheeler n & R. Sederoff n

author keywords: Genomics; Chestnut; Restoration
TL;DR: A strategy of map-based cloning, association genetics, and genetic engineering, combined with traditional and marker-assisted backcross breeding is proposed for the long-term genetic restoration of this iconic tree species. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Comparative analysis of transcript abundance in Pinus sylvestris after challenge with a saprotrophic, pathogenic or mutualistic fungus

TREE PHYSIOLOGY, 28(6), 885–897.

By: A. Adomas n, G. Heller n, A. Olson*, J. Osborne n, M. Karlsson*, J. Nahalkova*, L. Van Zyl n, R. Sederoff n ...

author keywords: defence; ectomycorrhiza; Heterobasidion annostan; Laccaria bicolor; microarray; recognition; Trichoderma aureoviride
MeSH headings : Basidiomycota / pathogenicity; Cell Communication; Microscopy, Electron, Scanning; Pinus sylvestris / genetics; Pinus sylvestris / microbiology; Pinus sylvestris / physiology; Plant Diseases / microbiology; Plant Proteins / metabolism; Plant Roots / microbiology; Plant Roots / ultrastructure; Ribosomal Proteins / biosynthesis; Ribosomal Proteins / metabolism; Seedlings / microbiology; Transcription, Genetic; Trichoderma / pathogenicity; Trichoderma / ultrastructure
TL;DR: There were specific transcriptional responses depending on whether the conifer roots were challenged with mutualistic, saprotrophic or pathogenic fungi, suggesting that pine trees are able to recognize diverse fungal species and specifically distinguish whether they are pathogenic, neutral or beneficial microbial agents. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

BMC GENOMICS, 9.

By: E. Novaes*, D. Drost*, W. Farmerie*, G. Pappas*, D. Grattapaglia*, R. Sederoff n, M. Kirst*

MeSH headings : Alleles; DNA, Complementary / biosynthesis; Eucalyptus / genetics; Expressed Sequence Tags; Gene Library; Genes, Plant; Genetic Variation; Haplotypes; Polymorphism, Single Nucleotide / genetics; Reproducibility of Results; Sequence Analysis, DNA / methods; Software; Transcription, Genetic
TL;DR: It is demonstrated that SNPs sampled in large-scale with 454 pyrosequencing can be used to detect evolutionary signatures among genes, providing one of the first genome-wide assessments of nucleotide diversity and Ka/Ks for a non-model plant species. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Transcriptional analysis of Pinus sylvestris roots challenged with the ectomycorrhizal fungus Laccaria bicolor

BMC Plant Biology, 8.

By: G. Heller, A. Adomas, G. Li, J. Osborne, L. Van Zyl, R. Sederoff, R. Finlay, J. Stenlid, F. Asiegbu

Source: NC State University Libraries
Added: August 6, 2018

2007 article

Regulatory science in forest biotechnology

Sederoff, R. (2007, April). TREE GENETICS & GENOMES, Vol. 3, pp. 71–74.

By: R. Sederoff n

TL;DR: The development of a regulatory framework in many countries, the absence of evidence ofharm in large numbers of field tests, and increasing familiarity has made this level of acceptance possible, and there is an inherent paradox in much of the regulation incurrent practice. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Synthesis of hydroxyphenylpropanoid beta-D-glucosides

JOURNAL OF WOOD CHEMISTRY AND TECHNOLOGY, 27(1), 1–8.

By: M. Mazur*, K. Hope-Ross*, J. Kadla*, R. Sederoff n & H. Chang n

author keywords: dihydroconiferyl alcohol glucoside; coniferin; synthesis; monolignol
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Trranscript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion

TREE PHYSIOLOGY, 27(10), 1441–1458.

By: A. Adomas*, G. Heller*, G. Li*, A. Olson*, T. Chu*, J. Osborne n, D. Craig n, L. Van Zyl n ...

author keywords: antimicrobial peptide; microarray; peroxidase; phenylopropanoid pathway; pine; plant defence
MeSH headings : Fungi / physiology; Gene Expression Profiling; Gene Expression Regulation, Plant; Oligonucleotide Array Sequence Analysis; Pinus sylvestris / metabolism; Plant Diseases / microbiology; Plant Proteins / genetics; Plant Proteins / metabolism; Plant Roots / metabolism; Plant Roots / microbiology; Plant Roots / ultrastructure; Seedlings
TL;DR: The similarity of the expression profiling pattern observed in this pathosystem to those documented in crop pathology suggests that angiosperms and gymnosperms use similar genetic programs in responding to invasive growth by microbial pathogens. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2005 journal article

Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays

BMC Genomics, 6(61).

By: J. Wadenback, D. Clapham, D. Craig, R. Sederoff, G. Peter, S. Von Arnold, U. Egertsdotter

Source: NC State University Libraries
Added: August 6, 2018

2005 journal article

Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid

GENETICS, 169(4), 2295–2303.

By: M. Kirst n, C. Basten n, A. Myburg*, Z. Zeng n & R. Sederoff n

MeSH headings : Cell Differentiation; Chimera; Chromosome Mapping; Crosses, Genetic; Eucalyptus / genetics; Gene Expression Regulation; Genes, Plant; Genetic Linkage; Genetic Markers; Genetic Variation; Genome, Plant; Genotype; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; Phylogeny; Quantitative Trait Loci; RNA, Messenger / metabolism
TL;DR: To analyze and compare the genetic architecture of transcript regulation in different genetic backgrounds of Eucalyptus, microarrays were used to examine variation in mRNA abundance in the differentiating xylem of a E. grandis pseudobackcross population. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2005 conference paper

Variation of a-cellulose content and related metabolites during wood formation in loblolly pine

13th ISWFPC Proceedings, 13.

By: C. Morris, B. Goldfarb, F. Isik, C. Li, H. Chang, R. Sederoff, J. Kadla

Source: NC State University Libraries
Added: August 6, 2018

2005 journal article

Verification of QTL linked markers for propagation traits in Eucalyptus

TREE GENETICS & GENOMES, 1(3), 103–108.

