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Ma Y, Fu W, Wan S, Li Y, Mao H, Khalid E, Zhang W, Ming R. Gene Regulatory Network Controlling Flower Development in Spinach ( Spinacia oleracea L.). Int J Mol Sci 2024; 25:6127. [PMID: 38892313 PMCID: PMC11173220 DOI: 10.3390/ijms25116127] [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: 04/15/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Spinach (Spinacia oleracea L.) is a dioecious, diploid, wind-pollinated crop cultivated worldwide. Sex determination plays an important role in spinach breeding. Hence, this study aimed to understand the differences in sexual differentiation and floral organ development of dioecious flowers, as well as the differences in the regulatory mechanisms of floral organ development of dioecious and monoecious flowers. We compared transcriptional-level differences between different genders and identified differentially expressed genes (DEGs) related to spinach floral development, as well as sex-biased genes to investigate the flower development mechanisms in spinach. In this study, 9189 DEGs were identified among the different genders. DEG analysis showed the participation of four main transcription factor families, MIKC_MADS, MYB, NAC, and bHLH, in spinach flower development. In our key findings, abscisic acid (ABA) and gibberellic acid (GA) signal transduction pathways play major roles in male flower development, while auxin regulates both male and female flower development. By constructing a gene regulatory network (GRN) for floral organ development, core transcription factors (TFs) controlling organ initiation and growth were discovered. This analysis of the development of female, male, and monoecious flowers in spinach provides new insights into the molecular mechanisms of floral organ development and sexual differentiation in dioecious and monoecious plants in spinach.
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Affiliation(s)
- Yaying Ma
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.M.); (W.F.)
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Wenhui Fu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.M.); (W.F.)
| | - Suyan Wan
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Yikai Li
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Haoming Mao
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Ehsan Khalid
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Wenping Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
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Audoor S, Bilcke G, Pargana K, Belišová D, Thierens S, Van Bel M, Sterck L, Rijsdijk N, Annunziata R, Ferrante MI, Vandepoele K, Vyverman W. Transcriptional chronology reveals conserved genes involved in pennate diatom sexual reproduction. Mol Ecol 2024; 33:e17320. [PMID: 38506152 DOI: 10.1111/mec.17320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/23/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Sexual reproduction is a major driver of adaptation and speciation in eukaryotes. In diatoms, siliceous microalgae with a unique cell size reduction-restitution life cycle and among the world's most prolific primary producers, sex also acts as the main mechanism for cell size restoration through the formation of an expanding auxospore. However, the molecular regulators of the different stages of sexual reproduction and size restoration are poorly explored. Here, we combined RNA sequencing with the assembly of a 55 Mbp reference genome for Cylindrotheca closterium to identify patterns of gene expression during different stages of sexual reproduction. These were compared with a corresponding transcriptomic time series of Seminavis robusta to assess the degree of expression conservation. Integrative orthology analysis revealed 138 one-to-one orthologues that are upregulated during sex in both species, among which 56 genes consistently upregulated during cell pairing and gametogenesis, and 11 genes induced when auxospores are present. Several early, sex-specific transcription factors and B-type cyclins were also upregulated during sex in other pennate and centric diatoms, pointing towards a conserved core regulatory machinery for meiosis and gametogenesis across diatoms. Furthermore, we find molecular evidence that the pheromone-induced cell cycle arrest is short-lived in benthic diatoms, which may be linked to their active mode of mate finding through gliding. Finally, we exploit the temporal resolution of our comparative analysis to report the first marker genes for auxospore identity called AAE1-3 ("Auxospore-Associated Expression"). Altogether, we introduce a multi-species model of the transcriptional dynamics during size restoration in diatoms and highlight conserved gene expression dynamics during different stages of sexual reproduction.
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Affiliation(s)
- Sien Audoor
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
| | - Gust Bilcke
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Katerina Pargana
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
| | - Darja Belišová
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Sander Thierens
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Lieven Sterck
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nadine Rijsdijk
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Naples, Italy
- Associate to the National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for AI & Computational Biology, VIB, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
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Ning C, Yang Y, Chen Q, Zhao W, Zhou X, He L, Li L, Zong D, Chen J. An R2R3 MYB transcription factor PsFLP regulates the symmetric division of guard mother cells during stomatal development in Pisum sativum. PHYSIOLOGIA PLANTARUM 2023; 175:e13943. [PMID: 37260122 DOI: 10.1111/ppl.13943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/03/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023]
Abstract
MYB transcriptional regulators belong to one of the most significant transcription factors families in plants, among which R2R3-MYB transcription factors are involved in plant growth and development, hormone signal transduction, and stress response. Two R2R3-MYB transcription factors, FLP and its paralogous AtMYB88, redundantly regulate the symmetrical division of guard mother cells (GMCs), and abiotic stress response in Arabidopsis thaliana. Only one orthologue gene of FLP was identified in pea (Pisum sativum FLP; PsFLP). In this study, we explored the gene function of PsFLP by virus-induced gene silencing (VIGS) technology. The phenotypic analysis displayed that the silencing of PsFLP expression led to the abnormal development of stomata and the emergence of multiple guard cells tightly united. In addition, the abnormal stomata of flp could be fully rescued by PsFLP driven by the FLP promoter. In conclusion, the results showed that PsFLP plays a conservative negative role in regulating the symmetric division of GMC during stomatal development. Based on real-time quantitative PCR, the relative expressions of AAO3, NCED3, and SnRK2.3 significantly increased in the flp pFLP::PsFLP plants compared to mutant, indicating that PsFLP might be involved in drought stress response. Thus, PsFLP regulates the genes related to cell cycle division during the stomatal development of peas and participates in response to drought stress. The study provides a basis for further research on its function and application in leguminous crop breeding.
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Affiliation(s)
- Conghui Ning
- College of Life Science, Southwest Forestry University, Kunming, Yunnan, China
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yating Yang
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiyi Chen
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Weiyue Zhao
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xuan Zhou
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Liangliang He
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Laigeng Li
- College of Life Science, Southwest Forestry University, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dan Zong
- College of Life Science, Southwest Forestry University, Kunming, Yunnan, China
| | - Jianghua Chen
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
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Li P, Chen L, Gu X, Zhao M, Wang W, Hou S. FOUR LIPS plays a role in meristemoid-to-GMC fate transition during stomatal development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:424-436. [PMID: 36786686 DOI: 10.1111/tpj.16146] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/07/2023] [Indexed: 05/10/2023]
Abstract
Meristemoids, which are stomatal precursor cells, exhibit self-renewal and differentiation abilities. However, the only known core factor associated with meristemoid division termination and fate transition is the heterodimer formed by the basic helix-loop-helix proteins MUTE and SCREAMs (SCRMs). FOUR LIPS (FLP), a well-known transcription factor that restricts guard mother cell (GMC) division, is a direct target of MUTE. Whether FLP involves in meristemoid differentiation is unknown. Through sensitized genetic screening of flp-1, we identified a mute-like (mutl) mutant with arrested meristemoids. The mutant carried a novel allele of the MUTE locus, i.e., mute-4. Intriguingly, mute-4 is a hypomorphic allele that exhibits wild-type appearance with slightly delayed meristemoid-to-GMC transition, whereas it renders an unexpected mutl epidermis with most meristemoids arrested and very few stomata when combined with flp (flp mute-4), suggesting that FLP is a positive regulator during this transition process. Consistently, the expression of FLP increased during GMC commitment, and the number of cells at this stage was markedly increased in flp. flp scrm double mutants produced arrested meristemoids similar to mute, and FLP was able to interact physically with SCRM. Taken together, our results demonstrate that FLP functions together with MUTE and SCRMs to direct meristemoid-to-GMC fate transition.
