@article{chen_yu_wang_wang_zhang_zhou_he_meng_wang_liu_et al._2023, title={Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'}, ISSN={["1755-0998"]}, DOI={10.1111/1755-0998.13770}, abstractNote={Abstract}, journal={MOLECULAR ECOLOGY RESOURCES}, author={Chen, Song and Yu, Yue and Wang, Xinyu and Wang, Sui and Zhang, Tianjiao and Zhou, Yan and He, Ruihan and Meng, Nan and Wang, Yiran and Liu, Wenxuan and et al.}, year={2023}, month={Feb} }
 @article{sulis_jiang_yang_marques_matthews_miller_lan_cofre-vega_liu_sun_et al._2023, title={Multiplex CRISPR editing of wood for sustainable fiber production}, volume={381}, ISSN={["1095-9203"]}, url={http://europepmc.org/abstract/med/37440632}, DOI={10.1126/science.add4514}, abstractNote={The domestication of forest trees for a more sustainable fiber bioeconomy has long been hindered by the complexity and plasticity of lignin, a biopolymer in wood that is recalcitrant to chemical and enzymatic degradation. Here, we show that multiplex CRISPR editing enables precise woody feedstock design for combinatorial improvement of lignin composition and wood properties. By assessing every possible combination of 69,123 multigenic editing strategies for 21 lignin biosynthesis genes, we deduced seven different genome editing strategies targeting the concurrent alteration of up to six genes and produced 174 edited poplar variants. CRISPR editing increased the wood carbohydrate-to-lignin ratio up to 228% that of wild type, leading to more-efficient fiber pulping. The edited wood alleviates a major fiber-production bottleneck regardless of changes in tree growth rate and could bring unprecedented operational efficiencies, bioeconomic opportunities, and environmental benefits.}, number={6654}, journal={SCIENCE}, author={Sulis, Daniel B. and Jiang, Xiao and Yang, Chenmin and Marques, Barbara M. and Matthews, Megan L. and Miller, Zachary and Lan, Kai and Cofre-Vega, Carlos and Liu, Baoguang and Sun, Runkun and et al.}, year={2023}, month={Jul}, pages={216-+} }
 @article{peng_tong_lee_wang_yu_huang_wen_makarem_pang_hinjan_et al._2023, title={Overexpression of a gibberellin 20-oxidase gene in poplar xylem led to an increase in the size of nanocellulose fibrils and improved paper properties}, volume={314}, ISSN={["1879-1344"]}, DOI={10.1016/j.carbpol.2023.120959}, abstractNote={Cellulose, the major component of secondary cell walls, is the most abundant renewable long-chain polymer on earth. Nanocellulose has become a prominent nano-reinforcement agent for polymer matrices in various industries. We report the generation of transgenic hybrid poplar overexpressing the Arabidopsis gibberellin 20-oxidase1 gene driven by a xylem-specific promoter to increase gibberellin (GA) biosynthesis in wood. X-ray diffraction (XRD) and sum frequency generation spectroscopic (SFG) analyses showed that cellulose in transgenic trees was less crystalline, but the crystal size was larger. The nanocellulose fibrils prepared from transgenic wood had an increased size compared to those from wild type. When such fibrils were used as a reinforcing agent in sheet paper preparation, the mechanical strength of the paper was significantly enhanced. Engineering the GA pathway can therefore affect nanocellulose properties, providing a new strategy for expanding nanocellulose applications.}, journal={CARBOHYDRATE POLYMERS}, author={Peng, Xiaopeng and Tong, Botong and Lee, Jongcheol and Wang, Kun and Yu, Xiaojuan and Huang, Xiong and Wen, Jialong and Makarem, Mohamadamin and Pang, Hongying and Hinjan, Subin and et al.}, year={2023}, month={Aug} }
 @article{li_cai_han_zhang_sun_xie_han_guo_tigabu_sederoff_et al._2022, title={Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.850054}, abstractNote={Acer pseudosieboldianum (Pax) Komarov is an ornamental plant with prominent potential and is naturally distributed in Northeast China. Here, we obtained a chromosome-scale genome assembly of A. pseudosieboldianum combining HiFi and Hi-C data, and the final assembled genome size was 690.24 Mb and consisted of 287 contigs, with a contig N50 value of 5.7 Mb and a BUSCO complete gene percentage of 98.4%. Genome evolution analysis showed that an ancient duplication occurred in A. pseudosieboldianum. Phylogenetic analyses revealed that Aceraceae family could be incorporated into Sapindaceae, consistent with the present Angiosperm Phylogeny Group system. We further construct a gene-to-metabolite correlation network and identified key genes and metabolites that might be involved in anthocyanin biosynthesis pathways during leaf color change. Additionally, we identified crucial teosinte branched1, cycloidea, and proliferating cell factors (TCP) transcription factors that might be involved in leaf morphology regulation of A. pseudosieboldianum, Acer yangbiense and Acer truncatum. Overall, this reference genome is a valuable resource for evolutionary history studies of A. pseudosieboldianum and lays a fundamental foundation for its molecular breeding.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Li, Xiang and Cai, Kewei and Han, Zhiming and Zhang, Shikai and Sun, Anran and Xie, Ying and Han, Rui and Guo, Ruixue and Tigabu, Mulualem and Sederoff, Ronald and et al.}, year={2022}, month={Mar} }
 @article{zhao_guo_cao_tian_han_sun_li_yang_ji_sederoff_et al._2022, title={Genome-wide identification of the AlkB homologs gene family, PagALKBH9B and PagALKBH10B regulated salt stress response in Populus}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.994154}, abstractNote={The AlkB homologs (ALKBH) gene family regulates N6-methyladenosine (m6A) RNA methylation and is involved in plant growth and the abiotic stress response. Poplar is an important model plant for studying perennial woody plants. Poplars typically have a long juvenile period of 7–10 years, requiring long periods of time for studies of flowering or mature wood properties. Consequently, functional studies of the ALKBH genes in Populus species have been limited. Based on AtALKBHs sequence similarity with Arabidopsis thaliana, 23 PagALKBHs were identified in the genome of the poplar 84K hybrid genotype (P. alba  ×  P. tremula var. glandulosa), and gene structures and conserved domains were confirmed between homologs. The PagALKBH proteins were classified into six groups based on conserved sequence compared with human, Arabidopsis, maize, rice, wheat, tomato, barley, and grape. All homologs of PagALKBHs were tissue-specific; most were highly expressed in leaves. ALKBH9B and ALKBH10B are m6A demethylases and overexpression of their homologs PagALKBH9B and PagALKBH10B reduced m6A RNA methylation in transgenic lines. The number of adventitious roots and the biomass accumulation of transgenic lines decreased compared with WT. Therefore, PagALKBH9B and PagALKBH10B mediate m6A RNA demethylation and play a regulatory role in poplar growth and development. Overexpression of PagALKBH9B and PagALKBH10B can reduce the accumulation of H2O2 and oxidative damage by increasing the activities of SOD, POD, and CAT, and enhancing protection for Chl a/b, thereby increasing the salt tolerance of transgenic lines. However, overexpression lines were more sensitive to drought stress due to reduced proline content. This research revealed comprehensive information about the PagALKBH gene family and their roles in growth and development and responsing to salt stress of poplar.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Zhao, Ye and Guo, Qi and Cao, Sen and Tian, Yanting and Han, Kunjin and Sun, Yuhan and Li, Juan and Yang, Qingshan and Ji, Qingju and Sederoff, Ronald and et al.}, year={2022}, month={Sep} }
 @article{li_cai_zhao_li_wang_tigabu_sederoff_ma_zhao_2022, title={Morphological and Comparative Transcriptome Analysis of Three Species of Five-Needle Pines: Insights Into Phenotypic Evolution and Phylogeny}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.795631}, abstractNote={Pinus koraiensis, Pinus sibirica, and Pinus pumila are the major five-needle pines in northeast China, with substantial economic and ecological values. The phenotypic variation, environmental adaptability and evolutionary relationships of these three five-needle pines remain largely undecided. It is therefore important to study their genetic differentiation and evolutionary history. To obtain more genetic information, the needle transcriptomes of the three five-needle pines were sequenced and assembled. To explore the relationship of sequence information and adaptation to a high mountain environment, data on needle morphological traits [needle length (NL), needle width (NW), needle thickness (NT), and fascicle width (FW)] and 19 climatic variables describing the patterns and intensity of temperature and precipitation at six natural populations were recorded. Geographic coordinates of altitude, latitude, and longitude were also obtained. The needle morphological data was combined with transcriptome information, location, and climate data, for a comparative analysis of the three five-needle pines. We found significant differences for needle traits among the populations of the three five-needle pine species. Transcriptome analysis showed that the phenotypic variation and environmental adaptation of the needles of P. koraiensis, P. sibirica, and P. pumila were related to photosynthesis, respiration, and metabolites. Analysis of orthologs from 11 Pinus species indicated a closer genetic relationship between P. koraiensis and P. sibirica compared to P. pumila. Our study lays a foundation for genetic improvement of these five-needle pines and provides insights into the adaptation and evolution of Pinus species.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Li, Xiang and Cai, Kewei and Zhao, Qiushuang and Li, Hanxi and Wang, Xuelai and Tigabu, Mulualem and Sederoff, Ronald and Ma, Wenjun and Zhao, Xiyang}, year={2022}, month={Feb} }
 @article{li_cai_zhang_pei_chen_jiang_han_zhao_li_zhang_et al._2022, title={The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis}, volume={11}, ISSN={["2047-217X"]}, DOI={10.1093/gigascience/giac057}, abstractNote={Abstract}, journal={GIGASCIENCE}, author={Li, Xiang and Cai, Kewei and Zhang, Qinhui and Pei, Xiaona and Chen, Song and Jiang, Luping and Han, Zhiming and Zhao, Minghui and Li, Yan and Zhang, Xinxin and et al.}, year={2022} }
 @article{wang_lu_zhang_liu_cao_chang_liu_lu_yu_li_et al._2022, title={The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion}, volume={12}, ISSN={["1532-2548"]}, DOI={10.1093/plphys/kiac571}, abstractNote={Abstract}, journal={PLANT PHYSIOLOGY}, author={Wang, Hanhui and Lu, Yanan and Zhang, Tianxu and Liu, Zhi and Cao, Li and Chang, Qiaoying and Liu, Yueying and Lu, Xin and Yu, Song and Li, Huiyu and et al.}, year={2022}, month={Dec} }
 @article{huang_wang_gong_wickell_kuo_zhang_wen_kim_lu_zhao_et al._2022, title={The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence}, ISSN={["2055-0278"]}, DOI={10.1038/s41477-022-01146-6}, abstractNote={Abstract}, journal={NATURE PLANTS}, author={Huang, Xiong and Wang, Wenling and Gong, Ting and Wickell, David and Kuo, Li-Yaung and Zhang, Xingtan and Wen, Jialong and Kim, Hoon and Lu, Fachuang and Zhao, Hansheng and et al.}, year={2022}, month={May} }
 @article{tang_wang_chai_wang_xu_liu_he_liu_zhang_kong_et al._2022, title={Ubiquitinated DA1 negatively regulates vascular cambium activity through modulating the stability of WOX4 in Populus}, ISSN={["1532-298X"]}, DOI={10.1093/plcell/koac178}, abstractNote={Abstract}, journal={PLANT CELL}, author={Tang, Xianfeng and Wang, Congpeng and Chai, Guohua and Wang, Dian and Xu, Hua and Liu, Yu and He, Guo and Liu, Shuqing and Zhang, Yiran and Kong, Yingzhen and et al.}, year={2022}, month={Jun} }
 @article{matthews_wang_sederoff_chiang_williams_2021, title={A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa}, volume={19}, ISSN={["2001-0370"]}, url={http://europepmc.org/abstract/med/33425249}, DOI={10.1016/j.csbj.2020.11.046}, abstractNote={Understanding the mechanisms behind lignin formation is an important research area with significant implications for the bioenergy and biomaterial industries. Computational models are indispensable tools for understanding this complex process. Models of the monolignol pathway in Populus trichocarpa and other plants have been developed to explore how transgenic modifications affect important bioenergy traits. Many of these models, however, only capture one level of biological organization and are unable to capture regulation across multiple biological scales. This limits their ability to predict how gene modification strategies will impact lignin and other wood properties. While the first multiscale model of lignin biosynthesis in P. trichocarpa spanned the transcript, protein, metabolic, and phenotypic layers, it did not account for cross-regulatory influences that could impact abundances of untargeted monolignol transcripts and proteins. Here, we present a multiscale model incorporating these cross-regulatory influences for predicting lignin and wood traits from transgenic knockdowns of the monolignol genes. The three main components of this multiscale model are (1) a transcript-protein model capturing cross-regulatory influences, (2) a kinetic-based metabolic model, and (3) random forest models relating the steady state metabolic fluxes to 25 physical traits. We demonstrate that including the cross-regulatory behavior results in smaller predictive error for 23 of the 25 traits. We use this multiscale model to explore the predicted impact of novel combinatorial knockdowns on key bioenergy traits, and identify the perturbation of PtrC3H3 and PtrCAld5H1&2 monolignol genes as a candidate strategy for increasing saccharification efficiencies while reducing negative impacts on wood density and height.}, journal={COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}, author={Matthews, Megan L. and Wang, Jack P. and Sederoff, Ronald and Chiang, Vincent L. and Williams, Cranos M.}, year={2021}, pages={168–182} }
 @misc{li_li_zhao_pang_wei_tigabu_chiang_sederoff_sederoff_zhao_2021, title={An Overview of the Practices and Management Methods for Enhancing Seed Production in Conifer Plantations for Commercial Use}, volume={7}, ISSN={["2311-7524"]}, DOI={10.3390/horticulturae7080252}, abstractNote={Flowering, the beginning of the reproductive growth, is a significant stage in the growth and development of plants. Conifers are economically and ecologically important, characterized by straight trunks and a good wood quality and, thus, conifer plantations are widely distributed around the world. In addition, conifer species have a good tolerance to biotic and abiotic stress, and a stronger survival ability. Seeds of some conifer species, such as Pinus koraiensis, are rich in vitamins, amino acids, mineral elements and other nutrients, which are used for food and medicine. Although conifers are the largest (giant sequoia) and oldest living plants (bristlecone pine), their growth cycle is relatively long, and the seed yield is unstable. In the present work, we reviewed selected literature and provide a comprehensive overview on the most influential factors and on the methods and techniques that can be adopted in order to improve flowering and seed production in conifers species. 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. Furthermore, several flowering-related genes (FT, Flowering locus T and MADS-box, MCMI, AGAMOUS, DEFICIENCES and SRF) that play a crucial role in flowering in coniferous trees were identified. The results of this study can be useful for forest managers and for enhancing seed yields in conifer plantations for commercial use.}, number={8}, journal={HORTICULTURAE}, author={Li, Yan and Li, Xiang and Zhao, Ming-Hui and Pang, Zhong-Yi and Wei, Jia-Tong and Tigabu, Mulualem and Chiang, Vincent L. and Sederoff, Heike and Sederoff, Ronald and Zhao, Xi-Yang}, year={2021}, month={Aug} }
 @article{wang_dai_pang_cheng_huang_li_yan_lu_wei_sederoff_et al._2021, title={BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAl5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.695223}, abstractNote={Lignin is one of the major components of xylem cell walls in tree stems. The lignin in the wood of most flowering plants (dicotyledonous angiosperms) is typically polymerized from three monolignol precursors, coniferyl alcohol, sinapyl alcohol, and p-coumaroyl alcohol, resulting in guaiacyl (G), syringyl (S), and hydroxyphenyl (H) subunits, respectively. In this study, we focus on the transcriptional regulation of a coniferaldehyde 5-hydroxylase (CAld5H2) gene, which encodes a key enzyme for sinapyl alcohol biosynthesis. We carried out a yeast one-hybrid (Y1H) screen to identify candidate upstream transcription factors (TFs) regulating CAld5H2. We obtained 12 upstream TFs as potential regulators of CAld5H2. One of these TF genes, BLH6a, encodes a BEL1-like homeodomain (BLH) protein and negatively regulated the CAld5H2 promoter activity. The direct regulation of CAld5H2 promoter by BLH6a was supported by chromatin immunoprecipitation–quantitative polymerase chain reaction (ChIP–qPCR) and dominant repression of BLH6a in transgenic plants. Luciferase complementation imaging analyses showed extensive protein–protein interactions among these 12 TFs. We propose that BLH6a is a negative regulator of CAld5H2, which acts through combinatorial regulation of multiple TFs for sinapyl alcohol (S monolignol) biosynthesis in poplar.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Wang, Qiao and Dai, Xinren and Pang, Hongying and Cheng, Yanxia and Huang, Xiong and Li, Hui and Yan, Xiaojing and Lu, Fachuang and Wei, Hairong and Sederoff, Ronald R. and et al.}, year={2021}, month={Jun} }
 @article{wang_dai_pang_cheng_huang_li_yan_lu_wei_sederoff_et al._2021, title={BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAld5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar (vol 12,& nbsp;695223, 2021)}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.761291}, abstractNote={[This corrects the article DOI: 10.3389/fpls.2021.695223.].}, journal={FRONTIERS IN PLANT SCIENCE}, author={Wang, Qiao and Dai, Xinren and Pang, Hongying and Cheng, Yanxia and Huang, Xiong and Li, Hui and Yan, Xiaojing and Lu, Fachuang and Wei, Hairong and Sederoff, Ronald R. and et al.}, year={2021}, month={Sep} }
