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Li P, Wang J, Zhang Q, Yu A, Sun R, Liu A. Genome-wide identification and analysis of GH1-containing H1 histones among poplar species. BMC Genomics 2025; 26:287. [PMID: 40128684 PMCID: PMC11931866 DOI: 10.1186/s12864-025-11456-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Accepted: 03/06/2025] [Indexed: 03/26/2025] Open
Abstract
Histone H1s are basic nuclear proteins, which played key role in the binding of DNA and nucleosome, eventually the stability of eukaryotic chromatin. In most species, H1s possess an evolutionarily conserved nucleosome-DNA binding globular domain (GH1), which is conserved between species, especially in mammals. However, there is limited information on the phylogeny, structure and function of H1s in poplar. In the present research, 21 GH1-containing proteins found in Populus trichocarpa were classified into three subgroups (H1s, Myb (SANK) GH1 and AT-hook GH1) based on their domains. The Populus H1 proteins contained lysine-rich N-, C-terminal tails and a conserved GH1 domain, particularly the characteristic amino acids in the helix and strand structures of the five H1 subtypes. The phylogenetic and structure diversity analysis of GH1 proteins across different Populus species and model plants revealed three conserved subgroups with characteristic amino acids. The variation in the number of members across the five subtypes was consistent with the evolutionary relationships among Populus species. The conserved characteristic amino acids among same Populus subtype can be served as markers for subtype identification. Furthermore, the abundance analysis of H1s in Populus indicated their unique functions in young tissues and stages, which may be related to DNA methylation. The consistent expression pattern of H1 across Populus species was in accordance with collinearity pairs. Present analyses provided valuable information on the diversity and evolution of H1s in Populus, advocating further research of H1s in plants.
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Affiliation(s)
- Ping Li
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), College of Forestry, Southwest Forestry University, Kunming, China
| | - Jing Wang
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), College of Forestry, Southwest Forestry University, Kunming, China
| | - Qimin Zhang
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), College of Forestry, Southwest Forestry University, Kunming, China
| | - Anmin Yu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), College of Forestry, Southwest Forestry University, Kunming, China
| | - Rui Sun
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), College of Forestry, Southwest Forestry University, Kunming, China
| | - Aizhong Liu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), College of Forestry, Southwest Forestry University, Kunming, China.
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Liu X, Cai K, Zhang Q, An W, Qu G, Jiang L, Wang F, Zhao X. Unlocking the Growth Potential of Poplar: A Novel Transcriptomic-Metabolomic Approach to Evaluating the Impact of Divergent Pruning Strategies. PLANTS (BASEL, SWITZERLAND) 2024; 13:3391. [PMID: 39683183 DOI: 10.3390/plants13233391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/11/2024] [Accepted: 12/01/2024] [Indexed: 12/18/2024]
Abstract
Pruning is a common forest-tending method; its purpose is to promote growth and improve the overall stand quality. Poplar is a fast-growing, broad-leaved tree species with high ecological and economic value. It is a common management method to promote its growth by pruning and adjusting the spatial structure of the stand, but its potential regulatory mechanism remains unclear. In this study, transcriptome and metabolome data of different parts at all pruning intensities were determined and analyzed. The results showed that 7316 differentially expressed genes were identified in this study. In the plant hormone signal transduction pathway, candidate genes were found in eight kinds of plant hormones, among which the main expression was gibberellin, auxin, and brassinosteroid. Some candidate gene structures (beta-glucosidase, endoglucanase, hexokinase, glucan endo-1, 3-beta-D-glucosidase, beta-fructofuranosidase, fructokinase, maltase-glucoamylase, phosphoglucomutase, and sucrose) were specifically associated with starch and sucrose biosynthesis. In the starch and sucrose biosynthesis pathway, D-fructose 6-phosphate, D-glucose 1,6-bisphosphate, and glucose-1-phosphate were the highest in stems and higher in the first round of pruning than in no pruning. The bHLH plays a key role in the starch and sucrose synthetic pathway, and AP2/ERF-ERF is important in the plant hormone signal transduction pathway. These results laid a foundation for understanding the molecular mechanism of starch and sucrose biosynthesis and provided a theoretical basis for promoting tree growth through pruning.
