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Dang H, Yu C, Nan S, Li Y, Du S, Zhao K, Wang S. Genome-wide identification and gene expression networks of LBD transcription factors in Populus trichocarpa. BMC Genomics 2024; 25:920. [PMID: 39358710 PMCID: PMC11448377 DOI: 10.1186/s12864-024-10848-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 09/27/2024] [Indexed: 10/04/2024] Open
Abstract
The Lateral Organ Boundaries Domain (LBD) proteins, an exclusive family of transcription factors (TFs) found solely in plants, play pivotal roles in lateral organogenesis, stress adaptation, secondary growth, and hormonal signaling responses. In this study, a total of 55 PtLBD TFs from Populus trichocarpa were identified and systematically classified into two subfamilies, designated as subfamily-I and subfamily-II with seven distinct groups based on phylogenetic analysis. Gene structure detection indicated that the difference of phase numbers linking adjacent exons contribute to the variations in splicing patterns among different PtLBD groups. Numerous transcription factor binding sites and cis-elements pertinent to hormone signaling pathways and stress response mechanisms were identified within the upstream promoter regions of the PtLBD genes. Thirty-five PtLBDs were found to be engaged in either tandem or segmental duplications, and genomic collinearity analysis revealed a stronger alignment between PtLBD genes and eudicots plants compared to their relationship with monocots. GO enrichment and temporal-spatio expression patterns showed that PtLBD7 from subfamily-I and PtLBD20 from subfamily-II, along with other 13 PtLBDs, were involved in plant growth and development biological processes. The multilayered hierarchical gene networks (ML-hGRN) mediated by PtLBD7 and PtLBD20 indicated that PtLBDs were mainly function in poplar growth and stress tolerance through a multifaceted and intricate regulatory machinery. This study lays a solid groundwork for delving deeper into the roles and underlying mechanisms of LBD transcription factors in poplar, specifically those related to plant hormones and stress tolerance.
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Affiliation(s)
- Hui Dang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
- School of Innovation and Intrepreneurship, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Changhong Yu
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Siyuan Nan
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Yajing Li
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Shuhui Du
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Kai Zhao
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Shengji Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
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Jia M, Wang Y, Jin H, Li J, Song T, Chen Y, Yuan Y, Hu H, Li R, Wu Z, Jiao P. Comparative Genomics Analysis of the Populus Epidermal Pattern Factor (EPF) Family Revealed Their Regulatory Effects in Populus euphratica Stomatal Development. Int J Mol Sci 2024; 25:10052. [PMID: 39337538 PMCID: PMC11432118 DOI: 10.3390/ijms251810052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/14/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
Drought stress seriously threatens plant growth. The improvement of plant water use efficiency (WUE) and drought tolerance through stomatal regulation is an effective strategy for coping with water shortages. Epidermal patterning factor (EPF)/EPF-like (EPFL) family proteins regulate stomatal formation and development in plants and thus contribute to plant stress adaptation. Here, our analysis revealed the presence of 14 PeEPF members in the Populus euphratica genome, which exhibited a relatively conserved gene structure with 1-3 introns. Subcellular localisation prediction revealed that 9 PeEPF members were distributed in the chloroplasts of P. euphratica, and 5 were located extracellularly. Phylogenetic analysis indicated that PeEPFs can be divided into three clades, with genes within the same clade revealing a relatively conserved structure. Furthermore, we observed the evolutionary conservation of PeEPFs and AtEPF/EPFLs in certain domains, which suggests their conserved function. The analysis of cis-acting elements suggested the possible involvement of PeEPFs in plant response to multiple hormones. Transcriptomic analysis revealed considerable changes in the expression level of PeEPFs during treatment with polyethylene glycol and abscisic acid. The overexpression of PeEPF2 resulted in low stomatal density in transgenetic lines. These findings provide a basis for gaining insights into the function of PeEPFs in response to abiotic stress.
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Affiliation(s)
- Mingyu Jia
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar 843300, China
| | - Ying Wang
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar 843300, China
| | - Hongyan Jin
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar 843300, China
| | - Jing Li
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar 843300, China
| | - Tongrui Song
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar 843300, China
| | - Yongqiang Chen
- Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Yuan
- Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Honghong Hu
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar 843300, China
- Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruting Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Peipei Jiao
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar 843300, China
- Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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Yang Y, Sun J, Qiu C, Jiao P, Wang H, Wu Z, Li Z. Comparative genomic analysis of the Growth-Regulating Factors-Interacting Factors (GIFs) in six Salicaceae species and functional analysis of PeGIF3 reveals their regulatory role in Populus heteromorphic leaves. BMC Genomics 2024; 25:317. [PMID: 38549059 PMCID: PMC10976704 DOI: 10.1186/s12864-024-10221-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND The growth-regulating factor-interacting factor (GIF) gene family plays a vital role in regulating plant growth and development, particularly in controlling leaf, seed, and root meristem homeostasis. However, the regulatory mechanism of heteromorphic leaves by GIF genes in Populus euphratica as an important adaptative trait of heteromorphic leaves in response to desert environment remains unknown. RESULTS This study aimed to identify and characterize the GIF genes in P. euphratica and other five Salicaceae species to investigate their role in regulating heteromorphic leaf development. A total of 27 GIF genes were identified and characterized across six Salicaceae species (P. euphratica, Populus pruinose, Populus deltoides, Populus trichocarpa, Salix sinopurpurea, and Salix suchowensis) at the genome-wide level. Comparative genomic analysis among these species suggested that the expansion of GIFs may be derived from the specific Salicaceae whole-genome duplication event after their divergence from Arabidopsis thaliana. Furthermore, the expression data of PeGIFs in heteromorphic leaves, combined with functional information on GIF genes in Arabidopsis, indicated the role of PeGIFs in regulating the leaf development of P. euphratica, especially PeGIFs containing several cis-acting elements associated with plant growth and development. By heterologous expression of the PeGIF3 gene in wild-type plants (Col-0) and atgif1 mutant of A. thaliana, a significant difference in leaf expansion along the medial-lateral axis, and an increased number of leaf cells, were observed between the overexpressed plants and the wild type. CONCLUSION PeGIF3 enhances leaf cell proliferation, thereby resulting in the expansion of the central-lateral region of the leaf. The findings not only provide global insights into the evolutionary features of Salicaceae GIFs but also reveal the regulatory mechanism of PeGIF3 in heteromorphic leaves of P. euphratica.
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Affiliation(s)
- Yuqi Yang
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China
- College of Life Science and Technology, Tarim University, 843300, Alar, China
- Desert Poplar Research Center of Tarim University, 843300, Alar, China
| | - Jianhao Sun
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China
- College of Life Science and Technology, Tarim University, 843300, Alar, China
- Desert Poplar Research Center of Tarim University, 843300, Alar, China
| | - Chen Qiu
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China
- College of Life Science and Technology, Tarim University, 843300, Alar, China
- Desert Poplar Research Center of Tarim University, 843300, Alar, China
| | - Peipei Jiao
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China
- College of Life Science and Technology, Tarim University, 843300, Alar, China
- Desert Poplar Research Center of Tarim University, 843300, Alar, China
| | - Houling Wang
- College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, 321004, Jinhua, China.
| | - Zhijun Li
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China.
- College of Life Science and Technology, Tarim University, 843300, Alar, China.
- Desert Poplar Research Center of Tarim University, 843300, Alar, China.
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Zhou H, Song X, Lu MZ. Growth-regulating factor 15-mediated vascular cambium differentiation positively regulates wood formation in hybrid poplar ( Populus alba × P. glandulosa). FRONTIERS IN PLANT SCIENCE 2024; 15:1343312. [PMID: 38425797 PMCID: PMC10902170 DOI: 10.3389/fpls.2024.1343312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
Introduction Hybrid poplars are industrial trees in China. An understanding of the molecular mechanism underlying wood formation in hybrid poplars is necessary for molecular breeding. Although the division and differentiation of vascular cambial cells is important for secondary growth and wood formation, the regulation of this process is largely unclear. Methods In this study, mPagGRF15 OE and PagGRF15-SRDX transgenic poplars were generated to investigate the function of PagGRF15. RNA-seq and qRT-PCR were conducted to analyze genome-wide gene expression, while ChIP‒seq and ChIP-PCR were used to identified the downstream genes regulated by PagGRF15. Results and discussion We report that PagGRF15 from hybrid poplar (Populus alba × P. glandulosa), a growth-regulating factor, plays a critical role in the regulation of vascular cambium activity. PagGRF15 was expressed predominantly in the cambial zone of vascular tissue. Overexpression of mPagGRF15 (the mutated version of GRF15 in the miR396 target sequence) in Populus led to decreased plant height and internode number. Further stem cross sections showed that the mPagGRF15 OE plants exhibited significant changes in vascular pattern with an increase in xylem and a reduction in phloem. In addition, cambium cell files were decreased in the mPagGRF15 OE plants. However, dominant suppression of the downstream genes of PagGRF15 using PagGRF15-SRDX showed an opposite phenotype. Based on the RNA-seq and ChIP-seq results, combining qRT-PCR and ChIP-PCR analysis, candidate genes, such as WOX4b, PXY and GID1.3, were obtained and found to be mainly involved in cambial activity and xylem differentiation. Accordingly, we speculated that PagGRF15 functions as a positive regulator mediating xylem differentiation by repressing the expression of the WOX4a and PXY genes to set the pace of cambial activity. In contrast, PagGRF15 mediated the GA signaling pathway by upregulating GID1.3 expression to stimulate xylem differentiation. This study provides valuable information for further studies on vascular cambium differentiation mechanisms and genetic improvement of the specific gravity of wood in hybrid poplars.
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Affiliation(s)
- Houjun Zhou
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Horvat B, Shikakura Y, Ohtani M, Demura T, Kikuchi A, Watanabe KN, Oguchi T. Heterogeneous Expression of Arabidopsis Subclass II of SNF1-Related Kinase 2 Improves Drought Tolerance via Stomatal Regulation in Poplar. Life (Basel) 2024; 14:161. [PMID: 38276290 PMCID: PMC10817443 DOI: 10.3390/life14010161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/28/2023] [Accepted: 01/20/2024] [Indexed: 01/27/2024] Open
Abstract
Abscisic acid (ABA) is the most important phytohormone involved in the response to drought stress. Subclass II of SNF1-related kinase 2 (SnRK2) is an important signaling kinase related to ABA signal transduction. It regulates the phosphorylation of the target transcription factors controlling the transcription of a wide range of ABA-responsive genes in Arabidopsis thaliana. The transgenic poplars (Populus tremula × P. tremuloides, clone T89) ectopically overexpressing AtSnRK2.8, encoding a subclass II SnRK2 kinase of A. thaliana, have been engineered but almost no change in its transcriptome was observed. In this study, we evaluated osmotic stress tolerance and stomatal behavior of the transgenic poplars maintained in the netted greenhouse. The transgenic poplars, line S22, showed a significantly higher tolerance to 20% PEG treatment than non-transgenic controls. The stomatal conductance of the transgenic poplars tended to be lower than the non-transgenic control. Microscopic observations of leaf imprints revealed that the transgenic poplars had significantly higher stomatal closures under the stress treatment than the non-transgenic control. In addition, the stomatal index was lower in the transgenic poplars than in the non-transgenic controls regardless of the stress treatment. These results suggested that AtSnRK2.8 is involved in the regulation of stomatal behavior. Furthermore, the transgenic poplars overexpressing AtSnRK2.8 might have improved abiotic stress tolerance through this stomatal regulation.
