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Alisha A, Szweykowska-Kulinska Z, Sierocka I. Comparative analysis of SPL transcription factors from streptophyte algae and embryophytes reveals evolutionary trajectories of SPL family in streptophytes. Sci Rep 2024; 14:1611. [PMID: 38238367 PMCID: PMC10796333 DOI: 10.1038/s41598-024-51626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode plant-specific transcription factors which are important regulators of diverse plant developmental processes. We took advantage of available genome sequences of streptophyte algae representatives to investigate the relationships of SPL genes between freshwater green algae and land plants. Our analysis showed that streptophyte algae, hornwort and liverwort genomes encode from one to four SPL genes which is the smallest set, in comparison to other land plants studied to date. Based on the phylogenetic analysis, four major SPL phylogenetic groups were distinguished with Group 3 and 4 being sister to Group 1 and 2. Comparative motif analysis revealed conserved protein motifs within each phylogenetic group and unique bryophyte-specific motifs within Group 1 which suggests lineage-specific protein speciation processes. Moreover, the gene structure analysis also indicated the specificity of each by identifying differences in exon-intron structures between the phylogenetic groups, suggesting their evolutionary divergence. Since current understanding of SPL genes mostly arises from seed plants, the presented comparative and phylogenetic analyzes from freshwater green algae and land plants provide new insights on the evolutionary trajectories of the SPL gene family in different classes of streptophytes.
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Affiliation(s)
- Alisha Alisha
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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2
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Poethig RS, Fouracre J. Temporal regulation of vegetative phase change in plants. Dev Cell 2024; 59:4-19. [PMID: 38194910 PMCID: PMC10783531 DOI: 10.1016/j.devcel.2023.11.010] [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: 07/17/2023] [Revised: 10/11/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
During their vegetative growth, plants reiteratively produce leaves, buds, and internodes at the apical end of the shoot. The identity of these organs changes as the shoot develops. Some traits change gradually, but others change in a coordinated fashion, allowing shoot development to be divided into discrete juvenile and adult phases. The transition between these phases is called vegetative phase change. Historically, vegetative phase change has been studied because it is thought to be associated with an increase in reproductive competence. However, this is not true for all species; indeed, heterochronic variation in the timing of vegetative phase change and flowering has made important contributions to plant evolution. In this review, we describe the molecular mechanism of vegetative phase change, how the timing of this process is controlled by endogenous and environmental factors, and its ecological and evolutionary significance.
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Affiliation(s)
- R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jim Fouracre
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
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Wu X, Cheng C, Ma R, Xu J, Ma C, Zhu Y, Ren Y. Genome-wide identification, expression analysis, and functional study of the bZIP transcription factor family and its response to hormone treatments in pea (Pisum sativum L.). BMC Genomics 2023; 24:705. [PMID: 37993794 PMCID: PMC10666455 DOI: 10.1186/s12864-023-09793-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Basic leucine zipper (bZIP) protein is a plant-specific transcription factor involved in various biological processes, including light signaling, seed maturation, flower development, cell elongation, seed accumulation protein, and abiotic and biological stress responses. However, little is known about the pea bZIP family. RESULTS In this study, we identified 87 bZIP genes in pea, named PsbZIP1 ~ PsbZIP87, via homology analysis using Arabidopsis. The genes were divided into 12 subfamilies and distributed unevenly in 7 pea chromosomes. PsbZIPs in the same subfamily contained similar intron/exon organization and motif composition. 1 tandem repeat event and 12 segmental duplication events regulated the expansion of the PsbZIP gene family. To better understand the evolution of the PsbZIP gene family, we conducted collinearity analysis using Arabidopsis thaliana, Oryza sativa Japonica, Fagopyrum tataricum, Solanum lycopersicum, Vitis vinifera, and Brachypodium distachyon as the related species of pea. In addition, interactions between PsbZIP proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of PsbZIP expression was complex. We also evaluated the expression patterns of bZIP genes in different tissues and at different fruit development stages, all while subjecting them to five hormonal treatments. CONCLUSION These results provide a deeper understanding of PsbZIP gene family evolution and resources for the molecular breeding of pea. The findings suggested that PsbZIP genes, specifically PSbZIP49, play key roles in the development of peas and their response to various hormones.
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Affiliation(s)
- Xiaozong Wu
- Zhengzhou University of Light Industry, Zhengzhou, 450002, People's Republic of China
| | - Changhe Cheng
- China Tobacco Zhejiang Industrial Co., LTD, Hangzhou, 310000, People's Republic of China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jianbo Xu
- Zhengzhou University of Light Industry, Zhengzhou, 450002, People's Republic of China
| | - Congcong Ma
- College of Medical Technology, Luoyang Polytechnic, Luoyang, 471000, China
| | - Yutao Zhu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, 462500, China.
