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Zhang X, Peng W, Chen H, Xing H. BnAP2-12 overexpression delays ramie flowering: evidence from AP2/ERF gene expression. FRONTIERS IN PLANT SCIENCE 2024; 15:1367837. [PMID: 38590749 PMCID: PMC10999622 DOI: 10.3389/fpls.2024.1367837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/12/2024] [Indexed: 04/10/2024]
Abstract
Introduction The APETALA2/ethylene response factor (AP2/ERF) superfamily plays a significant role in regulating plant gene expression in response to growth and development. To date, there have been no studies into whether the ramie AP2/ERF genes are involved in the regulation of flower development. Methods Here, 84 BnAP2/ERF members were identified from the ramie genome database, and various bioinformatics data on the AP2/ERF gene family, structure, replication, promoters and regulatory networks were analysed. BnAP2-12 was transferred into Arabidopsis through the flower-dipping method. Results Phylogenetic analysis classified the 84 BnAP2/ERF members into four subfamilies: AP2 (18), RAV (3), ERF (42), and DREB (21). The functional domain analysis of genes revealed 10 conserved motifs. Genetic mapping localised the 84 members on 14 chromosomes, among which chromosomes 1, 3, 5, and 8 had more members. Collinearity analysis revealed that 43.37% possibly resulted from replication events during the evolution of the ramie genome. Promoter sequence analysis identified classified cis-acting elements associated with plant growth and development, and responses to stress, hormones, and light. Transcriptomic comparison identified 3,635 differentially expressed genes (DEGs) between male and female flowers (1,803 and 1,832 upregulated and downregulated genes, respectively). Kyoto Encyclopaedia of Genes and Genomes pathway analysis categorised DEGs involved in metabolic pathways and biosynthesis of secondary metabolites. Gene Ontology enrichment analysis further identified enriched genes associated with pollen and female gamete formations. Of the 84 BnAP2/ERFs genes, 22 and 8 upregulated and downregulated genes, respectively, were present in female flowers. Co-expression network analysis identified AP2/ERF members associated with flower development, including BnAP2-12. Subcellular localisation analysis showed that the BnAP2-12 protein is localised in the nucleus and cell membrane. Overexpression BnAP2-12 delayed the flowering time of Arabidopsis thaliana. Conclusion These findings provide insights into the mechanism of ramie flower development.
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Affiliation(s)
- Xiaoyang Zhang
- Agricultural College of Hunan Agricultural University, Changsha, China
- Ramie Research Institute of Hunan Agricultural University, Changsha, China
| | - Wenxian Peng
- Ramie Research Institute of Hunan Agricultural University, Changsha, China
- Changsha Tobacco Company, Ningxiang, China
| | - Hao Chen
- Agricultural College of Hunan Agricultural University, Changsha, China
| | - Hucheng Xing
- Agricultural College of Hunan Agricultural University, Changsha, China
- Ramie Research Institute of Hunan Agricultural University, Changsha, China
- Hunan Key Laboratory of Germplasm Resources Innovation and Resource Utilization Crop Breeding Center, Changsha, China
- Hunan Provincial Engineering Technology Research Center of Grass Crop Germplasm Innovation and Utilization, Changsha, China
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Chu X, Wang M, Fan Z, Li J, Yin H. Molecular Mechanisms of Seasonal Gene Expression in Trees. Int J Mol Sci 2024; 25:1666. [PMID: 38338945 PMCID: PMC10855862 DOI: 10.3390/ijms25031666] [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: 12/27/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
In trees, the annual cycling of active and dormant states in buds is closely regulated by environmental factors, which are of primary significance to their productivity and survival. It has been found that the parallel or convergent evolution of molecular pathways that respond to day length or temperature can lead to the establishment of conserved periodic gene expression patterns. In recent years, it has been shown in many woody plants that change in annual rhythmic patterns of gene expression may underpin the adaptive evolution in forest trees. In this review, we summarize the progress on the molecular mechanisms of seasonal regulation on the processes of shoot growth, bud dormancy, and bud break in response to day length and temperature factors. We focus on seasonal expression patterns of genes involved in dormancy and their associated epigenetic modifications; the seasonal changes in the extent of modifications, such as DNA methylation, histone acetylation, and histone methylation, at dormancy-associated loci have been revealed for their actions on gene regulation. In addition, we provide an outlook on the direction of research on the annual cycle of tree growth under climate change.
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Affiliation(s)
- Xian Chu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Minyan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| | - Zhengqi Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
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Tang J, Chen Y, Huang C, Li C, Feng Y, Wang H, Ding C, Li N, Wang L, Zeng J, Yang Y, Hao X, Wang X. Uncovering the complex regulatory network of spring bud sprouting in tea plants: insights from metabolic, hormonal, and oxidative stress pathways. FRONTIERS IN PLANT SCIENCE 2023; 14:1263606. [PMID: 37936941 PMCID: PMC10627156 DOI: 10.3389/fpls.2023.1263606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 11/09/2023]
Abstract
The sprouting process of tea buds is an essential determinant of tea quality and taste, thus profoundly impacting the tea industry. Buds spring sprouting is also a crucial biological process adapting to external environment for tea plants and regulated by complex transcriptional and metabolic networks. This study aimed to investigate the molecular basis of bud sprouting in tea plants firstly based on the comparisons of metabolic and transcriptional profiles of buds at different developmental stages. Results notably highlighted several essential processes involved in bud sprouting regulation, including the interaction of plant hormones, glucose metabolism, and reactive oxygen species scavenging. Particularly prior to bud sprouting, the accumulation of soluble sugar reserves and moderate oxidative stress may have served as crucial components facilitating the transition from dormancy to active growth in buds. Following the onset of sprouting, zeatin served as the central component in a multifaceted regulatory mechanism of plant hormones that activates a range of growth-related factors, ultimately leading to the promotion of bud growth. This process was accompanied by significant carbohydrate consumption. Moreover, related key genes and metabolites were further verified during the entire overwintering bud development or sprouting processes. A schematic diagram involving the regulatory mechanism of bud sprouting was ultimately proposed, which provides fundamental insights into the complex interactions involved in tea buds.
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Affiliation(s)
- Junwei Tang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yao Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Chao Huang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Congcong Li
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yue Feng
- Zhejiang Provincial Seed Management Station, Hangzhou, China
| | - Haoqian Wang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Changqing Ding
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Nana Li
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Lu Wang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jianming Zeng
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yajun Yang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyuan Hao
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xinchao Wang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs/National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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Liu Y, Chen S, Chen J, Wang J, Wei M, Tian X, Chen L, Ma J. Comprehensive analysis and expression profiles of the AP2/ERF gene family during spring bud break in tea plant (Camellia sinensis). BMC PLANT BIOLOGY 2023; 23:206. [PMID: 37081399 PMCID: PMC10116778 DOI: 10.1186/s12870-023-04221-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND AP2/ERF transcription factors (AP2/ERFs) are important regulators of plant physiological and biochemical metabolism. Evidence suggests that AP2/ERFs may be involved in the regulation of bud break in woody perennials. Green tea is economically vital in China, and its production value is significantly affected by the time of spring bud break of tea plant. However, the relationship between AP2/ERFs in tea plant and spring bud break remains largely unknown. RESULTS A total of 178 AP2/ERF genes (CsAP2/ERFs) were identified in the genome of tea plant. Based on the phylogenetic analysis, these genes could be classified into five subfamilies. The analysis of gene duplication events demonstrated that whole genome duplication (WGD) or segmental duplication was the primary way of CsAP2/ERFs amplification. According to the result of the Ka/Ks value calculation, purification selection dominated the evolution of CsAP2/ERFs. Furthermore, gene composition and structure analyses of CsAP2/ERFs indicated that different subfamilies contained a variety of gene structures and conserved motifs, potentially resulting in functional differences among five subfamilies. The promoters of CsAP2/ERFs also contained various signal-sensing elements, such as abscisic acid responsive elements, light responsive elements and low temperature responsive elements. The evidence presented here offers a theoretical foundation for the diverse functions of CsAP2/ERFs. Additionally, the expressions of CsAP2/ERFs during spring bud break of tea plant were analyzed by RNA-seq and grouped into clusters A-F according to their expression patterns. The gene expression changes in clusters A and B were more synchronized with the spring bud break of tea plant. Moreover, several potential correlation genes, such as D-type cyclin genes, were screened out through weighted correlation network analysis (WGCNA). Temperature and light treatment experiments individually identified nine candidate CsAP2/ERFs that may be related to the spring bud break of tea plant. CONCLUSIONS This study provides new evidence for role of the CsAP2/ERFs in the spring bud break of tea plant, establishes a theoretical foundation for analyzing the molecular mechanism of the spring bud break of tea plant, and contributes to the improvement of tea cultivars.