 @article{lin_sun_song_chen_shi_yang_liu_tunlaya-anukit_liu_loziuk_et al._2021, title={Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa}, volume={12}, ISSN={["1664-462X"]}, url={http://europepmc.org/abstract/med/34691108}, DOI={10.3389/fpls.2021.727932}, abstractNote={Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. InPopulus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation ofPtrHCTsreduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenicP. trichocarpa. The Ptr4CL/PtrHCT interactions were then validatedin vivousing biomolecular fluorescence complementation (BiFC) and protein pull-down assays inP. trichocarpaSDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation inP. trichocarpa.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Lin, Chien-Yuan and Sun, Yi and Song, Jina and Chen, Hsi-Chuan and Shi, Rui and Yang, Chenmin and Liu, Jie and Tunlaya-Anukit, Sermsawat and Liu, Baoguang and Loziuk, Philip L. and et al.}, year={2021}, month={Oct} }
 @article{wang_chen_ali_zhang_wang_zhang_wang_zhang_xie_jiang_et al._2021, title={Epigenetic modification associated with climate regulates betulin biosynthesis in birch}, volume={12}, ISSN={["1993-0607"]}, DOI={10.1007/s11676-021-01424-7}, abstractNote={Abstract}, journal={JOURNAL OF FORESTRY RESEARCH}, author={Wang, Jiang and Chen, Bowei and Ali, Shahid and Zhang, Tianxu and Wang, Yu and Zhang, He and Wang, Lishan and Zhang, Yonglan and Xie, Linan and Jiang, Tingbo and et al.}, year={2021}, month={Dec} }
 @misc{yan_pei_zhang_li_zhang_zhao_chiang_sederoff_zhao_2021, title={MYB-Mediated Regulation of Anthocyanin Biosynthesis}, volume={22}, ISSN={["1422-0067"]}, DOI={10.3390/ijms22063103}, abstractNote={Anthocyanins are natural water-soluble pigments that are important in plants because they endow a variety of colors to vegetative tissues and reproductive plant organs, mainly ranging from red to purple and blue. The colors regulated by anthocyanins give plants different visual effects through different biosynthetic pathways that provide pigmentation for flowers, fruits and seeds to attract pollinators and seed dispersers. The biosynthesis of anthocyanins is genetically determined by structural and regulatory genes. MYB (v-myb avian myeloblastosis viral oncogene homolog) proteins are important transcriptional regulators that play important roles in the regulation of plant secondary metabolism. MYB transcription factors (TFs) occupy a dominant position in the regulatory network of anthocyanin biosynthesis. The TF conserved binding motifs can be combined with other TFs to regulate the enrichment and sedimentation of anthocyanins. In this study, the regulation of anthocyanin biosynthetic mechanisms of MYB-TFs are discussed. The role of the environment in the control of the anthocyanin biosynthesis network is summarized, the complex formation of anthocyanins and the mechanism of environment-induced anthocyanin synthesis are analyzed. 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 anthocyanins for the improvement of crops for food quality, nutrition and human health.}, number={6}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Yan, Huiling and Pei, Xiaona and Zhang, Heng and Li, Xiang and Zhang, Xinxin and Zhao, Minghui and Chiang, Vincent L. and Sederoff, Ronald Ross and Zhao, Xiyang}, year={2021}, month={Mar} }
 @article{li_li_zhao_hu_meng_song_tigabu_chiang_sederoff_ma_et al._2021, title={Molecular and Metabolic Insights into Anthocyanin Biosynthesis for Leaf Color Change in Chokecherry (Padus virginiana)}, volume={22}, ISSN={["1422-0067"]}, DOI={10.3390/ijms221910697}, abstractNote={Chokecherry (Padus virginiana L.) is an important landscaping tree with high ornamental value because of its colorful purplish-red leaves (PRL). The quantifications of anthocyanins and the mechanisms of leaf color change in this species remain unknown. The potential biosynthetic and regulatory mechanisms and the accumulation patterns of anthocyanins in P. virginiana that determine three leaf colors were investigated by combined analysis of the transcriptome and the metabolome. The difference of chlorophyll, carotenoid and anthocyanin content correlated with the formation of P. virginiana leaf color. Using enrichment and correlation network analysis, we found that anthocyanin accumulation differed in different colored leaves and that the accumulation of malvidin 3-O-glucoside (violet) and pelargonidin 3-O-glucoside (orange-red) significantly correlated with the leaf color change from green to purple-red. The flavonoid biosynthesis genes (PAL, CHS and CHI) and their transcriptional regulators (MYB, HD-Zip and bHLH) exhibited specific increased expression during the purple-red periods. Two genes encoding enzymes in the anthocyanin biosynthetic pathway, UDP glucose-flavonoid 3-O-glucosyl-transferase (UFGT) and anthocyanidin 3-O-glucosyltransferase (BZ1), seem to be critical for suppressing the formation of the aforesaid anthocyanins. 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. These results may facilitate genetic modification or selection for further improvement in ornamental qualities of P. virginiana.}, number={19}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Li, Xiang and Li, Yan and Zhao, Minghui and Hu, Yanbo and Meng, Fanjuan and Song, Xingshun and Tigabu, Mulualem and Chiang, Vincent L. and Sederoff, Ronald and Ma, Wenjun and et al.}, year={2021}, month={Oct} }
 @article{liu_li_wang_fan_yang_wang_fu_ge_sederoff_sederoff_et al._2021, title={Qu-2, a robust poplar suspension cell line for molecular biology}, volume={32}, ISSN={["1993-0607"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85097191965&partnerID=MN8TOARS}, DOI={10.1007/s11676-020-01266-9}, abstractNote={Abstract}, number={2}, journal={JOURNAL OF FORESTRY RESEARCH}, author={Liu, Caixia and Li, Kailong and Wang, Meng and Fan, Erqin and Yang, Chuanping and Wang, Junhui and Fu, Pengyue and Ge, Xiaolan and Sederoff, Heike W. and Sederoff, Ronald R. and et al.}, year={2021}, month={Apr}, pages={733–740} }
 @article{li_dai_huang_xu_wang_yan_sederoff_li_2021, title={Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus}, ISSN={["1744-7909"]}, DOI={10.1111/jipb.13159}, abstractNote={Abstract}, journal={JOURNAL OF INTEGRATIVE PLANT BIOLOGY}, author={Li, Hui and Dai, Xinren and Huang, Xiong and Xu, Mengxuan and Wang, Qiao and Yan, Xiaojing and Sederoff, Ronald R. and Li, Quanzi}, year={2021}, month={Oct} }
 @misc{niu_wang_yuan_sederoff_sederoff_chiang_borriss_2020, title={Microbial Interactions Within Multiple-Strain Biological Control Agents Impact Soil-Borne Plant Disease}, volume={11}, ISSN={["1664-302X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85094139988&partnerID=MN8TOARS}, DOI={10.3389/fmicb.2020.585404}, abstractNote={Major losses of crop yield and quality caused by soil-borne plant diseases have long threatened the ecology and economy of agriculture and forestry. Biological control using beneficial microorganisms has become more popular for management of soil-borne pathogens as an environmentally friendly method for protecting plants. Two major barriers limiting the disease-suppressive functions of biocontrol microbes are inadequate colonization of hosts and inefficient inhibition of soil-borne pathogen growth, due to biotic and abiotic factors acting in complex rhizosphere environments. Use of a consortium of microbial strains with disease inhibitory activity may improve the biocontrol efficacy of the disease-inhibiting microbes. The mechanisms of biological control are not fully understood. In this review, we focus on bacterial and fungal biocontrol agents to summarize the current state of the use of single strain and multi-strain biological control consortia in the management of soil-borne diseases. We discuss potential mechanisms used by microbial components to improve the disease suppressing efficacy. We emphasize the interaction-related factors to be considered when constructing multiple-strain biological control consortia and propose a workflow for assembling them by applying a reductionist synthetic community approach.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Niu, Ben and Wang, Weixiong and Yuan, Zhibo and Sederoff, Ronald R. and Sederoff, Heike and Chiang, Vincent L. and Borriss, Rainer}, year={2020}, month={Oct} }
 @article{yan_liu_kim_liu_huang_yang_lin_chen_yang_wang_et al._2019, title={CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa}, volume={222}, ISSN={["1469-8137"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85055556739&partnerID=MN8TOARS}, DOI={10.1111/nph.15505}, abstractNote={Summary}, number={1}, journal={NEW PHYTOLOGIST}, author={Yan, Xiaojing and Liu, Jie and Kim, Hoon and Liu, Baoguang and Huang, Xiong and Yang, Zhichang and Lin, Ying-Chung Jimmy and Chen, Hao and Yang, Chenmin and Wang, Jack P. and et al.}, year={2019}, month={Apr}, pages={244–260} }
 @article{allona_kirst_boerjan_strauss_sederoff_2019, title={Editorial: Forest Genomics and Biotechnology}, volume={10}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2019.01187}, abstractNote={1 Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain, 2 Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain, 3 School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States, 4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium, 5 Center for Plant Systems Biology, VIB, Ghent, Belgium, 6 Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, United States, 7 Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States}, journal={FRONTIERS IN PLANT SCIENCE}, author={Allona, Isabel and Kirst, Matias and Boerjan, Wout and Strauss, Steven and Sederoff, Ronald}, year={2019}, month={Oct} }
 @misc{wang_liu_sun_chiang_sederoff_2019, title={Enzyme-Enzyme Interactions in Monolignol Biosynthesis}, volume={9}, ISSN={["1664-462X"]}, url={http://dx.doi.org/10.3389/fpls.2018.01942}, DOI={10.3389/fpls.2018.01942}, abstractNote={The enzymes that comprise the monolignol biosynthetic pathway have been studied intensively for more than half a century. A major interest has been the role of pathway in the biosynthesis of lignin and the role of lignin in the formation of wood. The pathway has been typically conceived as linear steps that convert phenylalanine into three major monolignols or as a network of enzymes in a metabolic grid. Potential interactions of enzymes have been investigated to test models of metabolic channeling or for higher order interactions. Evidence for enzymatic or physical interactions has been fragmentary and limited to a few enzymes studied in different species. Only recently the entire pathway has been studied comprehensively in any single plant species. 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. The most extensive experiments have been done on differentiating xylem of Populus trichocarpa, where genomic, biochemical, chemical, and cellular experiments have been carried out. Interactions affect the rate, direction, and specificity of both 3 and 4-hydroxylation in the monolignol biosynthetic pathway. Three monolignol P450 mono-oxygenases form heterodimeric and heterotetrameric protein complexes that activate specific hydroxylation of cinnamic acid derivatives. Other interactions include regulatory kinetic control of 4-coumarate CoA ligases through subunit specificity and interactions between a cinnamyl alcohol dehydrogenase and a cinnamoyl-CoA reductase. Monolignol enzyme interactions with other pathway proteins have been associated with biotic and abiotic stress response. Evidence challenging or supporting metabolic channeling in this pathway will be discussed.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Wang, Jack P. and Liu, Baoguang and Sun, Yi and Chiang, Vincent L. and Sederoff, Ronald R.}, year={2019}, month={Jan} }
 @article{naik_wang_sederoff_chiang_williams_ducoste_2018, title={Assessing the impact of the 4CL enzyme complex on the robustness of monolignol biosynthesis using metabolic pathway analysis}, volume={13}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0193896}, DOI={10.1371/journal.pone.0193896}, abstractNote={Lignin is a polymer present in the secondary cell walls of all vascular plants. It is a known barrier to pulping and the extraction of high-energy sugars from cellulosic biomass. The challenge faced with predicting outcomes of transgenic plants with reduced lignin is due in part to the presence of unique protein-protein interactions that influence the regulation and metabolic flux in the pathway. Yet, it is unclear why certain plants have evolved to create these protein complexes. In this study, we use mathematical models to investigate the role that the protein complex, formed specifically between Ptr4CL3 and Ptr4CL5 enzymes, have on the monolignol biosynthesis pathway. The role of this Ptr4CL3-Ptr4CL5 enzyme complex on the steady state flux distribution was quantified by performing Monte Carlo simulations. The effect of this complex on the robustness and the homeostatic properties of the pathway were identified by performing sensitivity and stability analyses, respectively. Results from these robustness and stability analyses suggest that the monolignol biosynthetic pathway is resilient to mild perturbations in the presence of the Ptr4CL3-Ptr4CL5 complex. Specifically, the presence of Ptr4CL3-Ptr4CL5 complex increased the stability of the pathway by 22%. The robustness in the pathway is maintained due to the presence of multiple enzyme isoforms as well as the presence of alternative pathways resulting from the presence of the Ptr4CL3-Ptr4CL5 complex.}, number={3}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Naik, Punith and Wang, Jack P. and Sederoff, Ronald and Chiang, Vincent and Williams, Cranos and Ducoste, Joel J.}, editor={Cullen, DanielEditor}, year={2018}, month={Mar}, pages={e0193896} }
 @article{wang_matthews_williams_shi_yang_tunlaya-anukit_chen_li_liu_lin_et al._2018, title={Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-018-03863-z}, DOI={10.1038/s41467-018-03863-z}, abstractNote={Abstract}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Wang, Jack P. and Matthews, Megan L. and Williams, Cranos M. and Shi, Rui and Yang, Chenmin and Tunlaya-Anukit, Sermsawat and Chen, Hsi-Chuan and Li, Quanzi and Liu, Jie and Lin, Chien-Yuan and et al.}, year={2018}, month={Apr}, pages={1579} }
 @article{lin_chen_li_li_wang_shi_tunlaya-anukit_shuai_wang_ma_et al._2017, title={Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa}, volume={114}, ISSN={["0027-8424"]}, url={http://europepmc.org/abstract/med/29078399}, DOI={10.1073/pnas.1714422114}, abstractNote={Significance}, number={45}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Lin, Ying-Chung Jimmy and Chen, Hao and Li, Quanzi and Li, Wei and Wang, Jack P. and Shi, Rui and Tunlaya-Anukit, Sermsawat and Shuai, Peng and Wang, Zhifeng and Ma, Hongyan and et al.}, year={2017}, month={Nov}, pages={E9722–E9729} }
 @article{shi_wang_lin_li_sun_chen_sederoff_chiang_2017, title={Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa}, volume={245}, ISSN={["1432-2048"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85009291513&partnerID=MN8TOARS}, DOI={10.1007/s00425-016-2640-1}, abstractNote={Co-expression networks based on transcriptomes of Populus trichocarpa major tissues and specific cell types suggest redundant control of cell wall component biosynthetic genes by transcription factors in wood formation. We analyzed the transcriptomes of five tissues (xylem, phloem, shoot, leaf, and root) and two wood forming cell types (fiber and vessel) of Populus trichocarpa to assemble gene co-expression subnetworks associated with wood formation. We identified 165 transcription factors (TFs) that showed xylem-, fiber-, and vessel-specific expression. Of these 165 TFs, 101 co-expressed (correlation coefficient, r > 0.7) with the 45 secondary cell wall cellulose, hemicellulose, and lignin biosynthetic genes. Each cell wall component gene co-expressed on average with 34 TFs, suggesting redundant control of the cell wall component gene expression. Co-expression analysis showed that the 101 TFs and the 45 cell wall component genes each has two distinct groups (groups 1 and 2), based on their co-expression patterns. The group 1 TFs (44 members) are predominantly xylem and fiber specific, and are all highly positively co-expressed with the group 1 cell wall component genes (30 members), suggesting their roles as major wood formation regulators. Group 1 TFs include a lateral organ boundary domain gene (LBD) that has the highest number of positively correlated cell wall component genes (36) and TFs (47). The group 2 TFs have 57 members, including 14 vessel-specific TFs, and are generally less correlated with the cell wall component genes. An exception is a vessel-specific basic helix-loop-helix (bHLH) gene that negatively correlates with 20 cell wall component genes, and may function as a key transcriptional suppressor. The co-expression networks revealed here suggest a well-structured transcriptional homeostasis for cell wall component biosynthesis during wood formation.}, number={5}, journal={PLANTA}, author={Shi, Rui and Wang, Jack P. and Lin, Ying-Chung and Li, Quanzi and Sun, Ying-Hsuan and Chen, Hao and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2017}, month={May}, pages={927–938} }
 @article{lin_li_tunlaya-anukit_shi_sun_wang_liu_loziuk_edmunds_miller_et al._2016, title={A cell wall-bound anionic peroxidase, PtrPO21, is involved in lignin polymerization in Populus trichocarpa}, volume={12}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-016-0978-Y}, DOI={10.1007/s11295-016-0978-y}, number={2}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Lin, Chien-Yuan and Li, Quanzi and Tunlaya-Anukit, Sermsawat and Shi, Rui and Sun, Ying-Hsuan and Wang, Jack P. and Liu, Jie and Loziuk, Philip and Edmunds, Charles W. and Miller, Zachary D. and et al.}, year={2016}, month={Mar} }