- Henan University of Urban Construction, Pingdingshan, 467036, Henan, China.
| | - Yanyan Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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4
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Ren Y, Ma R, Xie M, Fan Y, Feng L, Chen L, Yang H, Wei X, Wang X, Liu K, Cheng P, Wang B. Genome-wide identification, phylogenetic and expression pattern analysis of HSF family genes in the Rye (Secale cereale L.). BMC PLANT BIOLOGY 2023; 23:441. [PMID: 37726665 PMCID: PMC10510194 DOI: 10.1186/s12870-023-04418-1] [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: 02/23/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Heat shock factor (HSF), a typical class of transcription factors in plants, has played an essential role in plant growth and developmental stages, signal transduction, and response to biotic and abiotic stresses. The HSF genes families has been identified and characterized in many species through leveraging whole genome sequencing (WGS). However, the identification and systematic analysis of HSF family genes in Rye is limited. RESULTS In this study, 31 HSF genes were identified in Rye, which were unevenly distributed on seven chromosomes. Based on the homology of A. thaliana, we analyzed the number of conserved domains and gene structures of ScHSF genes that were classified into seven subfamilies. To better understand the developmental mechanisms of ScHSF family during evolution, we selected one monocotyledon (Arabidopsis thaliana) and five (Triticum aestivum L., Hordeum vulgare L., Oryza sativa L., Zea mays L., and Aegilops tauschii Coss.) specific representative dicotyledons associated with Rye for comparative homology mapping. The results showed that fragment replication events modulated the expansion of the ScHSF genes family. In addition, interactions between ScHSF proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of ScHSF expression was complex. A total of 15 representative genes were targeted from seven subfamilies to characterize their gene expression responses in different tissues, fruit developmental stages, three hormones, and six different abiotic stresses. CONCLUSIONS This study demonstrated that ScHSF genes, especially ScHSF1 and ScHSF3, played a key role in Rye development and its response to various hormones and abiotic stresses. These results provided new insights into the evolution of HSF genes in Rye, which could help the success of molecular breeding in Rye.
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Affiliation(s)
- Yanyan Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Muhua Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, People's Republic of China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610000, People's Republic of China
| | - Long Chen
- Tianfu New Area General Aviation Profession Academy, Meishan, 620564, China
| | - Hao Yang
- Agricultural Service Center of Langde Town of Leishan County, Qiandongnan Miao and Dong Autonomous Prefecture, 556019, China
| | - Xiaobao Wei
- Guizhou Provincial Center For Disease Control And Prevention, Guiyang, 550025, People's Republic of China
| | - Xintong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Kouhan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Yadav S, Yadava YK, Meena S, Singh L, Kansal R, Grover M, M S N, Bharadwaj C, Paul V, Gaikwad K, Jain PK. The SPL transcription factor genes are potential targets for epigenetic regulation in response to drought stress in chickpea (C. arietinum L.). Mol Biol Rep 2023; 50:5509-5517. [PMID: 37119417 DOI: 10.1007/s11033-023-08347-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/17/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND Crop improvement for tolerance to various biotic and abiotic stress factors necessitates understanding the key gene regulatory mechanisms. One such mechanism of gene regulation involves changes in cytosine methylation at the gene body and flanking regulatory sequences. The present study was undertaken to identify genes which might be potential targets of drought-induced DNA methylation in chickpea. METHODS AND RESULTS Two chickpea genotypes, which contrast for drought tolerance, were subjected to drought stress conditions and their differential response was studied by analysing different morpho-physiological traits. Utilizing the in-house, high throughput sequencing data, the SQUAMOSA promoter-binding (SBP) protein-like (SPL) transcription factor genes were identified to be differentially methylated and expressed amongst the two genotypes, in response to drought stress. The methylation status of one of these genes was examined and validated through bisulfite PCR (BS-PCR). The identified genes could be possible homologs to known epialleles and can therefore serve as potential epialleles which can be utilized for crop improvement in chickpea. CONCLUSION The SPL TF genes are potential targets of epigenetic regulation in response to drought stress in chickpea. Since these are TFs, they might play important roles in controlling the expression of other genes, thus contributing to differential drought response of the two genotypes.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Shashi Meena
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Lalbahadur Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Rekha Kansal
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Monender Grover
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Nimmy M S
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - C Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vijay Paul
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Pradeep K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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Ren Y, Ma R, Fan Y, Zhao B, Cheng P, Fan Y, Wang B. Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Quinoa (Chenopodium quinoa). BMC Genomics 2022; 23:773. [PMID: 36434504 PMCID: PMC9701020 DOI: 10.1186/s12864-022-08977-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/29/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Squamous promoter binding protein-like (SPL) proteins are a class of transcription factors that play essential roles in plant growth and development, signal transduction, and responses to biotic and abiotic stresses. The rapid development of whole genome sequencing has enabled the identification and characterization of SPL gene families in many plant species, but to date this has not been performed in quinoa (Chenopodium quinoa). RESULTS This study identified 23 SPL genes in quinoa, which were unevenly distributed on 18 quinoa chromosomes. Quinoa SPL genes were then classified into eight subfamilies based on homology to Arabidopsis thaliana SPL genes. We selected three dicotyledonous and monocotyledonous representative species, each associated with C. quinoa, for comparative sympatric mapping to better understand the evolution of the developmental mechanisms of the CqSPL family. Furthermore, we also used 15 representative genes from eight subfamilies to characterize CqSPLs gene expression in different tissues and at different fruit developmental stages under six different abiotic stress conditions. CONCLUSIONS This study, the first to identify and characterize SPL genes in quinoa, reported that CqSPL genes, especially CqSPL1, play a critical role in quinoa development and in its response to various abiotic stresses.