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Affiliation(s)
- Yujie Liu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Si Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Jiedan Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Junyu Wang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Mengyuan Wei
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Xiaomiao Tian
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Liang Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
| | - Jianqiang Ma
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
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Li Y, Guo L, Wang Z, Zhao D, Guo D, Carlson JE, Yin W, Hou X. Genome-wide association study of 23 flowering phenology traits and 4 floral agronomic traits in tree peony ( Paeonia section Moutan DC.) reveals five genes known to regulate flowering time. HORTICULTURE RESEARCH 2023; 10:uhac263. [PMID: 36793754 PMCID: PMC9926158 DOI: 10.1093/hr/uhac263] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/21/2022] [Indexed: 06/18/2023]
Abstract
Tree peony is a unique traditional flower in China, with large, fragrant, and colorful flowers. However, a relatively short and concentrated flowering period limits the applications and production of tree peony. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of flowering phenology traits and ornamental phenotypes in tree peony. A diverse panel of 451 tree peony accessions was phenotyped for 23 flowering phenology traits and 4 floral agronomic traits over 3 years. Genotyping by sequencing (GBS) was used to obtain a large number of genome-wide single-nucleotide polymorphisms (SNPs) (107 050) for the panel genotypes, and 1047 candidate genes were identified by association mapping. Eighty-two related genes were observed during at least 2 years for flowering, and seven SNPs repeatedly identified for multiple flowering phenology traits over multiple years were highly significantly associated with five genes known to regulate flowering time. We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of flower bud differentiation and flowering time in tree peony. This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony. The results expand our understanding of flowering time control in perennial woody plants. Identification of markers closely related to these flowering phenology traits can be used in tree peony breeding programs for important agronomic traits.
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Affiliation(s)
| | | | - Zhanying Wang
- Luoyang Academy of Agricultural and Forestry Sciences, Luoyang, Henan, 471000, China
| | - Dehui Zhao
- College of Agronomy/College of Tree Peony, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Dalong Guo
- College of Forestry, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - John E. Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Weilun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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Wu Y, Li X, Zhang J, Zhao H, Tan S, Xu W, Pan J, Yang F, Pi E. ERF subfamily transcription factors and their function in plant responses to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1042084. [PMID: 36531407 PMCID: PMC9748296 DOI: 10.3389/fpls.2022.1042084] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/09/2022] [Indexed: 06/09/2023]
Abstract
Ethylene Responsive Factor (ERF) subfamily comprise the largest number of proteins in the plant AP2/ERF superfamily, and have been most extensively studied on the biological functions. Members of this subfamily have been proven to regulate plant resistances to various abiotic stresses, such as drought, salinity, chilling and some other adversities. Under these stresses, ERFs are usually activated by mitogen-activated protein kinase induced phosphorylation or escape from ubiquitin-ligase enzymes, and then form complex with nucleic proteins before binding to cis-element in promoter regions of stress responsive genes. In this review, we will discuss the phylogenetic relationships among the ERF subfamily proteins, summarize molecular mechanism how the transcriptional activity of ERFs been regulated and how ERFs of different subgroup regulate the transcription of stress responsive genes, such as high-affinity K+ transporter gene PalHKT1;2, reactive oxygen species related genes LcLTP, LcPrx, and LcRP, flavonoids synthesis related genes FtF3H and LhMYBSPLATTER, etc. Though increasing researches demonstrate that ERFs are involved in various abiotic stresses, very few interact proteins and target genes of them have been comprehensively annotated. Hence, future research prospects are described on the mechanisms of how stress signals been transited to ERFs and how ERFs regulate the transcriptional expression of stress responsive genes.
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Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress. BIOLOGY 2022; 11:biology11101520. [PMID: 36290423 PMCID: PMC9598233 DOI: 10.3390/biology11101520] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary The ethylene-responsive element (AP2/ERF) is one of the key and conserved transcription factors (TFs) in plants, and it plays a crucial role in regulating plant growth, development, and stress response. The cultivated almond in Xinjiang is often affected by short-term ultralow temperature freezing stress during the winter dormancy period, resulting in the death of large-scale almond plants. In this study, we conducted the first genome-wide analysis of the PdAP2/ERF family in almond, including protein physicochemical properties, phylogenetic relationships, motif types, gene structures, gene replication types, collinearity relationships, and cis-element types in promoter regions. We further analyzed the expression patterns of the PdAP2/ERF gene in different tissues of almond and under freezing stress at different temperatures in annual dormant branches using transcriptome data. In addition, we also analyzed the expression levels of 13 PdAP2/ERF genes in four tissues of almond and in annual dormant branches treated with freezing stress at different temperatures using fluorescence quantitative technology. This study laid the foundation for further exploring the function of the PdAP2/ERF gene in almond. Abstract The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays an important role in regulating plant growth and development and the response to biotic and abiotic stresses. However, there is no report on the AP2/ERF gene family in almond (Prunus dulcis). In this study, a total of 136 PdAP2/ERF genes were identified from the almond genome, and their protein physicochemical properties were analyzed. The PdAP2/ERF members were divided into five subgroups: AP2, RAV, ERF, DREB, and Soloist. The PdAP2/ERF members in each subgroup had conserved motif types and exon/intron numbers. PdAP2/ERFS members are distributed on eight chromosomes, with 22 pairs of segmental duplications and 28 pairs of tandem duplications. We further explored the colinear relationship between almond and Arabidopsis thaliana, Oryza sativa, Malus domestica, and Prunus persicaAP2/ERF genes and their evolution. The results of cis-acting elements showed that PdAP2/ERF members are widely involved in various processes, such as growth and development, hormone regulation, and stress response. The results based on transcriptome expression patterns showed that PdAP2/ERF genes had significant tissue-specific expression characteristics and were involved in the response of annual dormant branches of almond to low-temperature freezing stress. In addition, the fluorescence quantitative relative expression results of 13 representative PdAP2/ERF genes in four tissues of ‘Wanfeng’ almond and under six low-temperature freezing treatments of annual dormant branches were consistent with the transcriptome results. It is worth noting that the fluorescence quantitative expression level showed that the PdERF24 gene was extremely significant at −30 °C, suggesting that this gene may play an important role in the response of almond dormancy to ultralow temperature freezing stress. Finally, we identified 7424 and 6971 target genes based on AP2 and ERF/DREB DNA-binding sites, respectively. The GO and KEGG enrichment results showed that these target genes play important roles in protein function and multiple pathways. In summary, we conducted bioinformatics and expression pattern studies on PdAP2/ERF genes, including 13 PdAP2/ERF genes, and performed fluorescence quantitative analysis of annual dormant shoots under different low-temperature freezing stress treatments to understand the tolerance of almond dormancy to freezing stress and suggest future improvements.
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Sun L, Nie T, Chen Y, Yin Z. From Floral Induction to Blooming: The Molecular Mysteries of Flowering in Woody Plants. Int J Mol Sci 2022; 23:ijms231810959. [PMID: 36142871 PMCID: PMC9500781 DOI: 10.3390/ijms231810959] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 12/04/2022] Open
Abstract
Flowering is a pivotal developmental process in response to the environment and determines the start of a new life cycle in plants. Woody plants usually possess a long juvenile nonflowering phase followed by an adult phase with repeated flowering cycles. The molecular mechanism underlying flowering regulation in woody plants is believed to be much more complex than that in annual herbs. In this review, we briefly describe the successive but distinct flowering processes in perennial trees, namely the vegetative phase change, the floral transition, floral organogenesis, and final blooming, and summarize in detail the most recent advances in understanding how woody plants regulate flowering through dynamic gene expression. Notably, the florigen gene FLOWERING LOCUS T(FT) and its antagonistic gene TERMINAL FLOWER 1 (TFL1) seem to play a central role in various flowering transition events. Flower development in different taxa requires interactions between floral homeotic genes together with AGL6 conferring floral organ identity. Finally, we illustrate the issues and corresponding measures of flowering regulation investigation. It is of great benefit to the future study of flowering in perennial trees.