By: C. Marques, V. Carocha, A. Sa, M. Oliveira, A. Pires, R. Sederoff n, N. Borralho*

author keywords: Eucalyptus; AFLP; QTL verification; vegetative propagation; marker-aided selection
TL;DR: This study highlights the importance of sample size in QTL detection for low-heritability traits and confirms stable QTL linked markers (detected in different years) for propagation traits in an independent set of the same segregating population and in two related crosses involving the original E. globulus parent. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

An auxin-inducible gene from loblolly pine ( Pinus taeda L.) is differentially expressed in mature and juvenile-phase shoots and encodes a putative transmembrane protein

Planta, 218(6), 916–927.

By: V. Busov n, E. Johannes n, R. Whetten n, R. Sederoff n, S. Spiker n, C. Lanz-Garcia n, B. Goldfarb n

author keywords: adventitious root formation; auxin; gene expression (5NG4); maturation; nodulin; Pinus
MeSH headings : Amino Acid Sequence; Arabidopsis / genetics; Down-Regulation; Gene Expression Regulation, Plant; Indoleacetic Acids / metabolism; Indoleacetic Acids / pharmacology; Molecular Sequence Data; Phylogeny; Pinus taeda / genetics; Pinus taeda / metabolism; Plant Proteins / genetics; Plant Proteins / metabolism; Plant Shoots / growth & development; Plant Shoots / metabolism; Sequence Alignment; Sequence Homology, Amino Acid
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2004 journal article

Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus

PLANT PHYSIOLOGY, 135(4), 2368–2378.

By: M. Kirst n, A. Myburg n, J. De Leon, M. Kirst n, J. Scott n & R. Sederoff n

MeSH headings : Base Sequence; Chromosome Mapping; Crosses, Genetic; DNA Primers; Eucalyptus / genetics; Eucalyptus / growth & development; Eucalyptus / metabolism; Gene Expression Profiling; Gene Expression Regulation, Plant; Lignin / metabolism; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis; Quantitative Trait Loci
TL;DR: The power of integrating quantitative analysis of gene expression data and genetic map information to discover genetic and metabolic networks regulating complex biological traits is illustrated. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Gene Expression during Formation of Earlywood and Latewood in Loblolly Pine: Expression Profiles of 350 Genes

Plant Biology, 6(6), 654–663.

By: U. Egertsdotter*, L. Zyl n, J. MacKay*, G. Peter*, M. Kirst n, C. Clark n, R. Whetten n, R. Sederoff n

author keywords: microarray analysis; Pinus taeda; earlywood; latewood; transcript abundance
MeSH headings : Expressed Sequence Tags; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Microarray Analysis; Pinus taeda / genetics; Pinus taeda / metabolism; Reverse Transcriptase Polymerase Chain Reaction; Seasons; Transcription, Genetic
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2004 journal article

Genetics of Postzygotic Isolation in Eucalyptus: Whole-Genome Analysis of Barriers to Introgression in a Wide Interspecific Cross of Eucalyptus grandis and E. globulus

Genetics, 166(3), 1405–1418.

By: A. Myburg n, C. Vogl*, A. Griffin*, R. Sederoff n & R. Whetten n

MeSH headings : Alleles; Bayes Theorem; Chi-Square Distribution; Chromosome Mapping; Chromosomes, Plant; Crosses, Genetic; Eucalyptus / genetics; Genetic Linkage; Genetic Markers; Genome, Plant; Hybridization, Genetic; Markov Chains; Monte Carlo Method; Pedigree; Polymorphism, Restriction Fragment Length; Species Specificity
TL;DR: Contrary to expectation, heterospecific (donor) alleles of TRDLs were favored as often as recurrent alleles in both backcrosses, suggesting that positive and negative heterOSpecific interactions affect introgression rates in this wide interspecific pedigree. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2004 journal article

Metabolic profiling: A new tool in the study of wood formation

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 52(6), 1427–1434.

By: C. Morris n, J. Scott n, H. Chang n, R. Sederoff n, . D O'Malley & J. Kadla n

author keywords: metabolic profiling; principal component analysis (PCA); loblolly pine; xylem tissue; lipid metabolites; polar metabolites
MeSH headings : Cellulose / analysis; Gas Chromatography-Mass Spectrometry; Genotype; Lipid Metabolism; Phenotype; Pinus taeda / chemistry; Pinus taeda / genetics; Pinus taeda / metabolism; Plant Extracts / chemistry; Wood
TL;DR: The first application of metabolic profiling on differentiating xylem tissue of loblolly pine is reported, demonstrating the use of metabolic profiles for the study of wood-forming tissue and as a tool in functional genomics. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Microarray analyses of gene expression during adventitious root development in Pinus contorta (1[w])

PLANT PHYSIOLOGY, 135(3), 1526–1539.

By: M. Brinker n, L. Zyl n, W. Liu n, D. Craig n, R. Sederoff n, D. Clapham n, S. Arnold n

MeSH headings : Cell Division; Gene Expression Regulation, Developmental / genetics; Gene Expression Regulation, Plant / genetics; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis / methods; Pinus / genetics; Pinus / growth & development; Plant Proteins / genetics; Plant Roots / genetics; Plant Roots / growth & development; Polymerase Chain Reaction
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
6. Clean Water and Sanitation (OpenAlex)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

The effect of reduced glutathione on morphology and gene expression of white spruce (Picea glauca) somatic embryos

JOURNAL OF EXPERIMENTAL BOTANY, 55(397), 695–709.