 @article{lin_wang_li_chen_liu_loziuk_song_williams_muddiman_sederoff_et al._2015, title={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}, volume={8}, ISSN={["1752-9867"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84925201417&partnerID=MN8TOARS}, DOI={10.1016/j.molp.2014.12.003}, abstractNote={Downregulation of 4-coumaric acid:coenzyme A ligase (4CL) can reduce lignin content in a number of plant species. In lignin precursor (monolignol) biosynthesis during stem wood formation in Populus trichocarpa, two enzymes, Ptr4CL3 and Ptr4CL5, catalyze the coenzyme A (CoA) ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. CoA ligation of 4-coumaric acid is essential for the 3-hydroxylation of 4-coumaroyl shikimic acid. This hydroxylation results from sequential reactions of 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) and 4-coumaric acid 3-hydroxylase 3 (PtrC3H3). Alternatively, 3-hydroxylation of 4-coumaric acid to caffeic acid may occur through an enzyme complex of cinnamic acid 4-hydroxylase 1 and 2 (PtrC4H1 and PtrC4H2) and PtrC3H3. We found that 4-coumaroyl and caffeoyl shikimic acids are inhibitors of Ptr4CL3 and Ptr4CL5. 4-Coumaroyl shikimic acid strongly inhibits the formation of 4-coumaroyl-CoA and caffeoyl-CoA. Caffeoyl shikimic acid inhibits only the formation of 4-coumaroyl-CoA. 4-Coumaroyl and caffeoyl shikimic acids both act as competitive and uncompetitive inhibitors. Metabolic flux in wild-type and PtrC3H3 downregulated P. trichocarpa transgenics has been estimated by absolute protein and metabolite quantification based on liquid chromatography–tandem mass spectrometry, mass action kinetics, and inhibition equations. Inhibition by 4-coumaroyl and caffeoyl shikimic acids may play significant regulatory roles when these inhibitors accumulate.}, number={1}, journal={MOLECULAR PLANT}, author={Lin, Chien-Yuan and Wang, Jack P. and Li, Quanzi and Chen, Hsi-Chuan and Liu, Jie and Loziuk, Philip and Song, Jina and Williams, Cranos and Muddiman, David C. and Sederoff, Ronald R. and et al.}, year={2015}, month={Jan}, pages={176–187} }
 @article{loziuk_parker_li_lin_wang_li_sederoff_chiang_muddiman_2015, title={Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa}, volume={14}, ISSN={["1535-3907"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84942916917&partnerID=MN8TOARS}, DOI={10.1021/acs.jproteome.5b00233}, abstractNote={Cellulose, the main chemical polymer of wood, is the most abundant polysaccharide in nature.1 The ability to perturb the abundance and structure of cellulose microfibrils is of critical importance to the pulp and paper industry as well as for the textile, wood products, and liquid biofuels industries. Although much has been learned at the transcript level about the biosynthesis of cellulose, a quantitative understanding at the proteome level has yet to be established. 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. Development of an effective discovery proteomic strategy through a combination of subcellular fractionation of stem differentiating xylem tissue (SDX) with recently optimized FASP digestion protocols, StageTip fractionation, as well as optimized instrument parameters for global proteomic analysis using the quadrupole-orbitrap mass spectrometer resulted in the deepest proteomic coverage of SDX protein from P. trichocarpa with 9,146 protein groups being identified (1% FDR). Of these, 20 cellulosic/hemicellulosic enzymes and 43 xylem-specific transcription factor groups were identified. Finally, selection of surrogate peptides led to an assay for absolute quantification of 14 cellulosic proteins in SDX of P. trichocarpa.}, number={10}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Loziuk, Philip L. and Parker, Jennifer and Li, Wei and Lin, Chien-Yuan and Wang, Jack P. and Li, Quanzi and Sederoff, Ronald R. and Chiang, Vincent L. and Muddiman, David C.}, year={2015}, month={Oct}, pages={4158–4168} }
 @article{wang_chuang_loziuk_chen_lin_shi_qu_muddiman_sederoff_chiang_2015, title={Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis}, volume={112}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.1510473112}, DOI={10.1073/pnas.1510473112}, abstractNote={Significance}, number={27}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Wang, Jack P. and Chuang, Ling and Loziuk, Philip L. and Chen, Hao and Lin, Ying-Chung and Shi, Rui and Qu, Guan-Zheng and Muddiman, David C. and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2015}, month={Jun}, pages={8481–8486} }
 @article{li_yeh_yang_song_chen_sederoff_chiang_2015, title={Populus trichocarpa}, volume={1224}, ISBN={["978-1-4939-1657-3"]}, ISSN={["1064-3745"]}, DOI={10.1007/978-1-4939-1658-0_28}, abstractNote={Populus trichocarpa Nisqually-1 is a clone of black cottonwood that is widely used as a model woody plant. It was the first woody plant to have a full genome sequence and remains today as the model for growth, metabolism, development, and adaptation for all woody dicotyledonous plants. It is one of the best-annotated plant genomes available. It is also currently studied to improve bioenergy feedstocks and to learn about responses to environmental variation that may result from climate change. It is the best characterized woody plant for lignin biosynthesis. In spite of its role as a model woody plant, many important genetic applications have been limited because it was particularly difficult for DNA transformation. The ability to transform P. trichocarpa is a central component of a systems biology approach to the study of metabolic and developmental processes, where in combination with genome and transcriptome sequencing, all the expressed genes for specific pathways can be defined, cloned, and characterized for biological function. We previously reported on a method for Agrobacterium-mediated genetic transformation in P. trichocarpa(Song et al. Plant Cell Physiol 47: 1582-1589, 2006). Since then, we have optimized the protocol based on many experiments that varied in tissue manipulation, media, DNA constructs and Agrobacterium strains. A modified step-by-step protocol for Agrobacterium-mediated transformation of stem explants is described here. The health of the tissue explants and the time of cocultivation are among the critical steps in the protocol for successful transformation. This updated protocol should be helpful to many laboratories that are currently carrying out P. trichocarpa transformation. It should also encourage many labs that have not yet had success with P. trichocarpa to try again.}, journal={AGROBACTERIUM PROTOCOLS, VOLUME 2, THIRD EDITION}, author={Li, Quanzi and Yeh, Ting-Feng and Yang, Chenmin and Song, Jingyuan and Chen, Zenn-Zong and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2015}, pages={357–363} }
 @article{li_lin_li_shi_lin_chen_chuang_qu_sederoff_chiang_2014, title={A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue}, volume={9}, ISSN={["1750-2799"]}, DOI={10.1038/nprot.2014.146}, abstractNote={Woody cells and tissues are recalcitrant to standard chromatin immunoprecipitation (ChIP) procedures. However, we recently successfully implemented ChIP in wood-forming tissue of the model woody plant Populus trichocarpa. Here we provide the detailed ChIP protocol optimized for wood-forming tissue that we used in those studies. By using stem-differentiating xylem (SDX; a wood-forming tissue), we identified all steps that were ineffective in standard ChIP protocols and systematically modified them to develop and optimize a robust ChIP protocol. The protocol includes tissue collection, cross-linking, nuclear isolation, chromatin extraction, DNA fragmentation, immunoprecipitation, DNA purification and sequence analysis. The protocol takes 2.5 d to complete and allows a robust 8-10-fold enrichment of transcription factor (TF)-bound genomic fragments (~150 ng/g of SDX) over nonspecific DNAs. The enriched DNAs are of high quality and can be used for subsequent PCR and DNA-seq analyses. We used this protocol to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation. Our protocol, which may be suitable for many tissue types, is so far the only working ChIP system for wood-forming tissue.}, number={9}, journal={NATURE PROTOCOLS}, author={Li, Wei and Lin, Ying-Chung and Li, Quanzi and Shi, Rui and Lin, Chien-Yuan and Chen, Hao and Chuang, Ling and Qu, Guan-Zheng and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2014}, month={Sep}, pages={2180–2193} }
 @article{lin_li_chen_li_sun_shi_lin_wang_chen_chuang_et al._2014, title={A simple improved-throughput xylem protoplast system for studying wood formation}, volume={9}, ISSN={["1750-2799"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84907026654&partnerID=MN8TOARS}, DOI={10.1038/nprot.2014.147}, abstractNote={Isolated protoplasts serve as a transient expression system that is highly representative of stable transgenics in terms of transcriptome responses. They can also be used as a cellular system to study gene transactivation and nucleocytoplasmic protein trafficking. They are particularly useful for systems studies in which stable transgenics and mutants are unavailable. We present 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. The method involves tissue preparation, digestion of SDX cell walls, protoplast isolation and DNA transfection. Our approach is markedly faster and provides better yields than previous protocols; small (milligrams)- to large (20 g)-scale SDX preparations can be achieved in ~60 s, with isolation of protoplasts and their subsequent transfection taking ~50 min. Up to ten different samples can be processed simultaneously in this time scale. Our protocol gives a high yield (~2.5 × 10(7) protoplasts per g of SDX) of protoplasts sharing 96% transcriptome identity with intact SDX.}, number={9}, journal={NATURE PROTOCOLS}, author={Lin, Ying-Chung and Li, Wei and Chen, Hao and Li, Quanzi and Sun, Ying-Hsuan and Shi, Rui and Lin, Chien-Yuan and Wang, Jack P. and Chen, Hsi-Chuan and Chuang, Ling and et al.}, year={2014}, month={Sep}, pages={2194–2205} }
 @article{neale_wegrzyn_stevens_zimin_puiu_crepeau_cardeno_koriabine_holtz-morris_liechty_et al._2014, title={Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies}, volume={15}, ISSN={["1474-760X"]}, DOI={10.1186/gb-2014-15-3-r59}, abstractNote={The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome.In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.}, number={3}, journal={GENOME BIOLOGY}, author={Neale, David B. and Wegrzyn, Jill L. and Stevens, Kristian A. and Zimin, Aleksey V. and Puiu, Daniela and Crepeau, Marc W. and Cardeno, Charis and Koriabine, Maxim and Holtz-Morris, Ann E. and Liechty, John D. and et al.}, year={2014} }
 @article{loziuk_sederoff_chiang_muddiman_2014, title={Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry}, volume={139}, ISSN={["1364-5528"]}, DOI={10.1039/c4an00567h}, abstractNote={Relative abundance values and their associated variability are dynamic and dependent on absolute abundance.}, number={21}, journal={ANALYST}, author={Loziuk, Philip L. and Sederoff, Ronald R. and Chiang, Vincent L. and Muddiman, David C.}, year={2014}, pages={5439–5450} }
 @article{chen_song_wang_lin_ducoste_shuford_liu_li_shi_nepomuceno_et al._2014, title={Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling}, volume={26}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.113.119685}, DOI={10.1105/tpc.113.119685}, abstractNote={This work shows that 4CL, an enzyme in monolignol biosynthesis, is found as a heterotetrameric complex of two isoforms in Populus trichocarpa. The activity of the heterotetramer can be described by a mathematical model that explains the effects of each isoform with mixtures of substrates and three types of inhibition, providing insights into the regulation of metabolic flux for this pathway. As a step toward predictive modeling of flux through the pathway of monolignol biosynthesis in stem differentiating xylem of Populus trichocarpa, we discovered that the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterotetrameric protein complex. This conclusion is based on laser microdissection, coimmunoprecipitation, chemical cross-linking, bimolecular fluorescence complementation, and mass spectrometry. The tetramer is composed of three subunits of 4CL3 and one of 4CL5. 4CL5 appears to have a regulatory role. This protein–protein interaction affects the direction and rate of metabolic flux for monolignol biosynthesis in P. trichocarpa. A mathematical model was developed for the behavior of 4CL3 and 4CL5 individually and in mixtures that form the enzyme complex. The model incorporates effects of mixtures of multiple hydroxycinnamic acid substrates, competitive inhibition, uncompetitive inhibition, and self-inhibition, along with characteristic of the substrates, the enzyme isoforms, and the tetrameric complex. Kinetic analysis of different ratios of the enzyme isoforms shows both inhibition and activation components, which are explained by the mathematical model and provide insight into the regulation of metabolic flux for monolignol biosynthesis by protein complex formation.}, number={3}, journal={The Plant Cell}, publisher={Oxford University Press (OUP)}, author={Chen, Hsi-Chuan and Song, Jina and Wang, Jack P. and Lin, Ying-Chung and Ducoste, Joel and Shuford, Christopher M. and Liu, Jie and Li, Quanzi and Shi, Rui and Nepomuceno, Angelito and et al.}, year={2014}, month={Mar}, pages={876–893} }
 @article{sederoff_2013, title={GENOMICS A spruce sequence}, volume={497}, ISSN={["0028-0836"]}, DOI={10.1038/nature12250}, number={7451}, journal={NATURE}, author={Sederoff, Ronald}, year={2013}, month={May}, pages={569–570} }
 @article{liu_peng_li_sun_chiang_sederoff_2013, title={High-level gene expression in differentiating xylem of tobacco driven by a 2.0 kb Poplar COMT2 promoter and a 4 x 35S enhancer}, volume={30}, ISSN={["1342-4580"]}, DOI={10.5511/plantbiotechnology.13.0213a}, abstractNote={Promoter constructs with high levels of xylem specific expression are needed to obtain efficient expression of candidate genes, microRNAs (miRNAs) and artificial microRNAs (amiRNAs) for the genetic modification of wood properties. The gene for caffeic acid O-methytransferase (PtrCOMT2) has the second most abundant transcript level of all the genes in monolignol biosynthesis in Populus trichocarpa and a high level of specificity in differentiating xylem. To characterize the PtrCOMT2 promoter, we cloned a short (2.0 kb) and a long (3.3 kb) promoter segment and compared their expression using GUS as a reporter gene in the differentiating xylem of Nicotiana tabacum. Both the 2.0 kb and the 3.3 kb promoter segments showed high specificity for differentiating xylem in this heterologous system. GUS activity increased as much as 5 times when the 4×35S enhancer was inserted in front of the 2.0 kb promoter, but GUS activity was only increased 2 times when the enhancer was inserted behind the promoter. The enhancer inserted upstream reduced the expression of the 3.3 kb promoter. While expression of some of the enhancer-plus-promoter constructs increased expression, there was a loss of specificity.}, number={2}, journal={PLANT BIOTECHNOLOGY}, author={Liu, Enying and Peng, Shaobing and Li, Quanzi and Sun, Ying-Hsuan and Chiang, Vincent L. and Sederoff, Ronald R.}, year={2013}, pages={191–198} }
 @article{chen_song_williams_shuford_liu_wang_li_shi_gokce_ducoste_et al._2013, title={Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes}, volume={161}, ISSN={["0032-0889"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84874626790&partnerID=MN8TOARS}, DOI={10.1104/pp.112.210971}, abstractNote={Abstract}, number={3}, journal={PLANT PHYSIOLOGY}, author={Chen, Hsi-Chuan and Song, Jina and Williams, Cranos M. and Shuford, Christopher M. and Liu, Jie and Wang, Jack P. and Li, Quanzi and Shi, Rui and Gokce, Emine and Ducoste, Joel and et al.}, year={2013}, month={Mar}, pages={1501–1516} }
 @article{lu_li_wei_chang_tunlaya-anukit_kim_liu_song_sun_yuan_et al._2013, title={Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa}, volume={110}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.1308936110}, DOI={10.1073/pnas.1308936110}, abstractNote={
            Laccases, as early as 1959, were proposed to catalyze the oxidative polymerization of monolignols. Genetic evidence in support of this hypothesis has been elusive due to functional redundancy of laccase genes. An
            Arabidopsis
            double mutant demonstrated the involvement of laccases in lignin biosynthesis. We previously identified a subset of laccase genes to be targets of a microRNA (miRNA) ptr-miR397a in
            Populus trichocarpa
            . To elucidate the roles of ptr-miR397a and its targets, we characterized the laccase gene family and identified 49 laccase gene models, of which 29 were predicted to be targets of ptr-miR397a. We overexpressed
            Ptr-MIR397a
            in transgenic
            P. trichocarpa
            . In each of all nine transgenic lines tested, 17
            PtrLAC
            s were down-regulated as analyzed by RNA-seq. Transgenic lines with severe reduction in the expression of these laccase genes resulted in an ∼40% decrease in the total laccase activity. Overexpression of
            Ptr-MIR397a
            in these transgenic lines also reduced lignin content, whereas levels of all monolignol biosynthetic gene transcripts remained unchanged. 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. Full transcriptome–based differential gene expression in the overexpressed transgenics and protein domain analyses implicate previously unidentified transcription factors and their targets in an extended hierarchical GRN including ptr-miR397a and laccases that coregulate lignin biosynthesis in wood formation. Ptr-miR397a, laccases, and other regulatory components of this network may provide additional strategies for genetic manipulation of lignin content.
