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Li YT, Liu DH, Luo Y, Abbas Khan M, Mahmood Alam S, Liu YZ. Transcriptome analysis reveals the key network of axillary bud outgrowth modulated by topping in citrus. Gene 2024; 926:148623. [PMID: 38821328 DOI: 10.1016/j.gene.2024.148623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Topping, an important tree shaping and pruning technique, can promote the outgrowth of citrus axillary buds. However, the underlying molecular mechanism is still unclear. In this study, spring shoots of Citrus reticulata 'Huagan No.2' were topped and transcriptome was compared between axillary buds of topped and untopped shoots at 6 and 11 days after topping (DAT). 1944 and 2394 differentially expressed genes (DEGs) were found at 6 and 11 DAT, respectively. KEGG analysis revealed that many DEGs were related to starch and sucrose metabolism, signal transduction of auxin, cytokinin and abscisic acid. Specially, transcript levels of auxin synthesis, transport, and signaling-related genes (SAURs and ARF5), cytokinin signal transduction related genes (CRE1, AHP and Type-A ARRs), ABA signal responsive genes (PYL and ABF) were up-regulated by topping; while transcript levels of auxin receptor TIR1, auxin responsive genes AUX/IAAs, ABA signal transduction related gene PP2Cs and synthesis related genes NCED3 were down-regulated. On the other hand, the contents of sucrose and fructose in axillary buds of topped shoots were significantly higher than those in untopped shoots; transcript levels of 16 genes related to sucrose synthase, hexokinase, sucrose phosphate synthase, endoglucanase and glucosidase, were up-regulated in axillary buds after topping. In addition, transcript levels of genes related to trehalose 6-phosphate metabolism and glycolysis/tricarboxylic acid (TCA) cycle, as well to some transcription factors including Pkinase, Pkinase_Tyr, Kinesin, AP2/ERF, P450, MYB, NAC and Cyclin_c, significantly responded to topping. Taken together, the present results suggested that topping promoted citrus axillary bud outgrowth through comprehensively regulating plant hormone and carbohydrate metabolism, as well as signal transduction. These results deepened our understanding of citrus axillary bud outgrowth by topping and laid a foundation for further research on the molecular mechanisms of citrus axillary bud outgrowth.
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Affiliation(s)
- Yan-Ting Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dong-Hai Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yin Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Muhammad Abbas Khan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shariq Mahmood Alam
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yong-Zhong Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China.
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Wang H, Li X, Meng B, Fan Y, Khan SU, Qian M, Zhang M, Yang H, Lu K. Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1897-1912. [PMID: 38386569 PMCID: PMC11182599 DOI: 10.1111/pbi.14309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
Silique number is a crucial yield-related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high-yielding rapeseed.
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Affiliation(s)
- Hui Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Xiaodong Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Boyu Meng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Mingchao Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Minghao Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Haikun Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
- Engineering Research Center of South Upland Agriculture, Ministry of EducationChongqingP.R. China
- Academy of Agricultural SciencesSouthwest UniversityBeibeiChongqingP.R. China
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3
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Niu MX, Feng CH, He F, Zhang H, Bao Y, Liu SJ, Liu X, Su Y, Liu C, Wang HL, Yin W, Xia X. The miR6445-NAC029 module regulates drought tolerance by regulating the expression of glutathione S-transferase U23 and reactive oxygen species scavenging in Populus. THE NEW PHYTOLOGIST 2024; 242:2043-2058. [PMID: 38515251 DOI: 10.1111/nph.19703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
MicroRNAs are essential in plant development and stress resistance, but their specific roles in drought stress require further investigation. Here, we have uncovered that a Populus-specific microRNAs (miRNA), miR6445, targeting NAC (NAM, ATAF, and CUC) family genes, is involved in regulating drought tolerance of poplar. The expression level of miR6445 was significantly upregulated under drought stress; concomitantly, seven targeted NAC genes showed significant downregulation. Silencing the expression of miR6445 by short tandem target mimic technology significantly decreased the drought tolerance in poplar. Furthermore, 5' RACE experiments confirmed that miR6445 directly targeted NAC029. The overexpression lines of PtrNAC029 (OE-NAC029) showed increased sensitivity to drought compared with knockout lines (Crispr-NAC029), consistent with the drought-sensitive phenotype observed in miR6445-silenced strains. PtrNAC029 was further verified to directly bind to the promoters of glutathione S-transferase U23 (GSTU23) and inhibit its expression. Both Crispr-NAC029 and PtrGSTU23 overexpressing plants showed higher levels of PtrGSTU23 transcript and GST activity while accumulating less reactive oxygen species (ROS). Moreover, poplars overexpressing GSTU23 demonstrated enhanced drought tolerance. Taken together, our research reveals the crucial role of the miR6445-NAC029-GSTU23 module in enhancing poplar drought tolerance by regulating ROS homeostasis. This finding provides new molecular targets for improving the drought resistance of trees.
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Affiliation(s)
- Meng-Xue Niu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Cong-Hua Feng
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Fang He
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Han Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yu Bao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shu-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiao Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yanyan Su
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chao Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hou-Ling Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Weilun Yin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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Han Y, Qu M, Liu Z, Kang C. Transcription factor FveMYB117a inhibits axillary bud outgrowth by regulating cytokinin homeostasis in woodland strawberry. THE PLANT CELL 2024; 36:2427-2446. [PMID: 38547429 PMCID: PMC11132891 DOI: 10.1093/plcell/koae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/11/2024] [Indexed: 05/30/2024]
Abstract
Shoot branching affects plant architecture. In strawberry (Fragaria L.), short branches (crowns) develop from dormant axillary buds to form inflorescences and flowers. While this developmental transition contributes greatly to perenniality and yield in strawberry, its regulatory mechanism remains unclear and understudied. In the woodland strawberry (Fragaria vesca), we identified and characterized 2 independent mutants showing more crowns. Both mutant alleles reside in FveMYB117a, a R2R3-MYB transcription factor gene highly expressed in shoot apical meristems, axillary buds, and young leaves. Transcriptome analysis revealed that the expression of several cytokinin pathway genes was altered in the fvemyb117a mutant. Consistently, active cytokinins were significantly increased in the axillary buds of the fvemyb117a mutant. Exogenous application of cytokinin enhanced crown outgrowth in the wild type, whereas the cytokinin inhibitors suppressed crown outgrowth in the fvemyb117a mutant. FveMYB117a binds directly to the promoters of the cytokinin homeostasis genes FveIPT2 encoding an isopentenyltransferase and FveCKX1 encoding a cytokinin oxidase to regulate their expression. Conversely, the type-B Arabidopsis response regulators FveARR1 and FveARR2b can directly inhibit the expression of FveMYB117a, indicative of a negative feedback regulation. In conclusion, we identified FveMYB117a as a key repressor of crown outgrowth by inhibiting cytokinin accumulation and provide a mechanistic basis for bud fate transition in an herbaceous perennial plant.
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Affiliation(s)
- Yafan Han
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Minghao Qu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Chunying Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Nakamura S, Kinoshita A, Koga H, Tsukaya H. Expression analyses of CUP-SHAPED COTYLEDON and SHOOT MERISTEMLESS in the one-leaf plant Monophyllaea glabra reveal neoteny evolution of shoot meristem. Sci Rep 2024; 14:11148. [PMID: 38750143 PMCID: PMC11096313 DOI: 10.1038/s41598-024-62049-4] [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: 11/24/2023] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
The one-leaf plant Monophyllaea glabra exhibits a unique developmental manner in which only one cotyledon continues growing without producing new vegetative organs. This morphology is formed by specific meristems, the groove meristem (GM) and the basal meristem (BM), which are thought to be modified shoot apical meristem (SAM) and leaf meristem. In this study, we analysed the expression of the organ boundary gene CUP-SHAPED COTYLEDON (CUC) and the SAM maintenance gene SHOOT MERISTEMLESS (STM) orthologs by whole-mount in situ hybridisation. We found that CUCs did not show clear border patterns around GM and BM during the vegetative phase. Furthermore, double-colour detection analysis at the cellular level revealed that CUC and STM expression overlapped in the GM region during the vegetative phase. We also found that this overlap is dissolved in the reproductive phase when normal shoot organogenesis is observed. Since co-expression of these genes occurs during SAM initiation under embryogenesis in Arabidopsis, our results demonstrate that GM is a prolonged stage of pre-mature SAM. Therefore, we propose that neotenic meristems could be a novel plant trait acquired by one-leaf plants.
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Affiliation(s)
- Shunji Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ayaka Kinoshita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroyuki Koga
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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6
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Fan N, Su L, Lv A, Wen W, Gao L, You X, Zhou P, An Y. PECTIN ACETYLESTERASE12 regulates shoot branching via acetic acid and auxin accumulation in alfalfa shoots. PLANT PHYSIOLOGY 2024; 195:518-533. [PMID: 38365203 DOI: 10.1093/plphys/kiae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/06/2023] [Accepted: 12/24/2023] [Indexed: 02/18/2024]
Abstract
Shoot branching is an important biological trait affecting alfalfa (Medicago sativa L.) production, but its development is complicated and the mechanism is not fully clear. In the present study, pectin acetylesterase 12 (MsPAE12) and NAM/ATAF/CUC-domain transcription factor gene (MsNAC73) were isolated from alfalfa. MsPAE12 was highly expressed in shoot apexes, and MsNAC73 was found to be a key transcriptional repressor of MsPAE12 by directly binding to salicylic acid (SA) and jasmonic acid (JA) elements in the MsPAE12 promoter. The biological functions of MsPAE12 and MsNAC73 were studied through overexpression (OE) and down-expression (RNAi) of the 2 genes in alfalfa. The numbers of shoot branches increased in MsPAE12-OE lines but decreased in MsPAE12-RNAi and MsNAC73-OE plants, which was negatively related to their indole-3-acetic acid (IAA) accumulation in shoot apexes. Furthermore, the contents of acetic acid (AA) in shoot apexes decreased in MsPAE12-OE plants but increased in MsPAE12-RNAi and MsNAC73-OE plants. The changes of AA contents were positively related to the expression of TRYPTOPHAN AMINOTRANSFERASE 1 (MsTAA1), TRYPTOPHAN AMINOTRANSFERASE-RELATED 2 (MsTAR2), and YUCCA flavin monooxygenase (MsYUCC4) and the contents of tryptophan (Trp), indole-3-pyruvic acid (IPA), and IAA in shoot apexes of MsPAE12-OE, MsPAE12-RNAi, and MsNAC73-OE plants. Exogenous application of AA to wild type (WT) and MsPAE12-OE plants increased Trp, IPA, and IAA contents and decreased branch number. Exogenous IAA suppressed shoot branching in MsPAE12-OE plants, but exogenous IAA inhibitors increased shoot branching in MsPAE12-RNAi plants. These results indicate that the MsNAC73-MsPAE12 module regulates auxin-modulated shoot branching via affecting AA accumulation in shoot apexes of alfalfa.