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Affiliation(s)
- Ping Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Liang Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoli Gu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Mingfeng Zhao
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wenjin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Suiwen Hou
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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Zhang C, Zhang J, Liu H, Qu X, Wang J, He Q, Zou J, Yang K, Le J. Transcriptomic analysis reveals the role of FOUR LIPS in response to salt stress in rice. PLANT MOLECULAR BIOLOGY 2022; 110:37-52. [PMID: 35583702 DOI: 10.1007/s11103-022-01282-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
An R2R3-MYB transcription factor FOUR LIPS associated with B-type Cyclin-Dependent Kinase 1;1 confers salt tolerance in rice. The Arabidopsis FOUR LIPS (AtFLP), an R2R3 MYB transcription factor, acts as an important stomatal development regulator. Only one orthologue protein of AtFLP, Oryza sativa FLP (OsFLP), was identified in rice. However, the function of OsFLP is largely unknown. In this study, we conducted RNA-seq and ChIP-seq to investigate the potential role of OsFLP in rice. Our results reveal that OsFLP is probably a multiple functional regulator involved in many biological processes in growth development and stress responses in rice. However, we mainly focus on the role of OsFLP in salt stress response. Consistently, phenotypic analysis under salt stress conditions showed that osflp exhibited significant sensitivity to salt stress, while OsFLP over-expression lines displayed obvious salt tolerance. Additionally, Yeast one-hybrid assay and electrophoretic mobility shift assay (EMSA) showed that OsFLP directly bound to the promoter region of Oryza sativa B-type Cyclin-Dependent Kinase 1;1 (OsCDKB1;1), and the expression of OsCDKB1;1 was repressed in osflp. Disturbing the expression of OsCDKB1;1 remarkably enhanced the tolerance to salt stress. Taken together, our findings reveal a crucial function of OsFLP regulating OsCDKB1;1 in salt tolerance and largely extend the knowledge about the role of OsFLP in rice.
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Affiliation(s)
- Chunxia Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huichao Liu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Qu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junxue Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Wenbo School, Jinan, 250100, China
| | - Qixiumei He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junjie Zou
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kezhen Yang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Wang Z, Li J, Yang X, Hu Y, Yin Y, Shen X. MdFLP enhances drought tolerance by regulating MdNAC019 in self-rooted apple stocks. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111331. [PMID: 35696930 DOI: 10.1016/j.plantsci.2022.111331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Self-rooted apple stocks are widely used for the production of apples worldwide. However, self-rooted apple stocks are weak due to shallow roots and poor grounding, resulting in poor drought resistance. Therefore, it is essential to understand the molecular mechanisms to develop self-rooted apple stock cultivars with drought resistance. We reported that MdFLP, an R2R3-MYB transcription factor, directly binds to the promoter of MdNAC019, activating its transcription and consequently enhancing drought tolerance in self-rooted apple stocks. In addition, MdFLP indirectly activates the transcriptional expression of abiotic stress-related genes, namely, MdERF6 and MdZAT10. The plants overexpressing MdFLP displayed stronger drought tolerance, whereas MdFLP-RNAi plants showed weak drought tolerance compared with non-transgenic "Gala" plants, indicating that MdFLP regulates drought tolerance in self-rooted apple stocks. Altogether, we believe that our findings provide novel insights into the functions of MdFLP in the regulation of drought tolerance in self-rooted apple stocks.
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Affiliation(s)
- Zenghui Wang
- Shandong Institute of Pomology, Tai'an, Shandong 271000, China
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xuemei Yang
- Shandong Institute of Pomology, Tai'an, Shandong 271000, China
| | - Yanli Hu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, Tai'an, Shandong 271018, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yanlei Yin
- Shandong Institute of Pomology, Tai'an, Shandong 271000, China.
| | - Xiang Shen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, Tai'an, Shandong 271018, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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Lal M, Bhardwaj E, Chahar N, Yadav S, Das S. Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies. Funct Integr Genomics 2022; 22:371-405. [PMID: 35260976 DOI: 10.1007/s10142-022-00836-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/10/2022] [Accepted: 02/23/2022] [Indexed: 11/28/2022]
Abstract
Myeloblastosis (MYB) family, the largest plant transcription factor family, has been subcategorised based on the number and type of repeats in the MYB domain. In spite of several reports, evolution of MYB genes and repeats remains enigmatic. Brassicaceae members are endowed with complex genomes, including dysploidy because of its unique history with multiple rounds of polyploidisation, genomic fractionations and rearrangements. The present study is an attempt to gain insights into the complexities of MYB family diversity, understand impacts of genome evolution on gene families and develop an evolutionary framework to understand the origin of various subcategories of MYB gene family. We identified and analysed 1129 MYBs that included 1R-, 2R-, 3R- and atypical-MYBs across sixteen species representing protists, fungi, animals and plants and exclude MYB identified from Brassicaceae except Arabidopsis thaliana; in addition, a total of 1137 2R-MYB genes from six Brassicaceae species were also analysed. Comparative analysis revealed predominance of 1R-MYBs in protists, fungi, animals and lower plants. Phylogenetic reconstruction and analysis of selection pressure suggested ancestral nature of R1-type repeat containing 1R-MYBs that might have undergone intragenic duplication to form multi-repeat MYBs. Distinct differences in gene structure between 1R-MYB and 2R-MYBs were observed regarding intron number, the ratio of gene length to coding DNA sequence (CDS) length and the length of exons encoding the MYB domain. Conserved as well as novel and lineage-specific intron phases were identified. Analyses of physicochemical properties revealed drastic differences indicating functional diversification in MYBs. Phylogenetic reconstruction of 1R- and 2R-MYB genes revealed a shared structure-function relationship in clades which was supported when transcriptome data was analysed in silico. Comparative genomics to study distribution pattern and mapping of 2R-MYBs revealed congruency and greater degree of synteny and collinearity among closely related species. Micro-synteny analysis of genomic segments revealed high conservation of genes that are immediately flanking the surrounding tandemly organised 2R-MYBs along with instances of local duplication, reorganisations and genome fractionation. In summary, polyploidy, dysploidy, reshuffling and genome fractionation were found to cause loss or gain of 2R-MYB genes. The findings need to be supported with functional validation to understand gene structure-function relationship along the evolutionary lineage and adaptive strategies based on comparative functional genomics in plants.
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Affiliation(s)
- Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Nishu Chahar
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Shobha Yadav
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110007, India.
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Xu Z, Liu Q, Chen Y, He Y, Hu F. miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis. BMC PLANT BIOLOGY 2022; 22:149. [PMID: 35346036 PMCID: PMC8962573 DOI: 10.1186/s12870-022-03539-3] [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: 08/16/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND miR390s is an ancient family with a high level of conservation among plant miRNAs. Through the auxin signal transduction pathway, miR390 participates in diverse biological processes of plant growth and development. As an important Chinese traditional orchid, Cymbidium goeringii has unique flower shape and elegant fragrance. But its development has been greatly restricted because of the low flower bud differentiation and the difficult reproduction. This study aims to provide guidance for the role of cgo-miR390 in reproductive organ development to enhance the ornamental and economic value of Cymbidium. RESULTS MIR390a, MIR390b and MIR390c of C. goeringii were cloned, and their length ranged from 130 to 150 nt. Each precursor sequence of cgo-miR390 contains 2 to 3 mature miRNAs. Three kinds of cgo-miR390s displayed distinct temporal and spatial expression patterns during floral development in C. goeringii. The overexpression of MIR390s alters morphology and function of stamens and pistils in Arabidopsis, such as enlargement of anther aspect ratio and separation of stylar and stigmas, which affects the development of fruits and seeds. In particular, the pollen amount decreased and the seed abortion rate increased in cgo-MIR390c-overexpressed plants. CONCLUSIONS cgo-miR390 family affected the development of reproductive organs in transgenic Arabidopsis. The study provides references for the genetic improvement for orchid with potentially great economic benefit.