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Affiliation(s)
- Xiaoting Liu
- National Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Kewei Cai
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Qinhui Zhang
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Weizi An
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Guanzheng Qu
- National Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Luping Jiang
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Fusen Wang
- Qiqihar Branch of Heilongjiang Academy of Forestry, Qiqihar 161000, China
| | - Xiyang Zhao
- National Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
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Wang Z, Zhang W, Ding C, Xia Y, Yuan Z, Guo J, Yu J, Zhang B, Su X. RNA-seq reveals the gene expression in patterns in Populus × euramericana 'Neva' plantation under different precision water and fertilizer-intensive management. BMC PLANT BIOLOGY 2024; 24:759. [PMID: 39118015 PMCID: PMC11312740 DOI: 10.1186/s12870-024-05427-4] [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: 02/07/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Populus spp. is a crucial fast-growing and productive tree species extensively cultivated in the mid-latitude plains of the world. However, the impact of intensive cultivation management on gene expression in plantation remains largely unexplored. RESULTS Precision water and fertilizer-intensive management substantially increased key enzyme activities of nitrogen transport, assimilation, and photosynthesis (1.12-2.63 times than CK) in Populus × euramericana 'Neva' plantation. Meanwhile, this management approach had a significant regulatory effect on the gene expression of poplar plantations. 1554 differential expression genes (DEGs)were identified in drip irrigation (ND) compared with conventional irrigation. Relative to ND, 2761-4116 DEGs, predominantly up-regulated, were identified under three drip fertilization combinations, among which 202 DEGs were mainly regulated by fertilization. Moreover, drip irrigation reduced the expression of cell wall synthesis-related genes to reduce unnecessary water transport. Precision drip and fertilizer-intensive management promotes the synergistic regulation of carbon and nitrogen metabolism and up-regulates the expression of major genes in nitrogen transport and assimilation processes (5 DEGs), photosynthesis (15 DEGs), and plant hormone signal transduction (11 DEGs). The incorporation of trace elements further enhanced the up-regulation of secondary metabolic process genes. In addition, the co-expression network identified nine hub genes regulated by precision water and fertilizer-intensive management, suggesting a pivotal role in regulating the growth of poplar. CONCLUSION Precision water and fertilizer-intensive management demonstrated the ability to regulate the expression of key genes and transcription factor genes involved in carbon and nitrogen metabolism pathways, plant hormone signal transduction, and enhance the activity of key enzymes involved in related processes. This regulation facilitated nitrogen absorption and utilization, and photosynthetic abilities such as light capture, light transport, and electron transport, which faintly synergistically regulate the growth of poplar plantations. These results provide a reference for proposing highly efficient precision intensive management to optimize the expression of target genes.
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Affiliation(s)
- Zhou 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 State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Weixi Zhang
- 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 State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Changjun Ding
- 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 State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yongxiu Xia
- Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, 100023, P.R. China
| | - Zhengsai Yuan
- 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 State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jiangtao Guo
- Heibei Agricultural University, Baoding, 071001, P.R. China
| | - Jinjin Yu
- 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 State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Bingyu Zhang
- 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 State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Xiaohua Su
- 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 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, Nanjing, 210037, China.
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Bai Y, Ding G. Estimation of changes in carbon sequestration and its economic value with various stand density and rotation age of Pinus massoniana plantations in China. Sci Rep 2024; 14:16852. [PMID: 39039162 PMCID: PMC11263345 DOI: 10.1038/s41598-024-67307-z] [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: 03/27/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024] Open
Abstract
Plantations actively participate in the global carbon cycle and play a significant role in mitigating global climate change. However, the influence of forest management strategies, especially planting density management, on the biomass carbon storage and production value of plantations for ensuring carbon sink benefits is still unclear. In this study, we estimated the carbon sequestration and economic value of Pinus massoniana plantations with various stand densities and rotation ages using a growth model method. The results revealed that with increasing stand age, low-density plantations at 2000 trees·ha-1 (358.80 m3·ha-1), as well as high-density plantations at 4500 trees·ha-1 (359.10 m3·ha-1), exhibited nearly identical standing volumes, which indicated that reduced inter-tree competition intensity favors the growth of larger trees during later stages of development. Furthermore, an increase in planting density led to a decrease in the average carbon sequestration rate, carbon sink, and number of trees during the rapid growth period, indicating that broader spacing between trees is favorable for biomass carbon accumulation. Further, extending the rotation period from 15 to 20 years or 25 years and reducing the optimal planting density from 3000 to 2000 trees·ha-1 increased the overall benefits of combined timber and carbon sink income by 2.14 and 3.13 times, respectively. The results highlighted that optimizing the planting density positively impacts the timber productivity and carbon sink storage of Pinus massoniana plantations and boosts the expected profits of forest managers. Thus, future afforestation initiatives must consider stand age and planting density management to shift from a scale-speed pattern to a quality-benefit design.