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Affiliation(s)
- Borislav Horvat
- Degree Program in Life and Earth Science, Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
| | - Yuhei Shikakura
- Degree Program in Life and Earth Science, Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
| | - Misato Ohtani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Chiba, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
| | - Taku Demura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Center for Digital Green-Innovation, Nara Institute of Science and Technology, Ikoma 630-0192, Nara, Japan
| | - Akira Kikuchi
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
| | - Kazuo N. Watanabe
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
| | - Taichi Oguchi
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
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Wang S, Dong Y, Gu L, Chen X, Zhang C, Long L, Wang J, Yang M. Identification and adaptive evolution analysis of glutaredoxin genes in Populus spp. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:1154-1170. [PMID: 37703550 DOI: 10.1111/plb.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]
Abstract
Glutaredoxin (GRX) is a class of small redox proteins widely involved in cellular redox homeostasis and the regulation of various cellular processes. The role of GRX gene in the differentiation of Populus spp. is rarely reported. We compared the similarities and differences of GRX genes among four sections of poplar using bioinformatics, corrected the annotations of some GRX genes, and focused on analysing their transcript profiling and adaptive evolution in Populus spp. A total of 219 GRX genes were identified in four sections of poplar, among which annotations for 13 genes were corrected. Differences in GRX genes were found between sect. Turanga, represented by P. euphratica, and other poplar sections. Most notably, P. euphratica had the smallest number of duplication events for GRX genes (n = 9) and no tandem duplications, whereas there were >25 duplication events for all other poplars. Furthermore, we detected 18 pairs of GRX genes under positive selection pressure in various sections of poplar, and identified two groups of GRX genes in the Salicaceae that potentially underwent positive selection. Expression profiling results showed that the PtrGRX34 and its orthologous genes were upregulated under stress treatments. In summary, the GRX gene family underwent expansion during poplar differentiation, and some genes underwent rapid evolution during this process, which may be beneficial for Populus spp. to adapt to environmental changes. This study may provide more insights into the molecular mechanisms of Populus spp. adaptation to environmental changes and the adaptive evolution of GRX genes.
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Affiliation(s)
- S Wang
- Institute of Forest Biotechnology, College of Forestry, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Y Dong
- Institute of Forest Biotechnology, College of Forestry, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - L Gu
- Institute of Forest Biotechnology, College of Forestry, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - X Chen
- Institute of Forest Biotechnology, College of Forestry, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - C Zhang
- Institute of Forest Biotechnology, College of Forestry, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - L Long
- Institute of Forest Biotechnology, College of Forestry, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - J Wang
- Institute of Forest Biotechnology, College of Forestry, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - M Yang
- Institute of Forest Biotechnology, College of Forestry, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
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Zhou R, Jenkins JW, Zeng Y, Shu S, Jang H, Harding SA, Williams M, Plott C, Barry KW, Koriabine M, Amirebrahimi M, Talag J, Rajasekar S, Grimwood J, Schmitz RJ, Dawe RK, Schmutz J, Tsai CJ. Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1003-1017. [PMID: 37675609 DOI: 10.1111/tpj.16454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.
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Affiliation(s)
- Ran Zhou
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Shengqiang Shu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Scott A Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Melissa Williams
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | | | - Kerrie W Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mojgan Amirebrahimi
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chung-Jui Tsai
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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8
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Liu Y, Ma D, Constabel CP. CRISPR/Cas9 Disruption of MYB134 and MYB115 in Transgenic Poplar Leads to Differential Reduction of Proanthocyanidin Synthesis in Roots and Leaves. PLANT & CELL PHYSIOLOGY 2023; 64:1189-1203. [PMID: 37522631 DOI: 10.1093/pcp/pcad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/01/2023]
Abstract
Proanthocyanidins (PAs) are common specialized metabolites and particularly abundant in trees and woody plants. In poplar (Populus spp.), PA biosynthesis is stress-induced and regulated by two previously studied transcription factors MYB115 and MYB134. To determine the relative contribution of these regulators to PA biosynthesis, we created single- and double-knockout (KO) mutants for both genes in transgenic poplars using CRISPR/Cas9. Knocking out either MYB134 or MYB115 showed reduced PA accumulation and downregulated flavonoid genes in leaves, but MYB134 disruption had the greatest impact and reduced PAs to 30% of controls. In roots, by contrast, only the MYB134/MYB115 double-KOs showed a significant change in PA concentration. The loss of PAs paralleled the lower expression of PA biosynthesis genes and concentrations of flavan-3-ol PA precursors catechin and epicatechin. Interestingly, salicinoids were also affected in double-KOs, with distinct patterns in roots and shoots. We conclude that the regulatory pathways for PA biosynthesis differ in poplar leaves and roots. The residual PA content in the double-KO plants indicates that other transcription factors must also be involved in control of the PA pathway.
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Affiliation(s)
- Yalin Liu
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P5C3, Canada
| | - Dawei Ma
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P5C3, Canada
| | - C Peter Constabel
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P5C3, Canada
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Li P, Xiao L, Du Q, Quan M, Song Y, He Y, Huang W, Xie J, Lv C, Wang D, Zhou J, Li L, Liu Q, El‐Kassaby YA, Zhang D. Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2002-2018. [PMID: 37392407 PMCID: PMC10502748 DOI: 10.1111/pbi.14108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/03/2023]
Abstract
Heterozygous alleles are widespread in outcrossing and clonally propagated woody plants. The variation in heterozygosity that underlies population adaptive evolution and phenotypic variation, however, remains largely unknown. Here, we describe a de novo chromosome-level genome assembly of Populus tomentosa, an economic and ecologically important native tree in northern China. By resequencing 302 natural accessions, we determined that the South subpopulation (Pop_S) encompasses the ancestral strains of P. tomentosa, while the Northwest subpopulation (Pop_NW) and Northeast subpopulation (Pop_NE) experienced different selection pressures during population evolution, resulting in significant population differentiation and a decrease in the extent of heterozygosity. Analysis of heterozygous selective sweep regions (HSSR) suggested that selection for lower heterozygosity contributed to the local adaptation of P. tomentosa by dwindling gene expression and genetic load in the Pop_NW and Pop_NE subpopulations. Genome-wide association studies (GWAS) revealed that 88 single nucleotide polymorphisms (SNPs) within 63 genes are associated with nine wood composition traits. Among them, the selection for the homozygous AA allele in PtoARF8 is associated with reductions in cellulose and hemicellulose contents by attenuating PtoARF8 expression, and the increase in lignin content is attributable to the selection for decreases in exon heterozygosity in PtoLOX3 during adaptive evolution of natural populations. This study provides novel insights into allelic variations in heterozygosity associated with adaptive evolution of P. tomentosa in response to the local environment and identifies a series of key genes for wood component traits, thereby facilitating genomic-based breeding of important traits in perennial woody plants.
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Affiliation(s)
- Peng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Liang Xiao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qingzhang Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Mingyang Quan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuepeng Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuling He
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Weixiong Huang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jianbo Xie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Chenfei Lv
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Dan Wang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jiaxuan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Lianzheng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qing Liu
- CSIRO Agriculture and Food, Black MountainCanberraAustralian Capital TerritoryAustralia
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Deqiang Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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10
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Kim TL, Lim H, Denison MIJ, Oh C. Transcriptomic and Physiological Analysis Reveals Genes Associated with Drought Stress Responses in Populus alba × Populus glandulosa. PLANTS (BASEL, SWITZERLAND) 2023; 12:3238. [PMID: 37765403 PMCID: PMC10535988 DOI: 10.3390/plants12183238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023]
Abstract
Drought stress affects plant productivity by altering plant responses at the morphological, physiological, and molecular levels. In this study, we identified physiological and genetic responses in Populus alba × Populus glandulosa hybrid clones 72-30 and 72-31 after 12 days of exposure to drought treatment. After 12 days of drought treatment, glucose, fructose, and sucrose levels were significantly increased in clone 72-30 under drought stress. The Fv/Fo and Fv/Fm values in both clones also decreased under drought stress. The changes in proline, malondialdehyde, and H2O2 levels were significant and more pronounced in clone 72-30 than in clone 72-31. The activities of antioxidant-related enzymes, such as catalase and ascorbate peroxidase, were significantly higher in the 72-31 clone. To identify drought-related genes, we conducted a transcriptomic analysis in P. alba × P. glandulosa leaves exposed to drought stress. We found 883 up-regulated and 305 down-regulated genes in the 72-30 clone and 279 and 303 in the 72-31 clone, respectively. These differentially expressed genes were mainly in synthetic pathways related to proline, abscisic acid, and antioxidants. Overall, clone 72-31 showed better drought tolerance than clone 72-30 under drought stress, and genetic changes also showed different patterns.
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Affiliation(s)
- Tae-Lim Kim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (T.-L.K.); (C.O.)
| | - Hyemin Lim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (T.-L.K.); (C.O.)
| | | | - Changyoung Oh
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (T.-L.K.); (C.O.)
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11
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Li G, Chen Q, Bai Q, Feng Y, Mao K, Yang M, He L, Liu M, Liu J, Wan D. LncRNA expression analysis by comparative transcriptomics among closely related poplars and their regulatory roles in response to salt stress. TREE PHYSIOLOGY 2023:tpad041. [PMID: 37017317 DOI: 10.1093/treephys/tpad041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in regulating key biological processes; however, our knowledge of lncRNAs' roles in plant adaptive evolution is still limited. Here, we determined the divergence of conserved lncRNAs in closely related poplar species that were either tolerant or sensitive to salt stress by comparative transcriptome analysis. Among the 34,363 identified lncRNAs, approximately 3% were shared among poplar species with conserved sequences but diversified in their function, copy number, originating genomic region and expression patterns. Further cluster analysis revealed that the conserved lncRNAs showed more similar expression patterns within salt-tolerant poplars (P. euphratica and P. pruinosa) than between salt-tolerant and salt-sensitive poplars. Among these lncRNAs, the antisense lncRNA lncERF024 was induced by salt and differentiated expression between salt-sensitive and salt-tolerant poplars. Overexpression of lncERF024 in P. alba var. pyramidalis enhanced poplar tolerance to salt stress. Furthermore, RNA pull-down and RNA-seq analysis showed that numerous candidate genes or proteins associated with stress response and photosynthesis might be involved in salt resistance in PeulncERF024-OE poplars. Altogether, our study provided novel insight into how the diversification of lncRNA expression contributes to plant adaptation traits and showed that lncERF024 may be involved in the regulation both of gene expression and protein function conferring salt tolerance in Populus.