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Affiliation(s)
- Zihan Xu
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China
| | - Qian Liu
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China
| | - Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 310021, Hangzhou, Zhejiang Province, China
| | - Yuanhao He
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China
| | - Fengrong Hu
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China.
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Li Y, Xue S, He Q, Wang J, Zhu L, Zou J, Zhang J, Zuo C, Fan Z, Yue J, Zhang C, Yang K, Le J. Arabidopsis F-BOX STRESS INDUCED 4 is required to repress excessive divisions in stomatal development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:56-72. [PMID: 34817930 DOI: 10.1111/jipb.13193] [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: 08/21/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
During the terminal stage of stomatal development, the R2R3-MYB transcription factors FOUR LIPS (FLP/MYB124) and MYB88 limit guard mother cell division by repressing the transcript levels of multiple cell-cycle genes. In Arabidopsis thaliana possessing the weak allele flp-1, an extra guard mother cell division results in two stomata having direct contact. Here, we identified an ethylmethane sulfonate-mutagenized mutant, flp-1 xs01c, which exhibited more severe defects than flp-1 alone, producing giant tumor-like cell clusters. XS01C, encoding F-BOX STRESS-INDUCED 4 (FBS4), is preferentially expressed in epidermal stomatal precursor cells. Overexpressing FBS4 rescued the defective stomatal phenotypes of flp-1 xs01c and flp-1 mutants. The deletion or substitution of a conserved residue (Proline166) within the F-box domain of FBS4 abolished or reduced, respectively, its interaction with Arabidopsis Skp1-Like1 (ASK1), the core subunit of the Skp1/Cullin/F-box E3 ubiquitin ligase complex. Furthermore, the FBS4 protein physically interacted with CYCA2;3 and induced its degradation through the ubiquitin-26S proteasome pathway. Thus, in addition to the known transcriptional pathway, the terminal symmetric division in stomatal development is ensured at the post-translational level, such as through the ubiquitination of target proteins recognized by the stomatal lineage F-box protein FBS4.
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Affiliation(s)
- Yi Li
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan Xue
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- The Institute of Scientific and Technical Information of China, Beijing, 100038, China
| | - Qixiumei He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junxue Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Wenbo School, Jinan, 250100, China
| | - Lingling Zhu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junjie Zou
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoran Zuo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibin Fan
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junling Yue
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxia Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Kezhen Yang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Islam K, Rawoof A, Ahmad I, Dubey M, Momo J, Ramchiary N. Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:721265. [PMID: 34721453 PMCID: PMC8548648 DOI: 10.3389/fpls.2021.721265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/08/2021] [Indexed: 05/27/2023]
Abstract
Myeloblastosis (MYB) genes are important transcriptional regulators of plant growth, development, and secondary metabolic biosynthesis pathways, such as capsaicinoid biosynthesis in Capsicum. Although MYB genes have been identified in Capsicum annuum, no comprehensive study has been conducted on other Capsicum species. We identified a total of 251 and 240 MYB encoding genes in Capsicum chinense MYBs (CcMYBs) and Capsicum baccatum MYBs (CbMYBs). The observation of twenty tandem and 41 segmental duplication events indicated expansion of the MYB gene family in the C. chinense genome. Five CcMYB genes, i.e., CcMYB101, CcMYB46, CcMYB6, CcPHR8, and CcRVE5, and two CaMYBs, i.e., CaMYB3 and CaHHO1, were found within the previously reported capsaicinoid biosynthesis quantitative trait loci. Based on phylogenetic analysis with tomato MYB proteins, the Capsicum MYBs were classified into 24 subgroups supported by conserved amino acid motifs and gene structures. Also, a total of 241 CcMYBs were homologous with 225 C. annuum, 213 C. baccatum, 125 potato, 79 tomato, and 23 Arabidopsis MYBs. Synteny analysis showed that all 251 CcMYBs were collinear with C. annuum, C. baccatum, tomato, potato, and Arabidopsis MYBs spanning over 717 conserved syntenic segments. Using transcriptome data from three fruit developmental stages, a total of 54 CcMYBs and 81 CaMYBs showed significant differential expression patterns. Furthermore, the expression of 24 CcMYBs from the transcriptome data was validated by quantitative real-time (qRT) PCR analysis. Eight out of the 24 CcMYBs validated by the qRT-PCR were highly expressed in fiery hot C. chinense than in the lowly pungent C. annuum. Furthermore, the co-expression analysis revealed several MYB genes clustered with genes from the capsaicinoid, anthocyanin, phenylpropanoid, carotenoid, and flavonoids biosynthesis pathways, and related to determining fruit shape and size. The homology modeling of 126 R2R3 CcMYBs showed high similarity with that of the Arabidopsis R2R3 MYB domain template, suggesting their potential functional similarity at the proteome level. Furthermore, we have identified simple sequence repeat (SSR) motifs in the CcMYB genes, which could be used in Capsicum breeding programs. The functional roles of the identified CcMYBs could be studied further so that they can be manipulated for Capsicum trait improvement.
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Affiliation(s)
- Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Meenakshi Dubey
- Department of Biotechnology, Delhi Technological University, New Delhi, India
| | - John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Zhang D, Yang K, Kan Z, Dang H, Feng S, Yang Y, Li L, Hou N, Xu L, Wang X, Malnoy M, Ma F, Hao Y, Guan Q. The regulatory module MdBT2-MdMYB88/MdMYB124-MdNRTs regulates nitrogen usage in apple. PLANT PHYSIOLOGY 2021; 185:1924-1942. [PMID: 33793944 PMCID: PMC8133671 DOI: 10.1093/plphys/kiaa118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/18/2020] [Indexed: 05/04/2023]
Abstract
Less than 40% of the nitrogen (N) fertilizer applied to soil is absorbed by crops. Thus, improving the N use efficiency of crops is critical for agricultural development. However, the underlying regulation of these processes remains largely unknown, particularly in woody plants. By conducting yeast two-hybrid assays, we identified one interacting protein of MdMYB88 and MdMYB124 in apple (Malus × domestica), namely BTB and TAZ domain protein 2 (MdBT2). Ubiquitination and protein stabilization analysis revealed that MdBT2 ubiquitinates and degrades MdMYB88 and MdMYB124 via the 26S proteasome pathway. MdBT2 negatively regulates nitrogen usage as revealed by the reduced fresh weight, dry weight, N concentration, and N usage index of MdBT2 overexpression calli under low-N conditions. In contrast, MdMYB88 and MdMYB124 increase nitrate absorption, allocation, and remobilization by regulating expression of MdNRT2.4, MdNRT1.8, MdNRT1.7, and MdNRT1.5 under N limitation, thereby regulating N usage. The results obtained illustrate the mechanism of a regulatory module comprising MdBT2-MdMYB88/MdMYB124-MdNRTs, through which plants modulate N usage. These data contribute to a molecular approach to improve the N usage of fruit crops under limited N acquisition.
