Article
Plant Sciences
Michael F. Nagle, Jialin Yuan, Damanpreet Kaur, Cathleen Ma, Ekaterina Peremyslova, Yuan Jiang, Bahiya Zahl, Alexa Nino de Rivera, Wellington Muchero, Li Fuxin, Steven H. Strauss
Summary: Adventitious rooting (AR) plays a crucial role in tree propagation, breeding, and genetic engineering. However, the genetic basis of AR is not well-characterized. To identify genetic regulators of AR, a genome-wide association study (GWAS) was performed using 1148 Populus trichocarpa genotypes. A computer vision system was developed to measure various traits related to adventitious root development. GWAS analysis revealed 277 unique associations, indicating that genes involved in hormone signaling, cell division, and other root development processes play a role in AR. Numerous genes with unknown functions were also identified as candidates for further analysis.
HORTICULTURE RESEARCH
(2023)
Article
Plant Sciences
Hemeng Wang, Jin-Gui Chen, Ying Chang
Summary: OFPs are a family of plant growth regulators known to play diverse roles in physiological processes, with members like PtOFP1 having been shown to act as a transcriptional repressor. In Populus trichocarpa, 30 PtOFP genes were identified, grouped into four subfamilies, and found to be involved in hormonal responses and cellular processes. Overexpression of PtOFP1 in Arabidopsis enhanced tolerance to drought stress, highlighting its potential as a target for genetic modification in improving stress resistance in plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Huimin Zhao, Yani Niu, Hao Dong, Yaqi Jia, Yucheng Wang
Summary: The study identified two S1Fa-like TF genes, PtS1Fa1 and PtS1Fa2, in Populus trichocarpa. While PtS1Fa1 did not show significant effects, overexpression of PtS1Fa2 increased antioxidant activity and reduced ROS accumulation, playing a crucial role in drought tolerance in the plant.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Forestry
Haizhen Zhang, Xuetong Zhang, Meng Meng, Haoyang Di, Jingang Wang
Summary: Heat stress can severely hinder plant growth and reproduction, leading to significant financial losses and reduced crop yield. This study reveals the induction of heat shock transcription factor PtHSFA4a in Populus trichocarpa leaves under high temperatures. The ectopic expression of PtHSFA4a enhances heat stress tolerance in Arabidopsis thaliana by upregulating the antioxidant defense system and maintaining protein folding homeostasis. These findings provide new insights into the molecular mechanisms underlying the regulation of plant responses to heat stress mediated by PtHSFA4a.
Article
Biochemistry & Molecular Biology
Guiling Liu, Fengyi Li, Gongfa Shi, Lei Wang, Ling Wang, Lijuan Fan
Summary: This study systematically identified and characterized MADS-box genes in Iris laevigata, a plant species with beautiful flowers and strong cold resistance. The researchers found 41 putative MADS-box genes and selected IlSEP3 and IlSVP for functional studies. They showed that IlSEP3 promotes flowering, while IlSVP does not significantly affect phenotypes. This work fills the knowledge gap in key flowering control genes in I. laevigata and provides insights into the genetic regulation of flowering time in this plant species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Forestry
Xianqiang Wang, Shu Yao, Win Pa Pa Myo Htet, Yuchen Yue, Zhuanzhuan Zhang, Kuan Sun, Sijie Chen, Keming Luo, Di Fan, Isabel Allona
Summary: This study reveals the intricate regulatory mechanism of lignin biosynthesis in Populus tomentosa Carr., showing the interaction between miR828 and MYB171, MYB011 in regulating lignin synthesis through both transcriptional and post-transcriptional modulation.
Article
Forestry
Yang Ye, Haodong Xin, Xiting Gu, Jianwen Ma, Lingli Li
Summary: This study identified 233 PtbHLHs and 10 PtFBHs in the newest version of Populus trichocarpa genome, and analyzed their classification, distribution, expression patterns, and evolutionary pressures. The results suggest that PtbHLHs may be involved in plant growth and development, providing valuable clues for further investigations on the physiological and molecular functions of these genes.