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Affiliation(s)
- Guiting Li
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Qingyuan Chen
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qiuxian Bai
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Department of Pharmacology, Ningxia Medical University, Yinchuan,750004, China
| | - Yannan Feng
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Kaili Mao
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Mengran Yang
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Ling He
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Meijun Liu
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Jianquan Liu
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Dongshi Wan
- State Key Laboratory Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
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12
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Liu J, Zhang W, Liu Y, Zhu W, Yuan Z, Su X, Ding C. Differences in phyllosphere microbiomes among different Populus spp. in the same habitat. FRONTIERS IN PLANT SCIENCE 2023; 14:1143878. [PMID: 37063209 PMCID: PMC10098339 DOI: 10.3389/fpls.2023.1143878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION The above-ground parts of terrestrial plants are collectively known as the phyllosphere. The surface of the leaf blade is a unique and extensive habitat for microbial communities. Phyllosphere bacteria are the second most closely associated microbial group with plants after fungi and viruses, and are the most abundant, occupying a dominant position in the phyllosphere microbial community. Host species are a major factor influencing the community diversity and structure of phyllosphere microorganisms. METHODS In this study, six Populus spp. were selected for study under the same site conditions and their phyllosphere bacterial community DNA fragments were paired-end sequenced using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Based on the distribution of the amplicon sequence variants (ASVs), we assessed the alpha-diversity level of each sample and further measured the differences in species abundance composition among the samples, and predicted the metabolic function of the community based on the gene sequencing results. RESULTS The results revealed that different Populus spp. under the same stand conditions resulted in different phyllosphere bacterial communities. The bacterial community structure was mainly affected by the carbon and soluble sugar content of the leaves, and the leaf nitrogen, phosphorus and carbon/nitrogen were the main factors affecting the relative abundance of phyllosphere bacteria. DISCUSSION Previous studies have shown that a large proportion of the variation in the composition of phyllosphere microbial communities was explained by the hosts themselves. In contrast, leaf-borne nutrients were an available resource for bacteria living on the leaf surface, thus influencing the community structure of phyllosphere bacteria. These were similar to the conclusions obtained in this study. This study provides theoretical support for the study of the composition and structure of phyllosphere bacterial communities in woody plants and the factors influencing them.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuting Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), College of Forestry, Shenyang Agricultural University, Tieling, China
| | - Zhengsai Yuan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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13
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Genome-wide analysis of R2R3-MYB transcription factors reveals their differential responses to drought stress and ABA treatment in desert poplar (Populus euphratica). Gene 2023; 855:147124. [PMID: 36539045 DOI: 10.1016/j.gene.2022.147124] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The R2R3-MYB transcription factors are widely involved in the regulation of plant growth, biotic and abiotic stress responses. Meanwhile, seed germination, which is stimulated by internal and external environments, is a critical stage in the plant life cycle. However, the identification, characterization, and expression profiling of the Populus euphratica R2R3-MYB family in drought response during seed germination have been unknown. Our study attempted to identify and characterize the R2R3-MYB genes in P. euphratica (PeR2R3-MYBs) and explore how R2R3-MYBs trigger the drought and abscisic acid (ABA) response mechanism in its seedlings. Based on the analysis of comparative genomics, 174 PeR2R3-MYBs were identified and expanded driven by whole genome duplication or segment duplication events. The analysis of Ka/Ks ratios showed that, in contrast to most PeR2R3-MYBs, the other PeR2R3-MYBs were subjected to positive selection in P. euphratica. Further, the expression data of PeR2R3-MYBs under drought stress and ABA treatment, together with available functional data for Arabidopsis thaliana MYB genes, supported the hypothesis that PeR2R3-MYBs involved in response to drought are dependent or independent on ABA signaling pathway during seed germination, especially PeR2R3-MYBs with MYB binding sites (MBS) cis-element and/or tandem duplication. This study is the first report on the genome-wide analysis of PeR2R3-MYBs, as well as the other two Salicaceae species. The duplication events and differential expressions of PeR2R3-MYBs play important roles in enhancing the adaptation to drought desert environment. Our results provide a reference for prospective functional studies of R2R3-MYBs of poplars and lay the foundation for new breeding strategies to improve the drought tolerance of P. euphratica.
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14
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Gordon H, Fellenberg C, Lackus ND, Archinuk F, Sproule A, Nakamura Y, K�llner TG, Gershenzon J, Overy DP, Constabel CP. CRISPR/Cas9 disruption of UGT71L1 in poplar connects salicinoid and salicylic acid metabolism and alters growth and morphology. THE PLANT CELL 2022; 34:2925-2947. [PMID: 35532172 PMCID: PMC9338807 DOI: 10.1093/plcell/koac135] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/28/2022] [Indexed: 05/11/2023]
Abstract
Salicinoids are salicyl alcohol-containing phenolic glycosides with strong antiherbivore effects found only in poplars and willows. Their biosynthesis is poorly understood, but recently a UDP-dependent glycosyltransferase, UGT71L1, was shown to be required for salicinoid biosynthesis in poplar tissue cultures. UGT71L1 specifically glycosylates salicyl benzoate, a proposed salicinoid intermediate. Here, we analyzed transgenic CRISPR/Cas9-generated UGT71L1 knockout plants. Metabolomic analyses revealed substantial reductions in the major salicinoids, confirming the central role of the enzyme in salicinoid biosynthesis. Correspondingly, UGT71L1 knockouts were preferred to wild-type by white-marked tussock moth (Orgyia leucostigma) larvae in bioassays. Greenhouse-grown knockout plants showed substantial growth alterations, with decreased internode length and smaller serrated leaves. Reinserting a functional UGT71L1 gene in a transgenic rescue experiment demonstrated that these effects were due only to the loss of UGT71L1. The knockouts contained elevated salicylate (SA) and jasmonate (JA) concentrations, and also had enhanced expression of SA- and JA-related genes. SA is predicted to be released by UGT71L1 disruption, if salicyl salicylate is a pathway intermediate and UGT71L1 substrate. This idea was supported by showing that salicyl salicylate can be glucosylated by recombinant UGT71L1, providing a potential link of salicinoid metabolism to SA and growth impacts. Connecting this pathway with growth could imply that salicinoids are under additional evolutionary constraints beyond selective pressure by herbivores.
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Affiliation(s)
- Harley Gordon
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Christin Fellenberg
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Nathalie D Lackus
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Finn Archinuk
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Amanda Sproule
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Yoko Nakamura
- Department of Nuclear Magnetic Resonance, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Tobias G K�llner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - David P Overy
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
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15
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Wang J, Zhang L, Wang J, Hao Y, Xiao Q, Teng J, Shen S, Zhang Y, Feng Y, Bao S, Li Y, Yan Z, Wei C, Wang L, Wang J. Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow. BMC PLANT BIOLOGY 2022; 22:298. [PMID: 35710333 PMCID: PMC9205023 DOI: 10.1186/s12870-022-03684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remains poorly understood. RESULTS Here, through genomic synteny analyses, we identified duplicate genes generated by the Salicaceae common tetraploidization (SCT) in the poplar and willow genomes. We estimated that at least 0.58% and 0.25% of poplar and willow duplicates were affected by whole-gene conversion after the poplar-willow divergence, with more (5.73% and 2.66%) affected by partial-gene conversion. Moreover, we found that the converted duplicated genes were unevenly distributed on each chromosome in the two genomes, and the well-preserved homoeologous chromosome regions may facilitate the conversion of duplicates. Notably, we found that conversion maintained the similarity of duplicates, likely contributing to the conservation of certain sequences, but is essentially accelerated the rate of evolution and increased species divergence. In addition, we found that converted duplicates tended to have more similar expression patterns than nonconverted duplicates. We found that genes associated with multigene families were preferentially converted. We also found that the genes encoding conserved structural domains associated with specific traits exhibited a high frequency of conversion. CONCLUSIONS Extensive conversion between duplicate genes generated from the SCT contributes to the diversification of the family Salicaceae and has had long-lasting effects on those genes with important biological functions.
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Affiliation(s)
- Jianyu Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Lan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jiaqi Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yanan Hao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Qimeng Xiao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jia Teng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shaoqi Shen
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yishan Feng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shoutong Bao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yu Li
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Zimo Yan
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Chendan Wei
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Li Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
| | - Jinpeng Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
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16
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VanWallendael A, Lowry DB, Hamilton JA. One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102152. [PMID: 35065527 DOI: 10.1016/j.pbi.2021.102152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
A hundred years after Turesson first clearly described how locally adaptive variation is distributed within species, plant biologists are making major breakthroughs in our understanding of mechanisms underlying adaptation from local populations to the scale of continents. Although the genetics of local adaptation has typically been studied in smaller reciprocal transplant experiments, it is now being evaluated with whole genomes in large-scale networks of common garden experiments with perennial switchgrass and poplar trees. These studies support the hypothesis that a complex combination of loci, both with and without adaptive trade-offs, underlies local adaptation and that hybridization and adaptive introgression play a key role in the evolution of these species. Future studies incorporating high-throughput phenotyping, gene expression, and modeling will be used to predict responses of these species to climate change.
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Affiliation(s)
- Acer VanWallendael
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jill A Hamilton
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16801, USA
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17
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Cao HX, Vu GTH, Gailing O. From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees. Int J Mol Sci 2022; 23:966. [PMID: 35055150 PMCID: PMC8780650 DOI: 10.3390/ijms23020966] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.
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Affiliation(s)
- Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Giang Thi Ha Vu
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
- Center for Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Gottingen, Germany
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18
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Lan Y, Zhang K, He T, Wang H, Jiang C, Yan H, Xiang Y. Systematic analysis of the Serine/Arginine-Rich Protein Splicing Factors (SRs) and focus on salt tolerance of PtSC27 in Populus trichocarpa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 173:97-109. [PMID: 35121529 DOI: 10.1016/j.plaphy.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/09/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Serine/Arginine-Rich Protein Splicing Factors (SRs) are indispensable splicing factors, which play significant roles in spliceosome assembly, splicing regulation and regulation of plant stress. However, a comprehensive analysis and function research of SRs in the woody plant is still lacking. In this report, we conducted the identification and comprehensive analysis of the 71 SRs in poplar and three other dicots, including basic characterization, phylogenetic, conserved motifs, gene duplication, promoter and splice isoform of these genes. Based on the publicly available transcriptome data, expression pattern of SRs in poplar under low temperature, high temperature, drought and salt stress were further analyzed. Subsequently, a key candidate gene PtSC27 that responded to salt stress was screened. More importantly, overexpression of PtSC27 increased plant survival rate under salt stress, and enhanced salt tolerance by regulating malondialdehyde (MDA) content, peroxidase (POD) and catalase (CAT) enzyme activities in transgenic plants. Meanwhile, overexpression of PtSC27 made transgenic plants insensitive to exogenous ABA and improved the expression of some ABA signal-related genes under salt stress. Overall, our studies lay a foundation for understanding the structure and function of SRs in the poplar and provide useful gene resources for breeding through genetic engineering.
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Affiliation(s)
- Yangang Lan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Ting He
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Hao Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Chengzhi Jiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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19
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He H, Song XQ, Jiang C, Liu YL, Wang D, Wen SS, Chai GH, Zhao ST, Lu MZ. The role of senescence-associated gene101 (PagSAG101a) in the regulation of secondary xylem formation in poplar. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:73-86. [PMID: 34845845 DOI: 10.1111/jipb.13195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Wood is produced by the accumulation of secondary xylem via proliferation and differentiation of the cambium cells in woody plants. Identifying the regulators involved in this process remains a challenging task. In this study, we isolated PagSAG101a, the homolog of Arabidopsis thaliana SAG101, from a hybrid poplar (Populus alba × Populus glandulosa) clone 84K and investigated its role in secondary xylem development. PagSAG101a was expressed predominantly in lignified stems and localized in the nucleus. Compared with non-transgenic 84K plants, transgenic plants overexpressing PagSAG101a displayed increased plant height, internode number, stem diameter, xylem width, and secondary cell wall thickness, while opposite phenotypes were observed for PagSAG101a knock-out plants. Transcriptome analyses revealed that differentially expressed genes were enriched for those controlling cambium cell division activity and subsequent secondary cell wall deposition during xylem formation. In addition, the tandem CCCH zinc finger protein PagC3H17, which positively regulates secondary xylem width and secondary wall thickening in poplar, could bind to the promoter of PagSAG101a and mediate the regulation of xylem differentiation. Our results support that PagSAG101a, downstream of PagC3H17, functions in wood development.
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Affiliation(s)
- Hui He
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xue-Qin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Ying-Li Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Dian Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shuang-Shuang Wen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Guo-Hua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shu-Tang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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20
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Gao Y, Sun Y, Ou Y, Zheng X, Feng Q, Zhang H, Fei Y, Luo J, Resco de Dios V, Yao Y. Pretreating poplar cuttings with low nitrogen ameliorates salt stress responses by increasing stored carbohydrates and priming stress signaling pathways. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112801. [PMID: 34560614 DOI: 10.1016/j.ecoenv.2021.112801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Soil salinity is a widespread stress in semi-arid forests worldwide, but how to manage nitrogen (N) nutrition to improve plant saline tolerance remains unclear. Here, the cuttings of a widely distributed poplar from central Asia, Populus russikki Jabl., were exposed to either normal or low nitrogen (LN) concentrations for two weeks in semi-controlled greenhouse, and then they were added with moderate salt solution or not for another two weeks to evaluate their physiological, biochemical, metabolites and transcriptomic profile changes. LN-pretreating alleviated the toxicity caused by the subsequent salt stress in the poplar plants, demonstrated by a significant reduction in the influx of Na+ and Cl- and improvement of the K+/Na+ ratio. The other salt-stressed traits were also ameliarated, indicated by the variations of chlorophyll content, PSII photochemical activity and lipid peroxidation. Stress alleviation resulted from two different processes. First, LN pretreatment caused a significant increase of non-structural carbohydrates (NSC), allowed for an increased production of osmolytes and a higher potential fueling ion transport under subsequent salt condition, along with increased transcript levels of the cation/H+ ATPase. Second, LN pretreatment enhanced the transcript levels of stress signaling components and phytohormones pathway as well as antioxidant enzyme activities. The results indicate that early restrictions of N supply could enhance posterior survival under saline stress in poplar plants, which is important for plantation programs and restoration activities in semi-arid areas.