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Affiliation(s)
- Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kuo Yang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271000, China
| | - Zhiyong Kan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huan Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuxian Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yusen Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lingfei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaofei Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271000, China
| | - Mickael Malnoy
- Department of Biology and Genomics of Fruit Plants, Foundation Edmund Mach di San Michele all'Adige, Trento, Italy
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yujin Hao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271000, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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12
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Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta. ISME JOURNAL 2020; 15:562-576. [PMID: 33028976 PMCID: PMC8027222 DOI: 10.1038/s41396-020-00797-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/10/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022]
Abstract
Sexual reproduction is a fundamental phase in the life cycle of most diatoms. Despite its role as a source of genetic variation, it is rarely reported in natural circumstances and its molecular foundations remain largely unknown. Here, we integrate independent transcriptomic datasets to prioritize genes responding to sex inducing pheromones (SIPs) in the pennate diatom Seminavis robusta. We observe marked gene expression changes associated with SIP treatment in both mating types, including an inhibition of S phase progression, chloroplast division, mitosis, and cell wall formation. Meanwhile, meiotic genes are upregulated in response to SIP, including a sexually induced diatom specific cyclin. Our data further suggest an important role for reactive oxygen species, energy metabolism, and cGMP signaling during the early stages of sexual reproduction. In addition, we identify several genes with a mating type specific response to SIP, and link their expression pattern with physiological specialization, such as the production of the attraction pheromone diproline in mating type − (MT−) and mate-searching behavior in mating type + (MT+). Combined, our results provide a model for early sexual reproduction in pennate diatoms and significantly expand the suite of target genes to detect sexual reproduction events in natural diatom populations.
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13
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Yang J, Zhang G, An J, Li Q, Chen Y, Zhao X, Wu J, Wang Y, Hao Q, Wang W, Wang W. Expansin gene TaEXPA2 positively regulates drought tolerance in transgenic wheat (Triticum aestivum L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110596. [PMID: 32771153 DOI: 10.1016/j.plantsci.2020.110596] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 05/08/2023]
Abstract
Expansins loosen plant cell walls and are involved in cell enlargement and various abiotic stresses. In previous studies, we cloned the expansin gene TaEXPA2 from the wheat cultivar HF9703. Here, we studied its function and regulation in wheat drought stress tolerance. The results indicated that TaEXPA2-overexpressing wheat plants (OE) exhibited drought tolerant phenotypes, whereas down-regulation of TaEXPA2 by RNA interference (RNAi) resulted in elevated drought sensitivity, as measured by survival rate, photosynthetic rate and water containing ability under drought stress. Overexpression of TaEXPA2 enhanced the antioxidant capacity in wheat plants, via elevation of antioxidant enzyme activity and the increase of the transcripts of some ROS scavenging enzyme-related genes. Further investigation revealed that TaEXPA2 positively influenced lateral root formation under drought conditions. A MYB transcription factor of wheat named TaMPS activates TaEXPA2 expression directly by binding to its promoter. Overexpression of TaMPS in Arabidopsis conferred drought tolerance associated with improved lateral root number, and the close homolog genes of TaEXPA2 were up-regulated in Arabidopsis roots overexpressing TaMPS, which suggest that TaMPS may function as one of the regulator of TaEXPA2 gene expression in the root lateral development under drought stress. These findings suggest that TaEXPA2 positively regulates drought stress tolerance in wheat.
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Affiliation(s)
- Junjiao Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Guangqiang Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jie An
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Qinxue Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yanhui Chen
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China; Research Institute of Pomology of Chinese Academy of Agricultural Sciences, Xingcheng 125100, Liaoning, China
| | - Xiaoyu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Qunqun Hao
- College of Life Sciences, Zaozhuang University, Zaozhuang 277160, Shandong, China
| | - Wenqiang Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang 277160, Shandong, China.
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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14
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Singh V, Kumar N, Dwivedi AK, Sharma R, Sharma MK. Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome. Curr Genomics 2020; 21:138-154. [PMID: 32655308 PMCID: PMC7324873 DOI: 10.2174/1389202921666200326152119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/30/2022] Open
Abstract
Background Large scale cultivation of sorghum for food, feed, and biofuel requires concerted efforts for engineering multipurpose cultivars with optimised agronomic traits. Due to their vital role in regulating the biosynthesis of phenylpropanoid-derived compounds, biomass composition, biotic, and abiotic stress response, R2R3-MYB family transcription factors are ideal targets for improving environmental resilience and economic value of sorghum. Methods We used diverse computational biology tools to survey the sorghum genome to identify R2R3-MYB transcription factors followed by their structural and phylogenomic analysis. We used in-house generated as well as publicly available high throughput expression data to analyse the R2R3 expression patterns in various sorghum tissue types. Results We have identified a total of 134 R2R3-MYB genes from sorghum and developed a framework to predict gene functions. Collating information from the physical location, duplication, structural analysis, orthologous sequences, phylogeny, and expression patterns revealed the role of duplications in clade-wise expansion of the R2R3-MYB family as well as intra-clade functional diversification. Using publicly available and in-house generated RNA sequencing data, we provide MYB candidates for conditioning biofuel syndrome by engineering phenylpropanoid biosynthesis and sugar signalling pathways in sorghum. Conclusion The results presented here are pivotal to prioritize MYB genes for functional validation and optimize agronomic traits in sorghum.
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Affiliation(s)
- Vinay Singh
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Neeraj Kumar
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Anuj K Dwivedi
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Rita Sharma
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Manoj K Sharma
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
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Gangwar M, Shankar J. Molecular Mechanisms of the Floral Biology of Jatropha curcas: Opportunities and Challenges as an Energy Crop. FRONTIERS IN PLANT SCIENCE 2020; 11:609. [PMID: 32582231 PMCID: PMC7296989 DOI: 10.3389/fpls.2020.00609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Fossil fuel sources are a limited resource and could eventually be depleted. Biofuels have emerged as a renewable alternative to fossil fuels. Jatropha has grown in significance as a potential bioenergy crop due to its high content of seed oil. However, Jatropha's lack of high-yielding seed genotypes limits its potential use for biofuel production. The main cause of lower seed yield is the low female to male flower ratio (1:25-10), which affects the total amount of seeds produced per plant. Here, we review the genetic factors responsible for floral transitions, floral organ development, and regulated gene products in Jatropha. We also summarize potential gene targets to increase seed production and discuss challenges ahead.
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16
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Genome-Wide Association Analysis Identifies Candidate Genes Regulating Seed Number Per Silique in Arabidopsis thaliana. PLANTS 2020; 9:plants9050585. [PMID: 32370287 PMCID: PMC7284809 DOI: 10.3390/plants9050585] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/10/2020] [Accepted: 04/15/2020] [Indexed: 12/19/2022]
Abstract
Seed weight and number ultimately determine seed yield. Arabidopsis seed number comprised of silique number and seed number per silique (SNS). Comparing seed development and weight, determinants of seed number remain largely uncharacterized. In this study, taking advantage of 107 available Arabidopsis accessions, genome-wide association analysis (GWAS) was employed to identify the candidate genes regulating SNS. GWAS-based genotype and phenotype association analysis identified 38 most significant SNPs marker sites that were mapped to specific chromosomal positions and allowed us to screen for dozens of candidate genes. One of them (PIN3) was selected for functional validation based on gene expression analysis. It is a positive regulator of Arabidopsis SNS. Although silique length of PIN3 loss of function mutant was not significantly changed, its SNS and seed density (SD) were significantly reduced as compared with the wild type. Notably, PIN3 overexpression lines driven by a placenta-specific promoter STK exhibited significantly shorter siliques, slightly reduced SNS, but significant increased SD compared with wild type, suggesting that PIN3 positively regulates SD through inducing ovule primordia initiation regardless of the placenta size. Ovule initiation determines the maximal possibility of SNS, and new genes and mechanism regulating SNS through modulating ovule initiation is worth further investigated.