          }, number={26}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Lu, S. and Li, Q. and Wei, H. and Chang, M.-J. and Tunlaya-Anukit, S. and Kim, H. and Liu, J. and Song, J. and Sun, Y.-H. and Yuan, L. and et al.}, year={2013}, month={Jun}, pages={10848–10853} }
 @article{shi_shuford_wang_sun_yang_chen_tunlaya-anukit_li_liu_muddiman_et al._2013, title={Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa}, volume={238}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84882877816&partnerID=MN8TOARS}, DOI={10.1007/s00425-013-1905-1}, abstractNote={Phenylalanine ammonia-lyase (PAL) catalyzes the initial step of phenylpropanoid biosynthesis in plants. Five PAL genes (PtrPAL1 to 5) have been identified in Populus trichocarpa. These genes are classified into two subgroups according to their transcript sequence similarity and tissue specificity. However, the regulation of these genes and their protein functions are not well understood. In this study, enzymatic properties of each PtrPALs were characterized based on their recombinant proteins expressed in E.coli. Subcellular localizations of each PtrPALs in stem wood forming tissue were investigated and individual PtrPAL protein abundances in cytosol and membrane protein fractions were measured using protein cleavage-isotope dilution mass spectrometry (PC-IDMS). Protein/mRNA ratios of PtrPALs were further verified using RNA-Seq and gel-enhanced liquid chromatography mass spectrometry (GeLC-MS). All PtrPALs have similar catalytic properties for the deamination of L-phenylalanine, their major substrate. All PtrPALs have similar subcellular locations in stem wood forming tissue, with major amount in the cytosol (93-96 %) and less in the membrane (4-7 %). However, the protein/mRNA ratios of subgroup A (PtrPAL2, 4 and 5) are about five times that of subgroup B (PtrPAL1 and 3) in stem wood forming tissue, while all PtrPALs have similar transcript abundances. These results indicate a greater functional significance of subgroup A PtrPALs for stem wood formation, and highlight the role of gene post-transcriptional regulation.}, number={3}, journal={Planta}, author={Shi, R. and Shuford, C. M. and Wang, Jack P. and Sun, Y. H. and Yang, Z. C. and Chen, H. C. and Tunlaya-Anukit, S. and Li, Q. Z. and Liu, J. and Muddiman, David and et al.}, year={2013}, pages={487–497} }
 @article{lin_li_sun_kumari_wei_li_tunlaya-anukit_sederoff_chiang_2013, title={SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa}, volume={25}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.113.117697}, abstractNote={Novel methods were developed and demonstrated for the discovery of genetic regulatory networks in wood-forming tissues. Transfection of protoplasts from differentiating xylem with the transcription factor gene Ptr-SND1-B1 and novel computational analysis revealed a three-level hierarchical genetic regulatory network that was verified by ChIP and Ptr-SND1-B1 overexpression in transgenic plants. Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed 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. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexpressed Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1), a TF gene affecting wood formation, in these protoplasts and identified differentially expressed genes by RNA sequencing. Direct Ptr-SND1-B1–DNA interactions were then inferred by integration of time-course RNA sequencing data and top-down Graphical Gaussian Modeling–based algorithms. These Ptr-SND1-B1-DNA interactions were verified to function in differentiating xylem by anti-PtrSND1-B1 antibody-based chromatin immunoprecipitation (97% accuracy) and in stable transgenic P. trichocarpa (90% accuracy). In this way, we established a Ptr-SND1-B1–directed quantitative hGRN involving 76 direct targets, including eight TF and 61 enzyme-coding genes previously unidentified as targets. The network can be extended to the third layer from the second-layer TFs by computation or by overexpression of a second-layer TF to identify a new group of direct targets (third layer). This approach would allow the sequential establishment, one two-layered hGRN at a time, of all layers involved in a more comprehensive hGRN. Our approach may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable.}, number={11}, journal={PLANT CELL}, author={Lin, Ying-Chung and Li, Wei and Sun, Ying-Hsuan and Kumari, Sapna and Wei, Hairong and Li, Quanzi and Tunlaya-Anukit, Sermsawat and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2013}, month={Nov}, pages={4324–4341} }
 @article{albert_barbazuk_depamphilis_der_leebens-mack_ma_palmer_rounsley_sankoff_schuster_et al._2013, title={The Amborella Genome and the Evolution of Flowering Plants}, volume={342}, ISSN={["1095-9203"]}, url={http://science.sciencemag.org/content/342/6165/1241089.long}, DOI={10.1126/science.1241089}, abstractNote={Shaping Plant Evolution}, number={6165}, journal={Science}, author={Albert, Victor A. and Barbazuk, W. Bradley and dePamphilis, Claude W. and Der, Joshua P. and Leebens-Mack, James and Ma, Hong and Palmer, Jeffrey D. and Rounsley, Steve and Sankoff, David and Schuster, Stephan C. and et al.}, year={2013}, month={Dec}, pages={1456–1457} }
 @article{loziuk_wang_li_sederoff_chiang_muddiman_2013, title={Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments}, volume={12}, ISSN={["1535-3907"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84890109136&partnerID=MN8TOARS}, DOI={10.1021/pr4008442}, abstractNote={Workflows in bottom-up proteomics have traditionally implemented the use of proteolysis during sample preparation; enzymatic digestion is most commonly performed using trypsin. This results in the hydrolysis of peptide bonds forming tryptic peptides, which can then be subjected to LC-MS/MS analysis. While the structure, specificity, and kinetics of trypsin are well characterized, a lack of consensus and understanding has remained regarding fundamental parameters critical to obtaining optimal data from a proteomics experiment. These include the type of trypsin used, pH during digestion, incubation temperature as well as enzyme-to-substrate ratio. Through the use of design of experiments (DOE), we optimized these parameters, resulting in deeper proteome coverage and a greater dynamic range of measurement. The knowledge gained from optimization of a discovery-based proteomics experiment was applied to targeted LC-MS/MS experiments using protein cleavage-isotope dilution mass spectrometry for absolute quantification. We demonstrated the importance of these digest parameters with respect to our limit of detection as well as our ability to acquire more accurate quantitative measurements. Additionally, we were able to quantitatively account for peptide decay observed in previous studies, caused by nonspecific activity of trypsin. 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.}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Loziuk, Philip L. and Wang, Jack and Li, Quanzi and Sederoff, Ronald R. and Chiang, Vincent L. and Muddiman, David C.}, year={2013}, month={Dec}, pages={5820–5829} }
 @article{liu_shi_li_sederoff_chiang_2012, title={A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities}, volume={236}, ISSN={["0032-0935"]}, DOI={10.1007/s00425-012-1688-9}, abstractNote={Lignin content and composition are largely determined by the composition and quantity of the monolignol precursors. Individual enzymes of the monolignol biosynthetic pathway determine the composition and quantity of monolignols. Monolignol biosynthesis in angiosperms is mediated by ten enzyme families. We 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 Populus trichocarpa. As little as 300 mg fresh weight of SDX is sufficient for triplicate assays of all ten enzyme activities. To expand the effectiveness of the analysis, we quantified the reaction products directly by HPLC and developed a universal method that can separate the substrates and products of all enzymes. The specific activities measured with this simple approach are similar to those obtained with the optimum conditions previously established for each individual enzyme. This approach is applicable to the enzyme activity analysis for both P. trichocarpa (angiosperm) and Pinus taeda (gymnosperm) and is particularly useful when a large number of samples need to be analyzed for all monolignol biosynthetic enzymes.}, number={3}, journal={PLANTA}, author={Liu, Jie and Shi, Rui and Li, Quanzi and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2012}, month={Sep}, pages={879–885} }
 @article{kubisiak_nelson_staton_zhebentyayeva_smith_olukolu_fang_hebard_anagnostakis_wheeler_et al._2012, title={A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)}, volume={9}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-012-0579-3}, DOI={10.1007/s11295-012-0579-3}, abstractNote={The Chinese chestnut (Castanea mollissima) carries resistance to Cryphonectria parasitica, the fungal pathogen inciting chestnut blight. The pathogen, introduced from Asia, devastated the American chestnut (Castanea dentata) throughout its native range early in the twentieth century. A highly informative genetic map of Chinese chestnut was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut. Two mapping populations were established with three Chinese chestnut parents, ‘Mahogany’, ‘Nanking’, and ‘Vanuxem’, totaling 337 progeny. The transcriptome-based genetic map was created with 329 simple sequence repeat and 1,064 single nucleotide polymorphism markers all derived from expressed sequence tag sequences. Genetic maps for each parent were developed and combined to establish 12 consensus linkage groups spanning 742 cM, providing the the most comprehensive genetic map for a Fagaceae species to date. Over 75 % of the mapped markers from the Chinese chestnut consensus genetic map were placed on the physical map using overgo hybridization, providing a fully integrated genetic and physical map resource for Castanea spp. About half (57 %) of the Chinese chestnut genetic map could be assigned to regions of segmental homology with 58 % of the peach (Prunus persica) genome assembly. A three quantitative trait loci (QTL) model for blight resistance was verified using the new genetic markers and an existing interspecies (C. mollissima × C. dentata) F2 mapping population. Two of the blight resistance QTLs in chestnut shared synteny with two QTLs for powdery mildew resistance in peach, indicating the potential conservation of disease resistance genes at these loci.}, number={2}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Kubisiak, T. L. and Nelson, C. D. and Staton, M. E. and Zhebentyayeva, T. and Smith, C. and Olukolu, B. A. and Fang, G.-C. and Hebard, F. V. and Anagnostakis, S. and Wheeler, N. and et al.}, year={2012}, month={Nov}, pages={557–571} }
 @article{shuford_li_sun_chen_wang_shi_sederoff_chiang_muddiman_2012, title={Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry}, volume={11}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr300205a}, DOI={10.1021/pr300205a}, abstractNote={The economic value of wood/pulp from many tree species is largely dictated by the quantity and chemical properties of lignin, which is directly related to the composition and linkages of monolignols comprising the polymer. Although much is known regarding the monolignol biosynthetic pathway, our understanding is still deficient due to the lack of quantitative information at the proteomic level. We developed an assay based on protein cleavage isotope dilution mass spectrometry (PC-IDMS) for the determination of all potential, primary enzymes involved in the biosynthesis of monolignols and the peroxidases responsible for their polymerization to form lignin in the model tree species, Populus trichocarpa. Described is the identification of quantitative surrogate peptides through shotgun analysis of native and recombinant proteins, optimization of trypsin proteolysis using fractional factorial design of experiments, and development of a liquid chromatography-selected reaction monitoring method for specific detection of all targeted peptides. Of the 25 targeted enzymes, three were undetected in the normal xylem tissues, and all but two of the detectable species showed good day-to-day precision (CV < 10%). 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.}, number={6}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Shuford, Christopher M. and Li, Quanzi and Sun, Ying-Hsuan and Chen, Hsi-Chuan and Wang, Jack and Shi, Rui and Sederoff, Ronald. R. and Chiang, Vincent L. and Muddiman, David C.}, year={2012}, month={May}, pages={3390–3404} }
 @article{wang_shuford_li_song_lin_sun_chen_williams_muddiman_sederoff_et al._2012, title={Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis}, volume={236}, ISSN={["1432-2048"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84865584315&partnerID=MN8TOARS}, DOI={10.1007/s00425-012-1663-5}, abstractNote={Flowering plants have syringyl and guaiacyl subunits in lignin in contrast to the guaiacyl lignin in gymnosperms. The biosynthesis of syringyl subunits is initiated by coniferaldehyde 5-hydroxylase (CAld5H). In Populus trichocarpa there are two closely related CAld5H enzymes (PtrCAld5H1 and PtrCAld5H2) associated with lignin biosynthesis during wood formation. We used yeast recombinant PtrCAld5H1 and PtrCAld5H2 proteins to carry out Michaelis-Menten and inhibition kinetics with LC-MS/MS based absolute protein quantification. CAld5H, a monooxygenase, requires a cytochrome P450 reductase (CPR) as an electron donor. We cloned and expressed three P. trichocarpa CPRs in yeast and show that all are active with both CAld5Hs. The kinetic analysis shows both CAld5Hs have essentially the same biochemical functions. When both CAld5Hs are coexpressed in the same yeast membranes, the resulting enzyme activities are additive, suggesting functional redundancy and independence of these two enzymes. Simulated reaction flux based on Michaelis-Menten kinetics and inhibition kinetics confirmed the redundancy and independence. Subcellular localization of both CAld5Hs as sGFP fusion proteins expressed in P. trichocarpa differentiating xylem protoplasts indicate that they are endoplasmic reticulum resident proteins. These results imply that during wood formation, 5-hydroxylation in monolignol biosynthesis of P. trichocarpa requires the combined metabolic flux of these two CAld5Hs to maintain adequate biosynthesis of syringyl lignin. 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.}, number={3}, journal={PLANTA}, publisher={Springer Science + Business Media}, author={Wang, Jack P. and Shuford, Christopher M. and Li, Quanzi and Song, Jina and Lin, Ying-Chung and Sun, Ying-Hsuan and Chen, Hsi-Chuan and Williams, Cranos M. and Muddiman, David C. and Sederoff, Ronald R. and et al.}, year={2012}, month={Sep}, pages={795–808} }
 @article{sun_shi_zhang_chiang_sederoff_2012, title={MicroRNAs in trees}, volume={80}, ISSN={["0167-4412"]}, DOI={10.1007/s11103-011-9864-z}, abstractNote={MicroRNAs (miRNAs) are 20-24 nucleotide long molecules processed from a specific class of RNA polymerase II transcripts that mainly regulate the stability of mRNAs containing a complementary sequence by targeted degradation in plants. Many features of tree biology are regulated by miRNAs affecting development, metabolism, adaptation and evolution. MiRNAs may be modified and harnessed for controlled suppression of specific genes to learn about gene function, or for practical applications through genetic engineering. Modified (artificial) miRNAs act as dominant suppressors and are particularly useful in tree genetics because they bypass the generations of inbreeding needed for fixation of recessive mutations. The purpose of this review is to summarize the current status of information on miRNAs 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.}, number={1}, journal={PLANT MOLECULAR BIOLOGY}, author={Sun, Ying-Hsuan and Shi, Rui and Zhang, Xing-Hai and Chiang, Vincent L. and Sederoff, Ronald R.}, year={2012}, month={Sep}, pages={37–53} }
 @article{li_lin_sun_song_chen_zhang_sederoff_chiang_2012, title={Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa}, volume={109}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1212977109}, abstractNote={
            Secondary Wall-Associated NAC Domain 1s (SND1s) are transcription factors (TFs) known to activate a cascade of
            TF
            and pathway genes affecting secondary cell wall biosynthesis (xylogenesis) in
            Arabidopsis
            and poplars. Elevated SND1 transcriptional activation leads to ectopic xylogenesis and stunted growth. Nothing is known about the upstream regulators of
            SND1
            . Here we report the discovery of a stem-differentiating xylem (SDX)-specific alternative
            SND1
            splice variant,
            PtrSND1
            -
            A2
            
              IR
            
            , that acts as a dominant negative of SND1 transcriptional network genes in
            Populus trichocarpa
            .
            PtrSND1
            -
            A2
            
              IR
            
            derives from
            PtrSND1-A2
            , one of the four fully spliced
            PtrSND1
            gene family members (
            PtrSND1
            -
            A1
            , -
            A2
            , -
            B1
            , and -
            B2
            ). Each full-size PtrSND1 activates its own gene, and all four full-size members activate a common
            MYB
            gene (
            PtrMYB021
            ). PtrSND1-A2
            IR
            represses the expression of its
            PtrSND1
            member genes and
            PtrMYB021
            . Repression of the autoregulation of a TF family by its only splice variant has not been previously reported in plants. PtrSND1-A2
            IR
            lacks DNA binding and transactivation abilities but retains dimerization capability. PtrSND1-A2
            IR
            is localized exclusively in cytoplasmic foci. In the presence of any full-size PtrSND1 member, PtrSND1-A2
            IR
            is translocated into the nucleus exclusively as a heterodimeric partner with full-size PtrSND1s. Our findings are consistent with a model in which the translocated PtrSND1-A2
            IR
            lacking DNA-binding and transactivating abilities can disrupt the function of full-size PtrSND1s, making them nonproductive through heterodimerization, and thereby modulating the SND1 transcriptional network. PtrSND1-A2
            IR
            may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth.
          }, number={36}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Li, Quanzi and Lin, Ying-Chung and Sun, Ying-Hsuan and Song, Jian and Chen, Hao and Zhang, Xing-Hai and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2012}, month={Sep}, pages={14699–14704} }
 @article{chen_li_shuford_liu_muddiman_sederoff_chiang_2011, title={Membrane protein complexes catalyze both 4-and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis}, volume={108}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1116416109}, abstractNote={
            The hydroxylation of 4- and 3-ring carbons of cinnamic acid derivatives during monolignol biosynthesis are key steps that determine the structure and properties of lignin. Individual enzymes have been thought to catalyze these reactions. In stem differentiating xylem (SDX) of
            Populus trichocarpa
            , two cinnamic acid 4-hydroxylases (PtrC4H1 and PtrC4H2) and a
            p
            -coumaroyl ester 3-hydroxylase (PtrC3H3) are the enzymes involved in these reactions. Here we present evidence that these hydroxylases interact, forming heterodimeric (PtrC4H1/C4H2, PtrC4H1/C3H3, and PtrC4H2/C3H3) and heterotrimeric (PtrC4H1/C4H2/C3H3) membrane protein complexes. Enzyme kinetics using yeast recombinant proteins demonstrated that the enzymatic efficiency (
            V
            max
            /
            k
            m
            ) for any of the complexes is 70–6,500 times greater than that of the individual proteins. The highest increase in efficiency was found for the PtrC4H1/C4H2/C3H3-mediated
            p
            -coumaroyl ester 3-hydroxylation. Affinity purification-quantitative mass spectrometry, bimolecular fluorescence complementation, chemical cross-linking, and reciprocal coimmunoprecipitation provide further evidence for these multiprotein complexes. The activities of the recombinant and SDX plant proteins demonstrate two protein-complex–mediated 3-hydroxylation paths in monolignol biosynthesis in
            P
            .
            trichocarpa
            SDX; one converts
            p
            -coumaric acid to caffeic acid and the other converts
            p
            -coumaroyl shikimic acid to caffeoyl shikimic acid. Cinnamic acid 4-hydroxylation is also mediated by the same protein complexes. These results provide direct evidence for functional involvement of membrane protein complexes in monolignol biosynthesis.