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Affiliation(s)
- Yunxing Bai
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, China
| | - Guijie Ding
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, China.
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Chen J, Li T, Cai J, Yu P, Guo Y. Physiological and Molecular Response of Liriodendron chinense to Varying Stand Density. PLANTS (BASEL, SWITZERLAND) 2024; 13:508. [PMID: 38498462 PMCID: PMC10892427 DOI: 10.3390/plants13040508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 03/20/2024]
Abstract
Stand density affects the potentially superior productivity of forest ecosystems directly by regulating the light and nutrient availability of trees. Understanding how stand density influences the growth and development of trees is crucial for supporting forest management in the context of climate change. We focused on Liriodendron chinense in experimental plantations created in 2003, with planting densities ranging from 277 to 10,000 trees per hectare at six plots. The leaf structure and photosynthetic capacity of L. chinense changed significantly under different stand densities, which had a negative impact on their biomass (leaf mass) and nutrient (total carbohydrate content) accumulation. Transcriptional differences were observed among samples from plots with different planting densities. The expression of 1784 genes was negatively dependent on stand density, participating mainly in the biological processes of "circadian rhythm", "carbon metabolism", and "amino acid biosynthesis". Furthermore, we identified a photosynthesis-related module and constructed a gene regulatory network to discover that the transcription factors of MYB and bHLH may have important roles in the transcriptional regulation of photosynthesis biosynthesis by activating or repressing the expression of petA (Litul.15G096200), psbE (Litul.10G033900), and petD (Litul.17G061600) at different stand densities. Our study quantified the impact of stand density on tree growth at physiological and molecular levels. Our observations provide theoretical support for plantation establishment of L. chinense.
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Affiliation(s)
- Jun Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (J.C.); (T.L.); (J.C.)
| | - Ting Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (J.C.); (T.L.); (J.C.)
| | - Jinfeng Cai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (J.C.); (T.L.); (J.C.)
| | - Pengfei Yu
- Suining County Run Enterprises Investment Co., Ltd., Xuzhou 212100, China;
| | - Ying Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (J.C.); (T.L.); (J.C.)
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Sui J, Li C, Wang Y, Li X, Liu R, Hua X, Liu X, Qi H. Microecological Shifts in the Rhizosphere of Perennial Large Trees and Seedlings in Continuous Cropping of Poplar. Microorganisms 2023; 12:58. [PMID: 38257884 PMCID: PMC10820384 DOI: 10.3390/microorganisms12010058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
The cultivation of poplar trees is hindered by persistent cropping challenges, resulting in reduced wood productivity and increased susceptibility to soil-borne diseases. These issues primarily arise from alterations in microbial structure and the infiltration of pathogenic fungi. To investigate the impact on soil fertility, we conducted an analysis using soil samples from both perennial poplar trees and three successive generations of continuously cropped poplar trees. The quantity and community composition of bacteria and fungi in the rhizosphere were assessed using the Illumina MiSeq platform. The objective of this study is to elucidate the impact of continuous cropping challenges on soil fertility and rhizosphere microorganisms in poplar trees, thereby establishing a theoretical foundation for investigating the mechanisms underlying these challenges. The study found that the total bacteria in the BT group is 0.42 times higher than the CK group, and the total fungi is 0.33 times lower than the CK group. The BT and CK groups presented relatively similar bacterial richness and diversity, while the indices showed a significant (p < 0.05) higher fungal richness and diversity in the CK group. The fractions of Bacillus were 2.22% and 2.41% in the BT and CK groups, respectively. There was a 35.29% fraction of Inocybe in the BT group, whereas this was barely observed in the CK group. The fractions of Geopora were 26.25% and 5.99%, respectively in the BT and CK groups. Modifying the microbial community structure in soil subjected to continuous cropping is deemed as the most effective approach to mitigate the challenges associated with this agricultural practice.
