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Singh S, Praveen A, Bhadrecha P. Genome-wide identification and analysis of SPL gene family in chickpea (Cicer arietinum L.). PROTOPLASMA 2024; 261:799-818. [PMID: 38378886 DOI: 10.1007/s00709-024-01936-z] [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: 09/18/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
A transcription factor in plants encodes SQUAMOSA promoter binding protein-like (SPL) serves a broad spectrum of important roles for the plant, like, growth, flowering, and signal transduction. A gene family that encodes SPL proteins is documented in various model plant species, including Arabidopsis thaliana and Oryza sativa. Chickpea (Cicer arietinum), a leguminous crop, has not been thoroughly explored with regard to the SPL protein-encoding gene family. Chickpea SPL family genes were located and characterized computationally using a genomic database. Gene data of chickpea were obtained from the phytozome repository and was examined using bioinformatics methods. For investigating the possible roles of SPLs in chickpea, genome-wide characterization, expression, as well as structural analyses of this SPL gene family were performed. Cicer arietinum genome had 19 SPL genes, whereas, according to phylogenetic analysis, the SPLs in chickpea are segregated among four categories: Group-I has 2 introns, Group-II and IV have 1-2 introns (except CaSPL13 and CaSPL15 having 3 introns), and Group-III has 9 introns (except CaSPL1 and CaSPL11 with 1 and 8 introns, respectively). The SBP domain revealed that SPL proteins featured two zinc-binding sites, i.e., C3H and C2HC and one nuclear localization signal. All CaSPL proteins are found to contain highly conserved motifs, i.e., Motifs 1, 2, and 4, except CaSPL10 in which Motifs 1 and 4 were absent. Following analysis, it was found that Motifs 1 and 2 of the chickpea SBP domain are Zinc finger motifs, and Motif 4 includes a nuclear localization signal. All pairs of CaSPL paralogs developed by purifying selection. The CaSPL promoter investigation discovered cis-elements that are responsive to stress, light, and phytohormones. Examination of their expression patterns highlighted major CaSPLs to be evinced primarily among younger pods and flowers. Indicating their involvement in the plant's growth as well as development, along with their capacity to react as per different situations by handling the regulation of target gene's expression, several CaSPL genes are also expressed under certain stress conditions, namely, cold, salt, and drought. The majority of the CaSPL genes are widely expressed and play crucial roles in terms of the plant's growth, development, and responses to the environmental-stress conditions. Our work provides extensive insight into the gene family CaSPL, which might facilitate further studies related to the evolution and functions of the SPL genes for chickpea and other plant species.
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Affiliation(s)
- Shilpy Singh
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, 203201, U.P., India.
| | - Afsana Praveen
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 67, India
| | - Pooja Bhadrecha
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
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Wu C, Cheng Z, Gao J. Mysterious Bamboo flowering phenomenon: A literature review and new perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168695. [PMID: 38000754 DOI: 10.1016/j.scitotenv.2023.168695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Bamboo, a globally distributed non-timber forest resource, plays a critical role in local ecosystems and economies. Despite its significance, the understanding of bamboo's long and unpredictable flowering cycles remains limited. Our bibliometric analysis of bamboo flowering-related literature from the Web of Science database reveals an initial focus on regeneration studies, with a recent trend shifting towards microscopic and molecular perspectives. Furthermore, our narrative review emphasizes the importance of considering factors such as the proportion of flowering culms and the duration of flowering in classifying bamboo flowering phenomena. While numerous studies have endorsed the predator saturation hypothesis as a suitable explanation for the synchronicity of bamboo flowering, no existing theory explains bamboo's prolonged flowering cycles. We propose a new natural selection hypothesis as a potential explanation for these extraordinary cycles, underscoring the need for further research in this area. Despite the substantial volume of data accumulated on bamboo flowering, these resources have not been fully exploited in recent research. Future studies would benefit from more comprehensive data collection methods, encompassing field observations, satellite remote sensing data, and omics data. The convergence of traditional ecological studies with molecular techniques may pave the way for significant advancements in bamboo flowering research.
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Affiliation(s)
- Chongyang Wu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing, PR China
| | - Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing, PR China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing, PR China.