          }, number={52}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Chen, Hsi-Chuan and Li, Quanzi and Shuford, Christopher M. and Liu, Jie and Muddiman, David C. and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2011}, month={Dec}, pages={21253–21258} }
 @article{wyatt_sederoff_flaishman_lev-yadun_2010, title={Arabidopsis thaliana as a model for gelatinous fiber formation}, volume={57}, ISSN={["1021-4437"]}, DOI={10.1134/s1021443710030076}, number={3}, journal={RUSSIAN JOURNAL OF PLANT PHYSIOLOGY}, author={Wyatt, S. E. and Sederoff, R. and Flaishman, M. A. and Lev-Yadun, S.}, year={2010}, month={May}, pages={363–367} }
 @article{kremer_sederoff_wheeler_2010, title={Genomics of forest and ecosystem health in the Fagaceae: meeting report}, volume={6}, ISSN={["1614-2942"]}, DOI={10.1007/s11295-010-0277-y}, abstractNote={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. Major conference themes targeted Genomic Tool Development for the Fagaceae and Application of Genomic Resources. The meeting provided a venue for reviewing the rapidly expanding knowledge base on Fagaceae genomics and for developing collaborations between scientists from Europe and North America.}, number={5}, journal={TREE GENETICS & GENOMES}, author={Kremer, Antoine and Sederoff, Ronald and Wheeler, Nicholas}, year={2010}, month={Oct}, pages={815–820} }
 @article{novaes_kirst_chiang_winter-sederoff_sederoff_2010, title={Lignin and Biomass: A Negative Correlation for Wood Formation and Lignin Content in Trees}, volume={154}, ISSN={["0032-0889"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957730551&partnerID=MN8TOARS}, DOI={10.1104/pp.110.161281}, abstractNote={Studies in populations of forest tree hybrids have shown a negative correlation of biomass growth (usually measured as wood volume) and lignin content ([Kirst et al., 2004][1]; [Novaes et al., 2009][2]). The control of growth and lignin appears to be highly regulated, implying that selection for}, number={2}, journal={PLANT PHYSIOLOGY}, author={Novaes, Evandro and Kirst, Matias and Chiang, Vincent and Winter-Sederoff, Heike and Sederoff, Ronald}, year={2010}, month={Oct}, pages={555–561} }
 @article{shi_yang_lu_sederoff_chiang_2010, title={Specific down-regulation of PAL genes by artificial microRNAs in Populus trichocarpa}, volume={232}, ISSN={["0032-0935"]}, DOI={10.1007/s00425-010-1253-3}, abstractNote={Artificial microRNAs (amiRNAs) are similar to microRNAs (miRNAs) in that they are able to reduce the abundance of specific transcripts in plants by RNA-Induced Silencing Complex (RISC)-mediated cleavage and degradation, but differ in that they are designed for specific targets. The long generation times of forest trees have limited the discovery of mutations by conventional genetics. AmiRNAs can create gene-specific transcript reduction in transgenic trees in a single generation and may have broad application for functional genomics of trees. In this paper, we describe the specific down-regulation of multiple genes in the phenylalanine ammonia-lyase (PAL) gene family of Populus trichocarpa using amiRNA sequences incorporated in a P. trichocarpa miRNA-producing precursor, ptc-MIR408. Two different amiRNA constructs were designed to specifically down-regulate two different subsets of PAL genes, revealing differential regulation within the gene family. Down-regulation of subset A (PAL2, PAL4 and PAL5) by amiRNA-palA led to an increase in transcript abundance of subset B (PAL1 and PAL3). The reciprocal effect was not observed.}, number={6}, journal={PLANTA}, author={Shi, Rui and Yang, Chenmin and Lu, Shanfa and Sederoff, Ronald and Chiang, Vincent L.}, year={2010}, month={Nov}, pages={1281–1288} }
 @misc{shi_sun_li_heber_sederoff_chiang_2010, title={Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes}, volume={51}, ISSN={["1471-9053"]}, DOI={10.1093/pcp/pcp175}, abstractNote={As a step toward a comprehensive description of lignin biosynthesis in Populus trichocarpa, we identified from the genome sequence 95 phenylpropanoid gene models in 10 protein families encoding enzymes for monolignol biosynthesis. Transcript abundance was determined for all 95 genes in xylem, leaf, shoot and phloem using quantitative real-time PCR (qRT-PCR). We identified 23 genes that most probably encode monolignol biosynthesis enzymes during wood formation. Transcripts for 18 of the 23 are abundant and specific to differentiating xylem. We found evidence suggesting functional redundancy at the transcript level for phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), p-hydroxycinnamoyl-CoA:quinate shikimate p-hydroxycinnamoyltransferase (HCT), caffeoyl-CoA O-methyltransferase (CCoAOMT) and coniferyl aldehyde 5-hydroxylase (CAld5H). We carried out an enumeration-based motif identification and discriminant analysis on the promoters of all 95 genes. Five core motifs correctly discriminate the 18 xylem-specific genes from the 77 non-xylem genes. These motifs are similar to promoter elements known to regulate phenylpropanoid gene expression. This work suggests that genes in monolignol biosynthesis are regulated by multiple motifs, often related in sequence.}, number={1}, journal={PLANT AND CELL PHYSIOLOGY}, author={Shi, Rui and Sun, Ying-Hsuan and Li, Quanzi and Heber, Steffen and Sederoff, Ronald and Chiang, Vincent L.}, year={2010}, month={Jan}, pages={144–163} }
 @article{barakat_diloreto_zhang_smith_baier_powell_wheeler_sederoff_carlson_2009, title={Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection}, volume={9}, ISSN={["1471-2229"]}, DOI={10.1186/1471-2229-9-51}, abstractNote={American chestnut (Castanea dentata) was devastated by an exotic pathogen in the beginning of the twentieth century. This chestnut blight is caused by Cryphonectria parasitica, a fungus that infects stem tissues and kills the trees by girdling them. Because of the great economic and ecological value of this species, significant efforts have been made over the century to combat this disease, but it wasn't until recently that a focused genomics approach was initiated. Prior to the Genomic Tool Development for the Fagaceae project, genomic resources available in public databases for this species were limited to a few hundred ESTs. To identify genes involved in resistance to C. parasitica, we have sequenced the transcriptome from fungal infected and healthy stem tissues collected from blight-sensitive American chestnut and blight-resistant Chinese chestnut (Castanea mollissima) trees using ultra high throughput pyrosequencing. We produced over a million 454 reads, totaling over 250 million bp, from which we generated 40,039 and 28,890 unigenes in total from C. mollissima and C. dentata respectively. The functions of the unigenes, from GO annotation, cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. In silico expression analyses showed that many of the stress response unigenes were expressed more in canker tissues versus healthy stem tissues in both American and Chinese chestnut. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either American or Chinese chestnut canker tissues. Our study resulted in the identification of a large set of cDNA unigenes from American chestnut and Chinese chestnut. The ESTs and unigenes from this study constitute an important resource to the scientific community interested in the discovery of genes involved in various biological processes in Chestnut and other species. The identification of many defense-related genes differentially expressed in canker vs. healthy stem in chestnuts provides many new candidate genes for developing resistance to the chestnut blight and for studying pathways involved in responses of trees to necrotrophic pathogens. We also identified several candidate genes that may underline the difference in resistance to Cryphonectria parasitica between American chestnut and Chinese chestnut.}, journal={BMC PLANT BIOLOGY}, author={Barakat, Abdelali and DiLoreto, Denis S. and Zhang, Yi and Smith, Chris and Baier, Kathleen and Powell, William A. and Wheeler, Nicholas and Sederoff, Ron and Carlson, John E.}, year={2009}, month={May} }
 @misc{grattapaglia_plomion_kirst_sederoff_2009, title={Genomics of growth traits in forest trees}, volume={12}, ISSN={["1879-0356"]}, DOI={10.1016/j.pbi.2008.12.008}, abstractNote={Growth traits in trees are fundamental components of adaptation in a forest ecosystem and of productivity in planted forests. A number of processes determine tree growth, which are controlled by genetic and epigenetic factors that respond dynamically to environmental signals throughout centuries. Advances in genomics have allowed an increased comprehension of the complex mechanisms of tree growth and adaptation. Yet, the application of genomics to improving forest productivity and sustainability still entails capturing a large proportion of the total genetic variation controlling the component traits. Nonetheless, genetics and genomics are unifying disciplines that will serve well to dissect the variables and mechanisms of tree growth and development.}, number={2}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Grattapaglia, Dario and Plomion, Christophe and Kirst, Matias and Sederoff, Ronald R.}, year={2009}, month={Apr}, pages={148–156} }
 @article{wheeler_sederoff_2009, title={Role of genomics in the potential restoration of the American chestnut}, volume={5}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-008-0180-y}, number={1}, journal={TREE GENETICS & GENOMES}, author={Wheeler, Nicholas and Sederoff, Ronald}, year={2009}, month={Jan}, pages={181–187} }
 @article{adomas_heller_olson_osborne_karlsson_nahalkova_van zyl_sederoff_stenlid_finlay_et al._2008, title={Comparative analysis of transcript abundance in Pinus sylvestris after challenge with a saprotrophic, pathogenic or mutualistic fungus}, volume={28}, ISSN={["1758-4469"]}, DOI={10.1093/treephys/28.6.885}, abstractNote={To investigate functional differences in the recognition and response mechanisms of conifer roots to fungi with different trophic strategies, Pinus sylvestris L. was challenged with a saprotrophic fungus Trichoderma aureoviride Rifai. The results were compared with separate studies investigating pine interactions with a pathogen, Heterobasidion annosum (Fr.) Bref. sensu stricto and an ectomycorrhizal symbiont, Laccaria bicolor Maire (Orton). Global changes in the expression of 2109 conifer genes were assayed 1, 5 and 15 days after inoculation. Gene expression data from a cDNA microarray were analyzed by the 2-interconnected mixed linear model statistical approach. The total number of genes differentially expressed compared with the uninfected control was similar after challenge with the pathogen and the ectomycorrhizal symbiont, but the number of differentially expressed genes increased over time for H. annosum, and decreased for L. bicolor. Inoculation of pine roots with T. aureoviride resulted overall in a much lower number of genes with changed transcript levels compared with inoculation with H. annosum or L. bicolor. Functional classification of the differentially expressed genes revealed that the ectomycorrhizal fungus triggered transient induction of defence-related genes. The response and induction of defence against the pathogen was delayed and the magnitude increased over time. Thus, there were specific transcriptional responses depending on whether the conifer roots were challenged with mutualistic, saprotrophic or pathogenic fungi. This suggests that pine trees are able to recognize diverse fungal species and specifically distinguish whether they are pathogenic, neutral or beneficial microbial agents.}, number={6}, journal={TREE PHYSIOLOGY}, author={Adomas, Aleksandra and Heller, Gregory and Olson, Ake and Osborne, Jason and Karlsson, Magnus and Nahalkova, Jarmila and Van Zyl, Len and Sederoff, Ron and Stenlid, Jan and Finlay, Roger and et al.}, year={2008}, month={Jun}, pages={885–897} }
 @article{novaes_drost_farmerie_pappas_grattapaglia_sederoff_kirst_2008, title={High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome}, volume={9}, ISSN={["1471-2164"]}, DOI={10.1186/1471-2164-9-312}, abstractNote={Abstract}, journal={BMC GENOMICS}, author={Novaes, Evandro and Drost, Derek R. and Farmerie, William G. and Pappas, Georgios J., Jr. and Grattapaglia, Dario and Sederoff, Ronald R. and Kirst, Matias}, year={2008}, month={Jun} }
 @article{heller_adomas_li_osborne_van zyl_sederoff_finlay_stenlid_asiegbu_2008, title={Transcriptional analysis of Pinus sylvestris roots challenged with the ectomycorrhizal fungus Laccaria bicolor}, volume={8}, journal={BMC Plant Biology}, author={Heller, G. and Adomas, A. and Li, G. S. and Osborne, J. and Van Zyl, L. and Sederoff, R. and Finlay, R. D. and Stenlid, J. and Asiegbu, F. O.}, year={2008} }
 @article{sederoff_2007, title={Regulatory science in forest biotechnology}, volume={3}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-006-0081-x}, number={2}, journal={TREE GENETICS & GENOMES}, author={Sederoff, Ronald}, year={2007}, month={Apr}, pages={71–74} }
 @article{mazur_hope-ross_kadla_sederoff_chang_2007, title={Synthesis of hydroxyphenylpropanoid beta-D-glucosides}, volume={27}, ISSN={["0277-3813"]}, DOI={10.1080/02773810701282264}, abstractNote={Abstract Dihydroconiferyl alcohol glucoside has been synthesized from cinnamic acid ethyl ester glucoside. Two reaction systems were investigated; one involving hydrogenation of the cinnamic acid ethyl ester glucoside intermediate followed by diisobutylaluminium hydride (DIBAL‐H) reduction of the ester to the alcohol, and the other involving DIBAL‐H reduction of the cinnamic acid ethyl ester to the alcohol (coniferin) followed by hydrogenation. Hydrogenation followed by DIBAL‐H reduction led to higher dihydroconiferyl alcohol glucoside yields and avoided by‐product formation associated with the hydrogenation of coniferin.}, number={1}, journal={JOURNAL OF WOOD CHEMISTRY AND TECHNOLOGY}, author={Mazur, Magdalena and Hope-Ross, Kyle and Kadla, John F. and Sederoff, Ron and Chang, Hou-min}, year={2007}, pages={1–8} }
 @article{adomas_heller_li_olson_chu_osborne_craig_van zyl_wolfinger_sederoff_et al._2007, title={Trranscript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion}, volume={27}, ISSN={["1758-4469"]}, DOI={10.1093/treephys/27.10.1441}, abstractNote={The mechanisms underlying defence reactions to a pathogen attack, though well studied in crop plants, are poorly understood in conifers. To analyze changes in gene transcript abundance in Pinus sylvestris L. root tissues infected by Heterobasidion annosum (Fr.) Bref. s.l., a cDNA microarray containing 2109 ESTs from P. taeda L. was used. Mixed model statistical analysis identified 179 expressed sequence tags differentially expressed at 1, 5 or 15 days post inoculation. In general, the total number of genes differentially expressed during the infection increased over time. The most abundant group of genes up-regulated upon infection coded for enzymes involved in metabolism (phenylpropanoid pathway) and defence-related proteins with antimicrobial properties. A class III peroxidase responsible for lignin biosynthesis and cell wall thickening had increased transcript abundance at all measurement times. Real-time RT-PCR verified the microarray results with high reproducibility. 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.}, number={10}, journal={TREE PHYSIOLOGY}, author={Adomas, Aleksandra and Heller, Gregory and Li, Guosheng and Olson, Ake and Chu, Tzu-Ming and Osborne, Jason and Craig, Deborah and Van Zyl, Len and Wolfinger, Russ and Sederoff, Ron and et al.}, year={2007}, month={Oct}, pages={1441–1458} }
 @article{wadenback_clapham_craig_sederoff_peter_von arnold_egertsdotter_2005, title={Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays}, volume={6}, number={61}, journal={BMC Genomics}, author={Wadenback, J. and Clapham, D. H. and Craig, D. and Sederoff, R. and Peter, G. F. and Von Arnold, S. and Egertsdotter, U.}, year={2005} }
 @article{kirst_basten_myburg_zeng_sederoff_2005, title={Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid}, volume={169}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.104.039198}, abstractNote={Abstract}, number={4}, journal={GENETICS}, author={Kirst, M and Basten, CJ and Myburg, AA and Zeng, ZB and Sederoff, RR}, year={2005}, month={Apr}, pages={2295–2303} }
 @inproceedings{morris_goldfarb_isik_li_chang_sederoff_kadla_2005, title={Variation of a-cellulose content and related metabolites during wood formation in loblolly pine}, volume={13}, booktitle={13th ISWFPC Proceedings}, author={Morris, C. R. and Goldfarb, B. and Isik, F. and Li, C. S. and Chang, H.-M. and Sederoff, R. and Kadla, J. F.}, year={2005} }
 @article{marques_carocha_sa_oliveira_pires_sederoff_borralho_2005, title={Verification of QTL linked markers for propagation traits in Eucalyptus}, volume={1}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-005-0013-1}, number={3}, journal={TREE GENETICS & GENOMES}, author={Marques, C. M. and Carocha, V. J. and Sa, A. R. Pereira and Oliveira, M. R. and Pires, A. M. and Sederoff, R. and Borralho, N. M. G.}, year={2005}, month={Nov}, pages={103–108} }
 @article{busov_johannes_whetten_sederoff_spiker_lanz-garcia_goldfarb_2004, title={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}, volume={218}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/s00425-003-1175-4}, DOI={10.1007/s00425-003-1175-4}, abstractNote={We have isolated a gene from loblolly pine, 5NG4, that is highly and specifically induced by auxin in juvenile loblolly pine shoots prior to adventitious root formation, but substantially down-regulated in physiologically mature shoots that are adventitious rooting incompetent. 5NG4 was highly auxin-induced in roots, stems and hypocotyls, organs that can form either lateral or adventitious roots following an auxin treatment, but was not induced to the same level in needles and cotyledons, organs that do not form roots. The deduced amino acid sequence shows homology to the MtN21 nodulin gene from Medicago truncatula. The expression pattern of 5NG4 and its homology to a protein from Medicago involved in a root-related process suggest a possible role for this gene in adventitious root formation. Homology searches also identified similar proteins in Arabidopsis thaliana and Oryza sativa. High conservation across these evolutionarily distant species suggests essential functions in plant growth and development. A 38-member family of genes homologous to 5NG4 was identified in the A. thaliana genome. The physiological significance of this redundancy is most likely associated with functional divergence and/or expression specificity of the different family members. The exact biochemical function of the gene is still unknown, but sequence and structure predictions and 5NG4::GFP fusion protein localizations indicate it is a transmembrane protein with a possible transport function.}, number={6}, journal={Planta}, publisher={Springer Science and Business Media LLC}, author={Busov, Victor B. and Johannes, Eva and Whetten, Ross W. and Sederoff, Ronald R. and Spiker, Steven L. and Lanz-Garcia, Carmen and Goldfarb, Barry}, year={2004}, month={Apr}, pages={916–927} }
 @article{kirst_myburg_de leon_kirst_scott_sederoff_2004, title={Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus}, volume={135}, ISSN={["1532-2548"]}, DOI={10.1104/pp.103.037960}, abstractNote={Abstract}, number={4}, journal={PLANT PHYSIOLOGY}, author={Kirst, M and Myburg, AA and De Leon, JPG and Kirst, ME and Scott, J and Sederoff, R}, year={2004}, month={Aug}, pages={2368–2378} }
 @article{egertsdotter_zyl_mackay_peter_kirst_clark_whetten_sederoff_2004, title={Gene Expression during Formation of Earlywood and Latewood in Loblolly Pine: Expression Profiles of 350 Genes}, volume={6}, ISSN={1435-8603 1438-8677}, url={http://dx.doi.org/10.1055/s-2004-830383}, DOI={10.1055/s-2004-830383}, abstractNote={Abstract:  The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy‐one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.}, number={6}, journal={Plant Biology}, publisher={Wiley}, author={Egertsdotter, U. and Zyl, L. M. and MacKay, J. and Peter, G. and Kirst, M. and Clark, C. and Whetten, R. and Sederoff, R.}, year={2004}, month={Nov}, pages={654–663} }
 @article{myburg_vogl_griffin_sederoff_whetten_2004, title={Genetics of Postzygotic Isolation in Eucalyptus: Whole-Genome Analysis of Barriers to Introgression in a Wide Interspecific Cross of Eucalyptus grandis and E. globulus}, volume={166}, ISSN={0016-6731 1943-2631}, url={http://dx.doi.org/10.1534/genetics.166.3.1405}, DOI={10.1534/genetics.166.3.1405}, abstractNote={Abstract}, number={3}, journal={Genetics}, publisher={Genetics Society of America}, author={Myburg, Alexander A. and Vogl, Claus and Griffin, A. Rod and Sederoff, Ronald R. and Whetten, Ross W.}, year={2004}, month={Mar}, pages={1405–1418} }