By: C. Stasolla*, M. Belmonte, L. Zyl, D. Craig, W. Liu, E. Yeung, R. Sederoff

author keywords: embryogenesis; glutathione; microarray; transcript levels
MeSH headings : Desiccation; Enzymes / genetics; Gene Expression Regulation, Developmental / genetics; Gene Expression Regulation, Plant / drug effects; Gene Expression Regulation, Plant / genetics; Glutathione / pharmacology; Glutathione Disulfide / metabolism; Picea / cytology; Picea / drug effects; Picea / embryology; Picea / genetics; Plant Proteins / genetics
TL;DR: Inclusions of reduced glutathione (GSH) in the maturation medium increased the conversion frequency of white spruce somatic embryos without the need of a partial drying treatment (PDT). (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Variation an transcript abundance during somatic embryogenesis in gymnosperms

TREE PHYSIOLOGY, 24(10), 1073–1085.

By: C. Stasolla*, P. Bozhkov*, T. Chu*, L. Van Zyl n, U. Egertsdotter, M. Suarez*, D. Craig n, R. Wolfinger*, S. Von Arnold*, R. Sederoff n

author keywords: embryo development; gene expression; hybridization; microarray; Picea abies; Pinus taeda
MeSH headings : Cycadopsida / genetics; Cycadopsida / physiology; Gene Expression Regulation, Plant / physiology; Genetic Variation / physiology; Oligonucleotide Array Sequence Analysis; Picea / genetics; Picea / physiology; Seeds / genetics; Seeds / physiology; Transcription, Genetic / physiology; Trees / genetics; Trees / physiology
TL;DR: Comparison of transcript levels between successive stages of embryogenesis allowed us to identify several genes that showed unique expression responses during normal development, including proteins involved in detoxification processes, methionine synthesis and utilization, and carbohydrate metabolism. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2003 journal article

An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine

Plant Molecular Biology, 52(1), 91–102.

By: Y. Zhang n, G. Brown, R. Whetten, C. Loopstra, D. Neale, M. Kieliszewski, R. Sederoff

author keywords: arabinogalactan proteins (AGPs); Pinus taeda; plant cell wall biosynthesis; xylem differentiation
MeSH headings : Amino Acid Sequence; Antibodies, Monoclonal / immunology; Antibody Specificity; Blotting, Western; Cell Wall / metabolism; Chromatography, High Pressure Liquid / methods; Chromosome Mapping; Escherichia coli / genetics; Haplotypes; Immunohistochemistry; Molecular Sequence Data; Mucoproteins / genetics; Mucoproteins / immunology; Mucoproteins / metabolism; Pinus / genetics; Pinus / metabolism; Pinus taeda; Plant Proteins; Plant Structures / growth & development; Plant Structures / metabolism; Recombinant Proteins / genetics; Recombinant Proteins / isolation & purification; Recombinant Proteins / metabolism; Sequence Alignment; Sequence Analysis, DNA; Sequence Homology, Amino Acid
TL;DR: Investigation of genetic characterization, partial purification and immunolocalization of a classical AGP in loblolly pine showed that the PtaAGP6 epitopes are restricted to a file of cells that just precede secondary cell wall thickening, suggesting roles in xylem differentiation and wood formation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2003 journal article

Analysis of lignin produced by cinnamyl alcohol dehydrogenase-deficient Pinus taeda cultured cells

PLANT PHYSIOLOGY AND BIOCHEMISTRY, 41(5), 439–445.

By: C. Stasolla*, J. Scott, U. Egertsdotter, J. Kadla*, . D O'Malley, R. Sederoff*, L. Zyl

author keywords: cinnamyl alcohol dehydrogenase; cultured cells; dihydroconiferyl alcohol; lignin; Pinus taeda; xylem
TL;DR: The striking similarities in lignin composition observed both in vivo and in vitro, open new possibilities for the use of culture systems aimed at revealing the mechanisms controlling lign in biosynthesis, and the formation of DHCA subunits. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2003 journal article

Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana

Proceedings of the National Academy of Sciences, 100(12), 7383–7388.

By: M. Kirst n, A. Johnson n, C. Baucom n, E. Ulrich n, K. Hubbard n, R. Staggs n, C. Paule n, E. Retzel n, R. Whetten n, R. Sederoff n

MeSH headings : 3' Untranslated Regions; 5' Untranslated Regions; Arabidopsis / genetics; Conserved Sequence; Contig Mapping; DNA, Complementary / genetics; DNA, Plant / genetics; Evolution, Molecular; Expressed Sequence Tags; Gene Expression; Genes, Plant; Genome, Plant; Molecular Sequence Data; Pinus / genetics; Pinus taeda; Retroelements / genetics; Sequence Homology, Nucleic Acid; Species Specificity; Wood
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2003 journal article

Characterisation of PtMYB1, an R2R3-MYB from pine xylem

Plant Molecular Biology, 53(4), 597–608.

By: A. Patzlaff*, L. Newman*, C. Dubos*, R. Whetten n, C. Smith*, S. McInnis*, M. Bevan*, R. Sederoff n, M. Campbell*

author keywords: MYB; phenylalanine ammonia-lyase; phenylpropanoid; pine; xylem
MeSH headings : Adenosine Triphosphate / genetics; Adenosine Triphosphate / metabolism; Base Sequence; Binding Sites / genetics; Cloning, Molecular; Cytidine Triphosphate / genetics; Cytidine Triphosphate / metabolism; DNA, Complementary / chemistry; DNA, Complementary / genetics; Electrophoretic Mobility Shift Assay; Molecular Sequence Data; Oligonucleotides / genetics; Oligonucleotides / metabolism; Phylogeny; Pinus / genetics; Plant Proteins / genetics; Plant Proteins / metabolism; Plant Structures / genetics; Protein Binding; Proto-Oncogene Proteins c-myb / genetics; Proto-Oncogene Proteins c-myb / metabolism; Recombinant Fusion Proteins / genetics; Recombinant Fusion Proteins / metabolism; Saccharomyces cerevisiae / genetics; Sequence Analysis, DNA; Transcription, Genetic / genetics
TL;DR: Rec recombinant PtMYB1 protein was able to bind to AC elements and induce AC-element-dependent shifts in the electrophoretic mobility of a plant promoter that contains three AC elements, the minimal PHENYLALANINE AMMONIA-LYASE 2 (PAL2) promoter from Phaseolus vulgaris. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2003 journal article

Characterisation of a pine MYB that regulates lignification

The Plant Journal, 36(6), 743–754.