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Affiliation(s)
- Nana Fan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Life Science, Yulin University, Yulin 719000, China
| | - Liantai Su
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aimin Lv
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Wuwu Wen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiangkai You
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuan An
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai 201101, China
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Peng C, Xu H, Xie S, Zhong X, Chen L, He Y, Li Z, Zhou Y, Duan L. Unveiling the Regulatory Role of miRNAs in Internode Elongation: Integrated Analysis of MicroRNA and mRNA Expression Profiles across Diverse Dwarfing Treatments in Maize ( Zea mays L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7533-7545. [PMID: 38527761 DOI: 10.1021/acs.jafc.3c09507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
MicroRNAs are crucial regulators of gene expression in maize. However, the mechanisms through which miRNAs control internode elongation remain poorly understood. This study engineered varying levels of internode elongation inhibition, revealing that dwarfing treatments diminished gibberellin levels, curtailed cell longitudinal growth, and slowed the rate of internode elongation. Comprehensive transcriptome and miRNA profiling of the internode elongation zone showed gene expression changes that paralleled the extent of the internode length reduction. We identified 543 genes and 29 miRNAs with significant correlations to internode length, predominantly within families, including miR164 and miR396. By incorporating target gene expression levels, we pinpointed nine miRNA-mRNA pairs that are significantly associated with the regulation of the internode elongation. The inhibitory effects of these miRNAs on their target genes were confirmed through dual-luciferase reporter assays. Overexpression of miR164h in maize resulted in increased internode and cell length, suggesting a novel genetic avenue for manipulating plant stature. These miRNAs may also serve as precise spatiotemporal regulators for in vitro plant development.
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Affiliation(s)
- Chuanxi Peng
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Haidong Xu
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shipeng Xie
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xingyu Zhong
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Limei Chen
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yan He
- National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yuyi Zhou
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Liusheng Duan
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
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Segura M, García A, Gamarra G, Benítez Á, Iglesias-Moya J, Martínez C, Jamilena M. An miR164-resistant mutation in the transcription factor gene CpCUC2B enhances carpel arrest and ectopic boundary specification in Cucurbita pepo flower development. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1948-1966. [PMID: 38066672 DOI: 10.1093/jxb/erad486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/08/2023] [Indexed: 03/28/2024]
Abstract
The sex determination process in cucurbits involves the control of stamen or carpel development during the specification of male or female flowers from a bisexual floral meristem, a function coordinated by ethylene. A gain-of-function mutation in the miR164-binding site of CpCUC2B, ortholog of the Arabidopsis transcription factor gene CUC2, not only produced ectopic floral meristems and organs, but also suppressed the development of carpels and promoted the development of stamens. The cuc2b mutation induced the transcription of CpCUC2B in the apical shoots of plants after female flowering but repressed other CUC genes regulated by miR164, suggesting a conserved functional redundancy of these genes in the development of squash flowers. The synergistic androecious phenotype of the double mutant between cuc2b and etr2b, an ethylene-insensitive mutation that enhances the production of male flowers, demonstrated that CpCUC2B arrests the development of carpels independently of ethylene and CpWIP1B. The transcriptional regulation of CpCUC1, CpCUC2, and ethylene genes in cuc2b and ethylene mutants also confirms this conclusion. However, the epistasis of cuc2b over aco1a, a mutation that suppresses stamen arrest in female flowers, and the down-regulation of CpACS27A in cuc2b female apical shoots, indicated that CpCUC2B promotes stamen development by suppressing the late ethylene production.
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Affiliation(s)
- María Segura
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Alicia García
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Germán Gamarra
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Álvaro Benítez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Jessica Iglesias-Moya
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Cecilia Martínez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
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9
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Yuan Y, Du Y, Delaplace P. Unraveling the molecular mechanisms governing axillary meristem initiation in plants. PLANTA 2024; 259:101. [PMID: 38536474 DOI: 10.1007/s00425-024-04370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/22/2024] [Indexed: 04/24/2024]
Abstract
MAIN CONCLUSION Axillary meristems (AMs) located in the leaf axils determine the number of shoots or tillers eventually formed, thus contributing significantly to the plant architecture and crop yields. The study of AM initiation is unavoidable and beneficial for crop productivity. Shoot branching is an undoubted determinant of plant architecture and thus greatly impacts crop yield due to the panicle-bearing traits of tillers. The emergence of the AM is essential for the incipient bud formation, and then the bud is dormant or outgrowth immediately to form a branch or tiller. While numerous reviews have focused on plant branching and tillering development networks, fewer specifically address AM initiation and its regulatory mechanisms. This review synthesizes the significant advancements in the genetic and hormonal factors governing AM initiation, with a primary focus on studies conducted in Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.). In particular, by elaborating on critical genes like LATERAL SUPPRESSOR (LAS), which specifically regulates AM initiation and the networks in which they are involved, we attempt to unify the cascades through which they are positioned. We concentrate on clarifying the precise mutual regulation between shoot apical meristem (SAM) and AM-related factors. Additionally, we examine challenges in elucidating AM formation mechanisms alongside opportunities provided by emerging omics approaches to identify AM-specific genes. By expanding our comprehension of the genetic and hormonal regulation of AM development, we can develop strategies to optimize crop production and address global food challenges effectively.
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Affiliation(s)
- Yundong Yuan
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Yanfang Du
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Pierre Delaplace
- Plant Sciences, Gembloux Agro-Bio Tech, TERRA-Teaching and Research Center, Université de Liège, 5030, Gembloux, Belgium
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10
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Song X, Gu X, Chen S, Qi Z, Yu J, Zhou Y, Xia X. Far-red light inhibits lateral bud growth mainly through enhancing apical dominance independently of strigolactone synthesis in tomato. PLANT, CELL & ENVIRONMENT 2024; 47:429-441. [PMID: 37916615 DOI: 10.1111/pce.14758] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023]
Abstract
The ratio of red light to far-red light (R:FR) is perceived by light receptors and consequently regulates plant architecture. Regulation of shoot branching by R:FR ratio involves plant hormones. However, the roles of strigolactone (SL), the key shoot branching hormone and the interplay of different hormones in the light regulation of shoot branching in tomato (Solanum lycopersicum) are elusive. Here, we found that defects in SL synthesis genes CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7) and CCD8 in tomato resulted in more lateral bud growth but failed to reverse the FR inhibition of lateral bud growth, which was associated with increased auxin synthesis and decreased synthesis of cytokinin (CK) and brassinosteroid (BR). Treatment of auxin also inhibited shoot branching in ccd mutants. However, CK released the FR inhibition of lateral bud growth in ccd mutants, concomitant with the upregulation of BR synthesis genes. Furthermore, plants that overexpressed BR synthesis gene showed more lateral bud growth and the shoot branching was less sensitive to the low R:FR ratio. The results indicate that SL synthesis is dispensable for light regulation of shoot branching in tomato. Auxin mediates the response to R:FR ratio to regulate shoot branching by suppressing CK and BR synthesis.
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Affiliation(s)
- Xuewei Song
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaohua Gu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, People's Republic of China
| | - Shangyu Chen
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhenyu Qi
- Hainan Institute, Zhejiang University, Sanya, People's Republic of China
- Agricultural Experiment Station, Zhejiang University, Hangzhou, People's Republic of China
| | - Jingquan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, People's Republic of China
- Hainan Institute, Zhejiang University, Sanya, People's Republic of China
| | - Yanhong Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, People's Republic of China
- Hainan Institute, Zhejiang University, Sanya, People's Republic of China
| | - Xiaojian Xia
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, People's Republic of China
- Hainan Institute, Zhejiang University, Sanya, People's Republic of China
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11
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Lindsay P, Swentowsky KW, Jackson D. Cultivating potential: Harnessing plant stem cells for agricultural crop improvement. MOLECULAR PLANT 2024; 17:50-74. [PMID: 38130059 DOI: 10.1016/j.molp.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.
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Affiliation(s)
- Penelope Lindsay
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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12
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Chen Y, Ling Q, Li X, Ma Q, Tang S, Yuanzhi P, Liu QL, Jia Y, Yong X, Jiang B. Transcriptome analysis during axillary bud growth in chrysanthemum ( chrysanthemum× morifolium). PeerJ 2023; 11:e16436. [PMID: 38111658 PMCID: PMC10726743 DOI: 10.7717/peerj.16436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/19/2023] [Indexed: 12/20/2023] Open
Abstract
The chrysanthemum DgLsL gene, homologous with tomato Ls, is one of the earliest expressed genes controlling axillary meristem initiation. In this study, the wild-type chrysanthemum (CW) and DgLsL-overexpressed line 15 (C15) were used to investigate the regulatory mechanism of axillary bud development in chrysanthemum. Transcriptome sequencing was carried out to detect the differentially expressed genes of the axillary buds 0 h, 24 h and 48 h after decapitation. The phenotypic results showed that the number of axillary buds of C15 was significantly higher than CW. A total of 9,224 DEGs were identified in C15-0 vs. CW-0, 10,622 DEGs in C15-24 vs. CW-24, and 8,929 DEGs in C15-48 vs. CW-48.GO and KEGG pathway enrichment analyses showed that the genes of the flavonoid, phenylpropanoids and plant hormone pathways appeared to be differentially expressed, indicating their important roles in axillary bud germination. DgLsL reduces GA content in axillary buds by promoting GA2ox expression.These results confirmed previous studies on axillary bud germination and growth, and revealed the important roles of genes involved in plant hormone biosynthesis and signal transduction, aiding in the study of the gene patterns involved in axillary bud germination and growth.