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Ramakrishnan M, Yrjälä K, Vinod KK, Sharma A, Cho J, Satheesh V, Zhou M. Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry. Food Energy Secur 2020. [DOI: 10.1002/fes3.229] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Department of Forest Sciences University of Helsinki Helsinki Finland
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS) Chinese Academy of Sciences Shanghai China
| | - Viswanathan Satheesh
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High‐efficiency Utilization Zhejiang A&F University Hangzhou China
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Zhang H, Liu X, Yang X, Wu H, Zhu J, Zhang H. miRNA-mRNA Integrated Analysis Reveals Roles for miRNAs in a Typical Halophyte, Reaumuria soongorica, during Seed Germination under Salt Stress. PLANTS 2020; 9:plants9030351. [PMID: 32164348 PMCID: PMC7154850 DOI: 10.3390/plants9030351] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 01/02/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs that play a crucial role in plant growth, development, and environmental stress responses. Reaumuria soongorica is a typical halophyte that is widely distributed in saline–alkali desert regions. Under salt stress, R. soongorica can complete germination, a critical biological process in the life cycle of seed plants. To identify miRNAs and predict target mRNAs involved in seed germination during salt stress, nine small-RNA libraries were constructed and analyzed from R. soongorica seeds treated with various concentrations of NaCl. We also obtained transcriptome data under the same treatment conditions. Further analysis identified 88 conserved miRNAs representing 25 defined families and discovered 13 novel miRNAs from nine libraries. A co-expression analysis was performed on the same samples to identify putative miRNA–mRNA interactions that were responsive to salt stress. A comparative analysis of expression during germination under 273 (threshold) and 43 mM (optimal) NaCl treatments identified 13 differentially expressed miRNAs and 23 corresponding target mRNAs, while a comparison between 43 mM NaCl and non-salt-stress conditions uncovered one differentially expressed miRNA and one corresponding target mRNA. These results provide basic data for further study of molecular mechanisms involved in the germination of salt-stressed R. soongorica seeds, and also provide a reference for the improvement of salt tolerance during plant germination.
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Affiliation(s)
- Huilong Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Beijing 100091, China; (H.Z.); (X.L.); (X.Y.); (H.W.)
- Tianjin Research Institute of Forestry of Chinese Academy of Forestry, Tianjin 300450, China
| | - Xiaowei Liu
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Beijing 100091, China; (H.Z.); (X.L.); (X.Y.); (H.W.)
- Tianjin Research Institute of Forestry of Chinese Academy of Forestry, Tianjin 300450, China
| | - Xiuyan Yang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Beijing 100091, China; (H.Z.); (X.L.); (X.Y.); (H.W.)
- Tianjin Research Institute of Forestry of Chinese Academy of Forestry, Tianjin 300450, China
| | - Haiwen Wu
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Beijing 100091, China; (H.Z.); (X.L.); (X.Y.); (H.W.)
- Tianjin Research Institute of Forestry of Chinese Academy of Forestry, Tianjin 300450, China
| | - Jianfeng Zhu
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Beijing 100091, China; (H.Z.); (X.L.); (X.Y.); (H.W.)
- Tianjin Research Institute of Forestry of Chinese Academy of Forestry, Tianjin 300450, China
- Correspondence: (J.Z.); (H.Z.); Tel.: +86-10-6288-8900 (J.Z.); +86-10-6288-9343 (H.Z.)
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Beijing 100091, China; (H.Z.); (X.L.); (X.Y.); (H.W.)
- Tianjin Research Institute of Forestry of Chinese Academy of Forestry, Tianjin 300450, China
- Correspondence: (J.Z.); (H.Z.); Tel.: +86-10-6288-8900 (J.Z.); +86-10-6288-9343 (H.Z.)