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Affiliation(s)
- Yongfeng Gao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Yufang Sun
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yongbin Ou
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Xinhua Zheng
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Qian Feng
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Hao Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Yang Fei
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Jie Luo
- College of Horticulture and Forestry Sciences, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China
| | - Víctor Resco de Dios
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; Department of Crop and Forest Sciences & Joint Research Unit CTFC-AGROTECNIO-CERCA Center, Universitat de Lleida, 25198 Lleida,Spain.
| | - Yinan Yao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
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21
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Xiao L, Du Q, Fang Y, Quan M, Lu W, Wang D, Si J, El-Kassaby YA, Zhang D. Genetic architecture of the metabolic pathway of salicylic acid biosynthesis in Populus. TREE PHYSIOLOGY 2021; 41:2198-2215. [PMID: 33987676 DOI: 10.1093/treephys/tpab068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Salicylic acid (SA) is a vital hormone for adaptive responses to biotic and abiotic stresses, which facilitates growth-immunity trade-offs in plants. However, the genetic regulatory networks underlying the metabolic pathway of SA biosynthesis in perennial species remain unclear. Here, we integrated genome-wide association study (GWAS) with metabolite and expression profiling methodologies to dissect the genetic architecture of SA biosynthesis in Populus. First, we quantified nine intermediate metabolites of SA biosynthesis in 300 unrelated Populus tomentosa Carr. individuals. Then, we used a systematic genetic strategy to identify candidate genes for constructing the genetic regulatory network of SA biosynthesis. We focused on WRKY70, an efficient transcription factor, as the key causal gene in the regulatory network, and combined the novel genes coordinating the accumulation of SA. Finally, we identified eight GWAS signals and eight expression quantitative trait loci situated in a selective sweep, and showed the presence of large allele frequency differences among the three geographic populations, revealing that candidate genes subject to selection were involved in SA biosynthesis. This study provides an integrated strategy for dissecting the genetic architecture of the metabolic pathway of SA biosynthesis in Populus, thereby enhancing our understanding of genetic regulation of SA biosynthesis in trees, and accelerating marker-assisted breeding efforts toward high-resistance elite varieties of Populus.
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Affiliation(s)
- Liang Xiao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Yuanyuan Fang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Mingyang Quan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Wenjie Lu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Dan Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Jingna Si
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
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22
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Ahmed U, Rao MJ, Qi C, Xie Q, Noushahi HA, Yaseen M, Shi X, Zheng B. Expression Profiling of Flavonoid Biosynthesis Genes and Secondary Metabolites Accumulation in Populus under Drought Stress. Molecules 2021; 26:5546. [PMID: 34577017 PMCID: PMC8467073 DOI: 10.3390/molecules26185546] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 12/01/2022] Open
Abstract
Flavonoids are key secondary metabolites that are biologically active and perform diverse functions in plants such as stress defense against abiotic and biotic stress. In addition to its importance, no comprehensive information has been available about the secondary metabolic response of Populus tree, especially the genes that encode key enzymes involved in flavonoid biosynthesis under drought stress. In this study, the quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the expression of flavonoid biosynthesis genes (PtPAL, Pt4-CL, PtCHS, PtFLS-1, PtF3H, PtDFR, and PtANS) gradually increased in the leaves of hybrid poplar (P. tremula × P. alba), corresponding to the drought stress duration. In addition, the activity and capacity of antioxidants have also increased, which is positively correlated with the increment of phenolic, flavonoid, anthocyanin, and carotenoid compounds under drought stress. As the drought stress prolonged, the level of reactive oxygen species such as hydrogen peroxide (H2O2) and singlet oxygen (O2-) too increased. The concentration of phytohormone salicylic acid (SA) also increased significantly in the stressed poplar leaves. Our research concluded that drought stress significantly induced the expression of flavonoid biosynthesis genes in hybrid poplar plants and enhanced the accumulation of phenolic and flavonoid compounds with resilient antioxidant activity.
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Affiliation(s)
- Umair Ahmed
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (U.A.); (C.Q.); (Q.X.)
| | - Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China;
| | - Cheng Qi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (U.A.); (C.Q.); (Q.X.)
| | - Qi Xie
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (U.A.); (C.Q.); (Q.X.)
| | - Hamza Armghan Noushahi
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Muhammad Yaseen
- Wuzhishan National Long-Term Forest Ecosystem Monitoring Research Station, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Forestry, Hainan University, Haikou 570228, China;
| | - Xueping Shi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (U.A.); (C.Q.); (Q.X.)
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (U.A.); (C.Q.); (Q.X.)
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23
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Zuo Z, Sun X, Cao L, Zhang S, Yu J, Xu X, Xu Z, Liu G, Qu C. Genome-wide identification of FRK genes in Populus trichocarpa and their expression under different nitrogen treatments. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1919-1931. [PMID: 34616114 PMCID: PMC8484491 DOI: 10.1007/s12298-021-01055-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Fructokinase (FRK) is the main fructose phosphorylase and plays an important role in catalyzing the irreversible reaction of free fructose phosphorylation. In order to study the regulatory effect of different forms and concentrations of nitrogen on PtFRK genes in Populus trichocarpa, seven genes encoding the hypothetical FRK proteins were identified in Populus trichocarpa genome by bioinformatics method. Phylogenetic analysis revealed that PtFRK family genes can be divided into two subgroups: SI (PtFRK 1, 3, 4, 6) and SII (PtFRK 2, 5, 7). The tissue-specific expression data obtained from PopGenIE indicate that PtFRK2, 3, 4 and 5 are expressed highly in the stem. Quantitative real-time RT-PCR illustrate that PtFRK1-7 showed different expression patterns in different tissues under different concentrations and morphological nitrogen application. Under high nitrate treatment, the expression levels of PtFRK1, 2, 3 and 6 in stem increased significantly, while under low nitrate treatment, only the expression of PtFRK1, 4 in the upper stem and the expression of PtFRK3, 5 in the lower stem increased significantly. In contrast, ammonium tends to inhibit the expression of PtFRKs in lower stems, the expression levels of PtFRK2, 3, 4 and 5 are significantly reduced under ammonium treatment. However, high ammonium had significant effects on PtFRK6 in the apical bud and upper leaves, which were 6 and 8 times of the control, respectively. These results laid the foundation for the study of the PtFRK gene family of poplar and provided a theoretical basis for the molecular mechanism of nitrogen regulating cell wall development. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01055-6.
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Affiliation(s)
- Zhuang Zuo
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- Daxinganling Survey, Planning and Design Institute of State Forestry and Grassland Administration, Jiagedaqi, 165000 People’s Republic of China
| | - Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Lina Cao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Shuang Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040 People’s Republic of China
- College of Life Science, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Xiuyue Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040 People’s Republic of China
- College of Life Science, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- College of Forestry, Guizhou University, Guiyang, 550025 People’s Republic of China
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24
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Zhang L, Wang L, Zhang J, Song C, Li Y, Li J, Lu M. Expression and localization of SWEETs in Populus and the effect of SWEET7 overexpression in secondary growth. TREE PHYSIOLOGY 2021; 41:882-899. [PMID: 33147625 DOI: 10.1093/treephys/tpaa145] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
In trees, wood formation needs carbon import from the photosynthetic source tissues. Sugar transporters play important roles in carbohydrate transport into wood-forming cells. Sugars will eventually be exported transporters (SWEETs) play essential roles in many physiological processes. However, the roles of this family in the growth and development of woody plants have not been systematically investigated. In this study, 27 SWEET genes were identified in the Populus trichocarpa genome. These SWEET genes were classified into four clades based on their phylogenetic relationships, gene structures, conserved motifs and chromosomal locations. Representative SWEET members from each clade were selected for further studies. The PagSWEETs of Populus alba × Populus glandulosa were localized to plasma membrane, vacuolar, endoplasmic reticulum or Golgi. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that PagSWEETs have distinct expression patterns in various tissues, and PagSWEET5, 7, 10b, 10c, 15b, 17a and 17c exhibited high expression levels in stems. PagSWEET7 is localized to the cytoplasmic membrane and specifically expressed in the phloem as detected by histochemical GUS ($\beta $ - glucuronidase) assays. Xylem production and xylem sugar content were greater in developing wood of PagSWEET7 overexpression than wild-type lines. Collectively, these results provide valuable information for further investigating functions of PagSWEET genes, and identify PagSWEET7 as a candidate gene for using biotechnology to modify the wood formation in poplar.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- College of Agricultural and Biological engineering, Heze University, Heze, Shandong 274015, China
| | - Lijuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- State Key Laboratory of Subtropical Forestry, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Cai Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Non-wood Forest Product of State Forestry Administration, School of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yu Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jianbo Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- State Key Laboratory of Subtropical Forestry, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
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25
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Characterization and Expression of KT/HAK/KUP Transporter Family Genes in Willow under Potassium Deficiency, Drought, and Salt Stresses. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2690760. [PMID: 32596286 PMCID: PMC7303730 DOI: 10.1155/2020/2690760] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022]
Abstract
The K+ transporter/high-affinity K+/K+ uptake (KT/HAK/KUP) transporters dominate K+ uptake, transport, and allocation that play a pivotal role in mineral homeostasis and plant adaptation to adverse abiotic stresses. However, molecular mechanisms towards K+ nutrition in forest trees are extremely rare, especially in willow. In this study, we identified 22 KT/HAK/KUP transporter genes in purple osier willow (designated as SpuHAK1 to SpuHAK22) and examined their expression under K+ deficiency, drought, and salt stress conditions. Both transcriptomic and quantitative real-time PCR (qRT-PCR) analyses demonstrated that SpuHAKs were predominantly expressed in stems, and the expression levels of SpuHAK1, SpuHAK2, SpuHAK3, SpuHAK7, and SpuHAK8 were higher at the whole plant level, whereas SpuHAK9, SpuHAK11, SpuHAK20, and SpuHAK22 were hardly detected in tested tissues. In addition, both K+ deficiency and salt stress decreased the tissue K+ content, while drought increased the tissue K+ content in purple osier plant. Moreover, SpuHAK genes were differentially responsive to K+ deficiency, drought, and salt stresses in roots. K+ deficiency and salt stress mainly enhanced the expression level of responsive SpuHAK genes. Fifteen putative cis-acting regulatory elements, including the stress response, hormone response, circadian regulation, and nutrition and development, were identified in the promoter region of SpuHAK genes. Our findings provide a foundation for further functional characterization of KT/HAK/KUP transporters in forest trees and may be useful for breeding willow rootstocks that utilize potassium more efficiently.
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Qiu D, Bai S, Ma J, Zhang L, Shao F, Zhang K, Yang Y, Sun T, Huang J, Zhou Y, Galbraith DW, Wang Z, Sun G. The genome of Populus alba x Populus tremula var. glandulosa clone 84K. DNA Res 2020; 26:423-431. [PMID: 31580414 PMCID: PMC6796506 DOI: 10.1093/dnares/dsz020] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/09/2019] [Indexed: 01/22/2023] Open
Abstract
Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5 Mb) has a contig N50 size of 1.99 Mb and a scaffold N50 size of 19.6 Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356 Mb from P. alba (subgenome A) and 354 Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies.