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Affiliation(s)
- Yanyan Ren
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Rui Ma
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, 843100 Aksu, P.R. China
| | - Bingjie Zhao
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Peng Cheng
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Yu Fan
- grid.411292.d0000 0004 1798 8975School of Food and Biological Engineering, Chengdu University, Longquanyi District, 610106 Chengdu, P.R. China
| | - Baotong Wang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
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Zhao H, Cao H, Zhang M, Deng S, Li T, Xing S. Genome-Wide Identification and Characterization of SPL Family Genes in Chenopodium quinoa. Genes (Basel) 2022; 13:genes13081455. [PMID: 36011366 PMCID: PMC9408038 DOI: 10.3390/genes13081455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 12/02/2022] Open
Abstract
SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode a large family of plant-specific transcription factors that play important roles in plant growth, development, and stress responses. However, there is little information available on SPL genes in Chenopodiaceae. Here, 23 SPL genes were identified and characterized in the highly nutritious crop Chenopodium quinoa. Chromosome localization analysis indicated that the 23 CqSPL genes were unevenly distributed on 12 of 18 chromosomes. Two zinc finger-like structures and a nuclear location signal were present in the SBP domains of all CqSPLs, with the exception of CqSPL21/22. Phylogenetic analysis revealed that these genes were classified into eight groups (group I–VIII). The exon–intron structure and motif composition of the genes in each group were similar. Of the 23 CqSPLs, 13 were potential targets of miR156/7. In addition, 5 putative miR156-encoding loci and 13 putative miR157-encoding loci were predicted in the quinoa genome, and they were unevenly distributed on chromosome 1–4. The expression of several Cqu-MIR156/7 loci was confirmed by reverse transcription polymerase chain reaction in seedlings. Many putative cis-elements associated with light, stress, and phytohormone responses were identified in the promoter regions of CqSPLs, suggesting that CqSPL genes are likely involved in the regulation of key developmental processes and stress responses. Expression analysis revealed highly diverse expression patterns of CqSPLs among tissues. Many CqSPLs were highly expressed in leaves, flowers, and seeds, and their expression levels were low in the roots, suggesting that CqSPLs play distinct roles in the development and growth of quinoa. The expression of 13 of 23 CqSPL genes responded to salt treatment (11 up-regulated and 2 down-regulated). A total of 22 of 23 CqSPL genes responded to drought stress (21 up-regulated and 1 down-regulated). Moreover, the expression of 14 CqSPL genes was significantly altered following cadmium treatment (3 up-regulated and 11 down-regulated). CqSPL genes are thus involved in quinoa responses to salt/drought and cadmium stresses. These findings provide new insights that will aid future studies of the biological functions of CqSPLs in C. quinoa.
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Affiliation(s)
- Hongmei Zhao
- College of Biological Sciences and Technology, Jinzhong University, Jinzhong 030600, Shanxi, China
| | - Huaqi Cao
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Mian Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Sufang Deng
- College of Biological Sciences and Technology, Jinzhong University, Jinzhong 030600, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Tingting Li
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Shuping Xing
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
- Correspondence: ; Tel.: +86-186-0346-2517
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8
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Hussain A, Liu J, Mohan B, Burhan A, Nasim Z, Bano R, Ameen A, Zaynab M, Mukhtar MS, Pajerowska-Mukhtar KM. A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants. Sci Rep 2022; 12:12328. [PMID: 35853967 PMCID: PMC9296551 DOI: 10.1038/s41598-022-16602-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
Zinc finger (Zf)-BED proteins are a novel superfamily of transcription factors that controls numerous activities in plants including growth, development, and cellular responses to biotic and abiotic stresses. Despite their important roles in gene regulation, little is known about the specific functions of Zf-BEDs in land plants. The current study identified a total of 750 Zf-BED-encoding genes in 35 land plant species including mosses, bryophytes, lycophytes, gymnosperms, and angiosperms. The gene family size was somewhat proportional to genome size. All identified genes were categorized into 22 classes based on their specific domain architectures. Of these, class I (Zf-BED_DUF-domain_Dimer_Tnp_hAT) was the most common in the majority of the land plants. However, some classes were family-specific, while the others were species-specific, demonstrating diversity at different classification levels. In addition, several novel functional domains were also predicated including WRKY and nucleotide-binding site (NBS). Comparative genomics, transcriptomics, and proteomics provided insights into the evolutionary history, duplication, divergence, gene gain and loss, species relationship, expression profiling, and structural diversity of Zf-BEDs in land plants. The comprehensive study of Zf-BEDs in Gossypium sp., (cotton) also demonstrated a clear footprint of polyploidization. Overall, this comprehensive evolutionary study of Zf-BEDs in land plants highlighted significant diversity among plant species.