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Affiliation(s)
- Yijun Chen
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Qin Ling
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Xin Li
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Qiqi Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - ShaoKang Tang
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Pan Yuanzhi
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Qing-lin Liu
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Yin Jia
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Xue Yong
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Beibei Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
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13
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Robil JM. The many side jobs of Lateral suppressor (Ls) in plant development. PLANT PHYSIOLOGY 2023; 193:2254-2256. [PMID: 37706552 PMCID: PMC10663106 DOI: 10.1093/plphys/kiad496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023]
Affiliation(s)
- Janlo M Robil
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
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14
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Azad MF, Dawar P, Esim N, Rock CD. Role of miRNAs in sucrose stress response, reactive oxygen species, and anthocyanin biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1278320. [PMID: 38023835 PMCID: PMC10656695 DOI: 10.3389/fpls.2023.1278320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In plants, sucrose is the main transported disaccharide that is the primary product of photosynthesis and controls a multitude of aspects of the plant life cycle including structure, growth, development, and stress response. Sucrose is a signaling molecule facilitating various stress adaptations by crosstalk with other hormones, but the molecular mechanisms are not well understood. Accumulation of high sucrose concentrations is a hallmark of many abiotic and biotic stresses, resulting in the accumulation of reactive oxygen species and secondary metabolite anthocyanins that have antioxidant properties. Previous studies have shown that several MYeloBlastosis family/MYB transcription factors are positive and negative regulators of sucrose-induced anthocyanin accumulation and subject to microRNA (miRNA)-mediated post-transcriptional silencing, consistent with the notion that miRNAs may be "nodes" in crosstalk signaling by virtue of their sequence-guided targeting of different homologous family members. In this study, we endeavored to uncover by deep sequencing small RNA and mRNA transcriptomes the effects of exogenous high sucrose stress on miRNA abundances and their validated target transcripts in Arabidopsis. We focused on genotype-by-treatment effects of high sucrose stress in Production of Anthocyanin Pigment 1-Dominant/pap1-D, an activation-tagged dominant allele of MYB75 transcription factor, a positive effector of secondary metabolite anthocyanin pathway. In the process, we discovered links to reactive oxygen species signaling through miR158/161/173-targeted Pentatrico Peptide Repeat genes and two novel non-canonical targets of high sucrose-induced miR408 and miR398b*(star), relevant to carbon metabolic fluxes: Flavonoid 3'-Hydroxlase (F3'H), an important enzyme in determining the B-ring hydroxylation pattern of flavonoids, and ORANGE a post-translational regulator of Phytoene Synthase expression, respectively. Taken together, our results contribute to understanding the molecular mechanisms of carbon flux shifts from primary to secondary metabolites in response to high sugar stress.
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Affiliation(s)
- Md. Fakhrul Azad
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Nevzat Esim
- Department of Molecular Biology and Genetics, Bіngöl University, Bingöl, Türkiye
| | - Christopher D. Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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15
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Barrera-Rojas CH, Vicente MH, Pinheiro Brito DA, Silva EM, Lopez AM, Ferigolo LF, do Carmo RM, Silva CMS, Silva GFF, Correa JPO, Notini MM, Freschi L, Cubas P, Nogueira FTS. Tomato miR156-targeted SlSBP15 represses shoot branching by modulating hormone dynamics and interacting with GOBLET and BRANCHED1b. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5124-5139. [PMID: 37347477 DOI: 10.1093/jxb/erad238] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/19/2023] [Indexed: 06/23/2023]
Abstract
The miRNA156 (miR156)/SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL/SBP) regulatory hub is highly conserved among phylogenetically distinct species, but how it interconnects multiple pathways to converge to common integrators controlling shoot architecture is still unclear. Here, we demonstrated that the miR156/SlSBP15 node modulates tomato shoot branching by connecting multiple phytohormones with classical genetic pathways regulating both axillary bud development and outgrowth. miR156-overexpressing plants (156-OE) displayed high shoot branching, whereas plants overexpressing a miR156-resistant SlSBP15 allele (rSBP15) showed arrested shoot branching. Importantly, the rSBP15 allele was able to partially restore the wild-type shoot branching phenotype in the 156-OE background. rSBP15 plants have tiny axillary buds, and their activation is dependent on shoot apex-derived auxin transport inhibition. Hormonal measurements revealed that indole-3-acetic acid (IAA) and abscisic acid (ABA) concentrations were lower in 156-OE and higher in rSBP15 axillary buds, respectively. Genetic and molecular data indicated that SlSBP15 regulates axillary bud development and outgrowth by inhibiting auxin transport and GOBLET (GOB) activity, and by interacting with tomato BRANCHED1b (SlBRC1b) to control ABA levels within axillary buds. Collectively, our data provide a new mechanism by which the miR156/SPL/SBP hub regulates shoot branching, and suggest that modulating SlSBP15 activity might have potential applications in shaping tomato shoot architecture.
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Affiliation(s)
- Carlos Hernán Barrera-Rojas
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Mateus Henrique Vicente
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Diego Armando Pinheiro Brito
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Eder M Silva
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Aitor Muñoz Lopez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Leticia F Ferigolo
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Rafael Monteiro do Carmo
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Carolina M S Silva
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Geraldo F F Silva
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Joao P O Correa
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Marcela M Notini
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
| | - Luciano Freschi
- Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, CEP: 05508-090, Brazil
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Fabio T S Nogueira
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, CEP: 13418-900, Brazil
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16
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Liao G, Duan Y, Wang C, Zhuang Z, Wang H. Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Gene Family in Litchi chinensis. Genes (Basel) 2023; 14:1416. [PMID: 37510318 PMCID: PMC10379382 DOI: 10.3390/genes14071416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
NAC proteins play an essential role in the growth and development of litchi, especially during reproductive development. However, a comprehensive analysis of the litchi NAC gene family is currently absent. Based on information from the litchi genome, we found that the 112 NAC genes of litchi show an uneven distribution on the chromosomes. Phylogenetic and conserved structural domain analyses indicated that different types of variability were exhibited in the family of litchi NACs (LcNACs). Gene covariance analysis showed that the LcNACs showed better similarity in the same genus than with Arabidopsis. We further investigated the differential expression patterns of LcNACs in buds and rudimentary leaves of litchi. qRT-PCR results implied that they were involved in the process. Profiling of LcNAC promoter elements in litchi showed that they were extensively involved in light response, phytohormone regulation, abiotic stress response, and plant growth and development processes. This study provides new insights into the identification, structural characterization, tissue-specific expression analysis, and promoter response elements of LcNACs. It reveals the characteristics of the LcNACs and lays the foundation for the subsequent understanding of its biological functions and molecular regulatory mechanisms.
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Affiliation(s)
- Guihua Liao
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Yu Duan
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Congcong Wang
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Zebin Zhuang
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Haishi Wang
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
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17
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Ma L, Liu KW, Li Z, Hsiao YY, Qi Y, Fu T, Tang GD, Zhang D, Sun WH, Liu DK, Li Y, Chen GZ, Liu XD, Liao XY, Jiang YT, Yu X, Hao Y, Huang J, Zhao XW, Ke S, Chen YY, Wu WL, Hsu JL, Lin YF, Huang MD, Li CY, Huang L, Wang ZW, Zhao X, Zhong WY, Peng DH, Ahmad S, Lan S, Zhang JS, Tsai WC, Van de Peer Y, Liu ZJ. Diploid and tetraploid genomes of Acorus and the evolution of monocots. Nat Commun 2023; 14:3661. [PMID: 37339946 DOI: 10.1038/s41467-023-38829-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.
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Affiliation(s)
- Liang Ma
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Yiying Qi
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Tao Fu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guang-Da Tang
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei-Hong Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gui-Zhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xue-Die Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xing-Yu Liao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yu-Ting Jiang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yang Hao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jie Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xue-Wei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shijie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - You-Yi Chen
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wan-Lin Wu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Jui-Ling Hsu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yu-Fu Lin
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ming-Der Huang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Chia-Ying Li
- Department of Applied Chemistry, National Pingtung University, Pingtung City, Pingtung County, 900003, Taiwan
| | - Laiqiang Huang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | | | | | | | - Dong-Hui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Ji-Sen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan City, 701, Taiwan.
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Academy for Advanced Interdisciplinary Studies, Nanjing, 210095, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, China.
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18
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Li W, Wang T, Ma Y, Wang N, Wang W, Tang J, Zhang C, Hou X, Hou H. Ectopic Expression of BcCUC2 Involved in Sculpting the Leaf Margin Serration in Arabidopsis thaliana. Genes (Basel) 2023; 14:1272. [PMID: 37372452 DOI: 10.3390/genes14061272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Leaf margin serration is a morphological characteristic in plants. The CUC2 (CUP-SHAPED COTYLEDON 2) gene plays an important role in the outgrowth of leaf teeth and enhances leaf serration via suppression of growth in the sinus. In this study, we isolated the BcCUC2 gene from Pak-choi (Brassica rapa ssp. chinensis), which contains a 1104 bp coding sequence, encoding 367 amino acid residues. Multiple sequence alignment exhibited that the BcCUC2 gene has a typical conserved NAC domain, and phylogenetic relationship analysis showed that the BcCUC2 protein has high identity with Cruciferae plants (Brassica oleracea, Arabidopsis thaliana, and Cardamine hirsuta). The tissue-specific expression analysis displayed that the BcCUC2 gene has relatively high transcript abundance in floral organs. Meanwhile, the expression profile of BcCUC2 was relatively higher in the '082' lines with serrate leaf margins than the '001' lines with smooth leaf margins in young leaves, roots, and hypocotyls. In addition, the transcript level of BcCUC2 was up-regulated by IAA and GA3 treatment, especially at 1-3 h. The subcellular localization assay demonstrated that BcCUC2 was a nuclear-target protein. Furthermore, leaf serration occurred, and the number of the inflorescence stem was increased in the transgenic Arabidopsis thaliana plants' overexpressed BcCUC2 gene. These data illustrated that BcCUC2 is involved in the development of leaf margin serration, lateral branches, and floral organs, contributing to further uncovering and perfecting the regulation mechanism of leaf serration in Pak-choi.
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Affiliation(s)
- Wanqi Li
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Tongtong Wang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yu Ma
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Nan Wang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Wenjing Wang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Jun Tang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Changwei Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hualan Hou
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
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19
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Yang Q, Yuan C, Cong T, Zhang Q. The Secrets of Meristems Initiation: Axillary Meristem Initiation and Floral Meristem Initiation. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091879. [PMID: 37176937 PMCID: PMC10181267 DOI: 10.3390/plants12091879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023]
Abstract
The branching phenotype is an extremely important agronomic trait of plants, especially for horticultural crops. It is not only an important yield character of fruit trees, but also an exquisite ornamental trait of landscape trees and flowers. The branching characteristics of plants are determined by the periodic initiation and later development of meristems, especially the axillary meristem (AM) in the vegetative stage and the floral meristem (FM) in the reproductive stage, which jointly determine the above-ground plant architecture. The regulation of meristem initiation has made great progress in model plants in recent years. Meristem initiation is comprehensively regulated by a complex regulatory network composed of plant hormones and transcription factors. However, as it is an important trait, studies on meristem initiation in horticultural plants are very limited, and the mechanism of meristem initiation regulation in horticultural plants is largely unknown. This review summarizes recent research advances in axillary meristem regulation and mainly reviews the regulatory networks and mechanisms of AM and FM initiation regulated by transcription factors and hormones. Finally, considering the existing problems in meristem initiation studies and the need for branching trait improvement in horticulture plants, we prospect future studies to accelerate the genetic improvement of the branching trait in horticulture plants.