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Affiliation(s)
- Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shenglong Bai
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Jianchao Ma
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Lisha Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Fenjuan Shao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Kaikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,College of Horticulture, Agricultural University of Hebei, Baoding, China
| | - Yanfang Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Ting Sun
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Jinling Huang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yun Zhou
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - David W Galbraith
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China.,School of Plant Sciences and Bio5 Institute, The University of Arizona, Tucson, AZ, USA
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Guiling Sun
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
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Poplar PdPTP1 Gene Negatively Regulates Salt Tolerance by Affecting Ion and ROS Homeostasis in Populus. Int J Mol Sci 2020; 21:ijms21031065. [PMID: 32033494 PMCID: PMC7037657 DOI: 10.3390/ijms21031065] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022] Open
Abstract
High concentrations of Na+ in saline soil impair plant growth and agricultural production. Protein tyrosine phosphorylation is crucial in many cellular regulatory mechanisms. However, regulatory mechanisms of plant protein tyrosine phosphatases (PTPs) in controlling responses to abiotic stress remain limited. We report here the identification of a Tyrosine (Tyr)-specific phosphatase, PdPTP1, from NE19 (Populus nigra × (P. deltoides × P. nigra). Transcript levels of PdPTP1 were upregulated significantly by NaCl treatment and oxidative stress. PdPTP1 was found both in the nucleus and cytoplasm. Under NaCl treatment, transgenic plants overexpressing PdPTP1 (OxPdPTP1) accumulated more Na+ and less K+. In addition, OxPdPTP1 poplars accumulated more H2O2 and O2·-, which is consistent with the downregulation of enzymatic ROS-scavengers activity. Furthermore, PdPTP1 interacted with PdMAPK3/6 in vivo and in vitro. In conclusion, our findings demonstrate that PdPTP1 functions as a negative regulator of salt tolerance via a mechanism of affecting Na+/K+ and ROS homeostasis.
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28
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Zhao Y, Song X, Zhou H, Wei K, Jiang C, Wang J, Cao Y, Tang F, Zhao S, Lu MZ. KNAT2/6b, a class I KNOX gene, impedes xylem differentiation by regulating NAC domain transcription factors in poplar. THE NEW PHYTOLOGIST 2020; 225:1531-1544. [PMID: 31257603 DOI: 10.1111/nph.16036] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/22/2019] [Indexed: 05/21/2023]
Abstract
Wood formation is the terminal differentiation of xylem mother cells derived from cambial initials, and negative regulators play important roles in xylem differentiation. The molecular mechanism of the negative regulator of xylem differentiation PagKNAT2/6b was investigated. PagKNAT2/6b is an ortholog of Arabidopsis KNAT2 and KNAT6 that is highly expressed in phloem and xylem. Compared to nontransgenic control plants, transgenic poplar plants overexpressing PagKNAT2/6b present with altered vascular patterns, characterized by decreased secondary xylem with thin cell walls containing less cellulose, xylose and lignin. RNA sequencing analyses revealed that differentially expressed genes are enriched in xylem differentiation and secondary wall synthesis functions. Expression of NAM/ATAF/CUC (NAC) domain genes including PagSND1-A1, PagSND1-A2, PagSND1-B2 and PagVND6-C1 is downregulated by PagKNAT2/6b, while PagXND1a is directly upregulated. Accordingly, the dominant repression form of PagKNAT2/6b leads to increased xylem width per stem diameter through downregulation of PagXND1a. PagKNAT2/6b can inhibit cell differentiation and secondary wall deposition during wood formation in poplar by modulating the expression of NAC domain transcription factors. Direct activation of PagXND1a by PagKNAT2/6b is a key node in the negative regulatory network of xylem differentiation by KNOXs.
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Affiliation(s)
- Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Kaili Wei
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Cheng Jiang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yuan Cao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Shutang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
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Fang Q, Wang X, Wang H, Tang X, Liu C, Yin H, Ye S, Jiang Y, Duan Y, Luo K. The poplar R2R3 MYB transcription factor PtrMYB94 coordinates with abscisic acid signaling to improve drought tolerance in plants. TREE PHYSIOLOGY 2020; 40:46-59. [PMID: 31728530 DOI: 10.1093/treephys/tpz113] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/26/2019] [Accepted: 10/08/2019] [Indexed: 05/07/2023]
Abstract
In plants, R2R3 MYB transcription factors (TFs) consist of one large gene family and are involved in the regulation of many developmental processes and various stresses. However, the functions of most of MYB TFs in woody plants remain unknown. Here, PtrMYB94, an R2R3 MYB TF from Populus trichocarpa, is characterized to be involved in the regulation of drought responses and abscisic acid (ABA) signaling. PtrMYB94 encodes a nuclear-localized R2R3 MYB TF. RT-PCR results showed that the PtrMYB94 transcripts were relatively abundant in leaves and stems, and were induced rapidly in response to dehydration stress. Overexpression of PtrMYB94 improved plant drought responses, suggesting that this MYB TF may functionally regulate poplar adaptability to drought stress. Furthermore, the analysis of transcriptional expression and PtrMYB94 promoter: GUS activity showed that PtrMYB94 responded to ABA induction. PtrMYB94-overexpressing plants exhibited the inhibition of seed germination compared with the wild-type (WT) control under ABA exposure condition. The ABA content was evidently increased in the PtrMYB94-overexpressing plants relative to the WT plants. In addition, transcript levels of several ABA- and drought-responsive genes, such as ABA1 and DREB2B, were up-regulated. Taken together, our results suggest that PtrMYB94 is involved in an ABA-dependent drought stress regulation in Populus.
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Affiliation(s)
- Qing Fang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing 400715, China
- Hubei Key Laboratory of Biological Resources Protection and Utilization, School of Biological Science and Technology, Hubei Minzu University, Enshi 445000, China
| | - Xianqiang Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haiyang Wang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, School of Biological Science and Technology, Hubei Minzu University, Enshi 445000, China
| | - Xiaowen Tang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, School of Biological Science and Technology, Hubei Minzu University, Enshi 445000, China
| | - Chi Liu
- Hubei Key Laboratory of Biological Resources Protection and Utilization, School of Biological Science and Technology, Hubei Minzu University, Enshi 445000, China
| | - Heng Yin
- Hubei Key Laboratory of Biological Resources Protection and Utilization, School of Biological Science and Technology, Hubei Minzu University, Enshi 445000, China
| | - Shenglong Ye
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yuanzhong Jiang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yanjiao Duan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing 400715, China
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30
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Köbölkuti ZA, Cseke K, Benke A, Báder M, Borovics A, Németh R. Allelic variation in candidate genes associated with wood properties of cultivated poplars (Populus). Biol Futur 2019; 70:286-294. [PMID: 34554544 DOI: 10.1556/019.70.2019.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/26/2019] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Since Populus has veritable value as timber, plywood, pulp, and paper, genomic research should create the sound basis for further breeding toward desirable wood quality attributes. MATERIALS AND METHODS In this study, we addressed the need for a research methodology that initially identifies and then characterize candidate genes encoding enzymes with wood property phenotypic traits, toward the aim of developing a genomics-based breeding technology. RESULTS On 23 different poplar species/hybrid samples, we successfully amplified 55 primers designed on Populus trichocarpa L. Considering the number of polymorphic sites, out of 73,206 bp, 51 SNPs and 31 indel events were found. Non-synonymous single base mutations could be detected in number of 30, 21 out of 164 sequences were the number of minimum recombination events and 41 significant pairwise comparisons between loci could be detected. DISCUSSION AND CONCLUSION Our results provide a roadmap for a future association genetic study between nucleotide diversity and precise evaluation of phenotype.
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Affiliation(s)
- Zoltán Attila Köbölkuti
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary.
| | - Klára Cseke
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary
| | - Attila Benke
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary
| | - Mátyás Báder
- Simonyi Karoly Faculty of Engineering, Wood Sciences and Applied Arts, University of Sopron, Bajcsy Zs. u. 4, 9400, Sopron, Hungary
| | - Attila Borovics
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary
| | - Róbert Németh
- Simonyi Karoly Faculty of Engineering, Wood Sciences and Applied Arts, University of Sopron, Bajcsy Zs. u. 4, 9400, Sopron, Hungary
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31
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Qu C, Zhao H, Chen J, Zuo Z, Sun X, Huang J, Yang C, Zhang X, Zhang P, Quan X, Xu Z, Liu G. The transcriptional events and their relationship to physiological changes during poplar seed germination and post-germination. BMC Genomics 2019; 20:801. [PMID: 31684868 PMCID: PMC6829952 DOI: 10.1186/s12864-019-6180-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background Seed germination, the foundation of plant propagation, involves a series of changes at the molecular level. Poplar is a model woody plant, but the molecular events occurring during seed germination in this species are unclear. Results In this study, we investigated changes in gene transcriptional levels during different germination periods in poplar by high-throughput sequencing technology. Analysis of genes expressed at specific germination stages indicated that these genes are distributed in many metabolic pathways. Enrichment analysis of significantly differentially expressed genes based on hypergeometric testing revealed that multiple pathways, such as pathways related to glycolysis, lipid, amino acid, protein and ATP synthesis metabolism, changed significantly at the transcriptional level during seed germination. A comparison of ΣZ values uncovered a series of transcriptional changes in biological processes related to primary metabolism during poplar seed germination. Among these changes, genes related to CHO metabolism were the first to be activated, with subsequent expression of genes involved in lipid metabolism and then those associated with protein metabolism. The pattern of metabolomic and physiological index changes further verified the sequence of some biological events. Conclusions Our study revealed molecular events occurring at the transcriptional level during seed germination and determined their order. These events were further verified by patterns of changes of metabolites and physiological indexes. Our findings lay a foundation for the elucidation of the molecular mechanisms responsible for poplar seed germination.
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Affiliation(s)
- Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Hancheng Zhao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jinyuan Chen
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhuang Zuo
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jiahuan Huang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xiuli Zhang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Peng Zhang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xiankui Quan
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China. .,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
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32
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Expression Analysis of the NAC Transcription Factor Family of Populus in Response to Salt Stress. FORESTS 2019. [DOI: 10.3390/f10080688] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Research Highlights: Sequence phylogeny, genome organisation, gene structure, conserved motifs, promoter cis-element and expression profiling of poplar NACs related to salt stress were detected. In addition, expression of two salt-induced NACs was analysed. Background and Objectives: NAC transcription factor (TF) proteins are involved in a wide range of functions during plant development and stress-related endurance processes. To understand the function of Populus NAC TFs in salt stress tolerance, we characterised the structure and expression profile of a total of 289 NAC members. Materials and Methods: Sequence phylogeny, genome organisation, gene structure, motif composition and promoter cis-element were detected using bioinformatics. The expression pattern of Populus NAC TFs under salt stress was also detected using RNA-Seq and RT-qPCR. Results: Synteny analysis showed that 46 and 37 Populus NAC genes were involved in whole-genome duplication and tandem duplication events, respectively. The expression pattern of Populus NAC TFs under salt stress showed the expression of the 289 PtNACs of 84K poplar was induced. Similar expression trends of NACs were found in Populus simonii × P. nigra T. S. Hwang et Liang and Arabidopsis thaliana (L.) Heynh. Conclusions: The correlation analysis showed that the expression of two differentially expressed NAC genes PtNAC024 and PtNAC182 was significantly associated with most of the 63 differentially expressed genes tested. The expression of PtNAC024 and PtNAC182 in different tissues was also analysed in silico and different expression patterns were found. Together, this study provides a solid basis to explore stress-related NAC TF functions in Populus salt tolerance and development.