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Xu G, Huang J, Lei SK, Sun XG, Li X. Comparative gene expression profile analysis of ovules provides insights into Jatropha curcas L. ovule development. Sci Rep 2019; 9:15973. [PMID: 31685957 PMCID: PMC6828956 DOI: 10.1038/s41598-019-52421-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 10/03/2019] [Indexed: 02/02/2023] Open
Abstract
Jatropha curcas, an economically important biofuel feedstock with oil-rich seeds, has attracted considerable attention among researchers in recent years. Nevertheless, valuable information on the yield component of this plant, particularly regarding ovule development, remains scarce. In this study, transcriptome profiles of anther and ovule development were established to investigate the ovule development mechanism of J. curcas. In total, 64,325 unigenes with annotation were obtained, and 1723 differentially expressed genes (DEGs) were identified between different stages. The DEG analysis showed the participation of five transcription factor families (bHLH, WRKY, MYB, NAC and ERF), five hormone signaling pathways (auxin, gibberellic acid (GA), cytokinin, brassinosteroids (BR) and jasmonic acid (JA)), five MADS-box genes (AGAMOUS-2, AGAMOUS-1, AGL1, AGL11, and AGL14), SUP and SLK3 in ovule development. The role of GA and JA in ovule development was evident with increases in flower buds during ovule development: GA was increased approximately twofold, and JA was increased approximately sevenfold. In addition, the expression pattern analysis using qRT-PCR revealed that CRABS CLAW and AGAMOUS-2 were also involved in ovule development. The upregulation of BR signaling genes during ovule development might have been regulated by other phytohormone signaling pathways through crosstalk. This study provides a valuable framework for investigating the regulatory networks of ovule development in J. curcas.
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Affiliation(s)
- Gang Xu
- Institute for Forest Resources and Environment of Guizhou / College of Forestry, Guizhou University, Guiyang, 550025, P.R. China. .,Institute of Entomology, Guizhou University, Guiyang, Guizhou, P.R. China.
| | - Jian Huang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals of Guizhou University, Guiyang, Guizhou, P.R. China
| | - Shi-Kang Lei
- School of Life Science, Guizhou University, Guiyang, Guizhou, P.R. China
| | - Xue-Guang Sun
- Institute for Forest Resources and Environment of Guizhou / College of Forestry, Guizhou University, Guiyang, 550025, P.R. China
| | - Xue Li
- School of Life Science, Guizhou University, Guiyang, Guizhou, P.R. China
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Mátyás KK, Hegedűs G, Taller J, Farkas E, Decsi K, Kutasy B, Kálmán N, Nagy E, Kolics B, Virág E. Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weed Ambrosia artemisiifolia L. ( Asteraceae). PeerJ 2019; 7:e7421. [PMID: 31598422 PMCID: PMC6779118 DOI: 10.7717/peerj.7421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/06/2019] [Indexed: 12/31/2022] Open
Abstract
The highly allergenic and invasive weed Ambrosia artemisiifolia L. is a monoecius plant with separated male and female flowers. The genetic regulation of floral morphogenesis is a less understood field in the reproduction biology of this species. Therefore the objective of this work was to investigate the genetic control of sex determination during floral organogenesis. To this end, we performed a genome-wide transcriptional profiling of vegetative and generative tissues during the plant development comparing wild-growing and in vitro cultivated plants. RNA-seq on Illumina NextSeq 500 platform with an integrative bioinformatics analysis indicated differences in 80 floral gene expressions depending on photoperiodic and endogenous initial signals. Sex specificity of genes was validated based on RT-qPCR experiments. We found 11 and 16 uniquely expressed genes in female and male transcriptomes that were responsible particularly to maintain fertility and against abiotic stress. High gene expression of homologous such as FD, FT, TFL1 and CAL, SOC1, AP1 were characteristic to male and female floral meristems during organogenesis. Homologues transcripts of LFY and FLC were not found in the investigated generative and vegetative tissues. The repression of AP1 by TFL1 homolog was demonstrated in male flowers resulting exclusive expression of AP2 and PI that controlled stamen and carpel formation in the generative phase. Alterations of male and female floral meristem differentiation were demonstrated under photoperiodic and hormonal condition changes by applying in vitro treatments.
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Affiliation(s)
- Kinga Klára Mátyás
- Department of Plant Science and Biotechnology, University of Pannonia, Georgikon Faculty, Keszthely, Hungary
| | - Géza Hegedűs
- Department of Economic Methodology, University of Pannonia, Georgikon Faculty, Keszthely, Hungary
| | - János Taller
- Department of Plant Science and Biotechnology, University of Pannonia, Georgikon Faculty, Keszthely, Hungary
| | - Eszter Farkas
- Department of Plant Science and Biotechnology, University of Pannonia, Georgikon Faculty, Keszthely, Hungary
| | - Kincső Decsi
- Department of Plant Science and Biotechnology, University of Pannonia, Georgikon Faculty, Keszthely, Hungary
| | - Barbara Kutasy
- Department of Plant Science and Biotechnology, University of Pannonia, Georgikon Faculty, Keszthely, Hungary
| | - Nikoletta Kálmán
- Department of Biochemistry and Medical Chemistry, University of Pecs Medical School, Szentagothai Research Center, Pecs, Hungary
| | - Erzsébet Nagy
- Department of Plant Science and Biotechnology, University of Pannonia, Georgikon Faculty, Keszthely, Hungary
| | - Balázs Kolics
- Department of Plant Science and Biotechnology, University of Pannonia, Georgikon Faculty, Keszthely, Hungary
| | - Eszter Virág
- Department of Plant Science and Biotechnology, University of Pannonia, Georgikon Faculty, Keszthely, Hungary
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Wang Z, Li J, Mao Y, Zhang M, Wang R, Hu Y, Mao Z, Shen X. Transcriptional regulation of MdPIN3 and MdPIN10 by MdFLP during apple self-rooted stock adventitious root gravitropism. BMC PLANT BIOLOGY 2019; 19:229. [PMID: 31146692 PMCID: PMC6543673 DOI: 10.1186/s12870-019-1847-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/24/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The close planting of dwarfing self-rooted rootstocks is currently a widely used method for apple production; however, self-rooted rootstocks are weak with shallow roots and poor grounding. Therefore, understanding the molecular mechanisms that establish the gravitropic set-point angles (GSAs) of the adventitious roots of self-rooted apple stocks is important for developing self-rooted apple rootstock cultivars with deep roots. RESULTS We report that the apple FOUR LIPS (MdFLP), an R2R3-MYB transcription factor (TF), functions in establishing the GSA of the adventitious roots of self-rooted apple stocks in response to gravity. Biochemical analyses demonstrate that MdFLP directly binds to the promoters of two auxin efflux carriers, MdPIN3 and MdPIN10, that are involved in auxin transport, activates their transcriptional expression, and thereby promotes the development of adventitious roots in self-rooted apple stocks. Additionally, the apple auxin response factor MdARF19 influences the expression of those auxin efflux carriers and the establishment of the GSA of adventitious roots of apple in response to gravity by directly activating the expression of MdFLP. CONCLUSION Our findings provide new insights into the transcriptional regulation of MdFLP by the auxin response factor MdARF19 in the regulation of the GSA of adventitious roots of self-rooted apple stocks in response to gravity.