By: A. Patzlaff*, S. McInnis*, A. Courtenay*, C. Surman*, L. Newman*, C. Smith*, M. Bevan*, S. Mansfield* ...

author keywords: lignin; MYB; transcription; wood; pine; phenylpropanoid
MeSH headings : Amino Acid Sequence; Arabidopsis / genetics; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / genetics; Base Sequence; DNA, Complementary / genetics; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / genetics; Gene Expression Regulation, Plant / genetics; Gene Library; Genes, myb / genetics; Lignin / genetics; Molecular Sequence Data; Pinus / genetics; Plant Proteins / chemistry; Plant Proteins / genetics; Plants, Genetically Modified / genetics; Plants, Genetically Modified / metabolism; RNA, Plant / genetics; RNA, Plant / isolation & purification; Sequence Alignment; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Tobacco / metabolism; Transcription Factors / chemistry; Transcription Factors / genetics
TL;DR: Electrophoretic mobility shift assays showed that recombinant PtMYB4 protein is able to bind to DNA motifs known as AC elements, consistent with the hypothesis that PtmyB4 is sufficient to induce lignification, and that it may play this role during wood formation in pine. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2003 journal article

Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach

Theoretical and Applied Genetics, 107(6), 1028–1042.

By: A. Myburg n, A. Griffin*, R. Sederoff n & R. Whetten n

author keywords: comparative mapping; AFLP; Eucalyptus; transmission ratio distortion; genome synteny
MeSH headings : Chromosome Mapping; Chromosomes, Plant; Eucalyptus / genetics; Genetic Linkage; Genome, Plant; Inbreeding; Polymorphism, Genetic
TL;DR: The results suggest that hemizygous AFLP loci are dispersed throughout the E. grandis chromosomes of the F1 hybrid, which is characterized by hybrid inviability and hybrid abnormality. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2003 article

Genome studies and molecular genetics - The rice genome and comparative genomics of higher plants - Editorial overview

Sasaki, T., & Sederoff, R. R. (2003, April). CURRENT OPINION IN PLANT BIOLOGY, Vol. 6, pp. 97–100.

By: T. Sasaki* & R. Sederoff n

TL;DR: His team have been sequencing genes that are involved in wood formation and using microarrays to learn about the basis of wood properties, and they are also interested in the sequence relationships of angiosperms and gymnosperms. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2003 journal article

NMR analysis of lignins in CAD-deficient plants. Part 1. Incorporation of hydroxycinnamaldehydes and hydroxybenzaldehydes into lignins

ORGANIC & BIOMOLECULAR CHEMISTRY, 1(2), 268–281.

By: H. Kim*, J. Ralph*, F. Lu*, S. Ralph*, A. Boudet*, J. MacKay*, R. Sederoff n, T. Ito* ...

MeSH headings : Alcohol Oxidoreductases / deficiency; Alcohol Oxidoreductases / genetics; Benzaldehydes / chemistry; Benzaldehydes / metabolism; Carbon Isotopes; Cinnamates / chemistry; Cinnamates / metabolism; Dimerization; Down-Regulation; Lignin / biosynthesis; Lignin / chemistry; Nuclear Magnetic Resonance, Biomolecular; Pinus / enzymology; Pinus / genetics; Pinus / metabolism; Plants, Genetically Modified / enzymology; Plants, Genetically Modified / genetics; Plants, Genetically Modified / metabolism; Tobacco / enzymology; Tobacco / genetics; Tobacco / metabolism
TL;DR: Spectral data from dimers, oligomers, and synthetic polymers have allowed a more substantive assignment of aldehyde components in lignins isolated from a CAD-deficient pine mutant and an antisense-CAD-downregulated transgenic tobacco, suggesting that the aldehydes behave like the traditional monolignols and should probably be regarded as authentic lignin monomers in normal and CAD- deficient plants. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2003 journal article

Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine

Plant Physiology, 133(4), 1702–1716.

By: J. Watkinson, A. Sioson, C. Vasquez-Robinet, M. Shukla, D. Kumar, M. Ellis, L. Heath, N. Ramakrishnan ...

Source: NC State University Libraries
Added: August 6, 2018

2003 journal article

The effects of polyethylene glycol on gene expression of developing white spruce somatic embryos

PLANT PHYSIOLOGY, 131(1), 49–60.

By: C. Stasolla n, L. Zyl n, U. Egertsdotter, D. Craig n, W. Liu n & R. Sederoff n

MeSH headings : Arabidopsis Proteins / genetics; COP9 Signalosome Complex; Carbohydrate Metabolism; Cell Differentiation; Culture Techniques; DNA, Complementary / genetics; DNA, Complementary / metabolism; Disasters; GTP-Binding Proteins; Gene Expression Regulation, Developmental / drug effects; Gene Expression Regulation, Developmental / genetics; Gene Expression Regulation, Plant / drug effects; Gene Expression Regulation, Plant / genetics; Intracellular Signaling Peptides and Proteins; Meristem / genetics; Meristem / growth & development; Nitrogen / metabolism; Oligonucleotide Array Sequence Analysis / methods; Oxidative Stress; Picea / drug effects; Picea / genetics; Picea / growth & development; Pinus / genetics; Plant Roots / genetics; Plant Roots / growth & development; Plant Shoots / genetics; Plant Shoots / growth & development; Polyethylene Glycols / pharmacology; Proteins / genetics; RNA, Plant / genetics; Repressor Proteins; Seeds / drug effects; Seeds / genetics; Seeds / growth & development
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2003 journal article

Transcript profiles of stress-related genes in developing white spruce (Picea glauca) somatic embryos cultured with polyethylene glycol

PLANT SCIENCE, 165(4), 719–729.