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Affiliation(s)
- Liyong Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Department of Biology, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Tangjie Nie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yao Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zengfang Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-025-85427316
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Chen W, Tamada Y, Yamane H, Matsushita M, Osako Y, Gao-Takai M, Luo Z, Tao R. H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1015-1031. [PMID: 35699670 DOI: 10.1111/tpj.15868] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Bud dormancy helps woody perennials survive winter and activate robust plant development in the spring. For apple (Malus × domestica), short-term chilling induces bud dormancy in autumn, then prolonged chilling leads to dormancy release and a shift to a quiescent state in winter, with subsequent warm periods promoting bud break in spring. Epigenetic regulation contributes to seasonal responses such as vernalization. However, how histone modifications integrate seasonal cues and internal signals during bud dormancy in woody perennials remains largely unknown. Here, we show that H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. The global changes in gene expression strongly correlated with changes in H3K4me3, but not H3K27me3. High expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes, key regulators of dormancy, in autumn was associated with high H3K4me3 levels. In addition, known DAM/SHORT VEGETATIVE PHASE (SVP) target genes significantly overlapped with H3K4me3-modified genes as bud dormancy progressed. These data suggest that H3K4me3 contributes to the central dormancy circuit, consisting of DAM/SVP and abscisic acid (ABA), in autumn. In winter, the lower expression and H3K4me3 levels at DAMs and gibberellin metabolism genes control chilling-induced release of dormancy. Warming conditions in spring facilitate the expression of genes related to phytohormones, the cell cycle, and cell wall modification by increasing H3K4me3 toward bud break. Our study also revealed that activation of auxin and repression of ABA sensitivity in spring are conditioned at least partly through temperature-mediated epigenetic regulation in winter.
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Affiliation(s)
- Wenxing Chen
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
| | - Yosuke Tamada
- School of Engineering, Utsunomiya University, Utsunomiya, Japan
- National Institute for Basic Biology, Okazaki, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Miura-gun, Japan
| | - Hisayo Yamane
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Yutaro Osako
- Faculty of Agriculture, Shinshu University, Kamiina-gun, Japan
| | - Mei Gao-Takai
- Agricultural Experimental Station, Ishikawa Prefectural University, Nonoichi, Japan
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Lempe J, Peil A, Flachowsky H. Time-Resolved Analysis of Candidate Gene Expression and Ambient Temperature During Bud Dormancy in Apple. FRONTIERS IN PLANT SCIENCE 2022; 12:803341. [PMID: 35111181 PMCID: PMC8802299 DOI: 10.3389/fpls.2021.803341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Winter dormancy - a period of low metabolic activity and no visible growth - appears as an adaptation to harsh winter conditions and can be divided into different phases. It is tightly controlled by environmental cues, with ambient temperature playing a major role. During endodormancy, a cultivar-specific amount of cold needs to be perceived, and during ecodormancy, heat hours accumulate before bud burst and anthesis in spring. Expression analysis, performed in several key fruit tree species, proved to be very useful in elucidating the molecular control of onset and release of dormancy. However, the time resolution of these experiments has been limited. Therefore, in this study, dense time-series expression analysis was conducted for 40 candidate genes involved in dormancy control, under the cool-temperate climate conditions in Dresden. Samples were taken from the cultivars 'Pinova' and 'Gala,' which differ in flowering time. The set of candidate genes included well-established dormancy genes such as DAM genes, MdFLC-like, MdICE1, MdPRE 1, and MdPIF4. Furthermore, we tested genes from dormancy-associated pathways including the brassinosteroid, gibberellic acid, abscisic acid (ABA), cytokinin response, and respiratory stress pathways. The expression patterns of well-established dormancy genes were confirmed and could be associated with specific dormancy phases. In addition, less well-known transcription factors and genes of the ABA signaling pathway showed associations with dormancy progression. The three ABA signaling genes HAB1_chr15, HAI3, and ABF2 showed a local minimum of gene expression in proximity of the endodormancy to ecodormancy transition. The number of sampling points allowed us to correlate expression values with temperature data, which revealed significant correlations of ambient temperature with the expression of the Malus domestica genes MdICE1, MdPIF4, MdFLC-like, HAB1chr15, and the type-B cytokinin response regulator BRR9. Interestingly, the slope of the linear correlation of temperature with the expression of MdPIF4 differed between cultivars. Whether the strength of inducibility of MdPIF4 expression by low temperature differs between the 'Pinova' and 'Gala' alleles needs to be tested further.
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Li WF, Kang Y, Zhang Y, Zang QL, Qi LW. Concerted control of the LaRAV1-LaCDKB1;3 module by temperature during dormancy release and reactivation of larch. TREE PHYSIOLOGY 2021; 41:1918-1937. [PMID: 33847364 PMCID: PMC8498939 DOI: 10.1093/treephys/tpab052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Dormancy release and reactivation of temperate-zone trees involve the temperature-modulated expression of cell-cycle genes. However, information on the detailed regulatory mechanism is limited. Here, we compared the transcriptomes of the stems of active and dormant larch trees, emphasizing the expression patterns of cell-cycle genes and transcription factors and assessed their relationships and responses to temperatures. Twelve cell-cycle genes and 31 transcription factors were strongly expressed in the active stage. Promoter analysis suggested that these 12 genes might be regulated by transcription factors from 10 families. Altogether, 73 cases of regulation between 16 transcription factors and 12 cell-cycle genes were predicted, while the regulatory interactions between LaMYB20 and LaCYCB1;1, and LaRAV1 and LaCDKB1;3 were confirmed by yeast one-hybrid and dual-luciferase assays. Last, we found that LaRAV1 and LaCDKB1;3 had almost the same expression patterns during dormancy release and reactivation induced naturally or artificially by temperature, indicating that the LaRAV1-LaCDKB1;3 module functions in the temperature-modulated dormancy release and reactivation of larch trees. These results provide new insights into the link between temperature and cell-cycle gene expression, helping to understand the temperature control of tree growth and development in the context of climate change.
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Affiliation(s)
- Wan-Feng Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
| | - Yanhui Kang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
| | - Yao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
| | - Qiao-Lu Zang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
| | - Li-Wang Qi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
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Zhao X, Wen B, Li C, Liu L, Chen X, Li D, Li L, Fu X. PpEBB1 directly binds to the GCC box-like element of auxin biosynthesis related genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 306:110874. [PMID: 33775370 DOI: 10.1016/j.plantsci.2021.110874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/05/2021] [Accepted: 03/04/2021] [Indexed: 05/21/2023]
Abstract
EARLY BUD-BREAK 1 (EBB1) can promote bud break, and this function is likely conserved in woody plants. To get a more comprehensive understand of its function, peach (Prunus persica var. nectarina cultivar Zhongyou 4) PpEBB1 was overexpressed in Arabidopsis; the resultant phenotypes, including curved leaves, abnormal development of floral organs and low seed set, were similar to those of DORNRÖSCHEN-LIKE (DRNL) overexpression, indicating that PpEBB1 was a putative ortholog of AtDRNL. PpEBB1 bound to the GCC box-like element in the STYLISH1/SHI RELATED SEQUENCE5 (STY1/SRS5) promoter of peach, which has been proposed to occur in Arabidopsis as well. A GCC box-like element was also found in the YUCCA1 (YUC1) promoter, and PpEBB1 could bind to this element and activate the expression of YUC1. In addition to the elevated auxin content in the PpEBB1-oe plants as observed in our previous study, these results suggest that PpEBB1 can regulate auxin biosynthesis by directly activating related genes. Besides, we screened a zinc finger RING-finger protein, MYB30-INTERACTING E3 LIGASE 1 (PpMIEL1), showing interaction with PpEBB1, suggesting that the stability of PpEBB1 might be influenced by PpMIEL1 through ubiquitination.
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Affiliation(s)
- Xuehui Zhao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Chen Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Li Liu
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China.
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271000, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, China; Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Tai'an, Shandong, 271000, China.