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Affiliation(s)
- Qingqing Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Cunquan Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tianci Cong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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20
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Yang F, Njogu MK, Hesbon O, Wang Y, Lou Q, Cheng C, Zhou J, Li J, Chen J. Epistatic interaction between CsCEN and CsSHBY in regulating indeterminate/determinate growth of lateral branch in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:112. [PMID: 37052719 DOI: 10.1007/s00122-023-04350-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/20/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Two genetic loci, det-ma (CsCEN) and det-lb, showed epistatic interaction on indeterminate/determinate growth of LB in cucumber. CsSHBY was identified as the candidate gene for det-lb locus. Plant architecture depends on the spatial regulation of meristems from both main axis (MA) and lateral branches (LBs). Fate (indeterminate or determinate) of these meristems is a crucial source of architectural diversity determining crop productivity and management. CENTRORADIALIS/TERMINAL FLOWER 1/SELF-PRUNING (CETS) gene family have been well known as pivotal regulators for indeterminate/determinate growth of MA. Nevertheless, genes that regulate LB indeterminacy/determinacy remained unclear. Cucumber (Cucumis sativus L.) has typical monopodial growth and multiple lateral branches. Both MA and LBs had indeterminate or determinate growth, and indeterminate/determinate growth of LB was controlled by two distinct loci, det-ma (CsCEN) and det-lb. In our study, based on bulked segregant analysis (BSA) method, the det-lb locus was mapped on a 60.6 kb region on chromosome 1 harboring only one gene CsaV3_1G044330, which encoded a putative vacuolar-sorting protein (designated as CsSHBY). Multipoint mutations in CsSHBY were identified in D082 and D226, compared with CCMC, including nonsynonymous SNP mutations and a 6-bp deletion in exons. Further, qPCR showed that CsSHBY was highly expressed in lateral bud of CCMC, suggesting that CsSHBY might play an active role in regulating indeterminate/determinate growth of LB. Genetic analyses showed that det-ma (CsCEN) had an epistatic effect on det-lb (CsSHBY), and CsCEN could activate CsSHBY promoter by Dual luciferase and GUS activity assays. Meanwhile, Cscen or Csshby was found to influence auxin contents and CsYUCs and CsPINs expression levels. These findings provided new insights into precisely optimizing plant architecture for yield improvements.
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Affiliation(s)
- Fan Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Martin Kagiki Njogu
- Department of Plant Science, Chuka University, P.O. Box 109-60400, Chuka, Kenya
| | - Obel Hesbon
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuhui Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qunfeng Lou
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Cheng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junguo Zhou
- College of Horticulture and Landscape, Henan Institute of Science and Technology, Xinxiang, 453000, China.
| | - Ji Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jinfeng Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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21
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Yang Q, Cong T, Yao Y, Cheng T, Yuan C, Zhang Q. KNOX Genes Were Involved in Regulating Axillary Bud Formation of Chrysanthemum × morifolium. Int J Mol Sci 2023; 24:ijms24087081. [PMID: 37108245 PMCID: PMC10138332 DOI: 10.3390/ijms24087081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Branching is an important agronomic and economic trait in cut chrysanthemums. The axillary meristem (AM) formation of the axillary buds of cut chrysanthemums has a decisive role in its branching characteristics. However, little is known about the regulation mechanism of axillary meristem formation in chrysanthemums at the molecular level. Members of the Homeobox gene family especially genes belonging to the class I KNOX branch play a key role in regulating the axillary bud growth and development processes of plants. In this study, three genes belonging to the class I KNOX branch, CmKNAT1, CmKNAT6, and CmSTM were cloned from chrysanthemums, and their functions in regulating axillary bud formation were examined. The subcellular localization test showed that these three KNOX genes were expressed in the nucleus, so all of them might function as transcription factors. The results of the expression profile analysis showed that these three KNOX genes were highly expressed in the AM formation stage of axillary buds. Overexpression of KNOX genes result in a wrinkled leaf phenotype in tobacco and Arabidopsis, which may be related to the excessive division of leaf cells, resulting in the proliferation of leaf tissue. Furthermore, overexpression of these three KNOX genes enhances the regeneration ability of tobacco leaves, indicating that these three KNOX genes may participate in the regulation of cell meristematic ability, thus promoting the formation of buds. In addition, the results of fluorescence quantitative testing showed that these three KNOX genes may promote the formation of chrysanthemum axillary buds by promoting the cytokinin pathway while inhibiting the auxin and gibberellin pathways. In conclusion, this study demonstrated that CmKNAT1, CmKNAT6, and CmSTM genes were involved in regulating axillary bud formation of Chrysanthemum × morifolium and preliminarily revealed the molecular mechanism of their regulation of AM formation. These findings may provide a theoretical basis and candidate gene resources for genetic engineering breeding of new varieties of cut chrysanthemums without lateral branches.
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Affiliation(s)
- Qingqing Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tianci Cong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Yicen Yao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Cunquan Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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22
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Yang T, Jiao Y, Wang Y. Stem Cell Basis of Shoot Branching. PLANT & CELL PHYSIOLOGY 2023; 64:291-296. [PMID: 36416577 DOI: 10.1093/pcp/pcac165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
During their postembryonic development, plants continuously form branches to conquer more space and adapt to changing environments. In seed plants, this is achieved by lateral branching, in which axillary meristems (AMs) initiate at the leaf axils to form axillary buds. The developmental potential of AMs to form shoot branches is the same as that of embryonic shoot apical meristems (SAMs). Recent studies in Arabidopsis thaliana have revealed the cellular origin of AMs and have identified transcription factors and phytohormones that regulate sequential steps leading to AM initiation. In particular, a group of meristematic cells detached from the SAM are key to AM initiation, which constitutes an excellent system for understanding stem cell fate and de novo meristem formation.
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Affiliation(s)
- Tingting Yang
- College of Life Sciences, University of Chinese Academy of Sciences, 19A Yuquan Rd., Shijingshan District, Beijing 100049, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Center for Quantitative Biology, Peking University, 5 Summer Palace Rd., Haidian District, Beijing 100871, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, 19A Yuquan Rd., Shijingshan District, Beijing 100049, China
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23
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Liu J, Qiao Y, Li C, Hou B. The NAC transcription factors play core roles in flowering and ripening fundamental to fruit yield and quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1095967. [PMID: 36909440 PMCID: PMC9996081 DOI: 10.3389/fpls.2023.1095967] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Fruits are derived from flowers and play an important role in human food, nutrition, and health. In general, flowers determine the crop yield, and ripening affects the fruit quality. Although transcription factors (TFs) only account for a small part of plant transcriptomes, they control the global gene expression and regulation. The plant-specific NAC (NAM, ATAF, and CUC) TFs constitute a large family evolving concurrently with the transition of both aquatic-to-terrestrial plants and vegetative-to-reproductive growth. Thus, NACs play an important role in fruit yield and quality by determining shoot apical meristem (SAM) inflorescence and controlling ripening. The present review focuses on the various properties of NACs together with their function and regulation in flower formation and fruit ripening. Hitherto, we have a better understanding of the molecular mechanisms of NACs in ripening through abscisic acid (ABA) and ethylene (ETH), but how NACs regulate the expression of the inflorescence formation-related genes is largely unknown. In the future, we should focus on the analysis of NAC redundancy and identify the pivotal regulators of flowering and ripening. NACs are potentially vital manipulation targets for improving fruit quantity and quality.
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Affiliation(s)
- Jianfeng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuyuan Qiao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cui Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bingzhu Hou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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24
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Nicolas A, Maugarny-Calès A, Adroher B, Chelysheva L, Li Y, Burguet J, Bågman AM, Smit ME, Brady SM, Li Y, Laufs P. De novo stem cell establishment in meristems requires repression of organ boundary cell fate. THE PLANT CELL 2022; 34:4738-4759. [PMID: 36029254 PMCID: PMC9709991 DOI: 10.1093/plcell/koac269] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/24/2022] [Indexed: 05/27/2023]
Abstract
Stem cells play important roles in animal and plant biology, as they sustain morphogenesis and tissue replenishment following aging or injury. In plants, stem cells are embedded in multicellular structures called meristems. The formation of new meristems is essential for the plastic expansion of the highly branched shoot and root systems. In particular, axillary meristems (AMs) that produce lateral shoots arise from the division of boundary domain cells at the leaf base. The CUP-SHAPED COTYLEDON (CUC) genes are major determinants of the boundary domain and are required for AM initiation. However, how AMs get structured and how stem cells become established de novo remain elusive. Here, we show that two NGATHA-LIKE (NGAL) transcription factors, DEVELOPMENT-RELATED PcG TARGET IN THE APEX4 (DPA4)/NGAL3 and SUPPRESSOR OF DA1-1 7 (SOD7)/NGAL2, redundantly repress CUC expression in initiating AMs of Arabidopsis thaliana. Ectopic boundary fate leads to abnormal growth and organization of the AM and prevents de novo stem cell establishment. Floral meristems of the dpa4 sod7 double mutant show a similar delay in de novo stem cell establishment. Altogether, while boundary fate is required for the initiation of AMs, our work reveals how it is later repressed to allow proper meristem establishment and de novo stem cell niche formation.
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Affiliation(s)
- Antoine Nicolas
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
- Université Paris-Saclay, Orsay, 91405, France
| | - Aude Maugarny-Calès
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
- Université Paris-Saclay, Orsay, 91405, France
| | - Bernard Adroher
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Liudmila Chelysheva
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Yu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jasmine Burguet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Margot E Smit
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
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25
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The NGATHA-like Genes DPA4 and SOD7 Are Not Required for Stem Cell Specification during Embryo Development in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms231912007. [PMID: 36233309 PMCID: PMC9569844 DOI: 10.3390/ijms231912007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 01/09/2023] Open
Abstract
In plants, stem cells are embedded in structures called meristems. Meristems can be formed either during embryogenesis or during the plant's life such as, for instance, axillary meristems. While the regulation of the stem cell population in an established meristem is well described, how it is initiated in newly formed meristems is less well understood. Recently, two transcription factors of the NGATHA-like family, DEVELOPMENT-RELATED PcG TARGET IN THE APEX4 (DPA4)/NGAL3 and SUPPRESSOR OF DA1-1 7 (SOD7)/NGAL2 have been shown to facilitate de novo stem cell initiation in Arabidopsis thaliana axillary meristems. Here, we tested whether the DPA4 and SOD7 genes had a similar role during stem cell formation in embryo shoot apical meristems. Using DPA4 and SOD7 reporter lines, we characterized the expression pattern of these genes during embryo development, revealing only a partial overlap with the stem cell population. In addition, we showed that the expression of a stem cell reporter was not modified in dpa4-2 sod7-2 double mutant embryos compared to the wild type. Together, these observations suggest that DPA4 and SOD7 are not required for stem cell specification during embryo shoot apical meristem initiation. This work stresses the difference in the regulatory network leading to meristem formation during the embryonic and post-embryonic phases.