By: C. Stasolla*, L. Zyl, U. Egertsdotter, D. Craig, W. Liu & R. Sederoff*

author keywords: microarray; polyethylene glycol; transcript levels; white spruce
TL;DR: The transcript levels of several genes involved in cell aging and detoxification mechanisms, including peroxidases and chitinases, were developmentally regulated during the embryogenic process and differences in the expression of these genes were observed between control and PEG-treated embryos. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2003 journal article

Up, down and up again is a signature global gene expression pattern at the beginning of gymnosperm embryogenesis

GENE EXPRESSION PATTERNS, 3(1), 83–91.

By: L. Zyl n, P. Bozhkov*, D. Clapham*, R. Sederoff n & S. Arnold*

author keywords: Picea abies; embryogenesis; cDNA arrays; gene expression profile; transcriptionally repressive state; developmentally regulated genes; arrested cell line
MeSH headings : Gene Expression / physiology; Gene Expression Profiling; Gene Expression Regulation, Developmental; Phylogeny; Picea / embryology; Picea / metabolism
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2002 journal article

Conservation and synteny of SSR loci and QTLs for vegetative propagation in four Eucalyptus species

THEORETICAL AND APPLIED GENETICS, 105(2-3), 474–478.

By: C. Marques*, R. Brondani*, D. Grattapaglia* & R. Sederoff n

author keywords: SSR; mapping; QTLs; eucalyptus; synteny
TL;DR: Findings indicate high transferability of microsatellite markers between Eucalyptus species of the Symphyomyrtus subgenus and establish foundations for the use of synteny in the genetic analysis of this genus. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2002 journal article

Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P-taeda, P-sylvestris or Picea abies

COMPARATIVE AND FUNCTIONAL GENOMICS, 3(4), 306–318.

By: L. Zyl n, S. Arnold*, P. Bozhkov*, Y. Chen*, U. Egertsdotter, J. MacKay, R. Sederoff n, J. Shen n, L. Zelena, D. Clapham*

author keywords: cDNA array; conifer; normalization; functional genomics; pine; spruce
Source: Web Of Science
Added: August 6, 2018

2002 journal article

Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system

COMPARATIVE AND FUNCTIONAL GENOMICS, 3(3), 226–243.

By: L. Heath*, N. Ramakrishnan*, R. Sederoff n, R. Whetten n, B. Chevone*, C. Struble*, V. Jouenne*, D. Chen* ...

author keywords: microarrays; data mining; experiment management systems; inductive logic programming; reactive oxygen species; drought stress; Pinus taeda; microarray design
TL;DR: The design of Expresso is described as well as results of analysis with Expresso that suggest the importance of molecular chaperones and membrane transport proteins in mechanisms conferring successful adaptation to long-term drought stress. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2001 article

Elucidation of new structures in lignins of CAD- and COMT-deficient plants by NMR

Ralph, J., Lapierre, C., Marita, J. M., Kim, H., Lu, F. C., Hatfield, R. D., … Boerjan, W. (2001, July). PHYTOCHEMISTRY, Vol. 57, pp. 993–1003.

By: J. Ralph*, C. Lapierre*, J. Marita*, H. Kim*, F. Lu*, R. Hatfield*, S. Ralph*, C. Chapple* ...

author keywords: NMR; transgenic; mutant; O-methyltransferase; monolignol; coniferyl aldehyde; sinapyl aldehyde; 5-hydroxyconiferyl alcohol
MeSH headings : Alcohol Oxidoreductases / deficiency; Alcohol Oxidoreductases / metabolism; Cycadopsida / enzymology; Cycadopsida / metabolism; Lignin / biosynthesis; Lignin / chemistry; Methyltransferases / deficiency; Methyltransferases / metabolism; Models, Chemical; Molecular Structure; Nuclear Magnetic Resonance, Biomolecular / methods; Plants, Toxic; Tobacco / enzymology; Tobacco / metabolism
TL;DR: The recognition that novel units can incorporate into lignins portends significantly expanded opportunities for engineering the composition and consequent properties of lignin for improved utilization of valuable plant resources. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2001 journal article

Functional genomics and cell wall biosynthesis in loblolly pine

Plant Molecular Biology, 47(1/2), 275–291.

By: R. Whetten n, Y. Sun n, Y. Zhang n & R. Sederoff n

author keywords: EST sequencing; microarrays; Pinus taeda; xylogenesis; wood formation
TL;DR: Gene discovery by partial DNA sequence determination of cDNA clones is an effective means of building a knowledge base for molecular investigations of mechanisms governing aspects of pine growth and development, including the commercially relevant properties of secondary cell walls in wood. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2001 journal article

Genotypic control of high-frequency adventitious shoot regeneration via somatic organogenesis in loblolly pine

Plant Science, 161(2), 267–272.

By: W. Tang n, R. Whetten n & R. Sederoff n

author keywords: Pinus taedu L.; organogenesis; adventitious shoot regeneration; callus induction frequency; differentiation frequency
TL;DR: The in vitro regeneration procedure established in this investigation could be used for clonal micropropagation of some genotypes of loblolly pine, as well as for establishing a transformation system in coniferous species. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2001 personal communication

Grafting for transgene containment

Lev-Yadun, S., & Sederoff, R. (2001, December).

By: S. Lev-Yadun* & R. Sederoff n

MeSH headings : Biotechnology / methods; Biotechnology / trends; Containment of Biohazards / methods; Genetic Engineering / methods; Plants, Genetically Modified; Transgenes
TL;DR: Overall, broad consensus, if not unanimity, can be found in the following areas: • If GM forest trees are to play a part in intensification, much more research is needed to assess risks and benefits to the environment. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2001 journal article

High-throughput AFLP analysis using infrared dye-labeled primers and an automated DNA sequencer

BIOTECHNIQUES, 30(2), 348-+.