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Affiliation(s)
- Zenghui Wang
- State Key Laboratory of Crop Biology; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Jialin Li
- State Key Laboratory of Crop Biology; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Yunfei Mao
- State Key Laboratory of Crop Biology; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Manman Zhang
- State Key Laboratory of Crop Biology; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Rong Wang
- State Key Laboratory of Crop Biology; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Yanli Hu
- State Key Laboratory of Crop Biology; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Zhiquan Mao
- State Key Laboratory of Crop Biology; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Xiang Shen
- State Key Laboratory of Crop Biology; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018 Shandong China
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20
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Liu H, Wang R, Mao B, Zhao B, Wang J. Identification of lncRNAs involved in rice ovule development and female gametophyte abortion by genome-wide screening and functional analysis. BMC Genomics 2019; 20:90. [PMID: 30691391 PMCID: PMC6348626 DOI: 10.1186/s12864-019-5442-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/09/2019] [Indexed: 11/15/2022] Open
Abstract
Background As important female reproductive tissues, the rice (Oryza sativa L.) ovule and female gametophyte is significant in terms of their fertility. Long noncoding RNAs (lncRNAs) play important and wide-ranging roles in the growth and development of plants and have become a major research focus in recent years. Therefore, we explored the characterization and expression change of lncRNAs during ovule development and female gametophytic abortion. Results In our study, whole-transcriptome strand-specific RNA sequencing (ssRNA-seq) was performed in the ovules of a high-frequency female-sterile rice line (fsv1) and a wild-type rice line (Gui99) at the megaspore mother cell meiosis stage (stage 1), functional megaspore mitosis stage (stage 2) and female gametophyte mature stage (stage 3). By comparing two rice lines, we identified 152, 233, and 197 differentially expressed lncRNAs at the three ovule developmental stages. Functional analysis of the coherent target genes of these differentially expressed lncRNAs indicated that many lncRNAs participate in multiple pathways such as hormone and cellular metabolism and signal transduction. Moreover, there were many differentially expressed lncRNAs acting as the precursors of some miRNAs that are involved in the development of ovules and female gametophytes. In addition, we have found that lncRNAs can act as decoys, competing with mRNAs for binding to miRNAs to maintain the normal expression of genes related to ovule and female gametophyte development. Conclusion These results provide important clues for elucidating the female gametophyte abortion mechanism in rice. This study also expands our understanding about the biological functions of lncRNAs and the annotation of the rice genome. Electronic supplementary material The online version of this article (10.1186/s12864-019-5442-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helian Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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21
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Erbasol Serbes I, Palovaara J, Groß-Hardt R. Development and function of the flowering plant female gametophyte. Curr Top Dev Biol 2019; 131:401-434. [DOI: 10.1016/bs.ctdb.2018.11.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Geng D, Chen P, Shen X, Zhang Y, Li X, Jiang L, Xie Y, Niu C, Zhang J, Huang X, Ma F, Guan Q. MdMYB88 and MdMYB124 Enhance Drought Tolerance by Modulating Root Vessels and Cell Walls in Apple. PLANT PHYSIOLOGY 2018; 178:1296-1309. [PMID: 30190418 PMCID: PMC6236628 DOI: 10.1104/pp.18.00502] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/26/2018] [Indexed: 05/18/2023]
Abstract
Water deficit is one of the main limiting factors in apple (Malus × domestica Borkh.) cultivation. Root architecture plays an important role in the drought tolerance of plants; however, research efforts to improve drought tolerance of apple trees have focused on aboveground targets. Due to the difficulties associated with visualization and data analysis, there is currently a poor understanding of the genetic players and molecular mechanisms involved in the root architecture of apple trees under drought conditions. We previously observed that MdMYB88 and its paralog MdMYB124 regulate apple tree root morphology. In this study, we found that MdMYB88 and MdMYB124 play important roles in maintaining root hydraulic conductivity under long-term drought conditions and therefore contribute toward adaptive drought tolerance. Further investigation revealed that MdMYB88 and MdMYB124 regulate root xylem development by directly binding MdVND6 and MdMYB46 promoters and thus influence expression of their target genes under drought conditions. In addition, MdMYB88 and MdMYB124 were shown to regulate the deposition of cellulose and lignin root cell walls in response to drought. Taken together, our results provide novel insights into the importance of MdMYB88 and MdMYB124 in root architecture, root xylem development, and secondary cell wall deposition in response to drought in apple trees.
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Affiliation(s)
- Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lijuan Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaohua Huang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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23
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Li H, Zhang Q, Li L, Yuan J, Wang Y, Wu M, Han Z, Liu M, Chen C, Song W, Wang C. Ectopic Overexpression of bol-miR171b Increases Chlorophyll Content and Results in Sterility in Broccoli ( Brassica oleracea L var. italica). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9588-9597. [PMID: 30142272 DOI: 10.1021/acs.jafc.8b01531] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
MiR171 plays pleiotropic roles in the growth and development of several plant species. However, the mechanism underlying the miR171-mediated regulation of organ development in broccoli remains unknown. In this study, bol-miR171b was characterized and found to be differentially expressed in various broccoli organs. The ectopic overexpression of bol-miR171b in Arabidopsis affected the leaf and silique development of transgenic lines. In particular, the chlorophyll content of leaves from overexpressed bol-miR171b transgenic Arabidopsis was higher than that of the vector controls. The fertility and seed yield of Arabidopsis with overexpressed bol-miR171b were markedly lower than those of the vector controls. Similarly, overexpressed bol-miR171b transgenic broccoli exhibited dark green leaves with high chlorophyll content, and nearly all of the flowers were sterile. These results demonstrated that overexpression of bol-miR171b could increase the chlorophyll content of transgenic plants. Degradome sequencing was conducted to identify the targets of bol-miR171b. Two members of the GRAS gene family, BolSCL6 and BolSCL27, were cleaved by bol-miR171b-3p in broccoli. In addition to the genes targeted by bol-miR171b-3p, adenylylsulfate reductase 3 ( APSR3), which played important roles in plant sulfate assimilation and reduction, was speculated to be cleaved by bol-miR171b-5p, suggesting that the star sequence of bol-miR171b may also have functions in broccoli. Comparative transcriptome analysis further revealed that the genes involved in chloroplast development and sulfate homeostasis should participate in the bol-miR171b -mediated regulatory network. Taken together, these findings provided new insights into the function and regulation of bol-miR171b in broccoli and indicated the potential of bol-miR171b as a small RNA molecule that increased leaf chlorophyll in plants by genetic engineering.