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Affiliation(s)
- Athar Hussain
- Genomics Lab, School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Jinbao Liu
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA
| | - Binoop Mohan
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA
| | - Akif Burhan
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Zunaira Nasim
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Raveena Bano
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Ayesha Ameen
- Office of Research Innovation and Commercialization, University of Management and Technology, Lahore, 54770, Pakistan
| | - Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 51807, Guangdong, China
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA.
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Zhu H, Wang J, Jiang D, Hong Y, Xu J, Zheng S, Yang J, Chen W. The miR157-SPL-CNR module acts upstream of bHLH101 to negatively regulate iron deficiency responses in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1059-1075. [PMID: 35297168 DOI: 10.1111/jipb.13251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 05/23/2023]
Abstract
Iron (Fe) homeostasis is critical for plant growth, development, and stress responses. Fe levels are tightly controlled by intricate regulatory networks in which transcription factors (TFs) play a central role. A series of basic helix-loop-helix (bHLH) TFs have been shown to contribute to Fe homeostasis, but the regulatory layers beyond bHLH TFs remain largely unclear. Here, we demonstrate that the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) TF SlSPL-CNR negatively regulates Fe-deficiency responses in tomato (Solanum lycopersicum) roots. Fe deficiency rapidly repressed the expression of SlSPL-CNR, and Fe deficiency responses were intensified in two clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9-generated SlSPL-CNR knock-out lines compared to the wild-type. Comparative transcriptome analysis identified 47 Fe deficiency-responsive genes the expression of which is negatively regulated by SlSPL-CNR, one of which, SlbHLH101, helps regulate Fe uptake genes. SlSPL-CNR localizes the nucleus and interacts with the GTAC and BOX 4 (ATTAAT) motifs in the SlbHLH101 promoter to repress its expression. Inhibition of SlSPL-CNR expression in response to Fe deficiency was well correlated with the expression of the microRNA SlymiR157. SlymiR157-overexpressing tomato lines displayed enhanced Fe deficiency responses, as did SlSPL-CNR loss-of-function mutants. We propose that the SlymiR157-SlSPL-CNR module represents a novel pathway that acts upstream of SlbHLH101 to regulate Fe homeostasis in tomato roots.
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Affiliation(s)
- Huihui Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiayi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dan Jiang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jianli Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Weiwei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
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10
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The Mulberry SPL Gene Family and the Response of MnSPL7 to Silkworm Herbivory through Activating the Transcription of MnTT2L2 in the Catechin Biosynthesis Pathway. Int J Mol Sci 2022; 23:ijms23031141. [PMID: 35163065 PMCID: PMC8835075 DOI: 10.3390/ijms23031141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, as unique plant transcription factors, play important roles in plant developmental regulation and stress response adaptation. Although mulberry is a commercially valuable tree species, there have been few systematic studies on SPL genes. In this work, we identified 15 full-length SPL genes in the mulberry genome, which were distributed on 4 Morus notabilis chromosomes. Phylogenetic analysis clustered the SPL genes from five plants (Malus × domestica Borkh, Populus trichocarpa, M. notabilis, Arabidopsis thaliana, and Oryza sativa) into five groups. Two zinc fingers (Zn1 and Zn2) were found in the conserved SBP domain in all of the MnSPLs. Comparative analyses of gene structures and conserved motifs revealed the conservation of MnSPLs within a group, whereas there were significant structure differences among groups. Gene quantitative analysis showed that the expression of MnSPLs had tissue specificity, and MnSPLs had much higher expression levels in older mulberry leaves. Furthermore, transcriptome data showed that the expression levels of MnSPL7 and MnSPL14 were significantly increased under silkworm herbivory. Molecular experiments revealed that MnSPL7 responded to herbivory treatment through promoting the transcription of MnTT2L2 and further upregulating the expression levels of catechin synthesis genes (F3′H, DFR, and LAR).
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Li J, Fan R, Wu B, Ji X, Hao C. Genome-Wide Identification and Functional Exploration of SBP-Box Gene Family in Black Pepper ( Piper nigrum L.). Genes (Basel) 2021; 12:genes12111740. [PMID: 34828347 PMCID: PMC8625754 DOI: 10.3390/genes12111740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Black pepper (Piper nigrum L.), is dubbed "the King of Spices". However, the lack of genic knowledge has limited the understanding of its physiological processes and hindered the development of its molecular breeding. The SBP-box gene family is an important family in plant development and integrates multiple physiological processes. Here, we made a genome-wide identification of the pepper SBP-box gene family to provide evolutionary and functional information about this conserved transcription factor. In total, 34 SBP genes were identified in pepper. All these pepper SBP genes were clustered into eight groups, and one pepper group was not found in Arabidopsis thaliana. Segment duplications played the most important role in the expansion process of pepper SBP genes, and all these duplications were subjected to purifying selection. Half of pepper SBP genes were found miR156 target sites, and 17 miR156s were predicted. The tissue expression analysis revealed the differential expression of pepper SBP genes. Eleven SBP genes were found in four co-expression networks, and the GO enrichment further provides a functional prediction for pepper SBP genes. This study lays a foundation for further studies of pepper and provides a valuable reference for functional mining of pepper SBP genes.