By: A. Myburg n, D. Remington n, . DM O'Malley n, R. Sederoff n & R. Whetten n

MeSH headings : Electrophoresis; Genetic Markers; Genotype; Infrared Rays; Polymerase Chain Reaction; Polymorphism, Genetic; Sequence Analysis, DNA
TL;DR: A protocol for high-throughput AFLP analysis that allows up to 70,000 polymorphic marker genotype determinations per week on a single automated DNA sequencer is developed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2001 journal article

Molecular Cloning and Expression of Eight Laccase cDNAs in Loblolly Pine (Pinus taeda)*

Journal of Plant Research, 114(2), 147–155.

By: Y. Sato*, B. Wuli n, R. Sederoff n & R. Whetten n

author keywords: laccase; lignin synthesis; loblolly pine (Pinus taeda L); xylem differentiation
TL;DR: Northern analysis indicated that all eight of the laccase transcripts are most abundant in differentiating xylem of the six tissues and organs tested, suggesting that laccases play an important role in pine xyleM development. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2001 personal communication

Moribund funding in agricultural research

By: G. Robertson*, P. Barry*, F. Busta*, R. Collier*, N. Keen*, R. Sederoff n, W. Simpkins*, F. Stormshak*, T. Urban*

MeSH headings : Agriculture; Research; Research Support as Topic; United States; United States Department of Agriculture / economics
TL;DR: The double-digit increases in federal funding for basic research at the National Science Foundation and the National Institutes of Health for fiscal year 2001 are a welcome development, but does recognition of basic research as the engine that drives technology and economic growth not apply to agriculture? (via Semantic Scholar)
Source: NC State University Libraries
Added: August 6, 2018

2001 journal article

Pulping and bleaching of CAD-deficient wood

JOURNAL OF WOOD CHEMISTRY AND TECHNOLOGY, 21(1), 1–17.

By: D. Dimmel, J. MacKay*, E. Althen, C. Parks & R. Sederoff*

Source: Web Of Science
Added: August 6, 2018

2001 journal article

Regeneration of transgenic loblolly pine (Pinus taeda L.) from zygotic embryos transformed with Agrobacterium tumefaciens

PLANTA, 213(6), 981–989.

By: W. Tang n, R. Sederoff n & R. Whetten n

author keywords: genetic transformation; beta-glucuronidase gene; Pinus (transformation); plant DNA/T-DNA junction analysis; transgenic pine; zygotic embryo
MeSH headings : Agrobacterium tumefaciens / genetics; Base Sequence; Blotting, Southern; Culture Techniques; DNA, Bacterial / analysis; DNA, Bacterial / genetics; DNA, Plant / analysis; DNA, Plant / genetics; Glucuronidase / genetics; Glucuronidase / metabolism; Pinus / genetics; Pinus / physiology; Pinus taeda; Plant Shoots / genetics; Plant Shoots / physiology; Plant Structures / genetics; Plant Structures / physiology; Plants, Genetically Modified; Polymerase Chain Reaction; Recombinant Fusion Proteins / genetics; Recombinant Fusion Proteins / metabolism; Regeneration / physiology; Seeds / genetics; Seeds / physiology; Transformation, Genetic
TL;DR: The results suggest that an efficient A. tumefaciens-mediated transformation protocol for stable integration of foreign genes into loblolly pine has been developed and that this transformation system could be useful for future studies on transferring economically important genes to lobl Holly pine. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2000 journal article

Differential expression of genes encoding cell wall proteins in vascular tissues from vertical and bent loblolly pine trees

Tree Physiology, 20(7), 457–466.

By: Y. Zhang, R. Sederoff & I. Allona

Source: NC State University Libraries
Added: August 6, 2018

2000 journal article

Lignin structure in a mutant pine deficient in cinnamyl alcohol dehydrogenase

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 48(6), 2326–2331.

By: C. Lapierre n, B. Pollet n, J. MacKay n & R. Sederoff n

author keywords: lignification; altered lignin structure; pine (Pinus taeda L.); thioacidolysis; dihydroconiferyl alcohol
MeSH headings : Alcohol Oxidoreductases / genetics; Cycadopsida / enzymology; Cycadopsida / genetics; Lignin / biosynthesis; Lignin / chemistry; Mutation; Trees / enzymology; Trees / genetics
TL;DR: The results suggest that the CAD-deficient pines efficiently compensate for the shortage in normal lignin precursors by utilizing nontraditional wall phenolics to construct unusual lignins particularly enriched in resistant interunit bonds. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2000 patent

Methods for within family selection in woody perennials using genetic markers

Washington, DC: U.S. Patent and Trademark Office.

By: D. O'Malley, R. Sederoff & D. Grattapaglia

Source: NC State University Libraries
Added: August 6, 2018

2000 review

Pines as model gymnosperms to study evolution, wood formation, and perennial growth

[Review of ]. JOURNAL OF PLANT GROWTH REGULATION, 19(3), 290–305.

By: S. Lev-Yadun* & R. Sederoff n

author keywords: forest biotechnology; genomics; gymnosperms; Pinus; plant longevity; plant reproduction; wood formation; wood structure; xylogenesis
TL;DR: Many features of pine that make it a useful model for gymnosperms and woody plants are summarized and the influence of its reproductive system on methods for genetic analysis and the prospects for genomic studies and genetic engineering are described. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2000 journal article

Tree genomes: What will we understand about them by the year 2020 and how might we use that knowledge?

Forest Genetics and Sustainability, 23.

By: R. Sederoff*

TL;DR: The purpose of this paper is to speculate about the future applications of molecular genetics to the understanding and utilization of tree genomes and to provide an overview of ideas related to application to forest trees of existing technology in the relatively near future. (via Semantic Scholar)
Source: NC State University Libraries
Added: August 6, 2018

1999 article

Building better trees with antisense

Sederoff, R. (1999, August). NATURE BIOTECHNOLOGY, Vol. 17, pp. 750–751.