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Affiliation(s)
- Junkang Sui
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, China; (C.L.); (Y.W.); (X.L.); (R.L.); (X.H.)
| | - Chenyu Li
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, China; (C.L.); (Y.W.); (X.L.); (R.L.); (X.H.)
| | - Yinping Wang
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, China; (C.L.); (Y.W.); (X.L.); (R.L.); (X.H.)
| | - Xiangyu Li
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, China; (C.L.); (Y.W.); (X.L.); (R.L.); (X.H.)
| | - Rui Liu
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, China; (C.L.); (Y.W.); (X.L.); (R.L.); (X.H.)
| | - Xuewen Hua
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, China; (C.L.); (Y.W.); (X.L.); (R.L.); (X.H.)
| | - Xunli Liu
- College of Forestry, Shandong Agricultural University, Tai’an 271000, China;
| | - Hui Qi
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, China; (C.L.); (Y.W.); (X.L.); (R.L.); (X.H.)
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Chutimanukul P, Mosaleeyanon K, Janta S, Toojinda T, Darwell CT, Wanichananan P. Physiological responses, yield and medicinal substance (andrographolide, AP1) accumulation of Andrographis paniculata (Burm. f) in response to plant density under controlled environmental conditions. PLoS One 2022; 17:e0272520. [PMID: 35925998 PMCID: PMC9352076 DOI: 10.1371/journal.pone.0272520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Agricultural practice in adjusting planting density and harvest date are important factors for plant development and crop improvement, reaching maximum yields and enhancing the production of secondary metabolites. However, it is unclear as to the optimal planting densities during mass production that encourage consistent, high yield secondary metabolite content. For this, controlled environment, crop production facilities such as plant factories with artificial lighting (PFAL) offer opportunity to enhance quality and stabilize production of herbal plants. This study assessed the effect of plant density and harvest date on physiological responses, yield and andrographolide (AP1) content in Andrographis paniculata (Andrographis) using hydroponic conditions in a PFAL system. Andrographis, harvested at vegetative stage (30 days after transplanting; 30 DAT) and initial stage of flowering (60 DAT) exhibited no significant differences in growth parameters or andrographolide accumulation according to planting densities. Harvest time at flowering stage (90 DAT) showed the highest photosynthetic rates at a planting density of 15 plants m-2. Highest yield, number of leaves, and Andrographolide (AP1) content (mg per gram of DW in m2) were achieved at a more moderate planting density (30 plants m-2). Finally, five out of seventeen indices of leaf reflectance reveal high correlation (r = 0.8 to 1.0 and r = -0.8 to -1.0, P<0.01) with AP1 content. These results suggest that a planting density of 30 plants m-2 and harvest time of 90 DAT provide optimal growing condition under the hydroponic PFAL system.
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Affiliation(s)
- Panita Chutimanukul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kriengkrai Mosaleeyanon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supattana Janta
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Clive Terence Darwell
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Praderm Wanichananan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
- * E-mail:
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8
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Response of Poplar Leaf Transcriptome to Changed Management and Environmental Conditions in Pure and Mixed with Black Locust Stands. FORESTS 2022. [DOI: 10.3390/f13020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Mixed cropping in short rotation coppice can be an alternative to monocultures. To design optimized mixtures, field trials are needed. Poplar, as an economically important and fast-growing species, and black locust, as a nitrogen-fixing species, are promising candidates for such studies. RNA sequencing (RNA-seq) was used to monitor effects of mixed and pure cultivations on the gene expression of poplar along with growth measurements during 2017 and 2018. Both biomass production and leaf transcriptomes revealed a strong competition pressure of black locust and the abiotic environment on poplar trees. Gene expression differed between the two study sites and pure and mixed stands. Shading effects from black locust caused the downregulation of photosynthesis and upregulation of shade avoidance genes in mixed stands in 2017. As a result of higher light availability after cutting black locust, plant organ development genes were upregulated in mixed stands in 2018. Drought conditions during the summer of 2018 and competition for water between the two species caused the upregulation of drought stress response genes in mixed stands and at the unfavorable growing site. Further investigations are required to discover the mechanisms of interspecific competition and to develop stand designs, which could increase the success and productivity of mixed plantations.
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Cai K, Liu H, Chen S, Liu Y, Zhao X, Chen S. Genome-wide identification and analysis of class III peroxidases in Betula pendula. BMC Genomics 2021; 22:314. [PMID: 33932996 PMCID: PMC8088069 DOI: 10.1186/s12864-021-07622-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 04/15/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula. RESULTS We identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. CONCLUSIONS The research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.