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Affiliation(s)
- Jing Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Baoduo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Xunzhi Ji
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
- Correspondence:
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12
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Liu Y, Aslam M, Yao LA, Zhang M, Wang L, Chen H, Huang Y, Qin Y, Niu X. Genomic analysis of SBP gene family in Saccharum spontaneum reveals their association with vegetative and reproductive development. BMC Genomics 2021; 22:767. [PMID: 34706643 PMCID: PMC8549313 DOI: 10.1186/s12864-021-08090-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
Background SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SBP gene family has been identified and characterized in many species, but no systematic analysis of the SBP gene family has been carried out in sugarcane. Results In the present study, a total of 50 sequences for 30 SBP genes were identified by the genome-wide analysis and designated SsSBP1 to SsSBP30 based on their chromosomal distribution. According to the phylogenetic tree, gene structure and motif features, the SsSBP genes were classified into eight groups (I to VIII). By synteny analysis, 27 homologous gene pairs existed in SsSBP genes, and 37 orthologous gene pairs between sugarcane and sorghum were found. Expression analysis in different tissues, including vegetative and reproductive organs, showed differential expression patterns of SsSBP genes, indicating their functional diversity in the various developmental processes. Additionally, 22 SsSBP genes were predicted as the potential targets of miR156. The differential expression pattern of miR156 exhibited a negative correlation of transcription levels between miR156 and the SsSBP gene in different tissues. Conclusions The sugarcane genome possesses 30 SsSBP genes, and they shared similar gene structures and motif features in their subfamily. Based on the transcriptional and qRT-PCR analysis, most SsSBP genes were found to regulate the leaf initial and female reproductive development. The present study comprehensively and systematically analyzed SBP genes in sugarcane and provided a foundation for further studies on the functional characteristics of SsSBP genes during different development processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08090-3.
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Affiliation(s)
- Yanhui Liu
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.,College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mohammad Aslam
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Li-Ang Yao
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Man Zhang
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lulu Wang
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Huihuang Chen
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youmei Huang
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuan Qin
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China. .,College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xiaoping Niu
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.
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13
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Xiao Y, Wen J, Meng R, Meng Y, Zhou Q, Nie ZL. The expansion and diversity of the CYP75 gene family in Vitaceae. PeerJ 2021; 9:e12174. [PMID: 34616623 PMCID: PMC8449539 DOI: 10.7717/peerj.12174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
The CYP75 gene family plays an important role in flavonoid biosynthesis in plants. Little is known about the evolution of the gene family within the grape family. Here, we extracted the CYP75 genes from transcriptome data of 15 grape species and 36 representative genomes from other plants to explore the evolutionary history of the CYP75 gene family in Vitaceae. The structure of the CYP75 protein sequences is highly conserved with the variation mainly occurring in the N terminal and the middle region. The evolutionary analyses suggested classifying the CYP75 gene family into three groups in Vitaceae, namely Vitaceae A1, Vitaceae A2 and Vitaceae B. The Vitaceae A1 and A2 belong to the CYP75A subfamily and the Vitaceae B belongs to the CYP75B subfamily. Within the Vitaceae A1, most Vitaceae taxa present only one copy of the CYP75A protein sequence except for Vitis vinifera with a high number of sequences, which might have originated through recent gene duplications after its split from the other species. Vitaceae A2 contain only CYP75A sequences from Vitaceae sister to one from Camellia sinensis, probably representing a relict lineage. The CYP75B proteins were found to be dominated in Vitaceae and other angiosperms. Our results provide important insights into understanding the evolutionary history of the CYP75 gene family in Vitaceae and other angiosperms.