Article
Plant Sciences
Yanel Bernardi, Maria Agustina Ponso, Federico Belen, Abelardo C. Vegetti, Marcela C. Dotto
Summary: The miR394 pathway plays a crucial role in regulating flowering time in Arabidopsis plants in an LCR-independent manner. Mutations in the MIR394 genes result in early flowering, lower expression of FLC, and higher expression of FT and SOC1. The study also reveals that mir394a mir394b double mutants exhibit reduced branch production and lower seed yield. This research uncovers previously unknown aspects of development regulated by the miR394 pathway and contributes to a better understanding of the versatile functions of this plant regulatory miRNA.
PLANT CELL REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Wanqin Chen, Lirong Zhao, Lei Liu, Xia Li, Yang Li, Gang Liang, Houping Wang, Diqiu Yu
Summary: This study reveals that flowering time in Arabidopsis is significantly delayed by iron deficiency, mediated by the iron deficiency-induced transcription factors bHLH38/100/101 which regulate FT expression specifically under long days. Disrupting FT expression suppressed the early-flowering phenotype induced by bHLH38/100/101, indicating their dependence on functional FT. Additionally, bHLH38/100/101 interact with CO to regulate FT expression, suggesting that iron deficiency affects flowering through the bHLH38/100/101-CO-FT signaling pathway.
Article
Plant Sciences
Xiaorui Xu, Jingya Xu, Chen Yuan, Qianqian Chen, Qinggang Liu, Xuming Wang, Cheng Qin
Summary: BBX17, a member of the B-box (BBX) family, acts as a repressor of floral transition under long-day conditions. It interacts with CONSTANS (CO) and represses its ability to control FT expression, leading to delayed flowering phenotype in plants overexpressing BBX17. Additionally, the degradation of BBX17 is regulated by light and requires COP1 and 26S proteasome, making it a key factor in controlling flowering in Arabidopsis thaliana.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Plant Sciences
Xiaocen Ma, Na Luo, Wenping Bai, Xinru Wang, Congcong Wang, Nini Cheng, Heng Liu
Summary: This study identified six PtHMGR genes in Populus trichocarpa and revealed their crucial roles in plant growth and response to abiotic stresses. The genes were found to be regulated by light, hormones, and abiotic stresses, and transgenic expression of PtHMGR5 improved drought tolerance in plants.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Review
Biochemistry & Molecular Biology
Xiaopei Wang, Yanli Niu, Yuan Zheng
Summary: Plants face a more volatile environment due to their immobility, prompting the development of efficient mechanisms to adapt to stress. MYB transcription factors, a widespread family in plants, play critical roles in plant development and responses to stresses. Multiple studies have shown that MYB proteins are involved in diverse roles in responses to abiotic stresses, but their regulatory mechanism is still not well understood.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Qi Wang, Guang-Ling Wang, Shu-Yuan Song, Ya-Nan Zhao, Shan Lu, Fei Zhou
Summary: Floral transition is regulated by multiple pathways, and the OR protein negatively regulates flowering by repressing the expression of key flowering genes, independent of vernalization or GA-dependent pathways.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yijie Wang, Huiyan Zhou, Yuanrong He, Xiuping Shen, Sue Lin, Li Huang
Summary: This article provides an overview of the important roles of MYB transcription factors in the male reproductive development of plants, as well as their regulatory interactions with other transcription factors.