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33
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Fungal canker pathogens trigger carbon starvation by inhibiting carbon metabolism in poplar stems. Sci Rep 2019; 9:10111. [PMID: 31300723 PMCID: PMC6626041 DOI: 10.1038/s41598-019-46635-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
Carbon starvation is the current leading hypothesis of plant mortality mechanisms under drought stress; recently, it is also used to explain tree die-off in plant diseases. However, the molecular biology of the carbon starvation pathway is unclear. Here, using a punch inoculation system, we conducted transcriptome and physiological assays to investigate pathogen response in poplar stems at the early stages of Botryosphaeria and Valsa canker diseases. Transcriptome assays showed that the majority of differentially expressed genes (DEGs) in stem phloem and xylem, such as genes involved in carbon metabolism and transportation, aquaporin genes (in xylem) and genes related to the biosynthesis of secondary metabolites and the phenylpropanoid pathway (related to lignin synthesis), were downregulated at 7 days after inoculation (DAI). Results also showed that the expression of the majority of disease-resistance genes upregulated in poplar stems, which may be connected with the downregulation expression of the majority of WRKY family genes. Physiological assays showed that transpiration rate decreased but WUE (water use efficiency) increased the 3 and 7 DAI, while the net photosynthetic rate decreased at 11 DAI in Botryosphaeria infected poplars (ANOVA, P < 0.05). The NSC (non-structural carbohydrates) content assays showed that the soluble sugar content of stem phloem samples increased at 3, 7, and 11 DAI that might due to the impede of pathogen infection. However, soluble sugar content of stem xylem and root samples decreased at 11 DAI; in contrast, the starch content unchanged. Therefore, results revealed a chronological order of carbon related molecular and physiological performance: declination of genes involved in carbon and starch metabolism first (at least at 7 DAI), declination of assimilation and carbon reserve (at 11 DAI) second. Results implied a potential mechanism that affects the host carbon reserve, by directly inhibiting the expression of genes involved in carbon metabolism and transport.
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34
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Qu C, Hao B, Xu X, Wang Y, Yang C, Xu Z, Liu G. Functional Research on Three Presumed Asparagine Synthetase Family Members in Poplar. Genes (Basel) 2019; 10:E326. [PMID: 31035411 PMCID: PMC6562506 DOI: 10.3390/genes10050326] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/16/2019] [Accepted: 04/23/2019] [Indexed: 12/15/2022] Open
Abstract
Asparagine synthetase (AS), a key enzyme in plant nitrogen metabolism, plays an important role in plant nitrogen assimilation and distribution. Asparagine (Asn), the product of asparagine synthetase, is one of the main compounds responsible for organic nitrogen transport and storage in plants. In this study, we performed complementation experiments using an Asn-deficient Escherichia coli strain to demonstrate that three putative asparagine synthetase family members in poplar (Populussimonii× P.nigra) function in Asn synthesis. Quantitative real-time PCR revealed that the three members had high expression levels in different tissues of poplar and were regulated by exogenous nitrogen. PnAS1 and PnAS2 were also affected by diurnal rhythm. Long-term dark treatment resulted in a significant increase in PnAS1 and PnAS3 expression levels. Under long-term light conditions, however, PnAS2 expression decreased significantly in the intermediate region of leaves. Exogenous application of ammonium nitrogen, glutamine, and a glutamine synthetase inhibitor revealed that PnAS3 was more sensitive to exogenous glutamine, while PnAS1 and PnAS2 were more susceptible to exogenous ammonium nitrogen. Our results suggest that the various members of the PnAS gene family have distinct roles in different tissues and are regulated in different ways.
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Affiliation(s)
- Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China.
- School of Forestry, Northeast Forestry University, Harbin 150040, China.
| | - Bingqing Hao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China.
- School of Forestry, Northeast Forestry University, Harbin 150040, China.
- Guangxi Forestry Research Institute, Nanning 530000, China.
| | - Xiuyue Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China.
- School of Forestry, Northeast Forestry University, Harbin 150040, China.
| | - Yuchen Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China.
- School of Forestry, Northeast Forestry University, Harbin 150040, China.
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, Harbin 150040, China.
| | - Zhiru Xu
- School of Forestry, Northeast Forestry University, Harbin 150040, China.
- College of Life Science, Northeast Forestry University, Harbin 150040, China.
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China.
- School of Forestry, Northeast Forestry University, Harbin 150040, China.
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35
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Lu H, Klocko AL, Brunner AM, Ma C, Magnuson AC, Howe GT, An X, Strauss SH. RNA interference suppression of AGAMOUS and SEEDSTICK alters floral organ identity and impairs floral organ determinacy, ovule differentiation, and seed-hair development in Populus. THE NEW PHYTOLOGIST 2019; 222:923-937. [PMID: 30565259 PMCID: PMC6590139 DOI: 10.1111/nph.15648] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/09/2018] [Indexed: 05/24/2023]
Abstract
The role of the floral homeotic gene AGAMOUS (AG) and its close homologues in development of anemophilous, unisexual catkins has not previously been studied. We transformed two RNA interference (RNAi) constructs, PTG and its matrix-attachment-region flanked version MPG, into the early-flowering female poplar clone 6K10 (Populus alba) to suppress the expression of its two duplicate AG orthologues. By early 2018, six out of 22 flowering PTG events and 11 out of 12 flowering MPG events showed modified floral phenotypes in a field trial in Oregon, USA. Flowers in catkins from modified events had 'carpel-inside-carpel' phenotypes. Complete disruption of seed production was observed in seven events, and sterile anther-like organs in 10 events. Events with strong co-suppression of both the two AG and two SEEDSTICK (STK) paralogues lacked both seeds and associated seed hairs. Alterations in all of the modified floral phenotypes were stable over 4 yr of study. Trees from floral-modified events did not differ significantly (P < 0.05) from nonmodified transgenic or nontransgenic controls in biomass growth or leaf morphology. AG and STK genes show strong conservation of gene function during poplar catkin development and are promising targets for genetic containment of exotic or genetically engineered trees.
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Affiliation(s)
- Haiwei Lu
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
| | - Amy L. Klocko
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
- Department of BiologyUniversity of Colorado Colorado SpringsColorado SpringsCO80918USA
| | - Amy M. Brunner
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
- Department of Forest Resources and Environmental ConservationVirginia TechBlacksburgVA24061USA
| | - Cathleen Ma
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
| | - Anna C. Magnuson
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
| | - Glenn T. Howe
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
| | - Xinmin An
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and BiotechnologyBeijing Forestry UniversityBeijing100083China
| | - Steven H. Strauss
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
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Liu X, Chen M, Zhou X, Cao Z. Identification of novel miRNAs and their target genes from Populus szechuanica infected with Melampsora larici-populina. Mol Biol Rep 2019; 46:3083-3092. [PMID: 30859446 DOI: 10.1007/s11033-019-04746-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/05/2019] [Indexed: 01/21/2023]
Abstract
Two novel miRNAs were selected from a pre-constructed RNA library of Populus szechuanica infected with the foliar rust fungus Melampsora larici-populina in order to detect the genes regulated as targets of the miRNAs novel_mir_11 and novel_mir_357. The novel miRNAs were identified from P. szechuanica using stem-loop methods and their precursors were able to fold into a complete stem loop structure. The predicted target genes of the novel miRNAs were verified with RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-5'RACE). The full-length sequences of target genes, RPM1 and RPS2/5, in P. szechuanica were obtained through rapid amplification of cDNA ends (RACE) and officially named PsRPM1 and PsRPS2/5. These genes contain nucleotide binding site-leucine-rich repeats (NBS-LRR) domains typical of resistance genes. The expression levels of miRNAs and their target genes in different periods post infection were analysed with quantitative real-time PCR (qRT-PCR). After infection with the foliar rust fungus, the expression levels of the novel miRNAs and their target genes were dynamic. Both novel_mir_11 and novel_mir_357 negatively regulated the expression of their target genes. In this study, the regulatory effects of two novel miRNAs through their target genes were characterized to provide further mechanistic information regarding the interaction between Populus and a foliar rust fungus. Results of this study improve our understanding of the defence response mechanisms of Populus and will stimulate future work to characterize strategies to prevent and control Populus diseases.
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Affiliation(s)
- Xin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Min Chen
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue Zhou
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhimin Cao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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37
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Gourlay G, Constabel CP. Condensed tannins are inducible antioxidants and protect hybrid poplar against oxidative stress. TREE PHYSIOLOGY 2019; 39:345-355. [PMID: 30917196 DOI: 10.1093/treephys/tpy143] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 05/12/2023]
Abstract
Condensed tannins (CTs) have been studied extensively as potential defenses against pests and pathogens, and for their beneficial effects on human health. They are known to possess high in vitro antioxidant capacity, but whether they can function as in planta antioxidants for protection against oxidative stress has not been previously tested. Here, we show that stress induction of CTs in poplar (Populus) is matched closely by an increase in antioxidant activity under both high light and nitrogen deficiency. We also investigate the effects of CTs as in vivo antioxidants directly, using transgenic poplar plants which overexpress poplar MYB transcription factors that regulate the CT pathway. These transgenics have 50-fold higher CT concentrations than controls, and and also have dramatically higher antioxidant activity. High-CT and control poplar leaves were exposed to methyl viologen for 24 h. Chlorophyll fluorescence was used to measure maximum quantum efficiency of photosystem II photochemistry (Fv/Fm), and leaf discs were stained with 3,3'-diaminobenzidine (DAB) and nitroblue tetrazolium (NBT) to assess hydrogen peroxide and superoxide levels. After methyl viologen exposure, high-CT transgenics retained higher Fv/Fm ratios and accumulated less hydrogen peroxide and superoxide than the controls. Our findings indicate that high-CT concentrations protect poplar against methyl viologen-induced oxidative stress and suggest a broader function of CTs than previously supposed.
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Affiliation(s)
- Geraldine Gourlay
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC, Canada
| | - C Peter Constabel
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC, Canada
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38
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Ma J, Wan D, Duan B, Bai X, Bai Q, Chen N, Ma T. Genome sequence and genetic transformation of a widely distributed and cultivated poplar. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:451-460. [PMID: 30044051 PMCID: PMC6335071 DOI: 10.1111/pbi.12989] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 05/20/2023]
Abstract
Populus alba is widely distributed and cultivated in Europe and Asia. This species has been used for diverse studies. In this study, we assembled a de novo genome sequence of P. alba var. pyramidalis (= P. bolleana) and confirmed its high transformation efficiency and short transformation time by experiments. Through a process of hybrid genome assembly, a total of 464 M of the genome was assembled. Annotation analyses predicted 37 901 protein-coding genes. This genome is highly collinear to that of P. trichocarpa, with most genes having orthologs in the two species. We found a marked expansion of gene families related to histone and the hormone auxin but loss of disease resistance genes in P. alba if compared with the closely related P. trichocarpa. The genome sequence presented here represents a valuable resource for further molecular functional analyses of this species as a new tree model, poplar breeding practices and comparative genomic analyses across different poplars.
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Affiliation(s)
- Jianchao Ma
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Bingbing Duan
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Xiaotao Bai
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Qiuxian Bai
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ningning Chen
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Tao Ma
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduChina
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Lin Y, Min J, Lai R, Wu Z, Chen Y, Yu L, Cheng C, Jin Y, Tian Q, Liu Q, Liu W, Zhang C, Lin L, Zhang D, Thu M, Zhang Z, Liu S, Zhong C, Fang X, Wang J, Yang H, Varshney RK, Yin Y, Lai Z. Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics. Gigascience 2018; 6:1-14. [PMID: 28368449 PMCID: PMC5467034 DOI: 10.1093/gigascience/gix023] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 03/23/2017] [Indexed: 11/13/2022] Open
Abstract
Longan (Dimocarpus longan Lour.), an important subtropical fruit in the family Sapindaceae, is grown in more than 10 countries. Longan is an edible drupe fruit and a source of traditional medicine with polyphenol-rich traits. Tree size, alternate bearing, and witches' broom disease still pose serious problems. To gain insights into the genomic basis of longan traits, a draft genome sequence was assembled. The draft genome (about 471.88 Mb) of a Chinese longan cultivar, "Honghezi," was estimated to contain 31 007 genes and 261.88 Mb of repetitive sequences. No recent whole-genome-wide duplication event was detected in the genome. Whole-genome resequencing and analysis of 13 cultivated D. longan accessions revealed the extent of genetic diversity. Comparative transcriptome studies combined with genome-wide analysis revealed polyphenol-rich and pathogen resistance characteristics. Genes involved in secondary metabolism, especially those from significantly expanded (DHS, SDH, F3΄H, ANR, and UFGT) and contracted (PAL, CHS, and F3΄5΄H) gene families with tissue-specific expression, may be important contributors to the high accumulation levels of polyphenolic compounds observed in longan fruit. The high number of genes encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) and leucine-rich repeat receptor-like kinase proteins, as well as the recent expansion and contraction of the NBS-LRR family, suggested a genomic basis for resistance to insects, fungus, and bacteria in this fruit tree. These data provide insights into the evolution and diversity of the longan genome. The comparative genomic and transcriptome analyses provided information about longan-specific traits, particularly genes involved in its polyphenol-rich and pathogen resistance characteristics.