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Zheng X, Lin S, Fu H, Wan Y, Ding Y. The Bamboo Flowering Cycle Sheds Light on Flowering Diversity. FRONTIERS IN PLANT SCIENCE 2020; 11:381. [PMID: 32362903 PMCID: PMC7180196 DOI: 10.3389/fpls.2020.00381] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 03/17/2020] [Indexed: 05/16/2023]
Abstract
Bamboo is a perennial flowering plant with a distinctive life cycle: many bamboo species remain in the vegetative phase for decades, followed by mass synchronous flowering and subsequent death. The phenomenon of bamboo flowering is not fully understood, but its periodicity is a major research focus. Here, we collected information on bamboo flowering events by investigating historical documents and field studies at the Bamboo Research Institute of Nanjing Forestry University. We compiled information on more than 630 flowering events, 124 of which accurately recorded the flowering cycle time. We summarized the specific flowering cycles of 85 bamboo species, as well as four kinds of bamboo flowering habits in detail. We present a theory of the bamboo flowering cycle and discuss the reasons for the observed variations in bamboo flowering. This review also introduces two mechanisms by which bamboo forests are rejuvenated after flowering and explains the flowering phenomena of bamboo forests using the bamboo flowering cycle theory. Finally, we present suggestions for forest management strategies. Bamboo flowering is a normal physiological phenomenon, even though it has unique elements compared with flowering in other plants. The results presented here provide valuable reference material for understanding bamboo flowering and its periodicity.
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Affiliation(s)
- Xiao Zheng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
| | - Huajun Fu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yawen Wan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- *Correspondence: Yulong Ding
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Li Y, Zhang C, Yang K, Shi J, Ding Y, Gao Z. De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae). BMC Genomics 2019; 20:1035. [PMID: 31888463 PMCID: PMC6937737 DOI: 10.1186/s12864-019-6418-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/19/2019] [Indexed: 12/25/2022] Open
Abstract
Background Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.
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Affiliation(s)
- Ying Li
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Chunxia Zhang
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Kebin Yang
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Jingjing Shi
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Yulong Ding
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zhimin Gao
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China.
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Tong W, Yu J, Hou Y, Li F, Zhou Q, Wei C, Bennetzen JL. Circular RNA architecture and differentiation during leaf bud to young leaf development in tea (Camellia sinensis). PLANTA 2018; 248:1417-1429. [PMID: 30128600 DOI: 10.1007/s00425-018-2983-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
Circular RNA (circRNA) discovery, expression patterns and experimental validation in developing tea leaves indicates its correlation with circRNA-parental genes and potential roles in ceRNA interaction network. Circular RNAs (circRNAs) have recently emerged as a novel class of abundant endogenous stable RNAs produced by circularization with regulatory potential. However, identification of circRNAs in plants, especially in non-model plants with large genomes, is challenging. In this study, we undertook a systematic identification of circRNAs from different stage tissues of tea plant (Camellia sinensis) leaf development using rRNA-depleted circular RNA-seq. By combining two state-of-the-art detecting tools, we characterized 3174 circRNAs, of which 342 were shared by each approach, and thus considered high-confidence circRNAs. A few predicted circRNAs were randomly chosen, and 20 out of 24 were experimental confirmed by PCR and Sanger sequencing. Similar in other plants, tissue-specific expression was also observed for many C. sinensis circRNAs. In addition, we found that circRNA abundances were positively correlated with the mRNA transcript abundances of their parental genes. qRT-PCR validated the differential expression patterns of circRNAs between leaf bud and young leaf, which also indicated the low expression abundance of circRNAs compared to the standard mRNAs from the parental genes. We predicted the circRNA-microRNA interaction networks, and 54 of the differentially expressed circRNAs were found to have potential tea plant miRNA binding sites. The gene sets encoding circRNAs were significantly enriched in chloroplasts related GO terms and photosynthesis/metabolites biosynthesis related KEGG pathways, suggesting the candidate roles of circRNAs in photosynthetic machinery and metabolites biosynthesis during leaf development.