Article
Biochemistry & Molecular Biology
Xijuan Zhao, Lingling Tan, Shuo Wang, Yirong Shen, Liangyu Guo, Xiaoxue Ye, Shenkui Liu, Ying Feng, Wenwu Wu
Summary: This study identified 24 PtSR genes in Popolus trichocarpa, showing their constitutive expression in roots, stems, and leaves, and their response to various stresses. PtSCL30 may act as a negative regulator under cold and salt stress in woody plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Rongbin Hu, Jin Zhang, Sara Jawdy, Avinash Sreedasyam, Anna Lipzen, Mei Wang, Vivian Ng, Christopher Daum, Keykhosrow Keymanesh, Degao Liu, Haiwei Lu, Priya Ranjan, Jin-Gui Chen, Wellington Muchero, Timothy J. Tschaplinski, Gerald A. Tuskan, Jeremy Schmutz, Xiaohan Yang
Summary: In this study, we conducted genome-wide transcription sequencing analysis on leaf samples of an obligate CAM species, Kalanchoe fedtschenkoi, under moderate and severe drought treatments. We identified differentially expressed genes and created a whole genome wide co-expression network. Interestingly, we found that drought had little regulation on the expression of CAM-related genes in K. fedtschenkoi. Additionally, we observed some shared transcriptional changes between CAM species and C-3 species in response to drought stress.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Miaomiao Li, Tao Yao, Wanru Lin, Will E. E. Hinckley, Mary Galli, Wellington Muchero, Andrea Gallavotti, Jin-Gui Chen, Shao-shan Carol Huang
Summary: This study presents a new method to investigate how proteins interact to regulate gene activity. It reveals that certain proteins can expand their ability to recognize specific DNA sequences when they form complexes, leading to the regulation of a broader range of genes.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Nathan Bryant, Jin Zhang, Kai Feng, Mengjun Shu, Raphael Ployet, Jin-Gui Chen, Wellington Muchero, Chang Geun Yoo, Timothy J. Tschaplinski, Yunqiao Pu, Arthur J. Ragauskas
Summary: By characterizing a population of 409 naturally varying Populus trichocarpa genotypes, a genome-wide association study identified 756 genes significantly associated with lignin phenotypes, providing insights into the molecular mechanisms of lignin biosynthesis and new targets for genetic improvement in poplar.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Nathan Bryant, Wellington Muchero, Rachel A. Weber, Jaime Barros, Jin-Gui Chen, Timothy J. Tschaplinski, Yunqiao Pu, Arthur J. Ragauskas
Summary: The study found that the lignin content in the cell wall of Populus was significantly increased in the region infected by Septoria, and the composition of lignin in the infected region was also different. These results provide important insights into the wood characteristic changes of Populus during Septoria infection.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Tao Yao, Guoliang Yuan, Haiwei Lu, Yang Liu, Jin Zhang, Gerald A. Tuskan, Wellington Muchero, Jin-Gui Chen, Xiaohan Yang
Summary: The genus Populus is widely used for various purposes and has become a desirable crop for biofuel production and research. Modern biotechnologies, including CRISPR/Cas9, have been applied to improve its genetic and genomic traits. In this study, CRISPRa and CBE technologies were successfully used for gene expression regulation and precise gene engineering in two Populus species.
HORTICULTURE RESEARCH
(2023)
Article
Cell Biology
Him Shrestha, Tao Yao, Zhenzhen Qiao, Wellington Muchero, Robert L. L. Hettich, Jin-Gui Chen, Paul E. E. Abraham
Summary: PtLecRLK1 acts as a susceptibility factor in facilitating root colonization by Laccaria bicolor. It modifies multiple signaling pathways including plant defense, MAPK signaling, phytohormone signaling, ROS balance, endocytosis, cytoskeleton movement, and proteasomal degradation to establish and maintain L. bicolor colonization. Additionally, a cGMP-dependent protein kinase may be implicated as a substrate of PtLecRLK1.
Article
Plant Sciences
Hadia Hussain, Yuxin Cheng, Yating Wang, Yuan Yuan, Yingying Li, Hainan Tian, Saddam Hussain, Siyu Chen, Rao Lin, Tianya Wang, Shucai Wang
Summary: The plant hormone abscisic acid (ABA) plays an important role in regulating plant responses to abiotic stresses by regulating the expression of ABA-responsive genes. ASR1 and ASR2 are serine-rich novel transcription repressors closely related to ABA responses in Arabidopsis. They negatively regulate ABA responses in a redundant manner.