By: R. Sederoff n

MeSH headings : Cellulose / biosynthesis; Genetic Engineering; Lignin / genetics; Oligonucleotides, Antisense / genetics; Plants, Genetically Modified / genetics; Plants, Genetically Modified / growth & development; Trees / genetics; Trees / growth & development
Source: Web Of Science
Added: August 6, 2018

1999 journal article

Genetic dissection of vegetative propagation traits in Eucalyptus tereticornis and E-globulus

THEORETICAL AND APPLIED GENETICS, 99(6), 936–946.

By: C. Marques, J. Vasquez-Kool*, V. Carocha*, J. Ferreira*, . DM O'Malley, B. Liu*, R. Sederoff*

author keywords: AFLP; pseudo-testcross; Eucalyptus; QTL; vegetative propagation
TL;DR: Results indicate that phenotypic variation in these traits has a meaningful genetic component and that stable QTLs can be found in a family of reasonable size where no previous knowledge of the trait was available. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
3. Good Health and Well-being (OpenAlex)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

1999 journal article

High-efficiency Agrobacterium-mediated transformation of Norway spruce (Picea abies) and loblolly pine (Pinus taeda)

Plant Molecular Biology, 39(3), 407–416.

By: A. Wenck n, M. Quinn n, R. Whetten n, G. Pullman & R. Sederoff n

MeSH headings : Acetophenones / pharmacology; Agrobacterium tumefaciens / genetics; Agrobacterium tumefaciens / growth & development; Agrobacterium tumefaciens / pathogenicity; Base Sequence; Culture Techniques; DNA, Bacterial / analysis; DNA, Bacterial / genetics; Dose-Response Relationship, Drug; Molecular Sequence Data; Pinus taeda; Transformation, Genetic / drug effects; Virulence / genetics
TL;DR: Agrobacterium-mediated gene transfer is a useful technique for large-scale generation of transgenic Norway spruce and may prove useful for other conifer species. (via Semantic Scholar)
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018

1999 patent

Methods for within family selection of disease resistance in woody perennials using genetic markers

Washington, DC: U.S. Patent and Trademark Office.

By: H. Amerson, P. Wilcox, R. Sederoff, E. Kuhlman, D. O'Malley & D. Grattapaglia

Source: NC State University Libraries
Added: August 6, 2018

1999 journal article

Modified lignin and delignification with a CAD-deficient loblolly pine

HOLZFORSCHUNG, 53(4), 403–410.

By: J. MacKay*, T. Presnell, H. Jameel*, H. Taneda, . D O'Malley & R. Sederoff*

author keywords: pine; genetic modification; lignin mutant; delignification; soda pulping; coniferaldehyde
TL;DR: More extensive lignin removal, both in mild alkali treatment and in soda pulping, indicate that suppression of CAD in softwood trees may hold promise to produce woods well suited for “milder” pulping conditions that consume less chemicals and generate less waste. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

1999 journal article

Surfing on AG Biotech into genomics

Molecular Breeding, 5(1999), 485–491.

By: R. Sederoff

Source: NC State University Libraries
Added: August 6, 2018

1999 review

Unexpected variation in lignin

[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 2(2), 145–152.

By: R. Sederoff n, J. MacKay*, J. Ralph* & R. Hatfield*

MeSH headings : Alcohol Oxidoreductases / genetics; Alcohol Oxidoreductases / metabolism; Lignin / biosynthesis; Lignin / chemistry; Mutation; Phenols / metabolism; Plants, Genetically Modified; Trees / genetics; Trees / metabolism
TL;DR: The results argue in favor of an increased potential for genetic modification of lignin and indicate that the knowledge of the biosynthesis of lIGNin is far from complete. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

1998 journal article

AFLP genetic maps of Eucalyptus globulus and E-tereticornis

THEORETICAL AND APPLIED GENETICS, 96(6-7), 727–737.

By: C. Marques n, J. Araujo*, J. Ferreira*, R. Whetten n, . DM O'Malley n, B. Liu n, R. Sederoff n

author keywords: genetic map; linkage; Eucalyptus; AFLP marker
TL;DR: Amplified fragment length polymorphism analysis is a rapid and efficient technique for detecting large numbers of DNA markers in eucalypts and the linkage data developed in these maps will be used to detect loci controlling commercially important traits. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

1998 journal article

Analysis of xylem formation in pine by cDNA sequencing

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 95(16), 9693–9698.

By: I. Allona n, M. Quinn n, E. Shoop n, K. Swope n, S. St Cyr n, J. Carlis n, J. Riedl n, E. Retzel n ...

MeSH headings : DNA, Complementary; Gene Expression Regulation, Plant; Molecular Sequence Data; Trees / genetics; Trees / metabolism; Wood
TL;DR: Sequencing novel genes expressed during xylem formation will provide a powerful means of identifying mechanisms controlling this important differentiation pathway, as well as providing material for comparative analysis of gymnosperm and angiosperm sequences. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

1998 patent

Method of altering lignin in trees

Washington, DC: U.S. Patent and Trademark Office.

By: J. MacKay, D. O'Malley, R. Whetten & R. Sederoff

Source: NC State University Libraries
Added: August 6, 2018

1998 journal article

NMR applications in cell wall research

By: J. Ralph, R. Hatfield, L. Fanchuang, J. Marita, R. Ede, S. Junpeng, S. Quideau, R. Helm ...

Source: NC State University Libraries
Added: August 6, 2018

1998 review

Recent advances in understanding lignin biosynthesis

[Review of ]. ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY, 49(1998), 585–609.

By: R. Whetten n, J. MacKay n & R. Sederoff n

author keywords: monolignol biosynthesis; lignin composition; pulp manufacturing; forage quality; metabolic plasticity
TL;DR: These results argue that the accepted lignin biosynthetic pathway is either incomplete or incorrect, or both; and also suggest that plants may have a high level of metabolic plasticity in the formation of lignins. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

1998 journal article

The promise of forest biotechnology

Paper Age, (1998 Aug.), 13–18.