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26
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Best NB, Dilkes BP. Transcriptional responses to gibberellin in the maize tassel and control by DELLA domain proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:493-517. [PMID: 36050832 PMCID: PMC9826531 DOI: 10.1111/tpj.15961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The plant hormone gibberellin (GA) impacts plant growth and development differently depending on the developmental context. In the maize (Zea mays) tassel, application of GA alters floral development, resulting in the persistence of pistils. GA signaling is achieved by the GA-dependent turnover of DELLA domain transcription factors, encoded by dwarf8 (d8) and dwarf9 (d9) in maize. The D8-Mpl and D9-1 alleles disrupt GA signaling, resulting in short plants and normal tassel floret development in the presence of excess GA. However, D9-1 mutants are unable to block GA-induced pistil development. Gene expression in developing tassels of D8-Mpl and D9-1 mutants and their wild-type siblings was determined upon excess GA3 and mock treatments. Using GA-sensitive transcripts as reporters of GA signaling, we identified a weak loss of repression under mock conditions in both mutants, with the effect in D9-1 being greater. D9-1 was also less able to repress GA signaling in the presence of excess GA3 . We treated a diverse set of maize inbred lines with excess GA3 and measured the phenotypic consequences on multiple aspects of development (e.g., height and pistil persistence in tassel florets). Genotype affected all GA-regulated phenotypes but there was no correlation between any of the GA-affected phenotypes, indicating that the complexity of the relationship between GA and development extends beyond the two-gene epistasis previously demonstrated for GA and brassinosteroid biosynthetic mutants.
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Affiliation(s)
- Norman B. Best
- USDAAgriculture Research Service, Plant Genetics Research UnitColumbiaMissouri65211USA
| | - Brian P. Dilkes
- Department of BiochemistryPurdue University; West LafayetteIndiana47907USA
- Center for Plant BiologyPurdue UniversityWest LafayetteIndiana47907USA
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27
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Peng X, Feng C, Wang YT, Zhang X, Wang YY, Sun YT, Xiao YQ, Zhai ZF, Zhou X, Du BY, Wang C, Liu Y, Li TH. miR164g- MsNAC022 acts as a novel module mediating drought response by transcriptional regulation of reactive oxygen species scavenging systems in apple. HORTICULTURE RESEARCH 2022; 9:uhac192. [PMID: 36338839 PMCID: PMC9630969 DOI: 10.1093/hr/uhac192] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 08/22/2022] [Indexed: 05/27/2023]
Abstract
Under drought stress, reactive oxygen species (ROS) overaccumulate as a secondary stress that impairs plant performance and thus severely reduces crop yields. The mitigation of ROS levels under drought stress is therefore crucial for drought tolerance. MicroRNAs (miRNAs) are critical regulators of plant development and stress responses. However, the complex molecular regulatory mechanism by which they function during drought stress, especially in drought-triggered ROS scavenging, is not fully understood. Here, we report a newly identified drought-responsive miRNA, miR164g, in the wild apple species Malus sieversii and elucidate its role in apple drought tolerance. Our results showed that expression of miR164g is significantly inhibited under drought stress and it can specifically cleave transcripts of the transcription factor MsNAC022 in M. sieversii. The heterologous accumulation of miR164g in Arabidopsis thaliana results in enhanced sensitivity to drought stress, while overexpression of MsNAC022 in Arabidopsis and the cultivated apple line 'GL-3' (Malus domestica Borkh.) lead to enhanced tolerance to drought stress by raising the ROS scavenging enzymes activity and related genes expression levels, particularly PEROXIDASE (MsPOD). Furthermore, we showed that expression of MsPOD is activated by MsNAC022 in transient assays. Interestingly, Part1 (P1) region is the key region for the positive regulation of MsPOD promoter by MsNAC022, and the different POD expression patterns in M. sieversii and M. domestica is attributed to the specific fragments inserted in P1 region of M. sieversii. Our findings reveal the function of the miR164g-MsNAC022 module in mediating the drought response of M. sieversii and lay a foundation for breeding drought-tolerant apple cultivars.
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Affiliation(s)
- Xiang Peng
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chen Feng
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yan-Tao Wang
- Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiang Zhang
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yan-Yan Wang
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yue-Ting Sun
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yu-Qin Xiao
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ze-Feng Zhai
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xin Zhou
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Bing-Yang Du
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chao Wang
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yang Liu
- Corresponding authors. E-mails: ,
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Lee YK, Kumari S, Olson A, Hauser F, Ware D. Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis. Int J Mol Sci 2022; 23:ijms23158665. [PMID: 35955798 PMCID: PMC9369202 DOI: 10.3390/ijms23158665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
In plants, vegetative and reproductive development are associated with agronomically important traits that contribute to grain yield and biomass. Zinc finger homeodomain (ZF-HD) transcription factors (TFs) constitute a relatively small gene family that has been studied in several model plants, including Arabidopsis thaliana L. and Oryza sativa L. The ZF-HD family members play important roles in plant growth and development, but their contribution to the regulation of plant architecture remains largely unknown due to their functional redundancy. To understand the gene regulatory network controlled by ZF-HD TFs, we analyzed multiple loss-of-function mutants of ZF-HD TFs in Arabidopsis that exhibited morphological abnormalities in branching and flowering architecture. We found that ZF-HD TFs, especially HB34, negatively regulate the expression of miR157 and positively regulate SQUAMOSA PROMOTER BINDING-LIKE 10 (SPL10), a target of miR157. Genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq) analysis revealed that miR157D and SPL10 are direct targets of HB34, creating a feed-forward loop that constitutes a robust miRNA regulatory module. Network motif analysis contains overrepresented coherent type IV feedforward motifs in the amiR zf-HD and hbq mutant background. This finding indicates that miRNA-mediated ZF-HD feedforward modules modify branching and inflorescence architecture in Arabidopsis. Taken together, these findings reveal a guiding role of ZF-HD TFs in the regulatory network module and demonstrate its role in plant architecture in Arabidopsis.
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Affiliation(s)
- Young Koung Lee
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Institute of Plasma Technology, Korea Institute of Fusion Energy, 37, Dongjangsan-ro, Gunsan-si 54004, Korea
- Correspondence: (Y.K.L.); (D.W.)
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Felix Hauser
- Division of Biological Sciences, University of California–San Diego, La Jolla, CA 92093, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- USDA-ARS, Robert W. Holley Center, Ithaca, NY 14853, USA
- Correspondence: (Y.K.L.); (D.W.)
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29
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Zhang L, Fang W, Chen F, Song A. The Role of Transcription Factors in the Regulation of Plant Shoot Branching. PLANTS (BASEL, SWITZERLAND) 2022; 11:1997. [PMID: 35956475 PMCID: PMC9370718 DOI: 10.3390/plants11151997] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022]
Abstract
Transcription factors, also known as trans-acting factors, balance development and stress responses in plants. Branching plays an important role in plant morphogenesis and is closely related to plant biomass and crop yield. The apical meristem produced during plant embryonic development repeatedly produces the body of the plant, and the final aerial structure is regulated by the branching mode generated by axillary meristem (AM) activities. These branching patterns are regulated by two processes: AM formation and axillary bud growth. In recent years, transcription factors involved in regulating these processes have been identified. In addition, these transcription factors play an important role in various plant hormone pathways and photoresponses regulating plant branching. In this review, we start from the formation and growth of axillary meristems, including the regulation of hormones, light and other internal and external factors, and focus on the transcription factors involved in regulating plant branching and development to provide candidate genes for improving crop architecture through gene editing or directed breeding.
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Affiliation(s)
| | | | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (W.F.)
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (W.F.)
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30
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Du Q, Lv W, Guo Y, Yang J, Wang S, Li WX. MIR164b represses iron uptake by regulating the NAC domain transcription factor5-Nuclear Factor Y, Subunit A8 module in Arabidopsis. PLANT PHYSIOLOGY 2022; 189:1095-1109. [PMID: 35285505 PMCID: PMC9157116 DOI: 10.1093/plphys/kiac114] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Recent findings have revealed the important roles of microRNAs (miRNAs) in the secondary responses to oxidative damage caused by iron (Fe) excess. However, the functional importance of miRNAs in plant responses to Fe deficiency remains to be explored. Here, we show that the expression level of miR164 in Arabidopsis (Arabidopsis thaliana) roots was repressed by Fe deficiency. Primary root length, lateral root number, ferric reductase activity, and mRNA abundance of IRON-REGULATED TRANSPORTER1 (IRT1) and FERRIC REDUCTION OXIDASE2 (FRO2) were higher in the mir164b mutant than in the wild-type (WT) under Fe-deficient conditions. Analysis of the Fe concentrations and ferric reductase activities in the roots of miR164 knockdown transgenic plants showed that members of the miR164 family had different functions in Fe-deficiency responses. Promoter::GUS analysis showed that NAM/ATAF/CUC (NAC) domain transcription factor5 (NAC5) is regulated at both transcriptional and posttranscriptional levels under Fe-deficient conditions. Transgenic Arabidopsis plants overexpressing NAC5 were more tolerant of Fe deficiency than the WT. NAC5 has transactivation activity and directly transactivates the expression of Nuclear Factor Y, Subunit A8 (NFYA8), as demonstrated by chromatin immunoprecipitation followed by quantitative polymerase chain reaction, electrophoretic mobility shift assay (EMSA), and dual-luciferase reporter assay. Like overexpression of NAC5, overexpression of NFYA8 increases primary root length, lateral root number, ferric reductase activity, and mRNA abundance of IRT1 and FRO2 under Fe-deficient conditions. Thus, MIR164b is important for Fe-deficiency responses by its regulation of the NAC5-NFYA8 module.
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Affiliation(s)
- Qingguo Du
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenshuai Lv
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Guo
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Juan Yang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shanhong Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wen-Xue Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Liang J, Wu Z, Zheng J, Koskela EA, Fan L, Fan G, Gao D, Dong Z, Hou S, Feng Z, Wang F, Hytönen T, Wang H. The GATA factor HANABA TARANU promotes runner formation by regulating axillary bud initiation and outgrowth in cultivated strawberry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1237-1254. [PMID: 35384101 DOI: 10.1111/tpj.15759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
A runner, as an elongated branch, develops from the axillary bud (AXB) in the leaf axil and is crucial for the clonal propagation of cultivated strawberry (Fragaria × ananassa Duch.). Runner formation occurs in at least two steps: AXB initiation and AXB outgrowth. HANABA TARANU (HAN ) encodes a GATA transcription factor that affects AXB initiation in Arabidopsis and promotes branching in grass species, but the underlying mechanism is largely unknown. Here, the function of a strawberry HAN homolog FaHAN in runner formation was characterized. FaHAN transcripts can be detected in the leaf axils. Overexpression (OE) of FaHAN increased the number of runners, mainly by enhancing AXB outgrowth, in strawberry. The expression of the strawberry homolog of BRANCHED1 , a key inhibitor of AXB outgrowth in many plant species, was significantly downregulated in the AXBs of FaHAN -OE lines, whereas the expression of the strawberry homolog of SHOOT MERISTEMLESS, a marker gene for AXB initiation in Arabidopsis, was upregulated. Moreover, several genes of gibberellin biosynthesis and cytokinin signaling pathways were activated, whereas the auxin response pathway genes were repressed. Further assays indicated that FaHAN could be directly activated by FaNAC2, the overexpression of which in strawberry also increased the number of runners. The silencing of FaNAC2 or FaHAN inhibited AXB initiation and led to a higher proportion of dormant AXBs, confirming their roles in the control of runner formation. Taken together, our results revealed a FaNAC2-FaHAN pathway in the control of runner formation and have provided a means to enhance the vegetative propagation of cultivated strawberry.