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Yu J, Bennett D, Dardick C, Zhebentyayeva T, Abbott AG, Liu Z, Staton ME. Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach. Front Mol Biosci 2021; 8:612881. [PMID: 33968979 PMCID: PMC8098804 DOI: 10.3389/fmolb.2021.612881] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/15/2021] [Indexed: 11/15/2022] Open
Abstract
Bud dormancy is under the regulation of complex mechanisms including genetic and epigenetic factors. To study the function of regulatory non-coding RNAs in winter dormancy release, we analyzed the small RNA and long non-coding RNA (lncRNA) expression from peach (Prunus persica) floral buds in endodormancy, ecodormancy and bud break stages. Small RNAs underwent a major shift in expression primarily between dormancy and flowering with specific pairs of microRNAs and their mRNA target genes undergoing coordinated differential expression. From endodormancy to ecodormancy, ppe-miR6285 was significantly upregulated while its target gene, an ASPARAGINE-RICH PROTEIN involved in the regulation of abscisic acid signaling, was downregulated. At ecodormancy, ppe-miR2275, a homolog of meiosis-specific miR2275 across angiosperms, was significantly upregulated, supporting microsporogenesis in anthers at a late stage of dormancy. The expression of 785 lncRNAs, unlike the overall expression pattern in the small RNAs, demonstrated distinctive expression signatures across all dormancy and flowering stages. We predicted that a subset of lncRNAs were targets of microRNAs and found 18 lncRNA/microRNA target pairs with both differentially expressed across time points. The genome-wide differential expression and network analysis of non-coding RNAs and mRNAs from the same tissues provide new candidate loci for dormancy regulation and suggest complex noncoding RNA interactions control transcriptional regulation across these key developmental time points.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
| | - Dennis Bennett
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Christopher Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, The Pennsylvania State University, University Park, PA, United States
| | - Albert G Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
| | - Zongrang Liu
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Margaret E Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States.,Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
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A Complex Gene Network Mediated by Ethylene Signal Transduction TFs Defines the Flower Induction and Differentiation in Olea europaea L. Genes (Basel) 2021; 12:genes12040545. [PMID: 33918715 PMCID: PMC8070190 DOI: 10.3390/genes12040545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022] Open
Abstract
The olive tree (Olea europaea L.) is a typical Mediterranean crop, important for olive and oil production. The high tendency to bear fruits in an uneven manner, defined as irregular or alternate bearing, results in a significant economic impact for the high losses in olives and oil production. Buds from heavy loaded (‘ON’) and unloaded (‘OFF’) branches of a unique olive tree were collected in July and the next March to compare the transcriptomic profiles and get deep insight into the molecular mechanisms regulating floral induction and differentiation. A wide set of DEGs related to ethylene TFs and to hormonal, sugar, and phenylpropanoid pathways was identified in buds collected from ‘OFF’ branches. These genes could directly and indirectly modulate different pathways, suggesting their key role during the lateral bud transition to flowering stage. Interestingly, several genes related to the flowering process appeared as over-expressed in buds from March ‘OFF’ branches and they could address the buds towards flower differentiation. By this approach, interesting candidate genes related to the switch from vegetative to reproductive stages were detected and analyzed. The functional analysis of these genes will provide tools for developing breeding programs to obtain olive trees characterized by more constant productivity over the years.
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15
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Azeez A, Zhao YC, Singh RK, Yordanov YS, Dash M, Miskolczi P, Stojkovič K, Strauss SH, Bhalerao RP, Busov VB. EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy. Nat Commun 2021; 12:1123. [PMID: 33602938 PMCID: PMC7893051 DOI: 10.1038/s41467-021-21449-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/22/2021] [Indexed: 01/31/2023] Open
Abstract
Bud-break is an economically and environmentally important process in trees and shrubs from boreal and temperate latitudes, but its molecular mechanisms are poorly understood. Here, we show that two previously reported transcription factors, EARLY BUD BREAK 1 (EBB1) and SHORT VEGETATIVE PHASE-Like (SVL) directly interact to control bud-break. EBB1 is a positive regulator of bud-break, whereas SVL is a negative regulator of bud-break. EBB1 directly and negatively regulates SVL expression. We further report the identification and characterization of the EBB3 gene. EBB3 is a temperature-responsive, epigenetically-regulated, positive regulator of bud-break that provides a direct link to activation of the cell cycle during bud-break. EBB3 is an AP2/ERF transcription factor that positively and directly regulates CYCLIND3.1 gene. Our results reveal the architecture of a putative regulatory module that links temperature-mediated control of bud-break with activation of cell cycle.
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Affiliation(s)
- Abdul Azeez
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Yiru Chen Zhao
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Rajesh Kumar Singh
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Yordan S Yordanov
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL, USA
| | - Madhumita Dash
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Pal Miskolczi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Katja Stojkovič
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Steve H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Rishikesh P Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
| | - Victor B Busov
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
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Zhao X, Wen B, Li C, Tan Q, Liu L, Chen X, Li L, Fu X. Overexpression of the Peach Transcription Factor Early Bud-Break 1 Leads to More Branches in Poplar. FRONTIERS IN PLANT SCIENCE 2021; 12:681283. [PMID: 34220902 PMCID: PMC8247907 DOI: 10.3389/fpls.2021.681283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/11/2021] [Indexed: 05/05/2023]
Abstract
Shoot branching is an important adaptive trait that determines plant architecture. In a previous study, the Early bud-break 1 (EBB1) gene in peach (Prunus persica var. nectarina) cultivar Zhongyou 4 was transformed into poplar (Populus trichocarpa). PpEBB1-oe poplar showed a more branched phenotype. To understand the potential mechanisms underlying the EBB1-mediated branching, transcriptomic and proteomics analyses were used. The results showed that a large number of differentially expressed genes (DEGs)/differentially expressed proteins (DEPs) associated with light response, sugars, brassinosteroids (BR), and nitrogen metabolism were significantly enriched in PpEBB1-oe poplar. In addition, contents of sugars, BR, and amino acids were measured. Results showed that PpEBB1 significantly promoted the accumulation of fructose, glucose, sucrose, trehalose, and starch. Contents of brassinolide (BL), castasterone (CS), and 6-deoxocathasterone (6-deoxoCS) were all significantly changed with overexpressing PpEBB1. Various types of amino acids were measured and four of them were significantly improved in PpEBB1-oe poplar, including aspartic acid (Asp), arginine (Arg), cysteine (Cys), and tryptohpan (Trp). Taken together, shoot branching is a process controlled by a complex regulatory network, and PpEBB1 may play important roles in this process through the coordinating multiple metabolic pathways involved in shoot branching, including light response, phytohormones, sugars, and nitrogen.
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Affiliation(s)
- Xuehui Zhao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Chen Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Qiuping Tan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Li Liu
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
- Ling Li,
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Tai’an, China
- *Correspondence: Xiling Fu,
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Zhang M, Yang Q, Yuan X, Yan X, Wang J, Cheng T, Zhang Q. Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume. FRONTIERS IN PLANT SCIENCE 2021; 12:690841. [PMID: 34335659 PMCID: PMC8319914 DOI: 10.3389/fpls.2021.690841] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/28/2021] [Indexed: 05/12/2023]
Abstract
Prunus mume is one of the most important woody perennials for edible and ornamental use. Despite a substantial variation in the flowering phenology among the P. mume germplasm resources, the genetic control for flowering time remains to be elucidated. In this study, we examined five blooming time-related traits of 235 P. mume landraces for 2 years. Based on the phenotypic data, we performed genome-wide association studies, which included a combination of marker- and gene-based association tests, and identified 1,445 candidate genes that are consistently linked with flowering time across multiple years. Furthermore, we assessed the global transcriptome change of floral buds from the two P. mume cultivars exhibiting contrasting bloom dates and detected 617 associated genes that were differentially expressed during the flowering process. By integrating a co-expression network analysis, we screened out 191 gene candidates of conserved transcriptional pattern during blooming across cultivars. Finally, we validated the temporal expression profiles of these candidates and highlighted their putative roles in regulating floral bud break and blooming time in P. mume. Our findings are important to expand the understanding of flowering time control in woody perennials and will boost the molecular breeding of novel varieties in P. mume.