By: R. Sederoff

Source: NC State University Libraries
Added: August 6, 2018

1997 journal article

Abnormal lignin in a loblolly pine mutant

SCIENCE, 277(5323), 235–239.

By: J. Ralph n, J. MacKay n, R. Hatfield n, D. OMalley n, R. Whetten n & R. Sederoff n

MeSH headings : Alcohol Oxidoreductases / deficiency; Alcohol Oxidoreductases / genetics; Alcohol Oxidoreductases / metabolism; Aldehydes / analysis; Lignin / biosynthesis; Lignin / chemistry; Magnetic Resonance Spectroscopy; Mutation; Oxidation-Reduction; Phenols / analysis; Phenols / metabolism; Pinus taeda; Plant Proteins / genetics; Plant Proteins / metabolism
TL;DR: Novel lignin is formed in a mutant loblolly pine severely depleted in cinnamyl alcohol dehydrogenase, which converts coniferaldehyde to coniferyl alcohol, the primary lignIn precursor in pines. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

1997 article

Inheritance, gene expression, and lignin characterization in a mutant pine deficient in cinnamyl alcohol dehydrogenase

MacKay, J. J., OMalley, D. M., Presnell, T., Booker, F. L., Campbell, M. M., Whetten, R. W., & Sederoff, R. R. (1997, July 22). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol. 94, pp. 8255–8260.

By: J. MacKay n, D. OMalley n, T. Presnell n, F. Booker n, M. Campbell n, R. Whetten n, R. Sederoff n

MeSH headings : Alcohol Oxidoreductases / genetics; Alcohol Oxidoreductases / metabolism; Chromosome Mapping; Gene Expression Regulation, Enzymologic / genetics; Gene Expression Regulation, Plant / genetics; Homozygote; Lignin / metabolism; Mutation; Phenotype; Substrate Specificity; Trees / enzymology; Trees / genetics; Trees / metabolism
TL;DR: Lignin composition in this mutant loblolly pine shows dramatic modifications, including increased incorporation of the substrate of CAD (coniferaldehyde), indicating that CAD may modulate lign in composition in pine. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

1996 conference paper

Molecular markers, forest genetics, and tree breeding

In J. P. Gustafson & R. B. Flavell (Eds.), Genomes of Plants and Animals: 21 Stadler Genetics Symposium (pp. 87–102).

By: D. O'Malley n, D. Grattapaglia*, J. Chaparro n, P. Wilcox n, H. Amerson n, B. Liu n, R. Whetten n, S. McKeand n ...

Ed(s): J. Gustafson & R. Flavell

TL;DR: It is argued that important traits in forest trees such as wood volume, are likely to be controlled by large numbers of genes with small effects, and therefore, are unlikely to have useful marker trait associations. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018

1995 review

LIGNIN BIOSYNTHESIS

[Review of ]. PLANT CELL, 7(7), 1001–1013.

By: R. Whetten* & R. Sederoff*

Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

1994 journal article

Genetic regulation of lignin biosynthesis and the potential modification of wood by genetic engineering in loblolly pine

Genetic Engineering of Plant Secondary Metabolism, 313.

Ed(s): G. B. E. Ellis & H. Stafford

TL;DR: Lignin is needed to support the weight of the plant and to prevent the compression of vascular tissue that would collapse the cell walls, and thus plays an important role in resistance to disease and other adverse environmental stresses. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: NC State University Libraries
Added: August 6, 2018

1994 journal article

Genetic-linkage maps of eucalyptus-grandis and eucalyptus-urophylla using a pseudo-testcross - mapping strategy and rapd markers

Genetics, 137(4), 1121–1137.

By: D. Grattapaglia & R. Sederoff

Source: NC State University Libraries
Added: August 6, 2018

1993 conference paper

Application of genetic markers to tree breeding

Proceedings of the 22nd Southern Forest Tree Improvement Conference, 452–463.

By: D. Grattapaglia, J. Chaparro, P. Wilcox, S. McCord, B. Crane, H. Amerson, D. Werner, B. Liu ...

Source: NC State University Libraries
Added: August 6, 2018

1992 patent

Ballistic transformation of conifers

Washington, DC: U.S. Patent and Trademark Office.

By: A. Stomp, A. Weissinger & R. Sederoff

Source: NC State University Libraries
Added: August 6, 2018

1992 conference paper

Mapping in woody plants with RAPD markers: application to breeding in forestry and horticulture

Proceedings of the Symposium on the Applications of RAPD Technology to Plant Breeding, 37–40. Joint Plant Breeding Symposium Series, Crop Science Society of America, American Society for Horticultural Science, and American Genetics Association.

By: D. Grattapaglia, J. Chaparro, P. Wilcox, S. McCord, D. Werner, H. Amerson, S. McKeand, F. Bridgwater ...

Source: NC State University Libraries
Added: August 6, 2018

1989 patent

Method for transforming pine

Washington, DC: U.S. Patent and Trademark Office.

By: R. Sederoff, A. Stomp, L. Moore & S. Chilton

Source: NC State University Libraries
Added: August 6, 2018

1981 journal article

IMPROVED ESTIMATION OF DNA FRAGMENT LENGTHS FROM AGAROSE GELS

ANALYTICAL BIOCHEMISTRY, 115(1), 113–122.

By: H. Schaffer n & R. Sederoff n

MeSH headings : Bacteriophage lambda; Base Composition; Chromatography, Gel / methods; DNA / isolation & purification; DNA Restriction Enzymes; DNA, Viral / isolation & purification; Mathematics; Molecular Weight; Sepharose
TL;DR: An improved method for estimation of DNA fragment lengths from mobility on agarose gels is introduced, and the lengths of pBR322 fragments of known sequence were predicted with better than 1% accuracy. (via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

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