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Affiliation(s)
- Hui Li
- College of Life Sciences , Nankai University , Tianjin 300071 , People's Republic of China
- College of Horticulture and Landscape , Tianjin Agricultural University , Tianjin , People's Republic of China
| | - Qingli Zhang
- College of Life Sciences , Nankai University , Tianjin 300071 , People's Republic of China
| | - Lihong Li
- College of Life Sciences , Nankai University , Tianjin 300071 , People's Republic of China
| | - Jiye Yuan
- College of Life Sciences , Nankai University , Tianjin 300071 , People's Republic of China
| | - Yu Wang
- College of Life Sciences , Nankai University , Tianjin 300071 , People's Republic of China
| | - Mei Wu
- College of Life Sciences , Nankai University , Tianjin 300071 , People's Republic of China
| | - Zhanpin Han
- College of Horticulture and Landscape , Tianjin Agricultural University , Tianjin , People's Republic of China
| | - Min Liu
- College of Life Sciences , Shandong Normal University , Jinan , Shandong , People's Republic of China
| | - Chengbin Chen
- College of Life Sciences , Nankai University , Tianjin 300071 , People's Republic of China
| | - Wenqin Song
- College of Life Sciences , Nankai University , Tianjin 300071 , People's Republic of China
| | - Chunguo Wang
- College of Life Sciences , Nankai University , Tianjin 300071 , People's Republic of China
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RNA-seq Analysis Reveals Gene Expression Profiling of Female Fertile and Sterile Ovules of PinusTabulaeformis Carr. during Free Nuclear Mitosis of the Female Gametophyte. Int J Mol Sci 2018; 19:ijms19082246. [PMID: 30071597 PMCID: PMC6122031 DOI: 10.3390/ijms19082246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 01/08/2023] Open
Abstract
The development of the female gametophyte (FG) is one of the key processes of life cycle alteration between the haploid gametophyte and the diploid sporophytes in plants and it is required for successful seed development after fertilization. It is well demonstrated that free nuclear mitosis (FNM) of FG is crucial for the development of the ovule. However, studies of the molecular mechanism of ovule and FG development focused mainly on angiosperms, such as Arabidopsis thaliana and further investigation of gymnosperms remains to be completed. Here, Illumina sequencing of six transcriptomic libraries obtained from developing and abortive ovules at different stages during free nuclear mitosis of magagametophyte (FNMM) was used to acquire transcriptome data and gene expression profiles of Pinus tabulaeformis. Six cDNA libraries generated a total of 71.0 million high-quality clean reads that aligned with 63,449 unigenes and the comparison between developing and abortive ovules identified 7174 differentially expressed genes (DEGs). From the functional annotation results, DEGs involved in the cell cycle and phytohormone regulation were highlighted to reveal their biological importance in ovule development. Furthermore, validation of DEGs from the phytohormone signal transduction pathway was performed using quantitative real-time PCR analysis, revealing the dynamics of transcriptional networks and potential key components in the regulation of FG development in P. tabulaeformis were identified. These findings provide new insights into the regulatory mechanisms of ovule development in woody gymnosperms.
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Xie Y, Chen P, Yan Y, Bao C, Li X, Wang L, Shen X, Li H, Liu X, Niu C, Zhu C, Fang N, Shao Y, Zhao T, Yu J, Zhu J, Xu L, van Nocker S, Ma F, Guan Q. An atypical R2R3 MYB transcription factor increases cold hardiness by CBF-dependent and CBF-independent pathways in apple. THE NEW PHYTOLOGIST 2018; 218:201-218. [PMID: 29266327 DOI: 10.1111/nph.14952] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/13/2017] [Indexed: 05/19/2023]
Abstract
Apple (Malus × domestica) trees are vulnerable to freezing temperatures. However, there has been only limited success in developing cold-hardy cultivars. This lack of progress is due at least partly to lack of understanding of the molecular mechanisms of freezing tolerance in apple. In this study, we evaluated the potential roles for two R2R3 MYB transcription factors (TFs), MYB88 and the paralogous FLP (MYB124), in cold stress in apple and Arabidopsis. We found that MYB88 and MYB124 positively regulate freezing tolerance and cold-responsive gene expression in both apple and Arabidopsis. Chromatin-Immunoprecipitation-qPCR and electrophoretic mobility shift assays showed that MdMYB88/MdMYB124 act as direct regulators of the COLD SHOCK DOMAIN PROTEIN 3 (MdCSP3) and CIRCADIAN CLOCK ASSOCIATED 1 (MdCCA1) genes. Dual luciferase reporter assay indicated that MdCCA1 but not MdCSP3 activated the expression of MdCBF3 under cold stress. Moreover, MdMYB88 and MdMYB124 promoted anthocyanin accumulation and H2 O2 detoxification in response to cold. Taken together, our results suggest that MdMYB88 and MdMYB124 positively regulate cold hardiness and cold-responsive gene expression under cold stress by C-REPEAT BINDING FACTOR (CBF)-dependent and CBF-independent pathways.
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Affiliation(s)
- Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Yan Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Chana Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Liping Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Haiyan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Xiaofang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Chen Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Nan Fang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Yun Shao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Tao Zhao
- Biosystematics Group, Wageningen University, 6708, PB Wageningen, the Netherlands
| | - Jiantao Yu
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Jianhua Zhu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Lingfei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Steven van Nocker
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI, 48824, USA
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
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Yang H, Xue Q, Zhang Z, Du J, Yu D, Huang F. GmMYB181, a Soybean R2R3-MYB Protein, Increases Branch Number in Transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1027. [PMID: 30065741 PMCID: PMC6056663 DOI: 10.3389/fpls.2018.01027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/25/2018] [Indexed: 05/11/2023]
Abstract
Soybean (Glycine max) is an important economic crop that provides abundant oil and high quality protein for human beings. As the process of reproductive growth directly determines the crop seed yield and quality, we initiated studies to identify genes that regulate soybean floral organ development. One R2R3-MYB transcription factor gene, designated as GmMYB181, was found to be enriched in flowers based on microarray analysis and was further functionally investigated in transgenic Arabidopsis. GmMYB181 protein contains two MYB domains, which localized to the nucleus and displayed transcriptional activation in yeast hybrid system. Real-time quantitative PCR (qRT-PCR) results suggested GmMYB181 exclusively expressed in flower tissue. In Arabidopsis, overexpression of GmMYB181 altered the morphology of floral organs, fruit size and plant architecture, including outward curly sepals, smaller siliques, increased lateral branches and reduced plant height, indicating that GmMYB181 is involved in the development of reproductive organs and plays an important role in controlling plant architecture. Further, microarray analysis revealed that overexpressing GmMYB181 in Arabidopsis affected the expression of 3450 genes in mature flowers, including those involved in floral organ, seed/fruit development, and responded to different hormone signals.
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Genome-Wide Analysis of DNA Methylation During Ovule Development of Female-Sterile Rice fsv1. G3-GENES GENOMES GENETICS 2017; 7:3621-3635. [PMID: 28877971 PMCID: PMC5677159 DOI: 10.1534/g3.117.300243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The regulation of female fertility is an important field of rice sexual reproduction research. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during development processes. However, few reports have described the methylation profiles of female-sterile rice during ovule development. In this study, ovules were continuously acquired from the beginning of megaspore mother cell meiosis until the mature female gametophyte formation period, and global DNA methylation patterns were compared in the ovules of a high-frequency female-sterile line (fsv1) and a wild-type rice line (Gui99) using whole-genome bisulfite sequencing (WGBS). Profiling of the global DNA methylation revealed hypo-methylation, and 3471 significantly differentially methylated regions (DMRs) were observed in fsv1 ovules compared with Gui99. Based on functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis of differentially methylated genes (DMGs), we observed more DMGs enriched in cellular component, reproduction regulation, metabolic pathway, and other pathways. In particular, many ovule development genes and plant hormone-related genes showed significantly different methylation patterns in the two rice lines, and these differences may provide important clues for revealing the mechanism of female gametophyte abortion.
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Xanthopoulou A, Ganopoulos I, Psomopoulos F, Manioudaki M, Moysiadis T, Kapazoglou A, Osathanunkul M, Michailidou S, Kalivas A, Tsaftaris A, Nianiou-Obeidat I, Madesis P. De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers. Gene 2017; 622:50-66. [PMID: 28435133 DOI: 10.1016/j.gene.2017.04.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/15/2017] [Accepted: 04/19/2017] [Indexed: 01/03/2023]
Abstract
The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits.