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Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Ruilian Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lili Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Qilin Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Weihua Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Lixia Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dongmin Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Minkyaw Thu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shengcai Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chunshui Zhong
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.,School of Plant Biology, The University of Western Australia, Crawley, Perth, Australia
| | - Ye Yin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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40
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Kulkarni P, Dost M, Bulut ÖD, Welle A, Böcker S, Boland W, Svatoš A. Secondary ion mass spectrometry imaging and multivariate data analysis reveal co-aggregation patterns of Populus trichocarpa leaf surface compounds on a micrometer scale. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:193-206. [PMID: 29117637 DOI: 10.1111/tpj.13763] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/13/2017] [Accepted: 10/23/2017] [Indexed: 05/23/2023]
Abstract
Spatially resolved analysis of a multitude of compound classes has become feasible with the rapid advancement in mass spectrometry imaging strategies. In this study, we present a protocol that combines high lateral resolution time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging with a multivariate data analysis (MVA) approach to probe the complex leaf surface chemistry of Populus trichocarpa. Here, epicuticular waxes (EWs) found on the adaxial leaf surface of P. trichocarpa were blotted on silicon wafers and imaged using TOF-SIMS at 10 μm and 1 μm lateral resolution. Intense M+● and M-● molecular ions were clearly visible, which made it possible to resolve the individual compound classes present in EWs. Series of long-chain aliphatic saturated alcohols (C21 -C30 ), hydrocarbons (C25 -C33 ) and wax esters (WEs; C44 -C48 ) were clearly observed. These data correlated with the 7 Li-chelation matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, which yielded mostly molecular adduct ions of the analyzed compounds. Subsequently, MVA was used to interrogate the TOF-SIMS dataset for identifying hidden patterns on the leaf's surface based on its chemical profile. After the application of principal component analysis (PCA), a small number of principal components (PCs) were found to be sufficient to explain maximum variance in the data. To further confirm the contributions from pure components, a five-factor multivariate curve resolution (MCR) model was applied. Two distinct patterns of small islets, here termed 'crystals', were apparent from the resulting score plots. Based on PCA and MCR results, the crystals were found to be formed by C23 or C29 alcohols. Other less obvious patterns observed in the PCs revealed that the adaxial leaf surface is coated with a relatively homogenous layer of alcohols, hydrocarbons and WEs. The ultra-high-resolution TOF-SIMS imaging combined with the MVA approach helped to highlight the diverse patterns underlying the leaf's surface. Currently, the methods available to analyze the surface chemistry of waxes in conjunction with the spatial information related to the distribution of compounds are limited. This study uses tools that may provide important biological insights into the composition of the wax layer, how this layer is repaired after mechanical damage or insect feeding, and which transport mechanisms are involved in deploying wax constituents to specific regions on the leaf surface.
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Affiliation(s)
- Purva Kulkarni
- Lehrstuhl für Bioinformatik, Friedrich Schiller University, Ernst-Abbe-Platz 2, 07743, Jena, Germany
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
| | - Mina Dost
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
| | - Özgül Demir Bulut
- Institute of Functional Interfaces and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Alexander Welle
- Institute of Functional Interfaces and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Sebastian Böcker
- Lehrstuhl für Bioinformatik, Friedrich Schiller University, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
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41
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Xu Z, Gao L, Tang M, Qu C, Huang J, Wang Q, Yang C, Liu G, Yang C. Genome-wide identification and expression profile analysis of CCH gene family in Populus. PeerJ 2017; 5:e3962. [PMID: 29085758 PMCID: PMC5661435 DOI: 10.7717/peerj.3962] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/05/2017] [Indexed: 11/20/2022] Open
Abstract
Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone, CCH, is presently limited to Arabidopsis. This study reports the identification of 21 genes encoding putative CCH proteins in Populus trichocarpa. Besides sharing the conserved metal-binding motif MXCXXC and forming a βαββαβ secondary structure at the N-terminal, all the PtCCHs possessed the plant-exclusive extended C-terminal. Based on their gene structure, conserved motifs, and phylogenetic analysis, the PtCCHs were divided into three subgroups. Our analysis indicated that whole-genome duplication and tandem duplication events likely contributed to expansion of the CCH gene family in Populus. Tissue-specific data from PlantGenIE revealed that PtCCH genes had broad expression patterns in different tissues. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that PnCCH genes of P. simonii × P. nigra also had different tissue-specific expression traits, as well as different inducible-expression patterns in response to copper stresses (excessive and deficiency). In summary, our study of CCH genes in the Populus genome provides a comprehensive analysis of this gene family, and lays an important foundation for further investigation of their roles in copper homeostasis of poplar.
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Affiliation(s)
- Zhiru Xu
- College of Life Science, Northeast Forestry University, HarBin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
| | - Liying Gao
- College of Life Science, Northeast Forestry University, HarBin, China
| | - Mengquan Tang
- College of Life Science, Northeast Forestry University, HarBin, China
| | - Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
- School of Forestry, Northeast Forestry University, HarBin, China
| | - Jiahuan Huang
- College of Life Science, Northeast Forestry University, HarBin, China
| | - Qi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
- School of Forestry, Northeast Forestry University, HarBin, China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
- School of Forestry, Northeast Forestry University, HarBin, China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
- School of Forestry, Northeast Forestry University, HarBin, China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, HarBin, China
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42
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Chen Z, Ji L, Wang J, Jin J, Yang X, Rao P, Gao K, Liao W, Ye M, An X. Dynamic changes in the transcriptome of Populus hopeiensis in response to abscisic acid. Sci Rep 2017; 7:42708. [PMID: 28198429 PMCID: PMC5309881 DOI: 10.1038/srep42708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/13/2017] [Indexed: 11/09/2022] Open
Abstract
Abscisic acid (ABA) plays a fundamental role in plant response and adaptation to abiotic stresses, such as drought, high salinity and low temperature. Populus hopeiensis exhibits exceptional tolerance to water-deficit environments and is therefore an excellent choice for studying drought tolerance in trees. This study provides a global view of transcriptome dynamics in P. hopeiensis in response to exogenous ABA using Illumina RNA-sequencing. Endogenous ABA content increased and reached a peak at 8 h after ABA treatment and then significantly decreased at latter time points. Differential expression analysis and Gene ontology enrichment revealed that the number of transcripts exhibited significant increase during the first 8 hours after ABA treatment, which then significantly decreased at 12 and 24 h. Transcription factors (TFs) analysis showed that six different patterns were observed based on the expression of the six TFs families (AP2/ERF, NAC, MYB, MYB-related, bZIP and WRKY) and the majority of differentially expressed TFs increased rapidly after ABA treatment. This study provides a robust resource for investigating the functions of genes induced by ABA and will help to develop a better understanding of the molecular regulatory mechanism in response to drought in poplar.
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Affiliation(s)
- Zhong Chen
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Lexiang Ji
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China.,Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Jia Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Jinpu Jin
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Xiaoyu Yang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Pian Rao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Kai Gao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Weihua Liao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Meixia Ye
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Xinmin An
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
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43
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Kuzminsky E, Meschini R, Terzoli S, Pavani L, Silvestri C, Choury Z, Scarascia-Mugnozza G. Isolation of Mesophyll Protoplasts from Mediterranean Woody Plants for the Study of DNA Integrity under Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:1168. [PMID: 27574524 PMCID: PMC4983556 DOI: 10.3389/fpls.2016.01168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/20/2016] [Indexed: 05/24/2023]
Abstract
Abiotic stresses have considerable negative impact on Mediterranean plant ecosystems and better comprehension of the genetic control of response and adaptation of trees to global changes is urgently needed. The single cell gel electrophoresis (SCGE) assay could be considered a good estimator of DNA damage in an individual eukaryotic cell. This method has been mainly employed in animal tissues, because the plant cell wall represents an obstacle for the extraction of nuclei; moreover, in Mediterranean woody species, especially in the sclerophyll plants, this procedure can be quite difficult because of the presence of sclerenchyma and hardened cells. On the other hand, these plants represent an interesting material to be studied because of the ability of these plants to tolerate abiotic stress. For instance, holm oak (Quercus ilex L.) has been selected as the model plant to identify critical levels of O3 for Southern European forests. Consequently, a quantitative method for the evaluation of cell injury of leaf tissues of this species is required. Optimal conditions for high-yield nuclei isolation were obtained by using protoplast technology and a detailed description of the method is provided and discussed. White poplar (Populus alba L.) was used as an internal control for protoplast isolation. Such a method has not been previously reported in newly fully developed leaves of holm oak. This method combined with SCGE assay represents a new tool for testing the DNA integrity of leaf tissues in higher plants under stress conditions.
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Affiliation(s)
- Elena Kuzminsky
- Laboratory of Forest Biotechnology, Department for Innovation in Biological, Agro-food and Forest systems, University of TusciaViterbo, Italy
| | - Roberta Meschini
- Laboratory of Molecular Cytogenetic and Mutagenesis, Department of Ecological and Biological Science, University of TusciaViterbo, Italy
| | - Serena Terzoli
- Laboratory of Forest Biotechnology, Department for Innovation in Biological, Agro-food and Forest systems, University of TusciaViterbo, Italy
| | - Liliana Pavani
- Laboratory of Forest Biotechnology, Department for Innovation in Biological, Agro-food and Forest systems, University of TusciaViterbo, Italy
| | - Cristian Silvestri
- Laboratory of Tissue Culture and Biotechnology of Woody Plants, Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
| | - Zineb Choury
- Laboratory of Forest Biotechnology, Department for Innovation in Biological, Agro-food and Forest systems, University of TusciaViterbo, Italy
| | - Giuseppe Scarascia-Mugnozza
- Laboratory of Forest Biotechnology, Department for Innovation in Biological, Agro-food and Forest systems, University of TusciaViterbo, Italy
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Zhang Y, Han X, Sang J, He X, Liu M, Qiao G, Zhuo R, He G, Hu J. Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases. PeerJ 2016; 4:e2097. [PMID: 27330860 PMCID: PMC4906661 DOI: 10.7717/peerj.2097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/10/2016] [Indexed: 12/23/2022] Open
Abstract
Background.Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results. We carried out transcriptome sequencing at three different cultivation ages (7Y, 15Y and 21Y) generating 68.71 million reads (13.88 Gbp). A total of 140,486 unigenes with a mean size of 568.64 base pairs (bp) were obtained via de novo assembly. Of these, 27,427 unigenes (19.52%) were further annotated by comparison to public protein databases. A total of 5,331 (3.79%) unigenes were mapped into 118 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEG) analysis identified 3, 16 and 5,899 DEGs from the comparison of 7Y vs. 15Y, 7Y vs. 21Y and 15Y vs. 21Y, respectively, in the immature xylem tissues, including 2,638 significantly up-regulated and 3,280 significantly down-regulated genes. Besides, five NAC transcription factors, 190 MYB transcription factors, and 34 WRKY transcription factors were identified respectively from Chinese fir transcriptome. Conclusion. Our results revealed the active transcriptional pathways and identified the DEGs at different cultivation phases of Chinese fir wood formation. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of Chinese fir wood formation and contribute to future artificial production and applications.