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Affiliation(s)
- Jiahui Liang
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | - Ze Wu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Zheng
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Elli A Koskela
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | - Lingjiao Fan
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Guangxun Fan
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | - Dehang Gao
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhenfei Dong
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shengfan Hou
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zekun Feng
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Feng Wang
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
- NIAB EMR, Kent, ME19 6BJ, UK
| | - Hongqing Wang
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
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32
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Nicolas A, Laufs P. Meristem Initiation and de novo Stem Cell Formation. FRONTIERS IN PLANT SCIENCE 2022; 13:891228. [PMID: 35557739 PMCID: PMC9087721 DOI: 10.3389/fpls.2022.891228] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Plant aerial development relies on meristem activity which ensures main body plant axis development during plant life. While the shoot apical meristem (SAM) formed in the embryo only contributes to the main stem, the branched structure observed in many plants relies on axillary meristems (AMs) formed post-embryonically. These AMs initiate from a few cells of the leaf axil that retain meristematic characteristics, increase in number, and finally organize into a structure similar to the SAM. In this review, we will discuss recent findings on de novo establishment of a stem cell population and its regulatory niche, a key step essential for the indeterminate fate of AMs. We stress that de novo stem cell formation is a progressive process, which starts with a transient regulatory network promoting stem cell formation and that is different from the one acting in functional meristems. This transient stage can be called premeristems and we discuss whether this concept can be extended to the formation of meristems other than AMs.
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Affiliation(s)
- Antoine Nicolas
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- Université Paris-Saclay, Orsay, France
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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Yi M, Yang H, Yang S, Wang J. Overexpression of SHORT-ROOT2 transcription factor enhances the outgrowth of mature axillary buds in poplar trees. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2469-2486. [PMID: 35107566 DOI: 10.1093/jxb/erac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
SHORT-ROOT (SHR) transcription factors play important roles in asymmetric cell division and radial patterning of Arabidopsis roots. In hybrid poplar (P. tremula × P. alba clone INRA 717-1B4), PtaSHR2 was preferentially expressed in axillary buds (AXBs) and transcriptionally up-regulated during AXB maturation and activation. Overexpression of SHR2 (PtSHR2OE) induced an enhanced outgrowth of AXBs below the bud maturation point, with a simultaneous transition of an active shoot apex into an arrested terminal bud. The larger and more mature AXBs of PtSHR2OE trees revealed altered expression of genes involved in axillary meristem initiation and bud activation, as well as a higher ratio of cytokinin to auxin. To elucidate the underlying mechanism of PtSHR2OE-induced high branching, subsequent molecular and biochemical studies showed that compared with wild-type trees, decapitation induced a quicker bud outburst in PtSHR2OE trees, which could be fully inhibited by exogenous application of auxin or cytokinin biosynthesis inhibitor, but not by N-1-naphthylphthalamic acid. Our results indicated that overexpression of PtSHR2B disturbed the internal hormonal balance in AXBs by interfering with the basipetal transport of auxin, rather than causing auxin biosynthesis deficiency or auxin insensitivity, thereby releasing mature AXBs from apical dominance and promoting their outgrowth.
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Affiliation(s)
- Minglei Yi
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Heyu Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Shaohui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Jiehua Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
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Zhang C, Chang W, Li X, Yang B, Zhang L, Xiao Z, Li J, Lu K. Transcriptome and Small RNA Sequencing Reveal the Mechanisms Regulating Harvest Index in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:855486. [PMID: 35444672 PMCID: PMC9014204 DOI: 10.3389/fpls.2022.855486] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Harvest index (HI), the ratio of harvested seed weight to total aboveground biomass weight, is an economically critical value reflecting the convergence of complex agronomic traits. HI values in rapeseed (Brassica napus) remain much lower than in other major crops, and the underlying regulatory network is largely unknown. In this study, we performed mRNA and small RNA sequencing to reveal the mechanisms shaping HI in B. napus during the seed-filling stage. A total of 8,410 differentially expressed genes (DEGs) between high-HI and low-HI accessions in four tissues (silique pericarp, seed, leaves, and stem) were identified. Combining with co-expression network, 72 gene modules were identified, and a key gene BnaSTY46 was found to participate in retarded establishment of photosynthetic capacity to influence HI. Further research found that the genes involved in circadian rhythms and response to stimulus may play important roles in HI and that their transcript levels were modulated by differentially expressed microRNAs (DEMs), and we identified 903 microRNAs (miRNAs), including 46 known miRNAs and 857 novel miRNAs. Furthermore, transporter activity-related genes were critical to enhancing HI in good cultivation environments. Of 903 miRNAs, we found that the bna-miR396-Bna.A06SRp34a/Bna.A01EMB3119 pair may control the seed development and the accumulation of storage compounds, thus contributing to higher HI. Our findings uncovered the underlying complex regulatory network behind HI and offer potential approaches to rapeseed improvement.
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Affiliation(s)
- Chao Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Wei Chang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiaodong Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Bo Yang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Liyuan Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Zhongchun Xiao
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiana Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Kun Lu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
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Ivanova Z, Minkov G, Gisel A, Yahubyan G, Minkov I, Toneva V, Baev V. The Multiverse of Plant Small RNAs: How Can We Explore It?
. Int J Mol Sci 2022; 23:ijms23073979. [PMID: 35409340 PMCID: PMC8999349 DOI: 10.3390/ijms23073979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/22/2022] Open
Abstract
Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20–24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes—microRNAs (miRNAs) and small interfering RNAs (siRNAs)—which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study.
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Affiliation(s)
- Zdravka Ivanova
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
| | - Georgi Minkov
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Andreas Gisel
- Institute of Biomedical Technologies (ITB), CNR, 70126 Bari, Italy;
| | - Galina Yahubyan
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Ivan Minkov
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Valentina Toneva
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Vesselin Baev
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
- Correspondence:
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36
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Dong Q, Hu B, Zhang C. microRNAs and Their Roles in Plant Development. FRONTIERS IN PLANT SCIENCE 2022; 13:824240. [PMID: 35251094 PMCID: PMC8895298 DOI: 10.3389/fpls.2022.824240] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 05/26/2023]
Abstract
Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.
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Affiliation(s)
- Qingkun Dong
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Binbin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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RNA-Binding Protein MAC5A Is Required for Gibberellin-Regulated Stamen Development. Int J Mol Sci 2022; 23:ijms23042009. [PMID: 35216125 PMCID: PMC8874600 DOI: 10.3390/ijms23042009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 11/23/2022] Open
Abstract
The development of floral organs is coordinated by an elaborate network of homeotic genes, and gibberellin (GA) signaling is involved in floral organ development; however, the underlying molecular mechanisms remain elusive. In the present study, we found that MOS4-ASSOCIATED COMPLEX 5A (MAC5A), which is a protein containing an RNA-binding motif, was involved in the development of sepals, petals, and stamens; either the loss or gain of MAC5A function resulted in stamen malformation and a reduced seed set. The exogenous application of GA considerably exacerbated the defects in mac5a null mutants, including fewer stamens and male sterility. MAC5A was predominantly expressed in pollen grains and stamens, and overexpression of MAC5A affected the expression of homeotic genes such as APETALA1 (AP1), AP2, and AGAMOUS (AG). MAC5A may interact with RABBIT EARS (RBE), a repressor of AG expression in Arabidopsis flowers. The petal defect in rbe null mutants was at least partly rescued in mac5a rbe double mutants. These findings suggest that MAC5A is a novel factor that is required for the normal development of stamens and depends on the GA signaling pathway.
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Aslam M, She Z, Jakada BH, Fakher B, Greaves JG, Yan M, Chen Y, Zheng P, Cheng Y, Qin Y. Interspecific complementation-restoration of phenotype in Arabidopsis cuc2cuc3 mutant by sugarcane CUC2 gene. BMC PLANT BIOLOGY 2022; 22:47. [PMID: 35065620 PMCID: PMC8783490 DOI: 10.1186/s12870-022-03440-z] [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: 04/17/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In plants, a critical balance between differentiation and proliferation of stem cells at the shoot apical meristem zone is essential for proper growth. The spatiotemporal regulation of some crucial genes dictates the formation of a boundary within and around budding organs. The boundary plays a pivotal role in distinguishing one tissue type from another and provides a defined shape to the organs at their developed stage. NAM/CUC subfamily of the NAC transcription factors control the boundary formation during meristematic development. RESULTS Here, we have identified the CUP-SHAPED COTYLEDON (CUC) genes in sugarcane and named SsCUC2 (for the orthologous gene of CUC1 and CUC2) and SsCUC3. The phylogenetic reconstruction showed that SsCUCs occupy the CUC2 and CUC3 clade together with monocots, whereas eudicot CUC2 and CUC3 settled separately in the different clade. The structural analysis of CUC genes showed that most of the CUC3 genes were accompanied by an intron gain during eudicot divergence. Besides, the study of SsCUCs expression in the RNA-seq obtained during different stages of ovule development revealed that SsCUCs express in developing young tissues, and the expression of SsCUC2 is regulated by miR164. We also demonstrate that SsCUC2 (a monocot) could complement the cuc2cuc3 mutant phenotype of Arabidopsis (eudicot). CONCLUSIONS This study further supports that CUC2 has diverged in CUC1 and CUC2 during the evolution of monocots and eudicots from ancestral plants. The functional analysis of CUC expression patterns during sugarcane ovule development and ectopic expression of SsCUC2 in Arabidopsis showed that SsCUC2 has a conserved role in boundary formation. Overall, these findings improve our understanding of the functions of sugarcane CUC genes. Our results reveal the crucial functional role of CUC genes in sugarcane.
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Affiliation(s)
- Mohammad Aslam
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Zeyuan She
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Bello Hassan Jakada
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Beenish Fakher
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Joseph G Greaves
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Maokai Yan
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Yingzhi Chen
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Ping Zheng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Yan Cheng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Yuan Qin
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China.
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China.