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Affiliation(s)
- Man Zhang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qingqing Yang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xi Yuan
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | | | - Jia Wang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- *Correspondence: Qixiang Zhang
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Ma JJ, Liu SW, Han FX, Li W, Li Y, Niu SH. Comparative transcriptome analyses reveal two distinct transcriptional modules associated with pollen shedding time in pine. BMC Genomics 2020; 21:504. [PMID: 32698817 PMCID: PMC7374968 DOI: 10.1186/s12864-020-06880-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/02/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Seasonal flowering time is an ecologically and economically important trait in temperate trees. Previous studies have shown that temperature in many tree species plays a pivotal role in regulating flowering time. However, genetic control of flowering time is not synchronised in different individual trees under comparable temperature conditions, the underlying molecular mechanism is mainly to be investigated. RESULTS In the present study, we analysed the transcript abundance in male cones and needles from six early pollen-shedding trees (EPs) and six neighbouring late pollen-shedding trees (LPs) in Pinus tabuliformis at three consecutive time points in early spring. We found that the EPs and LPs had distinct preferred transcriptional modules in their male cones and, interestingly, the expression pattern was also consistently maintained in needles even during the winter dormancy period. Additionally, the preferred pattern in EPs was also adopted by other fast-growing tissues, such as elongating new shoots. Enhancement of nucleic acid synthesis and stress resistance pathways under cold conditions can facilitate rapid growth and maintain higher transcriptional activity. CONCLUSIONS During the cold winter and early spring seasons, the EPs were more sensitive to relatively warmer temperatures and showed higher transcriptomic activity than the LPs, indicating that EPs required less heat accumulation for pollen shedding than LPs. These results provided a transcriptomic-wide understanding of the temporal regulation of pollen shedding in pines.
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Affiliation(s)
- Jing-Jing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Shuang-Wei Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Fang-Xu Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Yue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
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19
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Zhao X, Han X, Wang Q, Wang X, Chen X, Li L, Fu X, Gao D. EARLY BUD BREAK 1 triggers bud break in peach trees by regulating hormone metabolism, the cell cycle, and cell wall modifications. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3512-3523. [PMID: 32507879 PMCID: PMC7475240 DOI: 10.1093/jxb/eraa119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/02/2020] [Indexed: 05/19/2023]
Abstract
In a previous study we identified EARLY BUD BREAK 1 (EBB1), an ERF transcription factor, in peach (Prunus persica var. nectarina cultivar Zhongyou 4); however, little is known of how PpEBB1 may regulate bud break. To verify the function of PpEBB1 in bud break, PpEBB1 was transiently transformed into peach buds, resulting in early bud break. Bud break occurred earlier in PpEBB1-oe poplar (Populus trichocarpa) obtained by heterologous transformation than in wild type (WT), consistent with the peach bud results, indicating that PpEBB1 can promote bud break. To explore how PpEBB1 affects bud break, differentially expressed genes (DEGs) between WT and PpEBB1-oe poplar plants were identified by RNA-sequencing. The expression of DEGs associated with hormone metabolism, cell cycle, and cell wall modifications changed substantially according to qRT-PCR. Auxin, ABA, and total trans-zeatin-type cytokinin levels were higher in the PpEBB1-oe plants than in WT plants, while the total N6-(Δ 2-isopentenyl)-adenine-type cytokinins was lower. Yeast two-hybrid and bimolecular fluorescence complementation assays verified that a cell wall modification-related protein (PpEXBL1) interacted with PpEBB1 suggesting that PpEBB1 could interact with these cell wall modification proteins directly. Overall, our study proposed a multifaceted explanation for how PpEBB1 regulates bud break and showed that PpEBB1 promotes bud break by regulating hormone metabolism, the cell cycle, and cell wall modifications.
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Affiliation(s)
- Xuehui Zhao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
| | - Xiaolun Han
- Laiyang City Bureau of Natural Resources and Planning, Yantai, Shangdong, China
| | - Qingjie Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
| | - Xuxu Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
- Correspondence: or
| | - Dongsheng Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
- Correspondence: or
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Yu J, Conrad AO, Decroocq V, Zhebentyayeva T, Williams DE, Bennett D, Roch G, Audergon JM, Dardick C, Liu Z, Abbott AG, Staton ME. Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach. FRONTIERS IN PLANT SCIENCE 2020; 11:180. [PMID: 32180783 PMCID: PMC7059448 DOI: 10.3389/fpls.2020.00180] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/06/2020] [Indexed: 05/07/2023]
Abstract
Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot (Prunus armeniaca) genotypes with contrasting bloom dates and peach (Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box (DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
| | - Anna O. Conrad
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States
| | - Véronique Decroocq
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Universite de Bordeaux, Villenave d'Ornon, France
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, the Pennsylvania State University, University Park, PA, United States
| | - Daniel E. Williams
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Dennis Bennett
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States
| | - Guillaume Roch
- GAFL Fruit and Vegetable Genetics and Breeding, INRA Centre PACA, Montfavet, France
| | - Jean-Marc Audergon
- GAFL Fruit and Vegetable Genetics and Breeding, INRA Centre PACA, Montfavet, France
| | - Christopher Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States
| | - Zongrang Liu
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States
| | - Albert G. Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
| | - Margaret E. Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
- Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
- *Correspondence: Margaret E. Staton,
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Jiang Z, Sun L, Wei Q, Ju Y, Zou X, Wan X, Liu X, Yin Z. A New Insight into Flowering Regulation: Molecular Basis of Flowering Initiation in Magnolia × soulangeana 'Changchun'. Genes (Basel) 2019; 11:genes11010015. [PMID: 31877931 PMCID: PMC7017242 DOI: 10.3390/genes11010015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 12/17/2022] Open
Abstract
Magnolia × soulangeana ‘Changchun’ are trees that bloom in spring and summer respectively after flower bud differentiation. Here, we use phenological and morphological observation and RNA-seq technology to study the molecular basis of flowering initiation in ‘Changchun’. During the process of flowering initiation in spring and summer, the growth of expanded flower buds increased significantly, and their shape was obviously enlarged, which indicated that flowering was initiated. A total of 168,120 expressed genes were identified in spring and summer dormant and expanded flower buds, of which 11,687 genes showed significantly differential expression between spring and summer dormant and expanded flower buds. These differentially expressed genes (DEGs) were mainly involved in plant hormone signal transduction, metabolic processes, cellular components, binding, and catalytic activity. Analysis of differential gene expression patterns revealed that gibberellin signaling, and some transcription factors were closely involved in the regulation of spring and summer flowering initiation in ‘Changchun’. A qRT-PCR (quantitative Real Time Polymerase Chain Reaction) analysis showed that BGISEQ-500 sequencing platform could truly reflect gene expression patterns. It also verified that GID1B (GIBBERELLIN INSENSITIVE DWARF1 B), GID1C, SPL8 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8), and GASA (GIBBERELLIC ACID-STIMULATED ARABIDOPSIS) family genes were expressed at high levels, while the expression of SPY (SPINDLY) was low during spring and summer flowering initiation. Meanwhile, the up- and down-regulated expression of, respectively, AGL6 (AGAMOUS-LIKE 6) and DREB3 (DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 3), AG15, and CDF1 (CYCLIC DOF FACTOR 1) might also be involved in the specific regulation of spring and summer flowering initiation. Obviously, flowering initiation is an important stage of the flowering process in woody plants, involving the specific regulation of relevant genes and transcription factors. This study provides a new perspective for the regulation of the flowering process in perennial woody plants.
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Affiliation(s)
- Zheng Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Z.J.); (L.S.); (Y.J.); (X.Z.); (X.W.); (X.L.)
| | - Liyong Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Z.J.); (L.S.); (Y.J.); (X.Z.); (X.W.); (X.L.)
| | - Qiang Wei
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China;
| | - Ye Ju
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Z.J.); (L.S.); (Y.J.); (X.Z.); (X.W.); (X.L.)
| | - Xuan Zou
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Z.J.); (L.S.); (Y.J.); (X.Z.); (X.W.); (X.L.)
| | - Xiaoxia Wan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Z.J.); (L.S.); (Y.J.); (X.Z.); (X.W.); (X.L.)
| | - Xu Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Z.J.); (L.S.); (Y.J.); (X.Z.); (X.W.); (X.L.)
| | - Zengfang Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Z.J.); (L.S.); (Y.J.); (X.Z.); (X.W.); (X.L.)