 @article{morris_scott_chang_sederoff_d o'malley_kadla_2004, title={Metabolic profiling: A new tool in the study of wood formation}, volume={52}, ISSN={["1520-5118"]}, DOI={10.1021/jf034688l}, abstractNote={In the realm of plant genomics, metabolic profiling has become a valuable tool with which to assess the effect of genetic and/or environmental factors on plant development. This paper reports the first application of metabolic profiling on differentiating xylem tissue of loblolly pine. A protocol is presented for the analysis of loblolly pine xylem tissue. The effects of sample preparation, extraction, and derivatization on the corresponding metabolite profiles and yields have been investigated and are reported. Gas chromatography-mass spectroscopy has been used to quantify >60 polar and lipophilic metabolites from wood-forming tissue. It was possible to assign chemical structures to approximately half of these compounds. Comparison of six loblolly pine genotypes, three high cellulose (50-52%) and three medium (45-48%) cellulose, showed distinct metabolic profiles. Principal component analysis enabled the assignment of metabolic phenotypes using these large data sets. Metabolic phenotype clustering occurred in which the three high-cellulose genotypes were segregated from the medium-cellulose genotypes. These results demonstrate the use of metabolic profiling for the study of wood-forming tissue and as a tool in functional genomics.}, number={6}, journal={JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY}, author={Morris, CR and Scott, JT and Chang, HM and Sederoff, RR and D O'Malley and Kadla, JF}, year={2004}, month={Mar}, pages={1427–1434} }
 @article{brinker_zyl_liu_craig_sederoff_clapham_arnold_2004, title={Microarray analyses of gene expression during adventitious root development in Pinus contorta (1[w])}, volume={135}, ISSN={["1532-2548"]}, DOI={10.1104/pp.103.032235}, abstractNote={Abstract}, number={3}, journal={PLANT PHYSIOLOGY}, author={Brinker, M and Zyl, L and Liu, WB and Craig, D and Sederoff, RR and Clapham, DH and Arnold, S}, year={2004}, month={Jul}, pages={1526–1539} }
 @article{stasolla_belmonte_zyl_craig_liu_yeung_sederoff_2004, title={The effect of reduced glutathione on morphology and gene expression of white spruce (Picea glauca) somatic embryos}, volume={55}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/erh074}, abstractNote={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). This beneficial effect was the result of major alterations in morphology and gene expression during the maturation period. Compared with control embryos, GSH-treated embryos showed a differential accumulation of storage products, i.e. preferential deposition of starch, the reduced formation of protein bodies, and increased vacuolation of cells. These morphological changes correlated with extensive alterations of gene expression occurring throughout the maturation period. The transcript profiles of stage-specific embryos matured with or without GSH were analysed using a DNA microarray containing 2 178 cDNAs from loblolly pine (Pinus taeda). The efficiency of heterologous hybridization between spruce and pine species on microarrays has previously been documented. The results indicate that several genes involved in a variety of signal regulatory pathways were differentially expressed in developing GSH- treated embryos. The transcript levels of many genes involved in carbohydrate metabolism and protein synthesis were altered by the presence of GSH and denoted differences in physiology between treatments. Extensive changes in the expression of genes participating in hormone synthesis, nucleotide metabolism, and meristem formation were also observed and related to the post-embryonic performance of the embryos.}, number={397}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Stasolla, C and Belmonte, MF and Zyl, L and Craig, DL and Liu, WB and Yeung, EC and Sederoff, RR}, year={2004}, month={Mar}, pages={695–709} }
 @article{stasolla_bozhkov_chu_van zyl_egertsdotter_suarez_craig_wolfinger_von arnold_sederoff_2004, title={Variation an transcript abundance during somatic embryogenesis in gymnosperms}, volume={24}, ISSN={["1758-4469"]}, DOI={10.1093/treephys/24.10.1073}, abstractNote={Somatic embryogenesis of Norway spruce (Picea abies L.) is a versatile model system to study molecular mechanisms regulating embryo development because it proceeds through defined developmental stages corresponding to specific culture treatments. Normal embryonic development involves early differentiation of proembryogenic masses (PEMs) into somatic embryos, followed by early and late embryogeny leading to the formation of mature cotyledonary embryos. In some cell lines there is a developmental arrest at the PEM-somatic embryo transition. To learn more about the molecular mechanisms regulating embryogenesis, we compared the transcript profiles of two normal lines and one developmentally arrested line. Ribonucleic acid, extracted from these cell lines at successive developmental stages, was analyzed on DNA microarrays containing 2178 expressed sequence tags (ESTs) (corresponding to 2110 unique cDNAs) from loblolly pine (Pinus taeda L.). Hybridization between spruce and pine species on microarrays has been shown to be effective (van Zyl et al. 2002, Stasolla et al. 2003). In contrast to the developmentally arrested line, the early phases of normal embryo development are characterized by a precise pattern of gene expression, i.e., repression followed by induction. Comparison of transcript levels between successive stages of embryogenesis allowed us to identify several genes that showed unique expression responses during normal development. Several of these genes encode proteins involved in detoxification processes, methionine synthesis and utilization, and carbohydrate metabolism. The potential role of these genes in embryo development is discussed.}, number={10}, journal={TREE PHYSIOLOGY}, author={Stasolla, C and Bozhkov, PV and Chu, TM and Van Zyl, L and Egertsdotter, U and Suarez, MF and Craig, D and Wolfinger, RD and Von Arnold, S and Sederoff, RR}, year={2004}, month={Oct}, pages={1073–1085} }
 @article{zhang_brown_whetten_loopstra_neale_kieliszewski_sederoff_2003, title={An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine}, volume={52}, ISSN={["0167-4412"]}, url={http://dx.doi.org/10.1023/a:1023978210001}, DOI={10.1023/A:1023978210001}, abstractNote={Arabinogalactan proteins (AGPs) are abundant plant proteoglycans implicated in plant growth and development. Here, we report the genetic characterization, partial purification and immunolocalization of a classical AGP (PtaAGP6, accession number AF101785) in loblolly pine (Pinus taeda L.). A PtaAGP6 full-length cDNA clone was expressed in bacteria. PtaAGP6 resembles tomato LeAGP-1 and Arabidopsis AtAGP17-19 in that they all possess a subdomain composed of basic amino acids. The accessibility of this domain in the glycoprotein makes it possible to label the PtaAGP6 epitopes on the cell surface or in the cell wall with polyclonal antibodies raised against this subdomain. The antibodies recognize the peptide of the basic subdomain and bind to the intact protein molecule. A soluble protein-containing fraction was purified from the differentiating xylem of pine trees by using beta-glucosyl Yariv reagent (beta-glcY) and was recognized by antibodies against the basic subdomain. Immunolocalization studies 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. The location of apparent labeling of the PtaAGP6 epitopes is separated from the location of lignin deposition. Multiple single nucleotide polymorphisms (SNPs) were detected in EST variants. Denaturing HPLC analysis of PCR products suggests that PtaAGP6 is encoded by a single gene. Mobility variation in denaturing gel electrophoresis was used to map PtaAGP6 SNPs to a site on linkage group 5.}, number={1}, journal={Plant Molecular Biology}, author={Zhang, Y. and Brown, G. and Whetten, R. and Loopstra, C.A. and Neale, D. and Kieliszewski, M.J. and Sederoff, R.R.}, year={2003}, pages={91–102} }
 @article{stasolla_scott_egertsdotter_kadla_d o'malley_sederoff_zyl_2003, title={Analysis of lignin produced by cinnamyl alcohol dehydrogenase-deficient Pinus taeda cultured cells}, volume={41}, ISSN={["0981-9428"]}, DOI={10.1016/S0981-9428(03)00051-2}, abstractNote={Comparative studies were conducted on composition of lignin produced both in vivo and in vitro by cinnamyl alcohol dehydrogenase (CAD)-deficient mutant loblolly pine (Pinus taeda L.). In vivo studies were performed using differentiating xylem obtained from two genotypes of heterozygous (CAD/cad) and two genotypes of homozygous (cad/cad) CAD-deficient mutant trees. In vitro studies were performed using a culture system in which cells, generated from the same genotypes, were induced to produce lignin in culture. Steady state RNA levels and enzyme activity of CAD were dramatically reduced in both xylem and cultured cells obtained from homozygous mutant trees, compared to their heterozygous counterparts. Light microscopic studies showed pronounced differences during the lignin formation between homozygous and heterozygous cells. Phenolic compounds in the heterozygous (CAD/cad) cells were deposited around the cell wall, accumulated preferentially in vacuoles of the homozygous (cad/cad) cells. Differences in lignin composition as revealed by thioacidolysis were also observed. Lignin of both xylem tissue and cultured cells obtained from CAD-deficient homozygotes showed lower levels of coniferyl alcohols and significant enrichments in dihydroconiferyl alcohol (DHCA) and coniferyl aldehyde, compared to their heterozygous counterparts. 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 lignin biosynthesis, and the formation of DHCA subunits.}, number={5}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Stasolla, C and Scott, J and Egertsdotter, U and Kadla, J and D O'Malley and Sederoff, R and Zyl, L}, year={2003}, month={May}, pages={439–445} }
 @article{kirst_johnson_baucom_ulrich_hubbard_staggs_paule_retzel_whetten_sederoff_2003, title={Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana}, volume={100}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1132171100}, DOI={10.1073/pnas.1132171100}, abstractNote={
            Pinus taeda
            L. (loblolly pine) and
            Arabidopsis thaliana
            differ greatly in form, ecological niche, evolutionary history, and genome  size.
            Arabidopsis
            is a small, herbaceous, annual dicotyledon, whereas  pines are large, long-lived, coniferous forest trees. Such diverse plants  might be expected to differ in a large number of functional genes. We have  obtained and analyzed 59,797 expressed sequence tags (ESTs) from wood-forming  tissues of loblolly pine and compared them to the gene sequences inferred from  the complete sequence of the
            Arabidopsis
            genome. Approximately 50% of  pine ESTs have no apparent homologs in
            Arabidopsis
            or any other  angiosperm in public databases. When evaluated by using contigs containing  long, high-quality sequences, we find a higher level of apparent homology  between the inferred genes of these two species. For those contigs 1,100 bp or  longer, ≈90% have an apparent
            Arabidopsis
            homolog (
            E
            value < 10
            -
            10
            ). Pines and
            Arabidopsis
            last  shared a common ancestor ≈300 million years ago. Few genes would be  expected to retain high sequence similarity for this time if they did not have  essential functions. These observations suggest substantial conservation of  gene sequence in seed plants.
          }, number={12}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Kirst, M. and Johnson, A. F. and Baucom, C. and Ulrich, E. and Hubbard, K. and Staggs, R. and Paule, C. and Retzel, E. and Whetten, R. and Sederoff, R.}, year={2003}, month={May}, pages={7383–7388} }
 @article{patzlaff_newman_dubos_whetten_smith_mcinnis_bevan_sederoff_campbell_2003, title={Characterisation of PtMYB1, an R2R3-MYB from pine xylem}, volume={53}, ISSN={0167-4412}, url={http://dx.doi.org/10.1023/b:plan.0000019066.07933.d6}, DOI={10.1023/B:PLAN.0000019066.07933.d6}, abstractNote={A cDNA encoding a member of the R2R3-MYB family of transcription factors was cloned from a library constructed from differentiating Pinus taeda (loblolly pine) xylem RNA. This MYB family member, Pinus taeda MYB1 (PtMYB1), was most abundantly expressed in differentiating xylem, as assessed by both ribonuclease protection assays, and by northern blot analysis with poly(A)-enriched RNA. Similar to other plant R2R3-MYB family members, recombinant Pt MYB1 protein was able to bind to AC elements in electrophoretic mobility shift assays (EMSAs). AC elements are DNA motifs rich in adenosine and cytosine that have been implicated in the xylem-localised regulation of genes encoding lignin biosynthetic enzymes. Pt MYB1 not only bound to AC elements, but was also able to 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. Transcriptional activation assays conducted using yeast showed that Pt MYB1 also activated transcription, and that it did so in an AC-element-dependent fashion. Pt MYB1 also activated transcription from the minimal PAL2 promoter in plant cells in an AC-element-dependent fashion, as revealed by transient transcriptional activation assays with microprojectile-bombarded tobacco NT-1 cells. Taken together, these finding are consistent with the hypothesis that Pt MYB1 may regulate transcription from cis -acting AC elements in pine xylem.}, number={4}, journal={Plant Molecular Biology}, publisher={Springer Nature}, author={Patzlaff, Astrid and Newman, Lisa J. and Dubos, Christian and Whetten, Ross W. and Smith, Caroline and McInnis, Stephanie and Bevan, Michael W. and Sederoff, Ronald R. and Campbell, Malcolm M.}, year={2003}, month={Nov}, pages={597–608} }
 @article{patzlaff_mcinnis_courtenay_surman_newman_smith_bevan_mansfield_whetten_sederoff_et al._2003, title={Characterisation of a pine MYB that regulates lignification}, volume={36}, ISSN={0960-7412 1365-313X}, url={http://dx.doi.org/10.1046/j.1365-313x.2003.01916.x}, DOI={10.1046/j.1365-313X.2003.01916.x}, abstractNote={Summary}, number={6}, journal={The Plant Journal}, publisher={Wiley}, author={Patzlaff, Astrid and McInnis, Stephanie and Courtenay, Adrian and Surman, Christine and Newman, Lisa J. and Smith, Caroline and Bevan, Michael W. and Mansfield, Shawn and Whetten, Ross W. and Sederoff, Ronald R. and et al.}, year={2003}, month={Dec}, pages={743–754} }
 @article{myburg_griffin_sederoff_whetten_2003, title={Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach}, volume={107}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-003-1347-4}, DOI={10.1007/s00122-003-1347-4}, abstractNote={Comparative genetic mapping in interspecific pedigrees presents a powerful approach to study genetic differentiation, genome evolution and reproductive isolation in diverging species. We used this approach for genetic analysis of an F(1) hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and Eucalyptus globulus (Labill.). This wide interspecific cross is characterized by hybrid inviability and hybrid abnormality. Approximately 20% of loci in the genome of the F(1) hybrid are expected to be hemizygous due to a difference in genome size between E. grandis (640 Mbp) and E. globulus (530 Mbp). We investigated the extent of colinearity between the two genomes and the distribution of hemizygous loci in the F(1) hybrid using high-throughput, semi-automated AFLP marker analysis. Two pseudo-backcross families (backcrosses of an F(1) individual to non-parental individuals of the parental species) were each genotyped with more than 800 AFLP markers. This allowed construction of de novo comparative genetic linkage maps of the F(1) hybrid and the two backcross parents. All shared AFLP marker loci in the three single-tree parental maps were found to be colinear and little evidence was found for gross chromosomal rearrangements. Our results suggest that hemizygous AFLP loci are dispersed throughout the E. grandis chromosomes of the F(1) hybrid.}, number={6}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Myburg, A. A. and Griffin, A. R. and Sederoff, R. R. and Whetten, R. W.}, year={2003}, month={Jul}, pages={1028–1042} }
 @article{sasaki_sederoff_2003, title={Genome studies and molecular genetics - The rice genome and comparative genomics of higher plants - Editorial overview}, volume={6}, ISSN={["1369-5266"]}, DOI={10.1016/S1369-5266(03)00018-9}, abstractNote={Rice varieties vary in their capacity for callus induction, growth, and regeneration. We identified the locus and candidate gene which conferred good callus growth and regenerative ability in the rice variety Koshihikari, a notorious poor rice line for genetic transformation. In addition, we succeeded in establishment of a new selectable marker system using the NiR gene for Agrobacterium-mediated transformation of rice, c.v. “Koshihikari.” The locus was mapped onto chromosome 1, and the nearest RFLP marker was C0178. A total of 500 segregating individuals (BC6F2 seeds) were screened for recombination by PCR-based screening and its location narrowed to a 540-kb region that had been sequenced by the International Rice Genome Sequencing Project. One ORF encoded a putative ferredoxin-nitrite reductase (NiR), which has been suggested to be required for callus induction and growth. The growth and regeneration ability of the calli initiated from Koshihikari was improved through integration of the NiR gene from Konansou. Analysis of ORFs and the promoter region of NiR indicated that the promoter region of NiR gene is responsible for growth and regeneration ability of calli in rice, c.v. Koshihikari. We established a NiR selection system for Agrobacterium-mediated transformation in rice, c.v. Koshihikari, by integration of the NiR gene isolated from rice c.v. Konansou. Transgenic rice plants regenerated from selected calli exhibited β-glucuronidase (GUS) activity. A transformation frequency of 9% was obtained. The results indicated that the NiR selection system is devoid of the disadvantages and concerns of using foreign genes (antibiotics and herbicide resistant) for selection.}, number={2}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Sasaki, T and Sederoff, RR}, year={2003}, month={Apr}, pages={97–100} }
 @article{kim_ralph_lu_ralph_boudet_mackay_sederoff_ito_kawai_ohashi_et al._2003, title={NMR analysis of lignins in CAD-deficient plants. Part 1. Incorporation of hydroxycinnamaldehydes and hydroxybenzaldehydes into lignins}, volume={1}, ISSN={["1477-0539"]}, DOI={10.1039/b209686b}, abstractNote={Peroxidase/H2O2-mediated radical coupling of 4-hydroxycinnamaldehydes produces 8-O-4-, 8-5-, and 8-8-coupled dehydrodimers as has been documented earlier, as well as the 5-5-coupled dehydrodimer. The 8-5-dehydrodimer is however produced kinetically in its cyclic phenylcoumaran form at neutral pH. Synthetic polymers produced from mixtures of hydroxycinnamaldehydes and normal monolignols provide the next level of complexity. 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. CAD-deficient pine lignin shows enhanced levels of the typical benzaldehyde and cinnamaldehyde end-groups, along with evidence for two types of 8-O-4-coupled coniferaldehyde units. The CAD-downregulated tobacco also has higher levels of hydroxycinnamaldehyde and hydroxybenzaldehyde (mainly syringaldehyde) incorporation, but the analogous two types of 8-O-4-coupled products are the dominant features. 8-8-Coupled units are also clearly evident. There is clear evidence for coupling of hydroxycinnamaldehydes to each other and then incorporation into the lignin, as well as for the incorporation of hydroxycinnamaldehyde monomers into the growing lignin polymer. Coniferaldehyde and sinapaldehyde (as well as vanillin and syringaldehyde) co-polymerize with the traditional monolignols into lignins and do so at enhanced levels when CAD-deficiency has an impact on the normal monolignol production. The implication is that, particularly in angiosperms, the aldehydes behave like the traditional monolignols and should probably be regarded as authentic lignin monomers in normal and CAD-deficient plants.}, number={2}, journal={ORGANIC & BIOMOLECULAR CHEMISTRY}, author={Kim, H and Ralph, J and Lu, FC and Ralph, SA and Boudet, AM and MacKay, JJ and Sederoff, RR and Ito, T and Kawai, S and Ohashi, H and et al.}, year={2003}, month={Jan}, pages={268–281} }
 @article{watkinson_sioson_vasquez-robinet_shukla_kumar_ellis_heath_ramakrishnan_chevone_watson_et al._2003, title={Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine}, volume={133}, DOI={10.1104/pp.103026914}, number={4}, journal={Plant Physiology}, author={Watkinson, J. I. and Sioson, A. A. and Vasquez-Robinet, C. and Shukla, M. and Kumar, D. and Ellis, M. and Heath, L. S. and Ramakrishnan, N. and Chevone, B. and Watson, L. T. and et al.}, year={2003}, pages={1702–1716} }