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Affiliation(s)
- Yang Xiao
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C., U.S.A
| | - Ran Meng
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ying Meng
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Qiang Zhou
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
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Xie X, Yue S, Shi B, Li H, Cui Y, Wang J, Yang P, Li S, Li X, Bian S. Comprehensive Analysis of the SBP Family in Blueberry and Their Regulatory Mechanism Controlling Chlorophyll Accumulation. FRONTIERS IN PLANT SCIENCE 2021; 12:703994. [PMID: 34276754 PMCID: PMC8281205 DOI: 10.3389/fpls.2021.703994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
SQUAMOSA Promoter Binding Protein (SBP) family genes act as central players to regulate plant growth and development with functional redundancy and specificity. Addressing the diversity of the SBP family in crops is of great significance to precisely utilize them to improve agronomic traits. Blueberry is an important economic berry crop. However, the SBP family has not been described in blueberry. In the present study, twenty VcSBP genes were identified through data mining against blueberry transcriptome databases. These VcSBPs could be clustered into eight groups, and the gene structures and motif compositions are divergent among the groups and similar within each group. The VcSBPs were differentially expressed in various tissues. Intriguingly, 10 VcSBPs were highly expressed at green fruit stages and dramatically decreased at the onset of fruit ripening, implying that they are important regulators during early fruit development. Computational analysis showed that 10 VcSBPs were targeted by miR156, and four of them were further verified by degradome sequencing. Moreover, their functional diversity was studied in Arabidopsis. Noticeably, three VcSBPs significantly increased chlorophyll accumulation, and qRT-PCR analysis indicated that VcSBP13a in Arabidopsis enhanced the expression of chlorophyll biosynthetic genes such as AtDVR, AtPORA, AtPORB, AtPORC, and AtCAO. Finally, the targets of VcSBPs were computationally identified in blueberry, and the Y1H assay showed that VcSBP13a could physically bind to the promoter region of the chlorophyll-associated gene VcLHCB1. Our findings provided an overall framework for individually understanding the characteristics and functions of the SBP family in blueberry.
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Affiliation(s)
- Xin Xie
- College of Plant Science, Jilin University, Changchun, China
| | - Shaokang Yue
- College of Plant Science, Jilin University, Changchun, China
| | - Baosheng Shi
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Hongxue Li
- College of Plant Science, Jilin University, Changchun, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON Canada
- Department of Biology, Western University, London, ON, Canada
| | - Jingying Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Pengjie Yang
- College of Plant Science, Jilin University, Changchun, China
| | - Shuchun Li
- Department of Pain, Second Hospital of Jilin University, Changchun, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, China
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, China
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15
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Feng G, Han J, Yang Z, Liu Q, Shuai Y, Xu X, Nie G, Huang L, Liu W, Zhang X. Genome-wide identification, phylogenetic analysis, and expression analysis of the SPL gene family in orchardgrass (Dactylis glomerata L.). Genomics 2021; 113:2413-2425. [PMID: 34058273 DOI: 10.1016/j.ygeno.2021.05.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
SPL (SQUAMOSA promoter binding protein-like) is a plant-specific transcription factor family that contains the conserved SBP domain, which plays a vital role in the vegetative-to-reproductive phase transition, flowering development and regulation, tillering/branching, and stress responses. Although the SPL family has been identified and characterized in various plant species, limited information about it has been obtained in orchardgrass, which is a critical forage crop worldwide. In this study, 17 putative DgSPL genes were identified among seven chromosomes, and seven groups that share similar gene structures and conserved motifs were determined by phylogenetic analysis. Of these, eight genes have potential target sites for miR156. cis-Element and gene ontology annotation analysis indicated DgSPLs may be involved in regulating development and abiotic stress responses. The expression patterns of eight DgSPL genes at five developmental stages, in five tissues, and under three stress conditions were determined by RNA-seq and qRT-PCR. These assays indicated DgSPLs are involved in vegetative-to-reproductive phase transition, floral development, and stress responses. The transient expression analysis in tobacco and heterologous expression assays in yeast indicated that miR156-targeted DG1G01828.1 and DG0G01071.1 are nucleus-localized proteins, that may respond to drought, salt, and heat stress. Our study represents the first systematic analysis of the SPL family in orchardgrass. This research provides a comprehensive assessment of the DgSPL family, which lays the foundation for further examination of the role of miR156/DgSPL in regulating development and stress responses in forages grasses.
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Affiliation(s)
- Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Jiating Han
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Qiuxu Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yang Shuai
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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16
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Jiang X, Chen P, Zhang X, Liu Q, Li H. Comparative analysis of the SPL gene family in five Rosaceae species: Fragaria vesca, Malus domestica, Prunus persica, Rubus occidentalis, and Pyrus pyrifolia. Open Life Sci 2021; 16:160-171. [PMID: 33817308 PMCID: PMC7968543 DOI: 10.1515/biol-2021-0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
SQUAMOSA promoter-binding protein-like (SPL) transcription factors are very important for the plant growth and development. Here 15 RoSPLs were identified in Rubus occidentalis. The conserved domains and motifs, phylogenetic relationships, posttranscriptional regulation, and physiological function of the 92 SPL family genes in Fragaria vesca, Malus domestica, Prunus persica, R. occidentalis, and Pyrus pyrifolia were analyzed. Sequence alignment and phylogenetic analysis showed the SPL proteins had sequence conservation, some FvSPLs could be lost or developed, and there was a closer relationship between M. domestica and P. pyrifolia, F. vesca and R. occidentalis, respectively. Genes with similar motifs clustering together in the same group had their functional redundancy. Based on the function of SPLs in Arabidopsis thaliana, these SPLs could be involved in vegetative transition from juvenile to adult, morphological change in the reproductive phase, anthocyanin biosynthesis, and defense stress. Forty-eight SPLs had complementary sequences of miR156, of which nine PrpSPLs in P. persica and eight RoSPLs in R. occidentalis as the potential targets of miR156 were reported for the first time, suggesting the conservative regulatory effects of miR156 and indicating the roles of miR156-SPL modules in plant growth, development, and defense response. It provides a basic understanding of SPLs in Rosaceae plants.