- Correspondence: ; Tel.: +86-025-8542-7316
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22
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Hu L, Zheng T, Cai M, Pan H, Wang J, Zhang Q. Transcriptome analysis during floral organ development provides insights into stamen petaloidy in Lagerstroemia speciosa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:510-518. [PMID: 31445476 DOI: 10.1016/j.plaphy.2019.08.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
As one of the most popular woody species that blooms in summer, Lagerstroemia speciosa has been used abundantly in urban landscape for its excellent floral beauty. For the first time, we discovered a double-flower variant with all petaloid stamens. To understand the molecular basis of this variation, we contrasted the transcriptomes of single- and double-flower buds at three stamen development stages. In total, 73,536 unigenes were mapped and 30,714 differently expressed genes (DEGs) were identified in the tissues. We focused on the DEGs expressing in both phenotypes and investigated the association of their expression profiles with their functions in transcription pathways. Furthermore, we performed WGCNA and identified co-expressed genes with four floral homeotic genes as hubs (MADS16, Unigene0026169; AP2, Unigene0042732; SOC1, Unigene0046314; AG, Unigene0056437). The expression of these hub genes has been conserved across the three developmental stages but significantly different between the two floral phenotypes. As a result, the robust transcriptional regulation of stamen petaloidy in double flowers was deduced. These findings will help to unravel the regulatory mechanisms of several specific genes, thereby providing a basis to study double-flower molecular breeding in L. speciosa.
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Affiliation(s)
- Ling Hu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ming Cai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.
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23
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Comparative Transcriptomic and Proteomic Analysis to Deeply Investigate the Role of Hydrogen Cyanamide in Grape Bud Dormancy. Int J Mol Sci 2019; 20:ijms20143528. [PMID: 31323865 PMCID: PMC6679053 DOI: 10.3390/ijms20143528] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 11/17/2022] Open
Abstract
Hydrogen cyanamide (HC) is an agrochemical compound that is frequently used to break bud dormancy in grapevines grown under mild winter conditions globally. The present study was carried out to provide an in-depth understanding of the molecular mechanism associated with HC releasing bud dormancy in grapevines. For this purpose, RNA-seq based transcriptomic and tandem mass tag (TMT)-based proteomic information was acquired and critically analyzed. The combined results of transcriptomic and proteomic analysis were utilized to demonstrate differential expression pattern of genes at the translational and transcriptional levels. The outcome of the proteomic analysis revealed that a total of 7135 proteins (p-value ≤ 0.05; fold change ≥ 1.5) between the treatments (HC treated versus control) were identified, out of which 6224 were quantified. Among these differentially expressed proteins (DEPs), the majority of these proteins were related to heat shock, oxidoreductase activity, and energy metabolism. Metabolic, ribosomal, and hormonal signaling pathways were found to be significantly enriched at both the transcriptional and translational levels. It was illustrated that genes associated with metabolic and oxidoreductase activity were mainly involved in the regulation of bud dormancy at the transcriptomic and proteomic levels. The current work furnishes a new track to decipher the molecular mechanism of bud dormancy after HC treatment in grapes. Functional characterization of key genes and proteins will be informative in exactly pinpointing the crosstalk between transcription and translation in the release of bud dormancy after HC application.
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24
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Xing X, Jiang J, Huang Y, Zhang Z, Song A, Ding L, Wang H, Yao J, Chen S, Chen F, Fang W. The Constitutive Expression of a Chrysanthemum ERF Transcription Factor Influences Flowering Time in Arabidopsis thaliana. Mol Biotechnol 2019; 61:20-31. [PMID: 30448907 DOI: 10.1007/s12033-018-0134-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
AP2/ERF transcription factors (TFs) represent valuable targets for the genetic manipulation of crop plants, as they participate in the control of metabolism, growth and development, as well as in the plants' response to environmental stimuli. Here, an ERF TF encoded by the chrysanthemum (Chrysanthemum morifolium) genome, designated CmERF110, was cloned and functionally characterized. The predicted CmERF110 polypeptide included a conserved DNA-binding AP2/ERF domain. A transient expression experiment revealed that the protein was deposited in the nucleus, and a transactivation experiment in yeast suggested that it had no transcriptional activity. The gene was transcribed in the chrysanthemum root, stem and leaf, with its transcript level following a circadian rhythm under both long and short days. The effect of constitutively expressing the gene in Arabidopsis thaliana was to accelerate flowering. Transcriptional profiling implied that its effect on floral initiation operated through the photoperiod pathway.
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Affiliation(s)
- Xiaojuan Xing
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China
| | - Jiafu Jiang
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China
| | - Yaoyao Huang
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China
| | - Zixin Zhang
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China
| | - Aiping Song
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China
| | - Lian Ding
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China
| | - Haibing Wang
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China
| | - Jianjun Yao
- Shanghai Honghua Horticulture Co. Ltd., Shanghai, 200070, China
| | - Sumei Chen
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China
| | - Fadi Chen
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China
| | - Weimin Fang
- Key Laboratory of Landscape Agriculture, College of Horticulture, Ministry of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, Republic of China.
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Conde D, Perales M, Sreedasyam A, Tuskan GA, Lloret A, Badenes ML, González-Melendi P, Ríos G, Allona I. Engineering Tree Seasonal Cycles of Growth Through Chromatin Modification. FRONTIERS IN PLANT SCIENCE 2019; 10:412. [PMID: 31024588 PMCID: PMC6459980 DOI: 10.3389/fpls.2019.00412] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/19/2019] [Indexed: 05/21/2023]
Abstract
In temperate and boreal regions, perennial trees arrest cell division in their meristematic tissues during winter dormancy until environmental conditions become appropriate for their renewed growth. Release from the dormant state requires exposure to a period of chilling temperatures similar to the vernalization required for flowering in Arabidopsis. Over the past decade, genomic DNA (gDNA) methylation and transcriptome studies have revealed signatures of chromatin regulation during active growth and winter dormancy. To date, only a few chromatin modification genes, as candidate regulators of these developmental stages, have been functionally characterized in trees. In this work, we summarize the major findings of the chromatin-remodeling role during growth-dormancy cycles and we explore the transcriptional profiling of vegetative apical bud and stem tissues during dormancy. Finally, we discuss genetic strategies designed to improve the growth and quality of forest trees.
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Affiliation(s)
- Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Gerald A. Tuskan
- Oak Ridge National Laboratory, Center for Bioenergy Innovation, Oak Ridge, TN, United States
| | - Alba Lloret
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - María L. Badenes
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Pablo González-Melendi
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
- *Correspondence: Isabel Allona, orcid.org/0000-0002-7012-2850
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Ito A, Sakaue T, Fujimaru O, Iwatani A, Ikeda T, Sakamoto D, Sugiura T, Moriguchi T. Comparative phenology of dormant Japanese pear (Pyrus pyrifolia) flower buds: a possible cause of 'flowering disorder'. TREE PHYSIOLOGY 2018; 38:825-839. [PMID: 29370432 DOI: 10.1093/treephys/tpx169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 12/04/2017] [Indexed: 05/03/2023]
Abstract
Mild winters influenced by global warming have increased the incidence of erratic flowering ('flowering disorder') in Japanese pear (Pyrus pyrifolia Nakai) trees in Japan. To discover how, when and what kind of disorder/damage occur in pear flower buds, we observed axillary flower buds of two cultivars, 'Kosui' (a mid-chill cultivar) and 'Niitaka' (a high-chill cultivar), grown at five locations. We focused on the phenology from autumn 2015 to spring 2016, when temperatures were higher than for average years, especially from September to January, and large fluctuations occurred due to El Niño. During the blooming season in the spring of 2016, both the percentage of blooming flower buds and the number of florets per flower bud decreased in trees located at lower latitudes (with lower chilling accumulation) with a more severe problem in 'Niitaka' than in 'Kosui'. As shown by forcing excised shoots, the onset and release of endodormancy occurred earlier in 'Kosui' than 'Niitaka' and occurred earlier in trees growing at higher latitudes than at lower latitudes (warmer regions). The freezing tolerance of flower buds, measured as the lethal temperature for 50% survival (LT50), was similar for the cultivars beginning in autumn and reached maximum levels, LT50 values of less than -12 °C, between late-December and mid-January in both cultivars, except for those in Kagoshima (the lowest latitude), where the maximum LT50 was only -5 °C throughout the season. We propose that warmer autumn-winter temperatures may prevent the acquisition of freezing tolerance, disturb endodormancy progression and disrupt floral organ development, thereby causing flowering disorder in pear trees. The risk of occurrence of flowering disorder in pear may be higher in high-chill cultivars than in low- or mid-chill cultivars and at lower latitudes compared with higher latitudes.