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Affiliation(s)
- Aliki Xanthopoulou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece; Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER (ex NAGREF), Thermi, Macedonia GR-57001, Greece
| | - Fotis Psomopoulos
- Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
| | - Maria Manioudaki
- Centre for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Aliki Kapazoglou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sofia Michailidou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Apostolos Kalivas
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER (ex NAGREF), Thermi, Macedonia GR-57001, Greece
| | - Athanasios Tsaftaris
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece; Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece
| | - Irini Nianiou-Obeidat
- Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece.
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece.
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Wang HZ, Yang KZ, Zou JJ, Zhu LL, Xie ZD, Morita MT, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nat Commun 2015; 6:8822. [PMID: 26578169 PMCID: PMC4673497 DOI: 10.1038/ncomms9822] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 10/07/2015] [Indexed: 12/29/2022] Open
Abstract
PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity. Plants respond to reorientation by altering the distribution of the plant hormone auxin causing roots to bend towards gravity. Here Wang et al. find that expression of the PIN3 and PIN7 auxin transporters in gravity sensing cells is controlled by concerted action of the FLP and MYB88 transcription factors.
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Affiliation(s)
- Hong-Zhe Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan (Fragrant Hill), Haidian, Beijing 100093, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ke-Zhen Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan (Fragrant Hill), Haidian, Beijing 100093, China
| | - Jun-Jie Zou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan (Fragrant Hill), Haidian, Beijing 100093, China
| | - Ling-Ling Zhu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan (Fragrant Hill), Haidian, Beijing 100093, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zi Dian Xie
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210, USA
| | - Miyo Terao Morita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masao Tasaka
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0101, Japan
| | - Jiří Friml
- Institute of Science and Technology of Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Erich Grotewold
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210, USA
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | - Steffen Vanneste
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | - Fred Sack
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan (Fragrant Hill), Haidian, Beijing 100093, China
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30
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Lei Q, Lee E, Keerthisinghe S, Lai L, Li M, Lucas JR, Wen X, Ren X, Sack FD. The FOUR LIPS and MYB88 transcription factor genes are widely expressed in Arabidopsis thaliana during development. AMERICAN JOURNAL OF BOTANY 2015; 102:1521-1528. [PMID: 26391711 DOI: 10.3732/ajb.1500056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/20/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY The FOUR LIPS (FLP) and MYB88 transcription factors, which are closely related in structure and function, control the development of stomata, as well as entry into megasporogenesis in Arabidopsis thaliana. However, other locations where these transcription factors are expressed are poorly described. Documenting additional locations where these genes are expressed might define new functions for these genes. METHODS Expression patterns were examined throughout vegetative and reproductive development. The expression from two transcriptional-reporter fusions were visualized with either β-glucuronidase (GUS) or green fluorescence protein (GFP). KEY RESULTS Both flp and myb88 genes were expressed in many, previously unreported locations, consistent with the possibility of additional functions for FLP and MYB88. Moreover, expression domains especially of FLP display sharp cutoffs or boundaries. CONCLUSIONS In addition to stomatal and reproductive development, FLP and MYB88, which are R2R3 MYB transcription factor genes, are expressed in many locations in cells, tissues, and organs.
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Affiliation(s)
- Qin Lei
- College of Horticulture, Northwest A&F University, Yangling, 712100, China Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - EunKyoung Lee
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sandra Keerthisinghe
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Lien Lai
- Department of Biochemistry, Ohio State University, Columbus, Ohio 43210 USA
| | - Meng Li
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jessica R Lucas
- Biology, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053 USA
| | - Xiaohong Wen
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Xiaolin Ren
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Fred D Sack
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
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31
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Jiang L, Yan S, Yang W, Li Y, Xia M, Chen Z, Wang Q, Yan L, Song X, Liu R, Zhang X. Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.). Sci Rep 2015; 5:8031. [PMID: 25619948 PMCID: PMC5379036 DOI: 10.1038/srep08031] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/18/2014] [Indexed: 11/09/2022] Open
Abstract
Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-Seq data were used to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expressed, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation for dissecting the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance.
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Affiliation(s)
- Li Jiang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Shuangshuang Yan
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Wencai Yang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Yanqiang Li
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Mengxue Xia
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Zijing Chen
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Qian Wang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Liying Yan
- College of Horticulture Science and Technology, Qinhuangdao 066004, China
| | - Xiaofei Song
- Analysis and Testing Centre, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Xiaolan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
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32
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Schmidt R, Schippers JHM, Mieulet D, Obata T, Fernie AR, Guiderdoni E, Mueller-Roeber B. MULTIPASS, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:258-73. [PMID: 23855375 DOI: 10.1111/tpj.12286] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 07/07/2013] [Accepted: 07/10/2013] [Indexed: 05/20/2023]
Abstract
Growth regulation is an important aspect of plant adaptation during environmental perturbations. Here, the role of MULTIPASS (OsMPS), an R2R3-type MYB transcription factor of rice, was explored. OsMPS is induced by salt stress and expressed in vegetative and reproductive tissues. Over-expression of OsMPS reduces growth under non-stress conditions, while knockdown plants display increased biomass. OsMPS expression is induced by abscisic acid and cytokinin, but is repressed by auxin, gibberellin and brassinolide. Growth retardation caused by OsMPS over-expression is partially restored by auxin application. Expression profiling revealed that OsMPS negatively regulates the expression of EXPANSIN (EXP) and cell-wall biosynthesis as well as phytohormone signaling genes. Furthermore, the expression of OsMPS-dependent genes is regulated by auxin, cytokinin and abscisic acid. Moreover, we show that OsMPS is a direct upstream regulator of OsEXPA4, OsEXPA8, OsEXPB2, OsEXPB3, OsEXPB6 and the endoglucanase genes OsGLU5 and OsGLU14. The multiple responses of OsMPS and its target genes to various hormones suggest an integrative function of OsMPS in the cross-talk between phytohormones and the environment to regulate adaptive growth.
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Affiliation(s)
- Romy Schmidt
- Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Straße 24-25, Haus 20, 14476, Potsdam, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
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33
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Xu XH, Wang F, Chen H, Sun W, Zhang XS. Transcript profile analyses of maize silks reveal effective activation of genes involved in microtubule-based movement, ubiquitin-dependent protein degradation, and transport in the pollination process. PLoS One 2013; 8:e53545. [PMID: 23301084 PMCID: PMC3536752 DOI: 10.1371/journal.pone.0053545] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/30/2012] [Indexed: 12/20/2022] Open
Abstract
Pollination is the first crucial step of sexual reproduction in flowering plants, and it requires communication and coordination between the pollen and the stigma. Maize (Zea mays) is a model monocot with extraordinarily long silks, and a fully sequenced genome, but little is known about the mechanism of its pollen-stigma interactions. In this study, the dynamic gene expression of silks at four different stages before and after pollination was analyzed. The expression profiles of immature silks (IMS), mature silks (MS), and silks at 20 minutes and 3 hours after pollination (20MAP and 3HAP, respectively) were compared. In total, we identified 6,337 differentially expressed genes in silks (SDEG) at the four stages. Among them, the expression of 172 genes were induced upon pollination, most of which participated in RNA binding, processing and transcription, signal transduction, and lipid metabolism processes. Genes in the SDEG dataset could be divided into 12 time-course clusters according to their expression patterns. Gene Ontology (GO) enrichment analysis revealed that many genes involved in microtubule-based movement, ubiquitin-mediated protein degradation, and transport were predominantly expressed at specific stages, indicating that they might play important roles in the pollination process of maize. These results add to current knowledge about the pollination process of grasses and provide a foundation for future studies on key genes involved in the pollen-silk interaction in maize.
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Affiliation(s)
- Xiao Hui Xu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Fang Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Hao Chen
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Wei Sun
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
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