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Li G, Xu B, Zhang Y, Xu Y, Khan NU, Xie J, Sun X, Guo H, Wu Z, Wang X, Zhang H, Li J, Xu J, Wang W, Zhang Z, Li Z. RGN1 controls grain number and shapes panicle architecture in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:158-167. [PMID: 34498389 PMCID: PMC8710824 DOI: 10.1111/pbi.13702] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 05/29/2023]
Abstract
Yield in rice is determined mainly by panicle architecture. Using map-based cloning, we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle architecture. Mutation of RGN1 caused an absence of lateral grains on secondary branches. We demonstrated that RGN1 controls lateral grain formation by regulation of LONELY GUY (LOG) expression, thus controlling grain number and shaping panicle architecture. A novel favourable allele, RGN1C , derived from the Or-I group in wild rice affected panicle architecture by means longer panicles. Identification of RGN1 provides a theoretical basis for understanding the molecular mechanism of lateral grain formation in rice; RGN1 will be an important gene resource for molecular breeding for higher yield.
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Affiliation(s)
- Gangling Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Bingxia Xu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yanpei Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yawen Xu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Najeeb Ullah Khan
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jianyin Xie
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xingming Sun
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Haifeng Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zhenyuan Wu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xueqiang Wang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jianlong Xu
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Wensheng Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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Vargas-Hernández BY, Núñez-Muñoz L, Calderón-Pérez B, Xoconostle-Cázares B, Ruiz-Medrano R. The NAC Transcription Factor ANAC087 Induces Aerial Rosette Development and Leaf Senescence in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:818107. [PMID: 35283930 PMCID: PMC8905224 DOI: 10.3389/fpls.2022.818107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/11/2022] [Indexed: 05/22/2023]
Abstract
CmNACP1 mRNA has been shown to move long distance through the phloem in Cucurbita maxima (pumpkin) and through a graft junction. Whereas the phloem transport of several different mRNAs has been documented in other systems as well, its function remains, for most of these RNAs, largely unknown. To gain insight into the possible role of these RNAs, we searched for the closest homologs of CmNACP1 in Arabidopsis, a model plant much more amenable for analysis. A phylogenetic approach using the predicted NAC domain indicated that ANAC059, ANAC092, ANAC079, ANAC100, ANAC046, and ANAC087 form a single clade with CmNACP1. In the present work, we analyzed the possible function of the ANAC087 gene in more detail. The promoter region of this gene directed expression in the vasculature, and also in trichomes, stem, apexes, and developing flowers which supports the notion that ANAC087 and CmNACP1 are orthologs. Overexpression of the ANAC087 gene induced increased branching in inflorescence stem, and also development of ectopic or aerial rosettes in T1 and T2 plants. Furthermore, overexpression of ANAC087 leads to accelerated leaf senescence in 44 days post-germination (dpg). Interestingly, a similar phenotype was observed in plants expressing the ANAC087 gene upstream region, also showing an increase in ANAC087 transcript levels. Finally, the results shown in this work indicate a role for ANAC087 in leaf senescence and also in rosette development.
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Wang Y. Stem Cell Basis for Fractal Patterns: Axillary Meristem Initiation. FRONTIERS IN PLANT SCIENCE 2021; 12:805434. [PMID: 34975997 PMCID: PMC8718902 DOI: 10.3389/fpls.2021.805434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Whereas stem cell lineages are of enormous importance in animal development, their roles in plant development have only been appreciated in recent years. Several specialized lineages of stem cells have been identified in plants, such as meristemoid mother cells and vascular cambium, as well as those located in the apical meristems. The initiation of axillary meristems (AMs) has recently gained intensive attention. AMs derive from existing stem cell lineages that exit from SAMs and define new growth axes. AMs are in fact additional rounds of SAMs, and display the same expression patterns and functions as the embryonic SAM, creating a fractal branching pattern. Their formation takes place in leaf-meristem boundaries and mainly comprises two key stages. The first stage is the maintenance of the meristematic cell lineage in an undifferentiated state. The second stage is the activation, proliferation, and re-specification to form new stem cell niches in AMs, which become the new postembryonic "fountain of youth" for organogenesis. Both stages are tightly regulated by spatially and temporally interwound signaling networks. In this mini-review, I will summarize the most up-to-date understanding of AM establishment and mainly focus on how the leaf axil meristematic cell lineage is actively maintained and further activated to become CLV3-expressed stem cells, which involves phytohormonal cascades, transcriptional regulations, epigenetic modifications, as well as mechanical signals.
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Garighan J, Dvorak E, Estevan J, Loridon K, Huettel B, Sarah G, Farrera I, Leclercq J, Grynberg P, Coiti Togawa R, Mota do Carmo Costa M, Costes E, Andrés F. The Identification of Small RNAs Differentially Expressed in Apple Buds Reveals a Potential Role of the Mir159-MYB Regulatory Module during Dormancy. PLANTS (BASEL, SWITZERLAND) 2021; 10:2665. [PMID: 34961136 PMCID: PMC8703471 DOI: 10.3390/plants10122665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022]
Abstract
Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warmer temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of 17 micro RNAs (miRNAs) that change their pattern of expression in apple buds during dormancy. Furthermore, the functional analysis of their predicted target genes suggests a main role of the 17 miRNAs in phenylpropanoid biosynthesis, gene regulation, plant development and growth, and response to stimulus. Finally, we studied the conservation of the Arabidopsis thaliana regulatory miR159-MYB module in apple in the context of the plant hormone abscisic acid homeostasis.
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Affiliation(s)
- Julio Garighan
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Etienne Dvorak
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Joan Estevan
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Karine Loridon
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Bruno Huettel
- Genome Centre, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany;
| | - Gautier Sarah
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Isabelle Farrera
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Julie Leclercq
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
- UMR AGAP Institute, CIRAD, F-34398 Montpellier, France
| | - Priscila Grynberg
- Bioinformatica Laboratory, Embrapa Recursos Genéticos e Biotecnologia—Cenargen, Brasilia 02372, Brazil; (P.G.); (R.C.T.); (M.M.d.C.C.)
| | - Roberto Coiti Togawa
- Bioinformatica Laboratory, Embrapa Recursos Genéticos e Biotecnologia—Cenargen, Brasilia 02372, Brazil; (P.G.); (R.C.T.); (M.M.d.C.C.)
| | - Marcos Mota do Carmo Costa
- Bioinformatica Laboratory, Embrapa Recursos Genéticos e Biotecnologia—Cenargen, Brasilia 02372, Brazil; (P.G.); (R.C.T.); (M.M.d.C.C.)
| | - Evelyne Costes
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Fernando Andrés
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
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Deng Z, Wu H, Li D, Li L, Wang Z, Yuan W, Xing Y, Li C, Liang D. Root-to-Shoot Long-Distance Mobile miRNAs Identified from Nicotiana Rootstocks. Int J Mol Sci 2021; 22:12821. [PMID: 34884626 PMCID: PMC8657949 DOI: 10.3390/ijms222312821] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/23/2022] Open
Abstract
Root-derived mobile signals play critical roles in coordinating a shoot's response to underground conditions. However, the identification of root-to-shoot long-distance mobile signals has been scant. In this study, we aimed to characterize root-to-shoot endogenous mobile miRNAs by using an Arabidopsis/Nicotiana interfamilial heterograft in which these two taxonomically distant species with clear genetic backgrounds had sufficient diversity in differentiating miRNA sources. Small RNA deep sequencing analysis revealed that 82 miRNAs from the Arabidopsis scion could travel through the graft union to reach the rootstock, whereas only a very small subset of miRNA (6 miRNAs) preferred the root-to-shoot movement. We demonstrated in an ex vivo RNA imaging experiment that the root-to-shoot mobile Nb-miR164, Nb-miR395 and Nb-miR397 were targeted to plasmodesmata using the bacteriophage coat protein MS2 system. Furthermore, the Nb-miR164 was shown to move from the roots to the shoots to induce phenotypic changes when its overexpressing line was used as rootstock, strongly supporting that root-derived Nb-miR164 was able to modify the scion trait via its long-distance movement.
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Affiliation(s)
- Zhuying Deng
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou 434023, China; (Z.D.); (H.W.); (D.L.); (L.L.); (Z.W.)
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434023, China
| | - Huiyan Wu
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou 434023, China; (Z.D.); (H.W.); (D.L.); (L.L.); (Z.W.)
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434023, China
| | - Dongyi Li
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou 434023, China; (Z.D.); (H.W.); (D.L.); (L.L.); (Z.W.)
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434023, China
| | - Luping Li
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou 434023, China; (Z.D.); (H.W.); (D.L.); (L.L.); (Z.W.)
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434023, China
| | - Zhipeng Wang
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou 434023, China; (Z.D.); (H.W.); (D.L.); (L.L.); (Z.W.)
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434023, China
| | - Wenya Yuan
- Hubei Collaborative Innovation Center for Green Transformation of BioResources, State Key Lab of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Yongzhong Xing
- National Center of Plant Gene Research (Wuhan), National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA 6150, Australia;
| | - Dacheng Liang
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou 434023, China; (Z.D.); (H.W.); (D.L.); (L.L.); (Z.W.)
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434023, China
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Wu B, Li Y, Li J, Xie Z, Luan M, Gao C, Shi Y, Chen S. Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L. Int J Mol Sci 2021; 22:ijms222111989. [PMID: 34769433 PMCID: PMC8584933 DOI: 10.3390/ijms222111989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
It is of significance to mine the structural genes related to the biosynthetic pathway of fatty acid (FA) and cellulose as well as explore the regulatory mechanism of alternative splicing (AS), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the biosynthesis of cannabinoids, FA and cellulose, which would enhance the knowledge of gene expression and regulation at post-transcriptional level in Cannabis sativa L. In this study, transcriptome, small RNA and degradome libraries of hemp 'Yunma No.1' were established, and comprehensive analysis was performed. As a result, a total of 154, 32 and 331 transcripts encoding key enzymes involved in the biosynthesis of cannabinoids, FA and cellulose were predicted, respectively, among which AS occurred in 368 transcripts. Moreover, 183 conserved miRNAs, 380 C. sativa-specific miRNAs and 7783 lncRNAs were predicted. Among them, 70 miRNAs and 17 lncRNAs potentially targeted 13 and 17 transcripts, respectively, encoding key enzymes or transporters involved in the biosynthesis of cannabinoids, cellulose or FA. Finally, the crosstalk between AS and miRNAs or lncRNAs involved in cannabinoids and cellulose was also predicted. In summary, all these results provided insights into the complicated network of gene expression and regulation in C. sativa.