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Affiliation(s)
- A Ito
- Division of Fruit Production and Postharvest Science, Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - T Sakaue
- Fruit Tree Division, Kagoshima Prefectural Institute of Agricultural Development, 2200 Oono, Kinpo, Minamisatsuma, Kagoshima 899-3401, Japan
| | - O Fujimaru
- Department of Deciduous Fruit Tree, Fruit Tree Research Institute, Kumamoto Prefectural Agricultural Research Center, 2566 Toyofuku, Matsubase, Uki, Kumamoto 869-0524, Japan
- Northern Kumamoto Administrative Headquarters, Kumamoto Prefectural Government, Tamana, Kumamoto 865-0016, Japan
| | - A Iwatani
- Department of Deciduous Fruit Tree, Fruit Tree Research Institute, Kumamoto Prefectural Agricultural Research Center, 2566 Toyofuku, Matsubase, Uki, Kumamoto 869-0524, Japan
| | - T Ikeda
- Laboratory of Fruit Growing and Breeding, Tottori Prefectural Horticultural Research Center, 2048 Yurashuku Hokuei, Tottori 689-2221, Japan
| | - D Sakamoto
- Division of Fruit Production and Postharvest Science, Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - T Sugiura
- Division of Fruit Production and Postharvest Science, Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - T Moriguchi
- Division of Fruit Production and Postharvest Science, Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
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Chandler JW. Class VIIIb APETALA2 Ethylene Response Factors in Plant Development. TRENDS IN PLANT SCIENCE 2018; 23:151-162. [PMID: 29074232 DOI: 10.1016/j.tplants.2017.09.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 05/21/2023]
Abstract
The APETALA2 (AP2) transcription factor superfamily in many plant species is extremely large. In addition to well-documented roles in stress responses, some AP2 members in arabidopsis, such as those of subgroup VIIIb, which includes DORNRÖSCHEN, DORNRÖSCHEN-LIKE, PUCHI, and LEAFY PETIOLE, are also important developmental regulators throughout the plant life cycle. Information is accumulating from orthologs of these proteins in important crop species that they influence key agronomic traits, such as the release of bud-burst in woody perennials and floral meristem identity and branching in cereals, and thereby represent potential for agronomic improvement. Given the increasing recognition of their developmental significance, this review highlights the function of these proteins and addresses their phylogenetic and evolutionary relationships.
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Affiliation(s)
- John W Chandler
- Institute for Developmental Biology, Cologne Biocenter, University of Cologne, Zuelpicher Strasse 47b, D-50674 Cologne, Germany.
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Falavigna VDS, Guitton B, Costes E, Andrés F. I Want to (Bud) Break Free: The Potential Role of DAM and SVP-Like Genes in Regulating Dormancy Cycle in Temperate Fruit Trees. FRONTIERS IN PLANT SCIENCE 2018; 9:1990. [PMID: 30687377 PMCID: PMC6335348 DOI: 10.3389/fpls.2018.01990] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 12/20/2018] [Indexed: 05/18/2023]
Abstract
Bud dormancy is an adaptive process that allows trees to survive the hard environmental conditions that they experience during the winter of temperate climates. Dormancy is characterized by the reduction in meristematic activity and the absence of visible growth. A prolonged exposure to cold temperatures is required to allow the bud resuming growth in response to warm temperatures. In fruit tree species, the dormancy cycle is believed to be regulated by a group of genes encoding MADS-box transcription factors. These genes are called DORMANCY-ASSOCIATED MADS-BOX (DAM) and are phylogenetically related to the Arabidopsis thaliana floral regulators SHORT VEGETATIVE PHASE (SVP) and AGAMOUS-LIKE 24. The interest in DAM and other orthologs of SVP (SVP-like) genes has notably increased due to the publication of several reports suggesting their role in the control of bud dormancy in numerous fruit species, including apple, pear, peach, Japanese apricot, and kiwifruit among others. In this review, we briefly describe the physiological bases of the dormancy cycle and how it is genetically regulated, with a particular emphasis on DAM and SVP-like genes. We also provide a detailed report of the most recent advances about the transcriptional regulation of these genes by seasonal cues, epigenetics and plant hormones. From this information, we propose a tentative classification of DAM and SVP-like genes based on their seasonal pattern of expression. Furthermore, we discuss the potential biological role of DAM and SVP-like genes in bud dormancy in antagonizing the function of FLOWERING LOCUS T-like genes. Finally, we draw a global picture of the possible role of DAM and SVP-like genes in the bud dormancy cycle and propose a model that integrates these genes in a molecular network of dormancy cycle regulation in temperate fruit trees.
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Lloret A, Badenes ML, Ríos G. Modulation of Dormancy and Growth Responses in Reproductive Buds of Temperate Trees. FRONTIERS IN PLANT SCIENCE 2018; 9:1368. [PMID: 30271422 PMCID: PMC6146825 DOI: 10.3389/fpls.2018.01368] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/29/2018] [Indexed: 05/20/2023]
Abstract
During autumn perennial trees cease growth and form structures called buds in order to protect meristems from the unfavorable environmental conditions, including low temperature and desiccation. In addition to increased tolerance to these abiotic stresses, reproductive buds modulate developmental programs leading to dormancy induction to avoid premature growth resumption, and flowering pathways. Stress tolerance, dormancy, and flowering processes are thus physically and temporarily restricted to a bud, and consequently forced to interact at the regulatory level. We review recent genomic, genetic, and molecular contributions to the knowledge of these three processes in trees, highlighting the role of epigenetic modifications, phytohormones, and common regulatory factors. Finally, we emphasize the utility of transcriptomic approaches for the identification of key structural and regulatory genes involved in bud processes, illustrated with our own experience using peach as a model.
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30
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Velappan Y, Signorelli S, Considine MJ. Cell cycle arrest in plants: what distinguishes quiescence, dormancy and differentiated G1? ANNALS OF BOTANY 2017; 120:495-509. [PMID: 28981580 PMCID: PMC5737280 DOI: 10.1093/aob/mcx082] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/29/2017] [Accepted: 06/06/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Quiescence is a fundamental feature of plant life, which enables plasticity, renewal and fidelity of the somatic cell line. Cellular quiescence is defined by arrest in a particular phase of the cell cycle, typically G1 or G2; however, the regulation of quiescence and proliferation can also be considered across wider scales in space and time. As such, quiescence is a defining feature of plant development and phenology, from meristematic stem cell progenitors to terminally differentiated cells, as well as dormant or suppressed seeds and buds. While the physiology of each of these states differs considerably, each is referred to as 'cell cycle arrest' or 'G1 arrest'. SCOPE Here the physiology and molecular regulation of (1) meristematic quiescence, (2) dormancy and (3) terminal differentiation (cell cycle exit) are considered in order to determine whether and how the molecular decisions guiding these nuclear states are distinct. A brief overview of the canonical cell cycle regulators is provided, and the genetic and genomic, as well as physiological, evidence is considered regarding two primary questions: (1) Are the canonical cell cycle regulators superior or subordinate in the regulation of quiescence? (2) Are these three modes of quiescence governed by distinct molecular controls? CONCLUSION Meristematic quiescence, dormancy and terminal differentiation are each predominantly characterized by G1 arrest but regulated distinctly, at a level largely superior to the canonical cell cycle. Meristematic quiescence is intrinsically linked to non-cell-autonomous regulation of meristem cell identity, and particularly through the influence of ubiquitin-dependent proteolysis, in partnership with reactive oxygen species, abscisic acid and auxin. The regulation of terminal differentiation shares analogous features with meristematic quiescence, albeit with specific activators and a greater role for cytokinin signalling. Dormancy meanwhile appears to be regulated at the level of chromatin accessibility, by Polycomb group-type histone modifications of particular dormancy genes.