Article
Plant Sciences
Yating Wang, Wei Wang, Qiming Jia, Hainan Tian, Xutong Wang, Yingying Li, Saddam Hussain, Hadia Hussain, Tianya Wang, Shucai Wang
Summary: This study identifies BIC2 as a regulator of ABA responses in Arabidopsis. BIC2 expression increases significantly in response to ABA treatment, while BIC1 expression remains largely unchanged. It is found that both BIC1 and BIC2 are mainly localized in the nucleus and can activate the expression of co-transfected reporter genes.
Article
Plant Sciences
Guoliang Yuan, Yang Liu, Tao Yao, Wellington Muchero, Jin-Gui Chen, Gerald A. Tuskan, Xiaohan Yang
Summary: Although CRISPR/Cas-based genome editing has been widely used in plant genetic engineering, its application in tree genetic improvement is limited due to challenges in Agrobacterium-mediated transformation. In this study, the researchers optimized the transformation protocol for eastern cottonwood and successfully applied a UV-visible reporter for non-invasive identification of transgenic events. They also examined the efficacy of CRISPR-based genome editing in poplar protoplasts and found high mutation efficiency in hybrid poplar clone, but no editing events in the eastern cottonwood clone. These findings highlight the potential of the eYGFPuv-assisted transformation and genome editing approach in poplar breeding and the need for further CRISPR research in the eastern cottonwood.
Article
Food Science & Technology
Mohamed S. Sheteiwy, Ahmed M. El-Sawah, Yoshihiro Kobae, Farwa Basit, Paul Holford, Haishui Yang, Ali El-Keblawy, Ghada G. Abdel-Fattah, Shucai Wang, Jose Luis Araus, Shereen Magdy Korany, Emad A. Alsherif, Hamada AbdElgawad
Summary: This study aimed to evaluate the individual and combined effects of arbuscular mycorrhizal fungi (AMF) and Bradyrhizobium on the growth, yield, and nutritional quality of guar plants. The results showed that inoculation with AMF and/or Bradyrhizobium improved the chemical composition and morpho-physiological traits of guar seeds and leaves. Furthermore, the inoculation increased the mineral, fiber, lipid, crude protein, and ash contents of guar, as well as the production of sugars, organic acids, amino acids, and fatty acids. This study sheds light on how AMF and Bradyrhizobium enhance guar yield and metabolism, and suggests that their combined inoculation is an innovative approach to improve the growth, yield, and quality of guar.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Engineering, Environmental
Jingui Chen, Jinxiu Zhao, Rui Feng, Hongmin Ma, Huan Wang, Xiang Ren, Qin Wei, Huangxian Ju
Summary: A photoelectrochemical aptamer sensor with a Fe2O3/g-C3N4 heterojunction substrate was developed for sensitive detection of Pb2+. The sensor showed good linearity, low detection limit, and stable performance, indicating its potential for the detection of Pb2+.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Plant Sciences
Tao Yao, Jin Zhang, Timothy B. Yates, Him K. Shrestha, Nancy L. Engle, Raphael Ployet, Cai John, Kai Feng, William Patrick Bewg, Margot S. S. Chen, Haiwei Lu, Scott A. Harding, Zhenzhen Qiao, Sara S. Jawdy, Mengjun Shu, Wenya Yuan, Khadijeh Mozaffari, Anne E. Harman-Ware, Renee M. Happs, Larry M. York, Brad M. Binder, Yuko Yoshinaga, Christopher Daum, Timothy J. Tschaplinski, Paul E. Abraham, Chung-Jui Tsai, Kerrie Barry, Anna Lipzen, Jeremy Schmutz, Gerald A. Tuskan, Jin-Gui Chen, Wellington Muchero
Summary: This study identified PtrXB38 as an expression quantitative trait loci (eQTL) hotspot, with predicted target genes involved in plant hormone responses and root development. Overexpression of PtrXB38 led to increased callusing and the formation of stem-born and base-born adventitious roots in Populus. Omics studies revealed the involvement of genes and proteins controlling auxin transport and signaling in PtrXB38-mediated root formation. Protein-protein interaction assays indicated that PtrXB38 interacts with components of the endocytosis pathway.