 @article{stasolla_zyl_egertsdotter_craig_liu_sederoff_2003, title={The effects of polyethylene glycol on gene expression of developing white spruce somatic embryos}, volume={131}, ISSN={["1532-2548"]}, DOI={10.1104/pp.015214}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Stasolla, C and Zyl, L and Egertsdotter, U and Craig, D and Liu, WB and Sederoff, RR}, year={2003}, month={Jan}, pages={49–60} }
 @article{stasolla_zyl_egertsdotter_craig_liu_sederoff_2003, title={Transcript profiles of stress-related genes in developing white spruce (Picea glauca) somatic embryos cultured with polyethylene glycol}, volume={165}, ISSN={["0168-9452"]}, DOI={10.1016/S0168-9452(03)00228-0}, abstractNote={The effect of polyethylene glycol (PEG) on the transcript level of 512 stress-related genes was analyzed by cDNA microarray. Major changes in gene expression between control and PEG-treated embryos were observed during the initial stages of development, upon transfer of the embryogenic tissue on maturation medium, and during the late phases of development, culminating with the generation of cotyledonary embryos. Only small changes in gene expression were observed during the intermediate phases of embryo development. The transcript levels of several genes involved in cell aging and detoxification mechanisms, including peroxidases and chitinases, were developmentally regulated during the embryogenic process. Major differences in the expression of these genes were observed between control and PEG-treated embryos. Based on their expression profiles, four different clusters of genes involved in stress response mechanisms were identified. The first group of genes, which included several heat shock proteins, was up-regulated in PEG-treated immature embryos. An opposite tendency was observed for a second cluster of genes, which included a glutathione-S-transferase, and a cysteine protease. The third class included genes repressed by PEG in fully developed embryos, whereas a fourth group of genes, which included several heat shock proteins and ubiquitin, was induced in PEG-treated embryos at the end of the culture period. Difference in transcript levels and profiles of several genes involved in cell wall and lignin biosynthesis were also observed between control and PEG-treated embryos.}, number={4}, journal={PLANT SCIENCE}, author={Stasolla, C and Zyl, L and Egertsdotter, U and Craig, D and Liu, WB and Sederoff, RR}, year={2003}, month={Oct}, pages={719–729} }
 @article{zyl_bozhkov_clapham_sederoff_arnold_2003, title={Up, down and up again is a signature global gene expression pattern at the beginning of gymnosperm embryogenesis}, volume={3}, ISSN={["1567-133X"]}, DOI={10.1016/S1567-133X(02)00068-6}, abstractNote={Somatic embryogenesis of a gymnosperm, Picea abies, represents a sequence of specifically regulated developmental stages including proembryogenic mass (PEM), PEM-to-embryo transition, and early and late embryogeny. Here, we report cDNA array analysis of expression patterns of 373 genes in the beginning of P. abies embryo development. The analysis revealed a group of 107 genes (29% of arrayed cDNAs) which were upregulated upon PEM-to-embryo transition, then downregulated during early embryogeny and finally upregulated again at the beginning of late embryogeny. This major gene expression pattern was abrogated in a developmentally arrested cell line that is unable to pass through the PEM-to-embryo transition. Thirty-five genes (9.4% of arrayed cDNAs) were found to be differentially expressed during normal embryonic pattern formation. Among them, 22 genes (5.9% of arrayed cDNAs) were directly associated with embryo pattern formation and can be considered as marker genes for early stages of P. abies embryogenesis. The majority of the marker genes encode for proteins involved in translation and posttranslational modification. Among them, 18 genes displayed the major expression pattern.}, number={1}, journal={GENE EXPRESSION PATTERNS}, author={Zyl, L and Bozhkov, PV and Clapham, DH and Sederoff, RR and Arnold, S}, year={2003}, month={Mar}, pages={83–91} }
 @article{marques_brondani_grattapaglia_sederoff_2002, title={Conservation and synteny of SSR loci and QTLs for vegetative propagation in four Eucalyptus species}, volume={105}, ISSN={["0040-5752"]}, DOI={10.1007/s00122-002-0899-z}, abstractNote={Conservation of microsatellite loci, heterozygous in Eucalyptus grandis, Eucalyptus urophylla, Eucalyptus tereticornis and Eucalyptus globulus, allowed us to propose homeologies among genetic linkage groups in these species, supported by at least three SSR loci in two different linkage groups. Marker-trait associations for sprouting and adventitious rooting ability were also compared in the four species. Putative quantitative trait loci (QTLs) influencing vegetative propagation traits were located on homeologous linkage groups. Our 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. Microsatellite markers should help integrate eucalypt genetic linkage maps from various sources. The availability of comparative linkage maps provides a basis of more-efficient use of genetic information for molecular breeding and evolutionary studies in Eucalyptus.}, number={2-3}, journal={THEORETICAL AND APPLIED GENETICS}, author={Marques, CM and Brondani, RPV and Grattapaglia, D and Sederoff, R}, year={2002}, month={Aug}, pages={474–478} }
 @article{zyl_arnold_bozhkov_chen_egertsdotter_mackay_sederoff_shen_zelena_clapham_2002, title={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}, volume={3}, ISSN={["1532-6268"]}, DOI={10.1002/cfg.199}, abstractNote={Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation betweenPinusandPiceawe have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem ofPinus taedawere printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures ofPinus taeda,P. sylvestrisandPicea abies, and with labelled cDNA from leaves ofNicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r2= 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2= 0.68 − 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r2= 0.52 − 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces.}, number={4}, journal={COMPARATIVE AND FUNCTIONAL GENOMICS}, author={Zyl, L and Arnold, S and Bozhkov, P and Chen, YZ and Egertsdotter, U and MacKay, J and Sederoff, RR and Shen, J and Zelena, L and Clapham, DH}, year={2002}, month={Aug}, pages={306–318} }
 @article{heath_ramakrishnan_sederoff_whetten_chevone_struble_jouenne_chen_van zyl_grene_et al._2002, title={Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system}, volume={3}, ISSN={["1532-6268"]}, DOI={10.1002/cfg.169}, abstractNote={Conception, design, and implementation of cDNA microarray experiments present a variety of bioinformatics challenges for biologists and computational scientists. The multiple stages of data acquisition and analysis have motivated the design of Expresso, a system for microarray experiment management. Salient aspects of Expresso include support for clone replication and randomized placement; automatic gridding, extraction of expression data from each spot, and quality monitoring; flexible methods of combining data from individual spots into information about clones and functional categories; and the use of inductive logic programming for higher-level data analysis and mining. The development of Expresso is occurring in parallel with several generations of microarray experiments aimed at elucidating genomic responses to drought stress in loblolly pine seedlings. The current experimental design incorporates 384 pine cDNAs replicated and randomly placed in two specific microarray layouts. We describe the design of Expresso 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.}, number={3}, journal={COMPARATIVE AND FUNCTIONAL GENOMICS}, author={Heath, L. S. and Ramakrishnan, N. and Sederoff, R. R. and Whetten, R. W. and Chevone, B. I. and Struble, C. A. and Jouenne, V. Y. and Chen, D. W. and Van Zyl, L. and Grene, R. and et al.}, year={2002}, month={Jun}, pages={226–243} }
 @article{ralph_lapierre_marita_kim_lu_hatfield_ralph_chapple_franke_hemm_et al._2001, title={Elucidation of new structures in lignins of CAD- and COMT-deficient plants by NMR}, volume={57}, ISSN={["0031-9422"]}, DOI={10.1016/S0031-9422(01)00109-1}, abstractNote={Studying lignin-biosynthetic-pathway mutants and transgenics provides insights into plant responses to perturbations of the lignification system, and enhances our understanding of normal lignification. When enzymes late in the pathway are downregulated, significant changes in the composition and structure of lignin may result. NMR spectroscopy provides powerful diagnostic tools for elucidating structures in the difficult lignin polymer, hinting at the chemical and biochemical changes that have occurred. COMT (caffeic acid O-methyl transferase) downregulation in poplar results in the incorporation of 5-hydroxyconiferyl alcohol into lignins via typical radical coupling reactions, but post-coupling quinone methide internal trapping reactions produce novel benzodioxane units in the lignin. CAD (cinnamyl alcohol dehydrogenase) downregulation results in the incorporation of the hydroxycinnamyl aldehyde monolignol precursors intimately into the polymer. Sinapyl aldehyde cross-couples 8-O-4 with both guaiacyl and syringyl units in the growing polymer, whereas coniferyl aldehyde cross-couples 8-O-4 only with syringyl units, reflecting simple chemical cross-coupling propensities. The incorporation of hydroxycinnamyl aldehyde and 5-hydroxyconiferyl alcohol monomers indicates that these monolignol intermediates are secreted to the cell wall for lignification. 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.}, number={6}, journal={PHYTOCHEMISTRY}, author={Ralph, J and Lapierre, C and Marita, JM and Kim, H and Lu, FC and Hatfield, RD and Ralph, S and Chapple, C and Franke, R and Hemm, MR and et al.}, year={2001}, month={Jul}, pages={993–1003} }
 @article{whetten_sun_zhang_sederoff_2001, title={Functional genomics and cell wall biosynthesis in loblolly pine}, volume={47}, ISSN={0167-4412}, url={http://dx.doi.org/10.1023/a:1010652003395}, DOI={10.1023/A:1010652003395}, number={1/2}, journal={Plant Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Whetten, Ross and Sun, Ying-Hsuan and Zhang, Yi and Sederoff, Ron}, year={2001}, month={Sep}, pages={275–291} }
 @article{tang_whetten_sederoff_2001, title={Genotypic control of high-frequency adventitious shoot regeneration via somatic organogenesis in loblolly pine}, volume={161}, ISSN={0168-9452}, url={http://dx.doi.org/10.1016/s0168-9452(01)00394-6}, DOI={10.1016/S0168-9452(01)00394-6}, abstractNote={Mature zygotic embryos of 24 genotypes of loblolly pine (Pinus taeda L.) were used as explants to establish an adventitious shoot regeneration system through somatic organogenesis. Callus formation frequencies of 18.2 (genotype 11-1103) -77.7% (genotype 7-100) have been induced from mature zygotic embryos of all genotypes tested on callus induction medium (basal salts) containing 2,4-dichlorophenoxyacetic acid (2,4-D) or alpha-naphthaleneacetic acid (NAA), 6-benzyladenine (BA), and kinetin. Adventitious shoot regeneration via organogenesis with the frequency of 5.4 (genotype 11-1103 and 7-2) -77.2% (genotype 8-1082) was obtained from callus and tissue cultures derived from mature zygotic embryos of 24 genotypes of loblolly pine. The highest mean number of 18 adventitious buds per piece of callus 0.5x0.5 cm(2) in size was obtained from genotype 8-1082. Elongation of adventitious buds was achieved on TE medium supplemented with 0.5 mg/l indole-3-butyric acid (IBA) and 1 mg/l BA. After rooting, regenerated plantlets were established in soil. These results suggested that adventitious shoot regeneration via somatic organogenesis was influenced by the genotypes. 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.}, number={2}, journal={Plant Science}, publisher={Elsevier BV}, author={Tang, Wei and Whetten, Ross and Sederoff, Ron}, year={2001}, month={Jul}, pages={267–272} }
 @misc{lev-yadun_sederoff_2001, title={Grafting for transgene containment}, volume={19}, ISSN={["1546-1696"]}, DOI={10.1038/nbt1201-1104}, number={12}, journal={NATURE BIOTECHNOLOGY}, author={Lev-Yadun, S and Sederoff, R}, year={2001}, month={Dec}, pages={1104–1104} }
 @article{myburg_remington_dm o'malley_sederoff_whetten_2001, title={High-throughput AFLP analysis using infrared dye-labeled primers and an automated DNA sequencer}, volume={30}, ISSN={["0736-6205"]}, DOI={10.2144/01302tt04}, abstractNote={ Amplified fragment length polymorphism (AFLP) analysis is currently the most powerful and efficient technique for the generation of large numbers of anonymous DNA markers in plant and animal genomes. We have developed 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. This throughput is based on multiplexed PCR amplification of AFLP fragments using two different infrared dyelabeled primer combinations. The multiplexed AFLPs are resolved on a two-dye, model 4200 LI-COR® automated DNA sequencer, and the digital images are scored using semi-automated scoring software specifically designed for complex AFLP banding patterns (AFLP-Quantar™). Throughput is enhanced by using high-quality genomic DNA templates obtained by a 96-well DNA isolation procedure. }, number={2}, journal={BIOTECHNIQUES}, author={Myburg, AA and Remington, DL and DM O'Malley and Sederoff, RR and Whetten, RW}, year={2001}, month={Feb}, pages={348-+} }
 @article{sato_wuli_sederoff_whetten_2001, title={Molecular Cloning and Expression of Eight Laccase cDNAs in Loblolly Pine (Pinus taeda)*}, volume={114}, ISSN={0918-9440}, url={http://dx.doi.org/10.1007/pl00013978}, DOI={10.1007/PL00013978}, number={2}, journal={Journal of Plant Research}, publisher={Springer Science and Business Media LLC}, author={Sato, Yasushi and Wuli, Bao and Sederoff, Ronald and Whetten, Ross}, year={2001}, month={Jun}, pages={147–155} }
 @misc{robertson_barry_busta_collier_keen_sederoff_simpkins_stormshak_urban_2001, title={Moribund funding in agricultural research}, volume={291}, DOI={10.1126/science.291.5511.2089c}, abstractNote={The double-digit increases in federal funding for basic research at the National Science Foundation (NSF) and the National Institutes of Health (NIH) for fiscal year 2001 are a welcome development ([1][1]), but does recognition of basic research as the engine that drives technology and economic growth not apply to agriculture?

The standard competitive grants program for basic research at the U.S. Department of Agriculture (USDA) began as the National Research Initiative 10 years ago after National Research Council (NRC) reports decried the lack of support for competitive research in the agricultural sciences. The program has outgrown its initiative status, yet it has been stalled for 9 years at a funding level that can only be described as moribund. Whereas support for competitive basic research programs at NSF and NIH combined have grown in constant dollars by 60% since 1992 ([2][2]), funding for the USDA's competitive grants program has decreased 14% in constant dollars since its 1992 appropriation of $100 million.

A report from the NRC noted the high quality of National Research Initiative research, its crucial contributions to agricultural productivity and environmental quality, and the more than three dozen studies that have placed the economic rate of return on public investment in food and fiber research at 35 to 60% per year ([3][3]). This is a phenomenal rate of return. New markets, new products, and environmental protection require new ideas, new approaches, and levels of research funding commensurate with the importance that society places on a safe, productive, and environmentally benign food and fiber production system.

In 30 years—the approximate time it takes basic research in the public sector to reach marketplace maturity—the world population will have increased by about 3 billion. Will we have funded the basic research necessary to feed and clothe them?

1. [↵][4]1. D. Malakoff
 , Science 291, 33 (2001) See, for example,.
 [OpenUrl][5][FREE Full Text][6]

2. [↵][7]American Association for the Advancement of Science, Historical data on federal R&D, FY 1976-2001. Available at .
 

3. [↵][8]1. National Research Council
 , National Research Initiative: A Vital Competitive Grants Program in Food, Fiber, and Natural-Resources Research (National Academy Press, Washington, DC, 2000).

 [1]: #ref-1
 [2]: #ref-2
 [3]: #ref-3
 [4]: #xref-ref-1-1 "View reference 1 in text"
 [5]: {openurl}?query=rft.jtitle%253DScience%26rft.stitle%253DScience%26rft.issn%253D0036-8075%26rft.aulast%253DMalakoff%26rft.auinit1%253DD.%26rft.volume%253D291%26rft.issue%253D5501%26rft.spage%253D33%26rft.epage%253D33%26rft.atitle%253D2001%2BU.S.%2BBUDGET%253A%2BRecord%2BYear%2Bfor%2BScience%252C%2BBut%2BCan%2BIt%2BBe%2BRepeated%253F%26rft_id%253Dinfo%253Adoi%252F10.1126%252Fscience.10.1126%252FSCIENCE.291.5501.33%26rft_id%253Dinfo%253Apmid%252F11192000%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx
 [6]: /lookup/ijlink/YTozOntzOjQ6InBhdGgiO3M6MTQ6Ii9sb29rdXAvaWpsaW5rIjtzOjU6InF1ZXJ5IjthOjQ6e3M6ODoibGlua1R5cGUiO3M6NDoiRlVMTCI7czoxMToiam91cm5hbENvZGUiO3M6Mzoic2NpIjtzOjU6InJlc2lkIjtzOjExOiIyOTEvNTUwMS8zMyI7czo0OiJhdG9tIjtzOjI1OiIvc2NpLzI5MS81NTExLzIwODkuMy5hdG9tIjt9czo4OiJmcmFnbWVudCI7czowOiIiO30=
 [7]: #xref-ref-2-1 "View reference 2 in text"
 [8]: #xref-ref-3-1 "View reference 3 in text"}, number={5511}, journal={Science}, author={Robertson, G. P. and Barry, P. J. and Busta, F. F. and Collier, R. J. and Keen, N. T. and Sederoff, R. R. and Simpkins, W. W. and Stormshak, F. and Urban, T. N.}, year={2001}, pages={2089–2090} }
 @article{dimmel_mackay_althen_parks_sederoff_2001, title={Pulping and bleaching of CAD-deficient wood}, volume={21}, ISSN={["1532-2319"]}, DOI={10.1081/WCT-100102651}, abstractNote={Mutant loblolly pine trees that are deficient in the enzyme cinnamyl alcohol dehydrogenase (CAD) have been obtained through directed breeding. The lignin in the wood of CAD-deficient trees has a different pool of precursors, resulting in high levels of pulping-resistant C-5 linkages. Wood from a 12-year-old CAD-deficient tree has been pulped under soda and kraft conditions in microdigestors. In comparison to a normal 12-year-old loblolly pine, the CAD-deficient wood was much more easily delignified. In addition, the pulp from CAD-deficient wood was as easy to bleach as a control pulp. The high reactivity of CAD-deficient wood may be related to the lignin size and phenolic content. The molecular weight of an isolated milled wood lignin from CAD-deficient pine was ∼35% less than that from a normal pine tree.}, number={1}, journal={JOURNAL OF WOOD CHEMISTRY AND TECHNOLOGY}, author={Dimmel, DR and MacKay, JJ and Althen, EM and Parks, C and Sederoff, RR}, year={2001}, pages={1–17} }
 @article{tang_sederoff_whetten_2001, title={Regeneration of transgenic loblolly pine (Pinus taeda L.) from zygotic embryos transformed with Agrobacterium tumefaciens}, volume={213}, ISSN={["1432-2048"]}, DOI={10.1007/s004250100566}, abstractNote={Embryos of 24 open-pollinated families of loblolly pine (Pinus teade L.) were used as explants to conduct in vitro regeneration. Then, Agrobacterium tumefaciens strain GV3101 harboring the plasmid pPCV6NFHygGUSINT was used to transform mature zygotic embryos of seven families of loblolly pine. The frequency of transformation varied among families infected with A. tumefaciens. The highest frequency (100%) of transient beta-glucuronidase (GUS)-expressing embryos was obtained from family 11-1029 with over 300 blue spots per embryo. Expression of the GUS reporter gene was observed in cotyledons, hypocotyls, and radicles of co-cultivated mature zygotic embryos, as well as in callus and shoots derived from co-cultivated mature zygotic embryos. Ninety transgenic plants were regenerated from hygromycin-resistant callus derived from families W03. 8-1082 and 11-1029. and 19 transgenic plantlets were established in soil. The presence of the GUS gene in the plant genome was confirmed by polymerase chain reaction. Southern blot, and plant DNA/T-DNA junction analysis. These 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 loblolly pine.}, number={6}, journal={PLANTA}, author={Tang, W and Sederoff, R and Whetten, R}, year={2001}, month={Oct}, pages={981–989} }
 @article{zhang_sederoff_allona_2000, title={Differential expression of genes encoding cell wall proteins in vascular tissues from vertical and bent loblolly pine trees}, volume={20}, number={7}, journal={Tree Physiology}, author={Zhang, Y. and Sederoff, R. R. and Allona, I.}, year={2000}, pages={457–466} }