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Affiliation(s)
- Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jie Yu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Hou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- School of Science, Anhui Agricultural University, Hefei, 230036, China
| | - Qiying Zhou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Henan Key Laboratory of Tea Plant Biology, College of Life Science, Xinyang Normal University, Xinyang, 464000, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
| | - Jeffrey L Bennetzen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
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Tian L, Liu H, Ren L, Ku L, Wu L, Li M, Wang S, Zhou J, Song X, Zhang J, Dou D, Liu H, Tang G, Chen Y. MicroRNA 399 as a potential integrator of photo-response, phosphate homeostasis, and sucrose signaling under long day condition. BMC PLANT BIOLOGY 2018; 18:290. [PMID: 30463514 PMCID: PMC6249786 DOI: 10.1186/s12870-018-1460-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/03/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Photoperiod-sensitivity is a critical endogenous regulatory mechanism for plant growth and development under specific environmental conditions, while phosphate and sucrose signaling processes play key roles in cell growth and organ initiation. MicroRNA399 is phosphate-responsive, but, whether it has roles in other metabolic processes remains unknown. RESULTS MicroRNA399 was determined to be sucrose-responsive through a microRNA array assay. High levels of sucrose inhibited the accumulation of microRNA399 family under phosphate starvation conditions in Arabidopsis thaliana. Similarly, exogenous sucrose supplementation also reduced microRNA399 expression in maize at developmental transition stages. RNA sequencing of a near-isogenic line(photoperiod-sensitive) line and its recurrent parent Huangzao4, a photoperiod-insensitive line, was conducted at various developmental stages. Members of microRNA399 family were down-regulated under long-day conditions in the photoperiod-sensitive near-isogenic line that accumulated more sucrose in vivo compared with the control line Huangzao4. CONCLUSION MicroRNA399s may play central roles in the integration of sucrose sensing and photoperiodic responses under long day conditions in maize.
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Affiliation(s)
- Lei Tian
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Haiping Liu
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | - Ligang Ren
- College of Life Science, Northwest Agriculture and Forestry University, Yangling, 712100 China
| | - Lixia Ku
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Liuji Wu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Mingna Li
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Shunxi Wang
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Jinlong Zhou
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Xiaoheng Song
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Jun Zhang
- Cereal Institute, Henan Academy of Agricultural Science/Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, 450002 China
| | - Dandan Dou
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Huafeng Liu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | - Yanhui Chen
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
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Li B, Xiao G, Luo K, Wang Z, Mao B, Lin X, Guo X. Overexpression of PvGF14c from Phyllostachys violascens Delays Flowering Time in Transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:105. [PMID: 29491870 PMCID: PMC5817094 DOI: 10.3389/fpls.2018.00105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/19/2018] [Indexed: 05/19/2023]
Abstract
14-3-3 Proteins are a family of highly conserved regulatory molecules expressed in all eukaryotic cells and regulate a diverse set of biological responses in plants. However, their functions in flowering of Phyllostachys violascens are poorly understood. In this study, four non-𝜀 Pv14-3-3 genes from P. violascens were identified and named PvGF14b, PvGF14c, PvGF14e, and PvGF14f. qRT-PCR analyses revealed that PvGF14b and PvGF14e exhibited widely expressed in all tested bamboo tissues. PvGF14b was highest expression in root and lowest in immature leaf. Whereas PvGF14c and PvGF14f showed tissue-specific expression. PvGF14c was mainly expressed in immature and mature leaves. PvGF14f was highest expression in mature leaves. These four genes were not significantly differentially expressed in mature leaf before bamboo flowering and during flower development. PvGF14b and PvGF14c were not induced by circadian rhythm. PvGF14c displayed subcellular localization in the cytoplasm and PvFT in nucleus and cytoplasm. Yeast two-hybrid screening and bimolecular fluorescence complementation confirmed the interaction between PvGF14c and PvFT. The overexpression of PvGF14b, PvGF14c, and PvGF14e significantly delayed flowering time in transgenic Arabidopsis under long-day condition. These findings suggested that at least three PvGF14 genes are involved in flowering and may act as a negative regulator of flowering by interacting with PvFT in bamboo.