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Affiliation(s)
- Yunxing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
- Institute of Architectural and Artistic Design, Henan Polytechnic University, Jiaozuo, Henan, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Jian Sang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Xuelian He
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Mingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Guiping He
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Ribeiro CL, Silva CM, Drost DR, Novaes E, Novaes CRDB, Dervinis C, Kirst M. Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus. BMC PLANT BIOLOGY 2016; 16:66. [PMID: 26983547 PMCID: PMC4793515 DOI: 10.1186/s12870-016-0753-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 03/06/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Adventitious roots (AR) develop from tissues other than the primary root, in a process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttings from a pseudo-backcross population of Populus deltoides and Populus trichocarpa. Quantitative trait loci (QTL) mapping and whole-transcriptome analysis of individuals with alternative QTL alleles for AR number were used to identify putative regulators of AR development. RESULTS Parental individuals and progeny showed extensive segregation for AR developmental traits. Quantitative trait loci for number of AR mapped consistently in the same interval of linkage group (LG) II and LG XIV, explaining 7-10 % of the phenotypic variation. A time series transcriptome analysis identified 26,121 genes differentially expressed during AR development, particularly during the first 24 h after cuttings were harvested. Of those, 1929 genes were differentially regulated between individuals carrying alternative alleles for the two QTL for number of AR, in one or more time point. Eighty-one of these genes were physically located within the QTL intervals for number of AR, including putative homologs of the Arabidopsis genes SUPERROOT2 (SUR2) and TRYPTOPHAN SYNTHASE ALPHA CHAIN (TSA1), both of which are involved in the auxin indole-3-acetic acid (IAA) biosynthesis pathway. CONCLUSIONS This study suggests the involvement of two genes of the tryptophan-dependent auxin biosynthesis pathway, SUR2 and TSA1, in the regulation of a critical trait for the clonal propagation of woody species. A possible model for this regulation is that poplar individuals that have poor AR formation synthesize auxin indole-3-acetic acid (IAA) primarily through the tryptophan (Trp) pathway. Much of the Trp pathway flux appears to be directed to the synthesis of indole glucosinolates (IG), as suggested by the over-expression of SUR2. Individuals that are efficient in AR formation may utilize alternative (non-Trp) pathways to synthesize IAA, based on the observation that they down-regulate the expression of TSA1, one of the critical steps in the synthesis of tryptophan.
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Affiliation(s)
- Cintia L. Ribeiro
- />School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL 32611 USA
- />Plant Molecular and Cellular Biology Graduate Program, University of Florida, P.O. Box 110690, Gainesville, FL 32611 USA
- />Present Address: Monsanto Company, 700 Chesterfield Pkwy W, Chesterfield, MO 63017 USA
| | - Cynthia M. Silva
- />School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL 32611 USA
| | - Derek R. Drost
- />School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL 32611 USA
- />Plant Molecular and Cellular Biology Graduate Program, University of Florida, P.O. Box 110690, Gainesville, FL 32611 USA
- />Present Address: Seminis, Inc., 37437 State Highway 16, Woodland, CA 95695 USA
| | - Evandro Novaes
- />School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL 32611 USA
- />Present Address: Universidade Federal de Goiás, Av. Esperança s/n°, Goiânia, GO 74001-970 Brazil
| | - Carolina R. D. B. Novaes
- />School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL 32611 USA
- />Present Address: Universidade Federal de Goiás, Av. Esperança s/n°, Goiânia, GO 74001-970 Brazil
| | - Christopher Dervinis
- />School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL 32611 USA
| | - Matias Kirst
- />School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL 32611 USA
- />Plant Molecular and Cellular Biology Graduate Program, University of Florida, P.O. Box 110690, Gainesville, FL 32611 USA
- />University of Florida Genetics Institute, University of Florida, P.O. Box 103610, Gainesville, FL 32611 USA
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Qu CP, Xu ZR, Hu YB, Lu Y, Yang CJ, Sun GY, Liu GJ. RNA-SEQ Reveals Transcriptional Level Changes of Poplar Roots in Different Forms of Nitrogen Treatments. FRONTIERS IN PLANT SCIENCE 2016; 7:51. [PMID: 26870068 PMCID: PMC4735414 DOI: 10.3389/fpls.2016.00051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/13/2016] [Indexed: 05/07/2023]
Abstract
Poplar has emerged as a model plant for better understanding cellular and molecular changes accompanying tree growth, development, and response to environment. Long-term application of different forms of nitrogen (such as [Formula: see text]-N and [Formula: see text]-N) may cause morphological changes of poplar roots; however, the molecular level changes are still not well-known. In this study, we analyzed the expression profiling of poplar roots treated by three forms of nitrogen: S1 ([Formula: see text]), S2 (NH4NO3), and S3 ([Formula: see text]) by using RNA-SEQ technique. We found 463 genes significantly differentially expressed in roots by different N treatments, of which a total of 112 genes were found to differentially express between S1 and S2, 171 genes between S2 and S3, and 319 genes between S1 and S3. A cluster analysis shows significant difference in many transcription factor families and functional genes family under different N forms. Through an analysis of Mapman metabolic pathway, we found that the significantly differentially expressed genes are associated with fermentation, glycolysis, and tricarboxylic acid cycle (TCA), secondary metabolism, hormone metabolism, and transport processing. Interestingly, we did not find significantly differentially expressed genes in N metabolism pathway, mitochondrial electron transport/ATP synthesis and mineral nutrition. We also found abundant candidate genes (20 transcription factors and 30 functional genes) regulating morphology changes of poplar roots under the three N forms. The results obtained are beneficial to a better understanding of the potential molecular and cellular mechanisms regulating root morphology changes under different N treatments.
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Affiliation(s)
- Chun-Pu Qu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
| | - Zhi-Ru Xu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Yan-Bo Hu
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Yao Lu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
| | - Cheng-Jun Yang
- School of Forestry, Northeast Forestry UniversityHarbin, China
| | - Guang-Yu Sun
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Guan-Jun Liu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
- *Correspondence: Guan-Jun Liu
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Strauss SH, Ma C, Ault K, Klocko AL. Lessons from Two Decades of Field Trials with Genetically Modified Trees in the USA: Biology and Regulatory Compliance. BIOSAFETY OF FOREST TRANSGENIC TREES 2016. [DOI: 10.1007/978-94-017-7531-1_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Zhang C, Meng S, Li M, Zhao Z. Genomic Identification and Expression Analysis of the Phosphate Transporter Gene Family in Poplar. FRONTIERS IN PLANT SCIENCE 2016; 7:1398. [PMID: 27695473 PMCID: PMC5025438 DOI: 10.3389/fpls.2016.01398] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/01/2016] [Indexed: 05/20/2023]
Abstract
Inorganic phosphate is one of key macronutrients essential for plant growth. The acquisition and distribution of phosphate are mediated by phosphate transporters functioning in various physiological and biochemical processes. In the present study, we comprehensively evaluated the phosphate transporter (PHT) gene family in the latest release of the Populus trichocarpa genome (version 3.0; Phytozome 11.0) and a total of 42 PHT genes were identified which formed five clusters: PHT1, PHT2, PHT3, PHT4, and PHO. Among the 42 PHT genes, 41 were localized to 15 Populus chromosomes. Analysis of these genes led to identification of 5-14 transmembrane segments, most of which were conserved within the same cluster. We identified 234 putative cis elements in the 2-kb upstream regions of the 42 PHT genes, many of which are related to development, stress, or hormone. Tissue-specific expression analysis of the 42 PtPHT genes revealed that 25 were highly expressed in the roots of P. tremula, suggesting that most of them might be involved in Pi uptake. Some PtPHT genes were highly expressed in more than six of the twelve investigated tissues of P. tremula, while the expression of a few of them was very low in all investigated tissues. In addition, the expression of the PtPHT genes was verified by quantitative real-time PCR in four tissues of P. simonii. Transcripts of 7 PtPHT genes were detected in all four tested tissues of P. simonii. Most PtPHT genes were expressed in the roots of P. simonii at high levels. Further, PtPHT1.2 and PtPHO9 expression was increased under drought conditions, irrespective of the phosphate levels. In particular, PtPHT1.2 expression was significantly induced by approximately 90-fold. However, the transcriptional changes of some PtPHT genes under drought stress were highly dependent on the phosphate levels. These results will aid in elucidation of the functions of PtPHT in the growth, development, and stress response of the poplar plant.
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Affiliation(s)
- Chunxia Zhang
- College of Forestry, Northwest A&F UniversityYangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F UniversityYangling, China
- *Correspondence: Chunxia Zhang
| | - Sen Meng
- College of Forestry, Northwest A&F UniversityYangling, China
| | - Mingjun Li
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Zhong Zhao
- College of Forestry, Northwest A&F UniversityYangling, China
- Zhong Zhao
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Zhang H, Yang J, Wang W, Li D, Hu X, Wang H, Wei M, Liu Q, Wang Z, Li C. Genome-wide identification and expression profiling of the copper transporter gene family in Populus trichocarpa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 97:451-460. [PMID: 26581045 DOI: 10.1016/j.plaphy.2015.10.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 06/05/2023]
Abstract
Copper transporters (COPT/Ctr) have important roles in the transport of copper (Cu) across the cell membrane in many different species. A comprehensive phylogeny and a molecular structure analysis of the COPT/Ctr family in plants and animals are presented, with an emphasis and bioinformatic analysis of the copper transporter family in Populus trichocarpa (PtCOPT). Structural analyses of PtCOPTs showed that most have 3 transmembrane domains (TMDs), with an exception of PtCOPT4 (2 TMDs). Gene structure, gene chromosomal location, and synteny analyses of PtCOPTs demonstrated that tandem and segmental duplications have likely contributed to the expansion and evolution of the PtCOPTs. Additionally, promoter analyses showed that the function of PtCOPTs is related to Cu and ferrum (Fe) transport. Tissue-specific expression of PtCOPT genes showed that most had relatively high transcript levels in roots and leaves. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that the expression of PtCOPT genes were induced not only in limited and excessive Cu, Fe, zinc (Zn) and manganese (Mn) stress, but also in lead (Pb), and cadmium (Cd) stress.
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Affiliation(s)
- Haizhen Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Jingli Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Weida Wang
- Wildlife Protection Department, Inner Mongolia Forestry Industrial Group, Yakeshi, Inner Mongolia 022150, China
| | - Dandan Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Xiaoqing Hu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Han Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Ming Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Quangang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Zhanchao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China.
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50
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Lanier C, Manier N, Cuny D, Deram A. The comet assay in higher terrestrial plant model: Review and evolutionary trends. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 207:6-20. [PMID: 26327498 DOI: 10.1016/j.envpol.2015.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/13/2015] [Indexed: 05/24/2023]
Abstract
The comet assay is a sensitive technique for the measurement of DNA damage in individual cells. Although it has been primarily applied to animal cells, its adaptation to higher plant tissues significantly extends the utility of plants for environmental genotoxicity research. The present review focuses on 101 key publications and discusses protocols and evolutionary trends specific to higher plants. General consensus validates the use of the percentage of DNA found in the tail, the alkaline version of the test and root study. The comet protocol has proved its effectiveness and its adaptability for cultivated plant models. Its transposition in wild plants thus appears as a logical evolution. However, certain aspects of the protocol can be improved, namely through the systematic use of positive controls and increasing the number of nuclei read. These optimizations will permit the increase in the performance of this test, namely when interpreting mechanistic and physiological phenomena.
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Affiliation(s)
- Caroline Lanier
- Université Lille 2, EA 4483, Laboratoire des Sciences Végétales et Fongiques - Faculté des Sciences Pharmaceutiques et Biologiques, B.P. 83, F-59006 Lille Cedex, France; Université Lille 2, Faculté Ingénierie et Management de la Santé (ILIS), EA 4483, 42, Rue Ambroise Paré, 59120 Loos, France
| | - Nicolas Manier
- INERIS, Parc Technologique ALATA, B.P. 2, 60550 Verneuil en Halatte, France
| | - Damien Cuny
- Université Lille 2, Faculté Ingénierie et Management de la Santé (ILIS), EA 4483, 42, Rue Ambroise Paré, 59120 Loos, France
| | - Annabelle Deram
- Université Lille 2, EA 4483, Laboratoire des Sciences Végétales et Fongiques - Faculté des Sciences Pharmaceutiques et Biologiques, B.P. 83, F-59006 Lille Cedex, France; Université Lille 2, Faculté Ingénierie et Management de la Santé (ILIS), EA 4483, 42, Rue Ambroise Paré, 59120 Loos, France.
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