 @article{lapierre_pollet_mackay_sederoff_2000, title={Lignin structure in a mutant pine deficient in cinnamyl alcohol dehydrogenase}, volume={48}, ISSN={["0021-8561"]}, DOI={10.1021/jf991398p}, abstractNote={Cinnamyl alcohol dehydrogenase (CAD) activity is deficient in loblolly pine (Pinus taeda L.) harboring a mutated allele of the cad gene (cad-n1). We compared lignin structure of CAD-deficient and wild-type pines, both types segregating within full-sib families obtained by controlled crosses. The type and frequency of lignin building units and distribution of interunit bonds were determined from the GC-MS analysis of thioacidolysis monomers and dimers. While the lignin content was only slightly reduced, the lignin structure was dramatically modified by the mutation in both mature and juvenile trees. Lignins from CAD-deficient pine displayed unusually high levels of coniferaldehyde and dihydroconiferyl alcohol. In addition, biphenyl and biphenyl ether bonds were in large excess in these abnormal lignins. These 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.}, number={6}, journal={JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY}, author={Lapierre, C and Pollet, B and MacKay, JJ and Sederoff, RR}, year={2000}, month={Jun}, pages={2326–2331} }
 @misc{o'malley_sederoff_grattapaglia_2000, title={Methods for within family selection in woody perennials using genetic markers}, volume={6,054,634}, number={2000 Apr. 25}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={O'Malley, D. M. and Sederoff, R. R. and Grattapaglia, D.}, year={2000} }
 @misc{lev-yadun_sederoff_2000, title={Pines as model gymnosperms to study evolution, wood formation, and perennial growth}, volume={19}, ISSN={["1435-8107"]}, DOI={10.1007/s003440000045}, number={3}, journal={JOURNAL OF PLANT GROWTH REGULATION}, author={Lev-Yadun, S and Sederoff, R}, year={2000}, month={Sep}, pages={290–305} }
 @article{sederoff_2000, title={Tree genomes: What will we understand about them by the year 2020 and how might we use that knowledge?}, ISBN={0792360117}, DOI={10.1007/978-94-017-1576-8_4}, abstractNote={The purpose of this paper is to speculate about the future applications of molecular genetics to the understanding and utilization of tree genomes. Biotechnology of forest trees is a young discipline. The first genetically engineered tree, a glyphosate tolerant hybrid poplar, was produced in 1987 (Fillatti et al., 1987). Since that time, biotechnology of forest trees has incorporated new technology of genetic mapping and has now entered the era of genomics. Much of what follows here is only one person’s speculations about scientific progress into a relatively near future. In general, scientists are less effective at predicting the future of science than are writers of fiction, who are less constrained about predictions. The time frame of this paper is to look forward to the year 2020, which is approximately one rotation age for a temperate pine, and as much as four rotations for a tropical hardwood. The purpose of this short review is not to be comprehensive, nor to provide access to key references, but to provide an overview of ideas related to application to forest trees of existing technology in the relatively near future.}, journal={Forest genetics and sustainability}, publisher={Dordrecht ;Boston : Kluwer Academic Publishers}, author={Sederoff, R. R.}, year={2000}, pages={23} }
 @article{sederoff_1999, title={Building better trees with antisense}, volume={17}, ISSN={["1087-0156"]}, DOI={10.1038/11678}, number={8}, journal={NATURE BIOTECHNOLOGY}, author={Sederoff, R}, year={1999}, month={Aug}, pages={750–751} }
 @article{marques_vasquez-kool_carocha_ferreira_dm o'malley_liu_sederoff_1999, title={Genetic dissection of vegetative propagation traits in Eucalyptus tereticornis and E-globulus}, volume={99}, ISSN={["1432-2242"]}, DOI={10.1007/s001220051400}, number={6}, journal={THEORETICAL AND APPLIED GENETICS}, author={Marques, CM and Vasquez-Kool, J and Carocha, VJ and Ferreira, JG and DM O'Malley and Liu, BH and Sederoff, R}, year={1999}, month={Oct}, pages={936–946} }
 @article{wenck_quinn_whetten_pullman_sederoff_1999, title={High-efficiency Agrobacterium-mediated transformation of Norway spruce (Picea abies) and loblolly pine (Pinus taeda)}, volume={39}, DOI={10.1023/a:1006126609534}, abstractNote={Agrobacterium-mediated gene transfer is the method of choice for many plant biotechnology laboratories; however, large-scale use of this organism in conifer transformation has been limited by difficult propagation of explant material, selection efficiencies and low transformation frequency. We have analyzed co-cultivation conditions and different disarmed strains of Agrobacterium to improve transformation. Additional copies of virulence genes were added to three common disarmed strains. These extra virulence genes included either a constitutively active virG or extra copies of virG and virB, both from pTiBo542. In experiments with Norway spruce, we increased transformation efficiencies 1000-fold from initial experiments where little or no transient expression was detected. Over 100 transformed lines expressing the marker gene beta-glucuronidase (GUS) were generated from rapidly dividing embryogenic suspension-cultured cells co-cultivated with Agrobacterium. GUS activity was used to monitor transient expression and to further test lines selected on kanamycin-containing medium. In loblolly pine, transient expression increased 10-fold utilizing modified Agrobacterium strains. Agrobacterium-mediated gene transfer is a useful technique for large-scale generation of transgenic Norway spruce and may prove useful for other conifer species.}, number={3}, journal={Plant Molecular Biology}, author={Wenck, A. R. and Quinn, M. and Whetten, Ross and Pullman, G. and Sederoff, R.}, year={1999}, pages={407–416} }
 @misc{amerson_wilcox_sederoff_kuhlman_o'malley_grattapaglia_1999, title={Methods for within family selection of disease resistance in woody perennials using genetic markers}, volume={5,908,978}, number={1999 June 1}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Amerson, H. V. and Wilcox, P. and Sederoff, R. R. and Kuhlman, E. G. and O'Malley, D. M. and Grattapaglia, D.}, year={1999} }
 @article{mackay_presnell_jameel_taneda_d o'malley_sederoff_1999, title={Modified lignin and delignification with a CAD-deficient loblolly pine}, volume={53}, ISSN={["0018-3830"]}, DOI={10.1515/HF.1999.067}, abstractNote={Summary}, number={4}, journal={HOLZFORSCHUNG}, author={MacKay, J and Presnell, T and Jameel, H and Taneda, H and D O'Malley and Sederoff, R}, year={1999}, pages={403–410} }
 @article{sederoff_1999, title={Surfing on AG Biotech into genomics}, volume={5}, number={1999}, journal={Molecular Breeding}, author={Sederoff, R. R.}, year={1999}, pages={485–491} }
 @misc{sederoff_mackay_ralph_hatfield_1999, title={Unexpected variation in lignin}, volume={2}, ISSN={["1879-0356"]}, DOI={10.1016/S1369-5266(99)80029-6}, abstractNote={Recent studies on mutant and transgenic plants indicate that lignification may be far more flexible than previously realized. Pines with a mutation affecting the biosynthesis of the major lignin precursor, coniferyl alcohol, show a high level of an unusual subunit, dihydroconiferyl alcohol. These results argue in favor of an increased potential for genetic modification of lignin and indicate that our knowledge of the biosynthesis of lignin is far from complete.}, number={2}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Sederoff, RR and MacKay, JJ and Ralph, J and Hatfield, RD}, year={1999}, month={Apr}, pages={145–152} }
 @article{marques_araujo_ferreira_whetten_dm o'malley_liu_sederoff_1998, title={AFLP genetic maps of Eucalyptus globulus and E-tereticornis}, volume={96}, ISSN={["1432-2242"]}, DOI={10.1007/s001220050795}, number={6-7}, journal={THEORETICAL AND APPLIED GENETICS}, author={Marques, CM and Araujo, JA and Ferreira, JG and Whetten, R and DM O'Malley and Liu, BH and Sederoff, R}, year={1998}, month={May}, pages={727–737} }
 @article{allona_quinn_shoop_swope_st cyr_carlis_riedl_retzel_campbell_sederoff_et al._1998, title={Analysis of xylem formation in pine by cDNA sequencing}, volume={95}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.95.16.9693}, abstractNote={
            Secondary xylem (wood) formation is likely to involve some genes expressed rarely or not at all in herbaceous plants. Moreover, environmental and developmental stimuli influence secondary xylem differentiation, producing morphological and chemical changes in wood. To increase our understanding of xylem formation, and to provide material for comparative analysis of gymnosperm and angiosperm sequences, ESTs were obtained from immature xylem of loblolly pine (
            Pinus taeda
            L.). A total of 1,097 single-pass sequences were obtained from 5′ ends of cDNAs made from gravistimulated tissue from bent trees. Cluster analysis detected 107 groups of similar sequences, ranging in size from 2 to 20 sequences. A total of 361 sequences fell into these groups, whereas 736 sequences were unique. About 55% of the pine EST sequences show similarity to previously described sequences in public databases. About 10% of the recognized genes encode factors involved in cell wall formation. Sequences similar to cell wall proteins, most known lignin biosynthetic enzymes, and several enzymes of carbohydrate metabolism were found. A number of putative regulatory proteins also are represented. Expression patterns of several of these genes were studied in various tissues and organs of pine. Sequencing novel genes expressed during xylem formation will provide a powerful means of identifying mechanisms controlling this important differentiation pathway.
          }, number={16}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Allona, I and Quinn, M and Shoop, E and Swope, K and St Cyr, S and Carlis, J and Riedl, J and Retzel, E and Campbell, MM and Sederoff, R and et al.}, year={1998}, month={Aug}, pages={9693–9698} }
 @misc{mackay_o'malley_whetten_sederoff_1998, title={Method of altering lignin in trees}, volume={5,824,842}, number={1998 Oct. 20}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={MacKay, J. and O'Malley, D. and Whetten, R. and Sederoff, R.}, year={1998} }
 @article{ralph_hatfield_fanchuang_marita_ede_junpeng_quideau_helm_grabber_kim_et al._1998, title={NMR applications in cell wall research}, number={1998}, journal={TAPPI Journal}, author={Ralph, J. and Hatfield, R. and Fanchuang, L. and Marita, J. M. and Ede, R. M. and Junpeng, S. R. and Quideau, S. and Helm, R. and Grabber, J. and Kim, H. and et al.}, year={1998} }
 @misc{whetten_mackay_sederoff_1998, title={Recent advances in understanding lignin biosynthesis}, volume={49}, ISSN={["1040-2519"]}, DOI={10.1146/annurev.arplant.49.1.585}, abstractNote={▪ Abstract  After a long period of little change, the basic concepts of lignin biosynthesis have been challenged by new results from genetic modification of lignin content and composition. New techniques for making directed genetic changes in plants, as well as improvements in the analytical techniques used to determine lignin content and composition in plant cell walls, have been used in experimental tests of the accepted lignin biosynthetic pathway. The lignins obtained from genetically modified plants have shown unexpected properties, and these findings have extended the known range of variation in lignin content and composition. 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. If this is so, the properties of novel lignins could be of significant scientific and practical interest.}, number={1998}, journal={ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY}, author={Whetten, RW and MacKay, JJ and Sederoff, RR}, year={1998}, pages={585–609} }
 @article{sederoff_1998, title={The promise of forest biotechnology}, number={1998 Aug.}, journal={Paper Age}, author={Sederoff, R. R.}, year={1998}, pages={13–18} }
 @article{ralph_mackay_hatfield_omalley_whetten_sederoff_1997, title={Abnormal lignin in a loblolly pine mutant}, volume={277}, ISSN={["1095-9203"]}, DOI={10.1126/science.277.5323.235}, abstractNote={
            Novel lignin is formed in a mutant loblolly pine (
            Pinus taeda
            L.) severely depleted in cinnamyl alcohol dehydrogenase (E.C. 1.1.1.195), which converts coniferaldehyde to coniferyl alcohol, the primary lignin precursor in pines. Dihydroconiferyl alcohol, a monomer not normally associated with the lignin biosynthetic pathway, is the major component of the mutant's lignin, accounting for ∼30 percent (versus ∼3 percent in normal pine) of the units. The level of aldehydes, including new 2-methoxybenzaldehydes, is also increased. The mutant pines grew normally indicating that, even within a species, extensive variations in lignin composition need not disrupt the essential functions of lignin.
          }, number={5323}, journal={SCIENCE}, author={Ralph, J and MacKay, JJ and Hatfield, RD and OMalley, DM and Whetten, RW and Sederoff, RR}, year={1997}, month={Jul}, pages={235–239} }
 @article{mackay_omalley_presnell_booker_campbell_whetten_sederoff_1997, title={Inheritance, gene expression, and lignin characterization in a mutant pine deficient in cinnamyl alcohol dehydrogenase}, volume={94}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.94.15.8255}, abstractNote={
            We have discovered a mutant loblolly pine (
            Pinus taeda
            L.) in which expression of the gene encoding cinnamyl alcohol dehydrogenase (CAD; EC
            1.1.1.195
            ) is severely reduced. The products of CAD, cinnamyl alcohols, are the precursors of lignin, a major cell wall polymer of plant vascular tissues. Lignin composition in this mutant shows dramatic modifications, including increased incorporation of the substrate of CAD (coniferaldehyde), indicating that CAD may modulate lignin composition in pine. The recessive
            cad-n1
            allele, which causes this phenotype, was discovered in a tree heterozygous for this mutant allele. It is inherited as a simple Mendelian locus that maps to the same genomic region as the
            cad
            locus. In mutant plants, CAD activity and abundance of
            cad
            RNA transcript are low, and free CAD substrate accumulates to a high level. The wood of the mutant is brown, whereas the wood in wild types is nearly white. The wood phenotype resembles that of brown midrib (
            bm
            ) mutants and some transgenic plants in which xylem is red-brown due to a reduction in CAD activity. However, unlike transgenics with reduced CAD, the pine mutant has decreased lignin content. Wood in which the composition of lignin varies beyond previous expectations still provides vascular function and mechanical support.
          }, number={15}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={MacKay, JJ and OMalley, DM and Presnell, T and Booker, FL and Campbell, MM and Whetten, RW and Sederoff, RR}, year={1997}, month={Jul}, pages={8255–8260} }
 @inproceedings{o'malley_grattapaglia_chaparro_wilcox_amerson_liu_whetten_mckeand_kuhlman_mccord_et al._1996, title={Molecular markers,  forest genetics, and tree breeding}, DOI={10.1007/978-1-4899-0280-1_7}, abstractNote={Several years ago, Strauss et al. (1992) thoughtfully evaluated the application of molecular markers in forest tree breeding for marker aided selection. The purpose of their paper was to emphasize the limitations and shortcomings of marker-aided selection particularly in conifers. They argued that studies of quantitative trait loci identified in agronomic crops, which have significant utility (e.g. Stuber, 1992; Stuber et al., 1992), are of little relevance to assessing the potential for marker aided selection in populations of forest trees, and that the near term usefulness of molecular markers for forest tree breeding will be limited. The major barriers to application included cost, the lack of association of markers with traits across breeding populations due to linkage equilibrium, variation in expression of loci affecting quantitative traits due to differences in genetic background, genotype environment interactions, and stability of marker-trait associations over multiple generations. In addition, Strauss et al. (1992) noted that marker-aided selection would be most useful for within family selection, where the economic values of the traits are high, the trait heritabilities are low, and where markers are able to explain much of the genetic variance. However, they 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.}, booktitle={Genomes of Plants and Animals: 21 Stadler Genetics Symposium}, publisher={Plenum Press,  NY}, author={O'Malley, D. M. and Grattapaglia, D. and Chaparro, J. X. and Wilcox, P. L. and Amerson, H. V. and Liu, B-H and Whetten, R. and McKeand, Steven and Kuhlman, E. G. and McCord, S. and et al.}, editor={Gustafson, J. P. and Flavell, R. B.Editors}, year={1996}, pages={87–102} }
 @misc{whetten_sederoff_1995, title={LIGNIN BIOSYNTHESIS}, volume={7}, ISSN={["1532-298X"]}, DOI={10.2307/3870053}, number={7}, journal={PLANT CELL}, author={WHETTEN, R and SEDEROFF, R}, year={1995}, month={Jul}, pages={1001–1013} }
 @article{sederoff_campbell_o'malley_whetten_1994, title={Genetic regulation of lignin biosynthesis and the potential modification of wood by genetic engineering in loblolly pine}, ISBN={0306448041}, DOI={10.1007/978-1-4615-2544-8_12}, journal={Genetic engineering of plant secondary metabolism}, publisher={New York :  Plenum Press}, author={Sederoff, R. and Campbell, M. and O'Malley, D. and Whetten, R.}, editor={B. E. Ellis, G. W. Kuroki and Stafford, H. A.Editors}, year={1994}, pages={313} }
 @article{grattapaglia_sederoff_1994, title={Genetic-linkage maps of eucalyptus-grandis and eucalyptus-urophylla using a pseudo-testcross - mapping strategy and rapd markers}, volume={137}, number={4}, journal={Genetics}, author={Grattapaglia, D. and Sederoff, R.}, year={1994}, pages={1121–1137} }
 @inproceedings{grattapaglia_chaparro_wilcox_mccord_crane_amerson_werner_liu_o'malley_whetten_et al._1993, title={Application of genetic markers to tree breeding}, booktitle={Proceedings of the 22nd Southern Forest Tree Improvement Conference}, author={Grattapaglia, D. and Chaparro, J. and Wilcox, P. and McCord, S. and Crane, B. and Amerson, H. and Werner, D. and Liu, B. H. and O'Malley, D. and Whetten, R. and et al.}, year={1993}, pages={452–463} }
 @misc{stomp_weissinger_sederoff_1992, title={Ballistic transformation of conifers}, volume={5,122,466}, number={1992 June 16}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Stomp, A. and Weissinger, A. and Sederoff, R.}, year={1992} }
 @inproceedings{grattapaglia_chaparro_wilcox_mccord_werner_amerson_mckeand_bridgwater_whetten_o'malley_et al._1992, title={Mapping in woody plants with RAPD markers: application to breeding in forestry and horticulture}, booktitle={Proceedings of the Symposium on the Applications of RAPD Technology to Plant Breeding}, publisher={Joint Plant Breeding Symposium Series,  Crop Science Society of America, American Society for Horticultural Science, and American Genetics Association}, author={Grattapaglia, D. and Chaparro, J. and Wilcox, P. and McCord, S. and Werner, D. and Amerson, H. and McKeand, S. and Bridgwater, F. and Whetten, R. and O'Malley, D. and et al.}, year={1992}, pages={37–40} }
 @misc{sederoff_stomp_moore_chilton_1989, title={Method for transforming pine}, volume={4886937}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Sederoff, R. R. and Stomp, A.-M. and Moore, L. W. and Chilton, S. W.}, year={1989} }
 @article{schaffer_sederoff_1981, title={IMPROVED ESTIMATION OF DNA FRAGMENT LENGTHS FROM AGAROSE GELS}, volume={115}, ISSN={["0003-2697"]}, DOI={10.1016/0003-2697(81)90533-9}, abstractNote={An improved method for estimation of DNA fragment lengths from mobility on agarose gels is introduced. Commonly, this estimation is done by graphing the logarithm of length against the mobility of standards, although this procedure produces a noticeably curved plot. The method presented here is based on the relationship of E. M. Southern (1979, Anal. Biochem., 100, 319–323), who showed that the reciprocal of mobility plotted against fragment length is linear. A least-squares analysis has been developed to use this relationship together with any number of standards to estimate fragment length. The method also tests internal consistency of the assigned lengths of a set of fragments. This analysis has been applied to sets of restriction fragments of λ DNA, indicating errors or inconsistencies in previously assigned lengths. Using a more consistent set of λ values, the lengths of pBR322 fragments of known sequence were predicted with better than 1% accuracy. No evidence of sequence-dependent migration was seen. A computer program to do this analysis is included.}, number={1}, journal={ANALYTICAL BIOCHEMISTRY}, author={SCHAFFER, HE and SEDEROFF, RR}, year={1981}, pages={113–122} }