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Affiliation(s)
- Bingjuan Li
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
| | - Guohui Xiao
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
| | - Kaisheng Luo
- School of Geography and Remote Sensing, Nanjing University of Information Science and Technology, Nanjing, China
| | - Zhengyi Wang
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bizeng Mao
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xinchun Lin
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
| | - Xiaoqin Guo
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Zhejiang A & F University, Hangzhou, China
- *Correspondence: Xiaoqin Guo,
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Li L, Cheng Z, Ma Y, Bai Q, Li X, Cao Z, Wu Z, Gao J. The association of hormone signalling genes, transcription and changes in shoot anatomy during moso bamboo growth. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:72-85. [PMID: 28499069 PMCID: PMC5785349 DOI: 10.1111/pbi.12750] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/10/2017] [Accepted: 04/21/2017] [Indexed: 05/13/2023]
Abstract
Moso bamboo is a large, woody bamboo with the highest ecological, economic and cultural value of all the bamboo types and accounts for up to 70% of the total area of bamboo grown. However, the spatiotemporal variation role of moso bamboo shoot during growth period is still unclear. We found that the bamboo shoot growth can be divided into three distinct periods, including winter growth, early growth and late growth based on gene expression and anatomy. In the early growth period, lateral buds germinated from the top of the bamboo joint in the shoot tip. Intercalary meristems grew vigorously during the winter growth period and early growth period, but in the late growth period, mitosis in the intercalary meristems decreased. The expression of cell cycle-associated genes and the quantity of differentially expressed genes were higher in early growth than those in late growth, appearing to be influenced by hormonal concentrations. Gene expression analysis indicates that hormone signalling genes play key roles in shoot growth, while auxin signalling genes play a central role. In situ hybridization analyses illustrate how auxin signalling genes regulate apical dominance, meristem maintenance and lateral bud development. Our study provides a vivid picture of the dynamic changes in anatomy and gene expression during shoot growth in moso bamboo, and how hormone signalling-associated genes participate in moso bamboo shoot growth.
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Affiliation(s)
- Long Li
- International Center for Bamboo and RattanKey Laboratory of Bamboo and Rattan Science and TechnologyState Forestry AdministrationBeijingChina
| | - Zhanchao Cheng
- International Center for Bamboo and RattanKey Laboratory of Bamboo and Rattan Science and TechnologyState Forestry AdministrationBeijingChina
| | - Yanjun Ma
- International Center for Bamboo and RattanKey Laboratory of Bamboo and Rattan Science and TechnologyState Forestry AdministrationBeijingChina
| | - Qingsong Bai
- International Center for Bamboo and RattanKey Laboratory of Bamboo and Rattan Science and TechnologyState Forestry AdministrationBeijingChina
| | - Xiangyu Li
- International Center for Bamboo and RattanKey Laboratory of Bamboo and Rattan Science and TechnologyState Forestry AdministrationBeijingChina
| | - Zhihua Cao
- Anhui Academy of ForestryHefeiAnhui ProvinceChina
| | - Zhongneng Wu
- Anhui Academy of ForestryHefeiAnhui ProvinceChina
| | - Jian Gao
- International Center for Bamboo and RattanKey Laboratory of Bamboo and Rattan Science and TechnologyState Forestry AdministrationBeijingChina
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Pan F, Wang Y, Liu H, Wu M, Chu W, Chen D, Xiang Y. Genome-wide identification and expression analysis of SBP-like transcription factor genes in Moso Bamboo (Phyllostachys edulis). BMC Genomics 2017; 18:486. [PMID: 28655295 PMCID: PMC5488377 DOI: 10.1186/s12864-017-3882-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 06/20/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The SQUAMOSA promoter binding protein-like (SPL) proteins are plant-specific transcription factors (TFs) that function in a variety of developmental processes including growth, flower development, and signal transduction. SPL proteins are encoded by a gene family, and these genes have been characterized in two model grass species, Zea mays and Oryza sativa. The SPL gene family has not been well studied in moso bamboo (Phyllostachys edulis), a woody grass species. RESULTS We identified 32 putative PeSPL genes in the P. edulis genome. Phylogenetic analysis arranged the PeSPL protein sequences in eight groups. Similarly, phylogenetic analysis of the SBP-like and SBP proteins from rice and maize clustered them into eight groups analogous to those from P. edulis. Furthermore, the deduced PeSPL proteins in each group contained very similar conserved sequence motifs. Our analyses indicate that the PeSPL genes experienced a large-scale duplication event ~15 million years ago (MYA), and that divergence between the PeSPL and OsSPL genes occurred 34 MYA. The stress-response expression profiles and tissue-specificity of the putative PeSPL gene promoter regions showed that SPL genes in moso bamboo have potential biological functions in stress resistance as well as in growth and development. We therefore examined PeSPL gene expression in response to different plant hormone and drought (polyethylene glycol-6000; PEG) treatments to mimic biotic and abiotic stresses. Expression of three (PeSPL10, -12, -17), six (PeSPL1, -10, -12, -17, -20, -31), and nine (PeSPL5, -8, -9, -14, -15, -19, -20, -31, -32) genes remained relatively stable after treating with salicylic acid (SA), gibberellic acid (GA), and PEG, respectively, while the expression patterns of other genes changed. In addition, analysis of tissue-specific expression of the moso bamboo SPL genes during development showed differences in their spatiotemporal expression patterns, and many were expressed at high levels in flowers and leaves. CONCLUSIONS The PeSPL genes play important roles in plant growth and development, including responses to stresses, and most of the genes are expressed in different tissues. Our study provides a comprehensive understanding of the PeSPL gene family and may enable future studies on the function and evolution of SPL genes in moso bamboo.