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Affiliation(s)
- Xuwen Jiang
- Dryland Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao, 266109, Shandong, China
| | - Peng Chen
- Department of Entomology, College of plant protection, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China.,Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Gongye North Road No. 202, Jinan, 250100, China
| | - Xiaowen Zhang
- Dryland Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao, 266109, Shandong, China
| | - Qizhi Liu
- Department of Entomology, College of plant protection, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
| | - Heqin Li
- Dryland Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao, 266109, Shandong, China
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17
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Jiang M, He Y, Chen X, Zhang X, Guo Y, Yang S, Huang J, Traw MB. CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1301-1314. [PMID: 32996244 DOI: 10.1111/tpj.15001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/14/2020] [Accepted: 09/03/2020] [Indexed: 05/07/2023]
Abstract
Although SQUAMOSA promoter-binding-like (SPL) transcription factors are important regulators of development in rice (Oryza sativa), prior assessments of the SPL family have been limited to single genes. A functional comparison across the full gene family in standardized genetic backgrounds has not been reported previously. Here, we demonstrate that the SPL gene family in rice is enriched due to the most recent whole genome duplication (WGD). Notably, 10 of 19 rice SPL genes (52%) cluster in four units that have persisted for at least 50 million years. We show that SPL gene grouping and retention following WGD is widespread in angiosperms, suggesting the conservatism and importance of this gene arrangement. We used Cas9 editing to generate transformation lines for all 19 SPL genes in a common set of backgrounds, and found that knockouts of 14 SPL genes exhibited defects in plant height, 10 exhibited defects in panicle size, and nine had altered grain lengths. We observed subfunctionalization of genes in the paleoduplicated pairs, but little evidence of neofunctionalization. Expression of OsSPL3 was negatively correlated with that of its closest neighbor in its synteny group, OsSPL4, and its sister paired gene, OsSPL12, in the opposing group. Nucleotide diversity was lower in eight of the nine singleton genes in domesticated rice, relative to wild rice, whereas the reverse was true for the paired genes. Together, these results provide functional information on eight previously unexamined OsSPL family members and suggest that paleoduplicate pair redundancy benefits plant survival and innovation.
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Affiliation(s)
- Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ying He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaonan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yanru Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - M Brian Traw
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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18
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Tripathi RK, Overbeek W, Singh J. Global analysis of SBP gene family in Brachypodium distachyon reveals its association with spike development. Sci Rep 2020; 10:15032. [PMID: 32929136 PMCID: PMC7490389 DOI: 10.1038/s41598-020-72005-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
SQUAMOSA-promoter binding like proteins (SBPs/SPLs) are plant specific transcription factors targeted by miR156 and involved in various biological pathways, playing multi-faceted developmental roles. This gene family is not well characterized in Brachypodium. We identified a total of 18 SBP genes in B. distachyon genome. Phylogenetic analysis revealed that SBP gene family in Brachypodium expanded through large scale duplication. A total of 10 BdSBP genes were identified as targets of miR156. Transcript cleavage analysis of selected BdSBPs by miR156 confirmed their antagonistic connection. Alternative splicing was observed playing an important role in BdSBPs and miR156 interaction. Characterization of T-DNA Bdsbp9 mutant showed reduced plant growth and spike length, reflecting its involvement in the spike development. Expression of a majority of BdSBPs elevated during spikelet initiation. Specifically, BdSBP1 and BdSBP3 differentially expressed in response to vernalization. Differential transcript abundance of BdSBP1, BdSBP3, BdSBP8, BdSBP9, BdSBP14, BdSBP18 and BdSBP23 genes was observed during the spike development under high temperature. Co-expression network, protein-protein interaction and biological pathway analysis indicate that BdSBP genes mainly regulate transcription, hormone, RNA and transport pathways. Our work reveals the multi-layered control of SBP genes and demonstrates their association with spike development and temperature sensitivity in Brachypodium.
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Affiliation(s)
- Rajiv K Tripathi
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Quebec, H9X 3V9, Canada.
| | - William Overbeek
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Quebec, H9X 3V9, Canada
| | - Jaswinder Singh
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Quebec, H9X 3V9, Canada.
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Zhu T, Liu Y, Ma L, Wang X, Zhang D, Han Y, Ding Q, Ma L. Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat. BMC PLANT BIOLOGY 2020; 20:420. [PMID: 32912142 PMCID: PMC7488452 DOI: 10.1186/s12870-020-02576-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/26/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. RESULTS In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). CONCLUSIONS The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.