Article
Biochemistry & Molecular Biology
Avinash Sreedasyam, Christopher Plott, Md Shakhawat Hossain, John T. Lovell, Jane Grimwood, Jerry W. Jenkins, Christopher Daum, Kerrie Barry, Joseph Carlson, Shengqiang Shu, Jeremy Phillips, Mojgan Amirebrahimi, Matthew Zane, Mei Wang, David Goodstein, Fabian B. Haas, Manuel Hiss, Pierre-Francois Perroud, Sara S. Jawdy, Yongil Yang, Rongbin Hu, Jenifer Johnson, Janette Kropat, Sean D. Gallaher, Anna Lipzen, Eugene Shakirov, Xiaoyu Weng, Ivone Torres-Jerez, Brock Weers, Daniel Conde, Marilia R. Pappas, Lifeng Liu, Andrew Muchlinski, Hui Jiang, Christine Shyu, Pu Huang, Jose Sebastian, Carol Laiben, Alyssa Medlin, Sankalpi Carey, Alyssa A. Carrell, Jin-Gui Chen, Mariano Perales, Kankshita Swaminathan, Isabel Allona, Dario Grattapaglia, Elizabeth A. Cooper, Dorothea Tholl, John P. Vogel, David J. Weston, Xiaohan Yang, Thomas P. Brutnell, Elizabeth A. Kellogg, Ivan Baxter, Michael Udvardi, Yuhong Tang, Todd C. Mockler, Thomas E. Juenger, John Mullet, Stefan A. Rensing, Gerald A. Tuskan, Sabeeha S. Merchant, Gary Stacey, Jeremy Schmutz
Summary: Gene functional descriptions are important for identifying candidate genes involved in trait variation, and plant responses to environmental cues can provide molecular targets for plant improvement. However, many genes across the plant phylogeny lack functional annotations. The Joint Genome Institute (JGI) Plant Gene Atlas is a valuable resource that integrates transcript abundance data from 18 diverse species to identify expression profiles and discover previously undocumented gene functions. The Gene Atlas is accessible through the JGI Plant Gene Atlas and Phytozome websites, allowing users to access differential gene expression, track orthologs, and visualize gene ontology and pathway enrichments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Patricia M. B. Saint-Vincent, Anna Furches, Stephanie Galanie, Erica Teixeira Prates, Jessa L. L. Aldridge, Audrey Labbe, Nan Zhao, Madhavi Z. Z. Martin, Priya Ranjan, Piet Jones, David Kainer, Udaya C. C. Kalluri, Jin-Gui Chen, Wellington Muchero, Daniel A. A. Jacobson, Timothy J. J. Tschaplinski
Summary: Metabolite genome-wide association studies (mGWASs) are important in plant genetics and metabolomics, but there is a lack of experimental validation. This study presents a functional genomics workflow for validating mGWAS-predicted enzyme-substrate relationships. Through high-throughput enzyme activity testing and metabolite screening, the study provides evidence for the role of UGTs in P. trichocarpa and identifies potential implications for sustainable biomass crop production.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Brennan Hyden, Dana L. Carper, Paul E. Abraham, Guoliang Yuan, Tao Yao, Leo Baumgart, Yu Zhang, Cindy Chen, Ronan O'Malley, Jin-Gui Chen, Xiaohan Yang, Robert L. Hettich, Gerald A. Tuskan, Lawrence B. Smart
Summary: In this study, Arabidopsis was used to investigate the sex determination genes and gender dimorphism genes in Salix purpurea. The results suggest that ARR17 and GATA15 may serve as master regulator genes for sex determination in S. purpurea, and two transcription factors may play a role in the downstream regulation of gender dimorphism.