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Affiliation(s)
- Feng Pan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yue Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Huanglong Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Min Wu
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wenyuan Chu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Danmei Chen
- 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. .,Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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12
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Ge W, Zhang Y, Cheng Z, Hou D, Li X, Gao J. Main regulatory pathways, key genes and microRNAs involved in flower formation and development of moso bamboo (Phyllostachys edulis). PLANT BIOTECHNOLOGY JOURNAL 2017; 15:82-96. [PMID: 27337661 PMCID: PMC5253477 DOI: 10.1111/pbi.12593] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/12/2016] [Accepted: 06/20/2016] [Indexed: 05/05/2023]
Abstract
Moso bamboo is characterized by infrequent sexual reproduction and erratic flowering habit; however, the molecular biology of flower formation and development is not well studied in this species. We studied the molecular regulation mechanisms of moso bamboo development and flowering by selecting three key regulatory pathways: plant-pathogen interaction, plant hormone signal transduction and protein processing in endoplasmic reticulum at different stages of flowering in moso bamboo. We selected PheDof1, PheMADS14 and six microRNAs involved in the three pathways through KEGG pathway and cluster analysis. Subcellular localization, transcriptional activation, Western blotting, in situ hybridization and qRT-PCR were used to further investigate the expression patterns and regulatory roles of pivotal genes at different flower development stages. Differential expression patterns showed that PheDof1, PheMADS14 and six miRNAs may play vital regulatory roles in flower development and floral transition in moso bamboo. Our research paves way for further studies on metabolic regulatory networks and provides insight into the molecular regulation mechanisms of moso bamboo flowering and senescence.
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Affiliation(s)
- Wei Ge
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry AdministrationInternational Centre for Bamboo and RattanBeijingChina
| | - Ying Zhang
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry AdministrationInternational Centre for Bamboo and RattanBeijingChina
- China National Engineering Research Center for Information Technology in AgricultureBeijingChina
| | - Zhanchao Cheng
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry AdministrationInternational Centre for Bamboo and RattanBeijingChina
| | - Dan Hou
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry AdministrationInternational Centre for Bamboo and RattanBeijingChina
| | - Xueping Li
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry AdministrationInternational Centre for Bamboo and RattanBeijingChina
| | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry AdministrationInternational Centre for Bamboo and RattanBeijingChina
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13
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Zheng Z, Yang X, Fu Y, Zhu L, Wei H, Lin X. Overexpression of PvPin1, a Bamboo Homolog of PIN1-Type Parvulin 1, Delays Flowering Time in Transgenic Arabidopsis and Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1526. [PMID: 28951734 PMCID: PMC5599775 DOI: 10.3389/fpls.2017.01526] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/21/2017] [Indexed: 05/03/2023]
Abstract
Because of the long and unpredictable flowering period in bamboo, the molecular mechanism of bamboo flowering is unclear. Recent study showed that Arabidopsis PIN1-type parvulin 1 (Pin1At) is an important floral activator and regulates floral transition by facilitating the cis/trans isomerization of the phosphorylated Ser/Thr residues preceding proline motifs in suppressor of overexpression of CO 1 (SOC1) and agamous-like 24 (AGL24). Whether bamboo has a Pin1 homolog and whether it works in bamboo flowering are still unknown. In this study, we cloned PvPin1, a homolog of Pin1At, from Phyllostachys violascens (Bambusoideae). Bioinformatics analysis showed that PvPin1 is closely related to Pin1-like proteins in monocots. PvPin1 was widely expressed in all tested bamboo