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Affiliation(s)
- Kewei Cai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Huixin Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yi Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
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Liu H, Gu H, Ye C, Guo C, Zhu Y, Huang H, Liu Y, He X, Yang M, Zhu S. Planting Density Affects Panax notoginseng Growth and Ginsenoside Accumulation by Balancing Primary and Secondary Metabolism. FRONTIERS IN PLANT SCIENCE 2021; 12:628294. [PMID: 33936125 PMCID: PMC8086637 DOI: 10.3389/fpls.2021.628294] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/26/2021] [Indexed: 05/24/2023]
Abstract
Adjusting planting density is a common agricultural practice used to achieve maximum yields. However, whether the quality of medicinal herbs can be improved by implementing appropriate planting densities is still uncertain. The medicinal crop Panax notoginseng was used to analyze the effects of planting density on growth and ginsenoside accumulation, and the possible mechanisms of these effects were revealed through metabonomics. The results showed that P. notoginseng achieved high ginsenoside accumulation at high planting densities (8 × 8 and 10 × 10 cm), while simultaneously achieved high biomass and ginsenoside accumulation at moderate planting density of 15 × 15 cm. At the moderate planting density, the primary metabolism (starch and sucrose metabolism) and secondary metabolism (the biosynthesis of phytohormone IAA and ginsenoside) of the plants were significantly enhanced. However, the strong intraspecific competition at the high planting densities resulted in stress as well as the accumulation of phytohormones (SA and JA), antioxidants (gentiobiose, oxalic acid, dehydroascorbic acid) and other stress resistance-related metabolites. Interestingly, the dry biomass and ginsenoside content were significantly lower at low densities (20 × 20 and 30 × 30 cm) with low intraspecific competition, which disturbed normal carbohydrate metabolism by upregulating galactose metabolism. In summary, an appropriate planting density was benefit for the growth and accumulation of ginsenosides in P. notoginseng by balancing primary metabolism and secondary metabolism.
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Affiliation(s)
- Haijiao Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Hongrui Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Chen Ye
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Cunwu Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yifan Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yixiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Xiahong He
- School of Landscape and Horticulture, Southwest Forestry University, Kunming, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
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11
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Niu J, Ma M, Yin X, Liu X, Dong T, Sun W, Yang F. Transcriptional and physiological analyses of reduced density in apple provide insight into the regulation involved in photosynthesis. PLoS One 2020; 15:e0239737. [PMID: 33044972 PMCID: PMC7549834 DOI: 10.1371/journal.pone.0239737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/13/2020] [Indexed: 11/18/2022] Open
Abstract
Different densities have a great influence on the physiological process and growth of orchard plants. Exploring the molecular basis and revealing key candidate genes for different densities management of orchard has great significance for production capacity improvement. In this study, transcriptome sequencing of apple trees was carried out at three different sampling heights to determine gene expression patterns under high density(HD) and low density(LD) and the physiological indices were measured to determine the effect of density change on plants. As a result, physiological indexes showed that the content of Chlorophyll, ACC, RUBP and PEP in the LD was apparently higher than that in control group(high density, HD). While the content of PPO and AO in the LD was noticeably lower than that in the HD. There were 3808 differentially expressed genes (DEGs) were detected between HD and LD, of which 1935, 2390 and 1108 DEGs were found in the three comparisons(middle-upper, lower-outer and lower-inner), respectively. 274 common differentially expressed genes (co-DEGs) were contained in all three comparisons. Functional enrichment and KEGG pathway analysis found these genes were involved in Carbon fixation in photosynthetic organisms, Circadian rhythm, Photosynthesis - antenna proteins, Photosynthesis, chlorophyll metabolism, Porphyrin, sugar metabolism and so on. Among these genes, LHCB family participated in photosynthesis as parts of photosystem II. In addition, SPA1, rbcL, SNRK2, MYC2, BSK, SAUR and PP2C are involved in Circadian rhythm, the expression of genes related to glycometabolism and hormone signaling pathway is also changed. The results revealed that the decrease of plant density changed the photosynthetic efficiency of leaves and the expression of photosynthesis-related genes, which provide a theoretical basis for the actual production regulation of apples.
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Affiliation(s)
- Junqiang Niu
- Institute of Fruit and Floriculture Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
| | - Ming Ma
- Institute of Fruit and Floriculture Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
| | - Xiaoning Yin
- Institute of Fruit and Floriculture Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
| | - Xinglu Liu
- Institute of Fruit and Floriculture Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
| | - Tie Dong
- Institute of Fruit and Floriculture Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
| | - Wentai Sun
- Institute of Fruit and Floriculture Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
| | - Fuxia Yang
- Institute of Fruit and Floriculture Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
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