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Affiliation(s)
- Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Yanni Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Jishuang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Zhenzhen Xie
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (M.L.); (C.G.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (M.L.); (C.G.)
| | - Yuhua Shi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
- Correspondence:
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Luo Z, Janssen BJ, Snowden KC. The molecular and genetic regulation of shoot branching. PLANT PHYSIOLOGY 2021; 187:1033-1044. [PMID: 33616657 PMCID: PMC8566252 DOI: 10.1093/plphys/kiab071] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/22/2021] [Indexed: 05/27/2023]
Abstract
The architecture of flowering plants exhibits both phenotypic diversity and plasticity, determined, in part, by the number and activity of axillary meristems and, in part, by the growth characteristics of the branches that develop from the axillary buds. The plasticity of shoot branching results from a combination of various intrinsic and genetic elements, such as number and position of nodes and type of growth phase, as well as environmental signals such as nutrient availability, light characteristics, and temperature (Napoli et al., 1998; Bennett and Leyser, 2006; Janssen et al., 2014; Teichmann and Muhr, 2015; Ueda and Yanagisawa, 2019). Axillary meristem initiation and axillary bud outgrowth are controlled by a complex and interconnected regulatory network. Although many of the genes and hormones that modulate branching patterns have been discovered and characterized through genetic and biochemical studies, there are still many gaps in our understanding of the control mechanisms at play. In this review, we will summarize our current knowledge of the control of axillary meristem initiation and outgrowth into a branch.
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Affiliation(s)
- Zhiwei Luo
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Bart J Janssen
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
| | - Kimberley C Snowden
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
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Chowdhury MR, Bahadur RP, Basak J. Genome-wide prediction of cauliflower miRNAs and lncRNAs and their roles in post-transcriptional gene regulation. PLANTA 2021; 254:72. [PMID: 34519918 DOI: 10.1007/s00425-021-03689-y] [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: 04/20/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
We have predicted miRNAs, their targets and lncRNAs from the genome of Brassica oleracea along with their functional annotation. Selected miRNAs and their targets are experimentally validated. Roles of these non-coding RNAs in post-transcriptional gene regulation are also deciphered. Cauliflower (Brassica oleracea var. Botrytis) is an important vegetable crop for its dietary and medicinal values with rich source of vitamins, dietary fibers, flavonoids and antioxidants. MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs), which regulate gene expression by inhibiting translation or by degrading messenger RNAs (mRNAs). On the other hand, long non-coding RNAs (lncRNAs) are responsible for the up regulation and the down regulation of transcription. Although the genome of cauliflower is reported, yet the roles of these ncRNAs in post-transcriptional gene regulation (PTGR) remain elusive. In this study, we have computationally predicted 355 miRNAs, of which 280 miRNAs are novel compared to miRBase 22.1. All the predicted miRNAs belong to 121 different families. We have also identified 934 targets of 125 miRNAs along with their functional annotation. These targets are further classified into biological processes, molecular functions and cellular components. Moreover, we have predicted 634 lncRNAs, of which 61 are targeted by 30 novel miRNAs. Randomly chosen 10 miRNAs and 10 lncRNAs are experimentally validated. Five miRNA targets including squamosa promoter-binding-like protein 9, homeobox-leucine zipper protein HDG12-like, NAC domain-containing protein 100, CUP-SHAPED COTYLEDON 1 and kinesin-like protein NACK2 of four miRNAs including bol-miR156a, bol-miR162a, bol-miR164d and bol-miR2673 are also experimentally validated. We have built network models of interactions between miRNAs and their target mRNAs, as well as between miRNAs and lncRNAs. Our findings enhance the knowledge of non-coding genome of cauliflower and their roles in PTGR, and might play important roles in improving agronomic traits of this economically important crop.
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Affiliation(s)
- Moumita Roy Chowdhury
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Jolly Basak
- Department of Biotechnology, Visva-Bharati University, Santiniketan, 731235, India.
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Zhan J, Chu Y, Wang Y, Diao Y, Zhao Y, Liu L, Wei X, Meng Y, Li F, Ge X. The miR164-GhCUC2-GhBRC1 module regulates plant architecture through abscisic acid in cotton. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1839-1851. [PMID: 33960609 PMCID: PMC8428825 DOI: 10.1111/pbi.13599] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/11/2021] [Accepted: 03/28/2021] [Indexed: 05/06/2023]
Abstract
Branching determines cotton architecture and production, but the underlying regulatory mechanisms remain unclear. Here, we report that the miR164-GhCUC2 (CUP-SHAPED COTYLEDON2) module regulates lateral shoot development in cotton and Arabidopsis. We generated OE-GhCUC2m (overexpression GhCUC2m) and STTM164 (short tandem target mimic RNA of miR164) lines in cotton and heterologous expression lines for gh-miR164, GhCUC2 and GhCUC2m in Arabidopsis to study the mechanisms controlling lateral branching. GhCUC2m overexpression resulted in a short-branch phenotype similar to STTM164. In addition, heterologous expression of GhCUC2m led to decreased number and length of branches compared with wild type, opposite to the effects of the OE-gh-pre164 line in Arabidopsis. GhCUC2 interacted with GhBRC1 and exhibited similar negative regulation of branching. Overexpression of GhBRC1 in the brc1-2 mutant partially rescued the mutant phenotype and decreased branch number. GhBRC1 directly bound to the NCED1 promoter and activated its transcription, leading to local abscisic acid (ABA) accumulation and response. Mutation of the NCED1 promoter disrupted activation by GhBRC1. This finding demonstrates a direct relationship between BRC1 and ABA signalling and places ABA downstream of BRC1 in the control of branching development. The miR164-GhCUC2-GhBRC1-GhNCED1 module provides a clear regulatory axis for ABA signalling to control plant architecture.
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Affiliation(s)
- Jingjing Zhan
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
| | - Yu Chu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
| | - Ye Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
| | - Yangyang Diao
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
| | - Yanyan Zhao
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
| | - Lisen Liu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
| | - Xi Wei
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
| | - Yuan Meng
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
| | - Fuguang Li
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
| | - Xiaoyang Ge
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
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López H, Schmitz G, Thoma R, Theres K. Super determinant1A, a RAWULdomain-containing protein, modulates axillary meristem formation and compound leaf development in tomato. THE PLANT CELL 2021; 33:2412-2430. [PMID: 34009392 PMCID: PMC8364250 DOI: 10.1093/plcell/koab121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/22/2021] [Indexed: 05/28/2023]
Abstract
Shoot branching and complex leaf development relies on the establishment of boundaries that precedes the formation of axillary meristems (AMs) and leaflets. The tomato (Solanum lycopersicum) super determinant mutant is compromised in both processes, due to a mutation in Sde1A. Sde1A encodes a protein with a RAWUL domain, which is also present in Polycomb Group Repressive Complex 1 (PRC1) RING finger proteins and WD Repeat Domain 48 proteins. Genetic analysis revealed that Sde1A and Bmi1A cooperate, whereas Bmi1C antagonizes both activities, indicating the existence of functionally opposing PRC1 complexes that interact with Sde1A. Sde1A is expressed at early stages of boundary development in a small group of cells in the center of the leaf-axil boundary, but its activity is required for meristem formation at later stages. This suggests that Sde1A and Bmi1A promote AM formation and complex leaf development by safeguarding a pool of cells in the developing boundary zones. Genetic and protein interaction analyses showed that Sde1A and Lateral suppressor (Ls) are components of the same genetic pathway. In contrast to ls, sde1a mutants are not compromised in inflorescence branching, suggesting that Sde1A is a potential target for breeding tomato cultivars with reduced side-shoot formation during vegetative development.
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Affiliation(s)
- Hernán López
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
| | - Gregor Schmitz
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
| | - Rahere Thoma
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
| | - Klaus Theres
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
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Feng J, Cheng L, Zhu Z, Yu F, Dai C, Liu Z, Guo WW, Wu XM, Kang C. GRAS transcription factor LOSS OF AXILLARY MERISTEMS is essential for stamen and runner formation in wild strawberry. PLANT PHYSIOLOGY 2021; 186:1970-1984. [PMID: 33890635 PMCID: PMC8331164 DOI: 10.1093/plphys/kiab184] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/03/2021] [Indexed: 05/19/2023]
Abstract
Axillary bud development is a major factor that impacts plant architecture. A runner is an elongated shoot that develops from axillary bud and is frequently used for clonal propagation of strawberry. However, the genetic control underlying runner production is largely unknown. Here, we identified and characterized loss of axillary meristems (lam), an ethyl methanesulfonate-induced mutant of the diploid woodland strawberry (Fragaria vesca) that lacked stamens in flowers and had reduced numbers of branch crowns and runners. The reduced branch crown and runner phenotypes were caused by a failure of axillary meristem initiation. The causative mutation of lam was located in FvH4_3g41310, which encodes a GRAS transcription factor, and was validated by a complementation test. lamCR mutants generated by CRISPR/Cas9 produced flowers without stamens and had fewer runners than the wild-type. LAM was broadly expressed in meristematic tissues. Gibberellic acid (GA) application induced runner outgrowth from the remaining buds in lam, but failed to do so at the empty axils of lam. In contrast, treatment with the GA biosynthesis inhibitor paclobutrazol converted the runners into branch crowns. Moreover, genetic studies indicated that lam is epistatic to suppressor of runnerless (srl), a mutant of FveRGA1 in the GA pathway, during runner formation. Our results demonstrate that LAM is required for stamen and runner formation and acts sequentially with GA from bud initiation to runner outgrowth, providing insights into the molecular regulation of these economically important organs in strawberry.
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Affiliation(s)
- Jia Feng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Laichao Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenying Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Feiqi Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunying Kang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Author for communication:
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Guo M, Long Y, Xu L, Zhang W, Liu T, Zhang C, Hou X, Li Y. CELL CYCLE SEITCH 52 regulates tillering by interacting with LATERAL SUPPRESSOR in non-heading Chinese cabbage. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 309:110934. [PMID: 34134841 DOI: 10.1016/j.plantsci.2021.110934] [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: 12/25/2020] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
With the discovery of essential genes regulating tillering, such as MONOCULM 1 (MOC1) in rice and LATERAL SUPPRESSOR (LAS in Arabidopsis, LS in tomato), research on tillering mechanisms has made great progress; however, the study of tillering in non-heading Chinese cabbage (NHCC) is rare. Here, we report that BcLAS, as a member of the GRAS family, plays an important role in the tillering of NHCC during its vegetative growth. BcLAS was almost not expressed in other examed parts except leaf axils throughout life. When the expression of BcLAS was silenced utilizing virus-induced gene silencing (VIGS) technology, we found that the tiller number of 'Maertou' decreased sharply. In 'Suzhouqing', overexpression of BcLAS significantly promoted tillering. BcCCS52, the orthologue to CELL CYCLE SEITCH 52 (CCS52), interacts with BcLAS. Downregulation of the expression of BcCCS52 promoted tillering of 'Suzhouqing'; therefore, we conclude that BcCCS52 plays a negative role in tillering regulation. Our findings reveal the tillering regulation mechanism of NHCCs at the vegetative stage and report an orthologue of CCS52 regulating tillering in NHCC.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Yan Long
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Lanlan Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Wei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China.
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