tissues, with the highest expression in young leaf and lowest in floral bud. Moreover, PvPin1 expression was high in leaves before bamboo flowering then declined during flower development. Overexpression of PvPin1 significantly delayed flowering time by downregulating SOC1 and AGL24 expression in Arabidopsis under greenhouse conditions and conferred a significantly late flowering phenotype by upregulating OsMADS56 in rice under field conditions. PvPin1 showed subcellular localization in both the nucleus and cytolemma. The 1500-bp sequence of the PvPin1 promoter was cloned, and cis-acting element prediction showed that ABRE and TGACG-motif elements, which responded to abscisic acid (ABA) and methyl jasmonate (MeJA), respectively, were characteristic of P. violascens in comparison with Arabidopsis. On promoter activity analysis, exogenous ABA and MeJA could significantly inhibit PvPin1 expression. These findings suggested that PvPin1 may be a repressor in flowering, and its delay of flowering time could be regulated by ABA and MeJA in bamboo.
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Affiliation(s)
- Zhigang Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
| | - Xiaoming Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
| | - Yaping Fu
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Longfei Zhu
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
| | - Hantian Wei
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry UniversityHangzhou, China
- *Correspondence: Xinchun Lin,
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14
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Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing. FORESTS 2016. [DOI: 10.3390/f7120318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Biswas P, Chakraborty S, Dutta S, Pal A, Das M. Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics. FRONTIERS IN PLANT SCIENCE 2016; 7:1900. [PMID: 28018419 PMCID: PMC5156695 DOI: 10.3389/fpls.2016.01900] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/01/2016] [Indexed: 05/16/2023]
Abstract
Bamboos are an important member of the subfamily Bambusoideae, family Poaceae. The plant group exhibits wide variation with respect to the timing (1-120 years) and nature (sporadic vs. gregarious) of flowering among species. Usually flowering in woody bamboos is synchronous across culms growing over a large area, known as gregarious flowering. In many monocarpic bamboos this is followed by mass death and seed setting. While in sporadic flowering an isolated wild clump may flower, set little or no seed and remain alive. Such wide variation in flowering time and extent means that the plant group serves as repositories for genes and expression patterns that are unique to bamboo. Due to the dearth of available genomic and transcriptomic resources, limited studies have been undertaken to identify the potential molecular players in bamboo flowering. The public release of the first bamboo genome sequence Phyllostachys heterocycla, availability of related genomes Brachypodium distachyon and Oryza sativa provide us the opportunity to study this long-standing biological problem in a comparative and functional genomics framework. We identified bamboo genes homologous to those of Oryza and Brachypodium that are involved in established pathways such as vernalization, photoperiod, autonomous, and hormonal regulation of flowering. Additionally, we investigated triggers like stress (drought), physiological maturity and micro RNAs that may play crucial roles in flowering. We also analyzed available transcriptome datasets of different bamboo species to identify genes and their involvement in bamboo flowering. Finally, we summarize potential research hurdles that need to be addressed in future research.
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Affiliation(s)
- Prasun Biswas
- Plant Genomics Laboratory, Department of Life Sciences, Presidency UniversityKolkata, India
| | - Sukanya Chakraborty
- Plant Genomics Laboratory, Department of Life Sciences, Presidency UniversityKolkata, India
| | - Smritikana Dutta
- Plant Genomics Laboratory, Department of Life Sciences, Presidency UniversityKolkata, India
| | - Amita Pal
- Division of Plant Biology, Bose InstituteKolkata, India
| | - Malay Das
- Plant Genomics Laboratory, Department of Life Sciences, Presidency UniversityKolkata, India
- *Correspondence: Malay Das
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