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Affiliation(s)
- Yazhini Velappan
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- The School of Molecular Sciences, and The UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Santiago Signorelli
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- The School of Molecular Sciences, and The UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Departamento de Biología Vegetal, Universidad de la República, Montevideo, 12900, Uruguay
| | - Michael J Considine
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- The School of Molecular Sciences, and The UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Department of Agriculture and Food Western Australia, South Perth, WA 6151, Australia
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
- For correspondence. Email
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31
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Conde D, Le Gac AL, Perales M, Dervinis C, Kirst M, Maury S, González-Melendi P, Allona I. Chilling-responsive DEMETER-LIKE DNA demethylase mediates in poplar bud break. PLANT, CELL & ENVIRONMENT 2017; 40:2236-2249. [PMID: 28707409 DOI: 10.1111/pce.13019] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 05/21/2023]
Abstract
Annual dormancy-growth cycle is a developmental and physiological process essential for the survival of deciduous trees in temperate and boreal forests. Seasonal control of shoot growth in woody perennials requires specific genetic programmes responding to environmental signals. The environmental-controlled mechanisms that regulate the shift between winter dormancy and the growth-promoting genetic programmes are still unknown. Here, we show that dynamics in genomic DNA methylation levels are involved in the regulation of dormancy-growth cycle in poplar. The reactivation of growth in the apical shoot during bud break process in spring is preceded by a progressive reduction of genomic DNA methylation in apex tissue. The induction in apex tissue of a chilling-dependent poplar DEMETER-LIKE 10 (PtaDML10) DNA demethylase precedes shoot growth reactivation. Transgenic poplars showing downregulation of PtaDML8/10 caused delayed bud break. Genome-wide transcriptome and methylome analysis and data mining revealed that the gene targets of DEMETER-LIKE-dependent DNA demethylation are genetically associated with bud break. These data point to a chilling-dependent DEMETER-like DNA demethylase mechanisms being involved in the shift from winter dormancy to a condition that precedes shoot apical vegetative growth in poplar.
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Affiliation(s)
- Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Anne-Laure Le Gac
- LBLGC EA1207, USC 1328 INRA, University Orléans, 45067, Orléans, France
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Christopher Dervinis
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Stéphane Maury
- LBLGC EA1207, USC 1328 INRA, University Orléans, 45067, Orléans, France
| | - Pablo González-Melendi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain
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32
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Carneros E, Yakovlev I, Viejo M, Olsen JE, Fossdal CG. The epigenetic memory of temperature during embryogenesis modifies the expression of bud burst-related genes in Norway spruce epitypes. PLANTA 2017; 246:553-566. [PMID: 28577177 PMCID: PMC5561168 DOI: 10.1007/s00425-017-2713-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/23/2017] [Indexed: 05/05/2023]
Abstract
Epigenetic memory affects the timing of bud burst phenology and the expression of bud burst-related genes in genetically identical Norway spruce epitypes in a manner usually associated with ecotypes. In Norway spruce, a temperature-dependent epigenetic memory established during embryogenesis affects the timing of bud burst and bud set in a reproducible and predictable manner. We hypothesize that the clinal variation in these phenological traits, which is associated with adaptation to growth under frost-free conditions, has an epigenetic component. In Norway spruce, dehydrins (DHNs) have been associated with extreme frost tolerance. DHN transcript levels decrease gradually prior to flushing, a time when trees are highly sensitive to frost. Furthermore, EARLY BUD BREAK 1 genes (EBB1) and the FT-TFL1-LIKE 2-gene (PaFTL2) were previously suggested to be implied in control of bud phenology. Here we report an analysis of transcript levels of 12 DHNs, 3 EBB1 genes and FTL2 in epitypes of the same genotype generated at different epitype-inducing temperatures, before and during spring bud burst. Earlier flushing of epitypes originating from embryos developed at 18 °C as compared to 28 °C, was associated with differential expression of these genes between epitypes and between buds and last year's needles. The majority of these genes showed significantly different expressions between epitypes in at least one time point. The general trend in DHN expression pattern in buds showed the expected reduction in transcript levels when approaching flushing, whereas, surprisingly, transcript levels peaked later in needles, mainly at the moment of bud burst. Collectively, our results demonstrate that the epigenetic memory of temperature during embryogenesis affects bud burst phenology and expression of the bud burst-related DHN, EBB1 and FTL2 genes in genetically identical Norway spruce epitypes.
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Affiliation(s)
- Elena Carneros
- Norwegian Institute of Bioeconomy Research, 1431, Ås, Norway
- Department of Life Sciences, University of Alcalá, Ctra. de Barcelona km 33.600, 28805, Alcalá De Henares, Madrid, Spain
| | - Igor Yakovlev
- Norwegian Institute of Bioeconomy Research, 1431, Ås, Norway
| | - Marcos Viejo
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jorunn E Olsen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432, Ås, Norway
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Tuan PA, Bai S, Saito T, Ito A, Moriguchi T. Dormancy-Associated MADS-Box (DAM) and the Abscisic Acid Pathway Regulate Pear Endodormancy Through a Feedback Mechanism. PLANT & CELL PHYSIOLOGY 2017; 58:1378-1390. [PMID: 28586469 DOI: 10.1093/pcp/pcx074] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/10/2017] [Indexed: 05/20/2023]
Abstract
In the pear 'Kosui' (Pyrus pyrifolia Nakai), the dormancy-associated MADS-box (PpDAM1 = PpMADS13-1) gene has been reported to play an essential role in bud endodormancy. Here, we found that PpDAM1 up-regulated expression of 9-cis-epoxycarotenoid dioxygenase (PpNCED3), which is a rate-limiting gene for ABA biosynthesis. Transient assays with a dual luciferase reporter system (LUC assay) and electrophoretic mobility shift assay (EMSA) showed that PpDAM1 activated PpNCED3 expression by binding to the CArG motif in the PpNCED3 promoter. PpNCED3 expression was increased toward endodormancy release in lateral flower buds of 'Kosui', which is consistent with the induced levels of ABA, its catabolism (ABA 8'-hydroxylase) and signaling genes (type 2C protein phosphatase genes and SNF1-related protein kinase 2 genes). In addition, we found that an ABA response element (ABRE)-binding transcription factor, PpAREB1, exhibiting high expression concomitant with endodormancy release, bound to three ABRE motifs in the promoter region of PpDAM1 and negatively regulated its activity. Taken together, our results suggested a feedback regulation between PpDAM1 and the ABA metabolism and signaling pathway during endodormancy of pear. This first evidence of an interaction between a DAM and ABA biosynthesis in vitro will provide further insights into bud endodormancy regulatory mechanisms of deciduous trees including pear.
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Affiliation(s)
- Pham Anh Tuan
- Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
| | - Songling Bai
- Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Takanori Saito
- Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Akiko Ito
- Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
| | - Takaya Moriguchi
- Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
- Institute of Fruit Tree and Tea Science, NARO, Okitsu-Nakacho Shimizu, Shizuoka 424-0292, Japan
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34
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Singh RK, Svystun T, AlDahmash B, Jönsson AM, Bhalerao RP. Photoperiod- and temperature-mediated control of phenology in trees - a molecular perspective. THE NEW PHYTOLOGIST 2017; 213:511-524. [PMID: 27901272 DOI: 10.1111/nph.14346] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/07/2016] [Indexed: 05/17/2023]
Abstract
Contents 511 I. 511 II. 512 III. 513 IV. 513 V. 517 VI. 517 VII. 521 VIII. 521 Acknowledgements 521 References 521 SUMMARY: Trees growing in boreal and temperate regions synchronize their growth with seasonal climatic changes in adaptive responses that are essential for their survival. These trees cease growth before the winter and establish a dormant state during which growth cessation is maintained by repression of responses to growth-promotive signals. Reactivation of growth in the spring follows the release from dormancy promoted by prolonged exposure to low temperature during the winter. The timing of the key events and regulation of the molecular programs associated with the key stages of the annual growth cycle are controlled by two main environmental cues: photoperiod and temperature. Recently, key components mediating photoperiodic control of growth cessation and bud set have been identified, and striking similarities have been observed in signaling pathways controlling growth cessation in trees and floral transition in Arabidopsis. Although less well understood, the regulation of bud dormancy and bud burst may involve cell-cell communication and chromatin remodeling. Here, we discuss current knowledge of the molecular-level regulation of the annual growth cycle of woody trees in temperate and boreal regions, and identify key questions that need to be addressed in the future.
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Affiliation(s)
- Rajesh Kumar Singh
- Department of Forest Genetics and Plant Physiology, SLU, S-901 83, Umeå, Sweden
| | - Tetiana Svystun
- Department of Physical Geography and Ecosystem Science, Lund University, Sölvegatan 12, S-223 62, Lund, Sweden
| | - Badr AlDahmash
- College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Anna Maria Jönsson
- Department of Physical Geography and Ecosystem Science, Lund University, Sölvegatan 12, S-223 62, Lund, Sweden
| | - Rishikesh P Bhalerao
- Department of Forest Genetics and Plant Physiology, SLU, S-901 83, Umeå, Sweden
- College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
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