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Affiliation(s)
- Ting Zhu
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yue Liu
- College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Liting Ma
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xiaoying Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Dazhong Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yucui Han
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Yangling, 712100, China.
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Wang Z, Ma W, Zhu T, Lu N, Ouyang F, Wang N, Yang G, Kong L, Qu G, Zhang S, Wang J. Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey. BMC Genomics 2020; 21:508. [PMID: 32698759 PMCID: PMC7376858 DOI: 10.1186/s12864-020-06918-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Floral transition plays an important role in development, and proper time is necessary to improve the value of valuable ornamental trees. The molecular mechanisms of floral transition remain unknown in perennial woody plants. "Bairihua" is a type of C. bungei that can undergo floral transition in the first planting year. RESULTS Here, we combined short-read next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing to provide a more complete view of transcriptome regulation during floral transition in C. bungei. The circadian rhythm-plant pathway may be the critical pathway during floral transition in early flowering (EF) C. bungei, according to horizontal and vertical analysis in EF and normal flowering (NF) C. bungei. SBP and MIKC-MADS-box were seemingly involved in EF during floral transition. A total of 61 hub genes were associated with floral transition in the MEturquoise model with Weighted Gene Co-expression Network Analysis (WGCNA). The results reveal that ten hub genes had a close connection with the GASA homologue gene (Cbu.gene.18280), and the ten co-expressed genes belong to five flowering-related pathways. Furthermore, our study provides new insights into the complexity and regulation of alternative splicing (AS). The ratio or number of isoforms of some floral transition-related genes is different in different periods or in different sub-genomes. CONCLUSIONS Our results will be a useful reference for the study of floral transition in other perennial woody plants. Further molecular investigations are needed to verify our sequencing data.
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Affiliation(s)
- Zhi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Fangqun Ouyang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Nan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Guijuan Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Lisheng Kong
- Department of Biology Centre for Forest Biology, University of Victoria, Victoria, BC 11 Canada
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 PR China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
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21
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Lai T, Wang X, Ye B, Jin M, Chen W, Wang Y, Zhou Y, Blanks AM, Gu M, Zhang P, Zhang X, Li C, Wang H, Liu Y, Gallusci P, Tör M, Hong Y. Molecular and functional characterization of the SBP-box transcription factor SPL-CNR in tomato fruit ripening and cell death. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2995-3011. [PMID: 32016417 PMCID: PMC7260717 DOI: 10.1093/jxb/eraa067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/01/2020] [Indexed: 05/19/2023]
Abstract
SlSPL-CNR, an SBP-box transcription factor (TF) gene residing at the epimutant Colourless non-ripening (Cnr) locus, is involved in tomato ripening. This epimutant provides a unique model to investigate the (epi)genetic basis of fruit ripening. Here we report that SlSPL-CNR is a nucleus-localized protein with a distinct monopartite nuclear localization signal (NLS). It consists of four consecutive residues ' 30KRKR33' at the N-terminus of the protein. Mutation of the NLS abolishes SlSPL-CNR's ability to localize in the nucleus. SlSPL-CNR comprises two zinc-finger motifs (ZFMs) within the C-terminal SBP-box domain. Both ZFMs contribute to zinc-binding activity. SlSPL-CNR can induce cell death in tomato and tobacco, dependent on its nuclear localization. However, the two ZFMs have differential impacts on SlSPL-CNR's induction of severe necrosis or mild necrotic ringspot. NLS and ZFM mutants cannot complement Cnr fruits to ripen. SlSPL-CNR interacts with SlSnRK1. Virus-induced SlSnRK1 silencing leads to reduction in expression of ripening-related genes and inhibits ripening in tomato. We conclude that SlSPL-CNR is a multifunctional protein that consists of a distinct monopartite NLS, binds to zinc, and interacts with SlSnRK1 to affect cell death and tomato fruit ripening.
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Affiliation(s)
- Tongfei Lai
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaohong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bishun Ye
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mingfei Jin
- School of Life Sciences, East China Normal University, Shanghai, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ying Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yingying Zhou
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Andrew M Blanks
- Cell and Developmental Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Mei Gu
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Chunyang Li
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Philippe Gallusci
- Laboratory of Grape Ecophysiology and Functional Biology, Bordeaux University, INRA, Bordeaux Science Agro, Villenave d’Ornon, France
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
- Correspondence: , or
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Roles of transcription factor SQUAMOSA promoter binding protein-like gene family in papaya (Carica papaya) development and ripening. Genomics 2020; 112:2734-2747. [PMID: 32194147 DOI: 10.1016/j.ygeno.2020.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 02/05/2023]
Abstract
SQUAMOSA promoter binding protein-like (SPL) family plays vital regulatory roles in plant growth and development. The SPL family in climacteric fruit Carica papaya has not been reported. This study identified 14 papaya SPLs (CpSPL) from papaya genome and analyzed their sequence features, phylogeny, intron/exon structure, conserved motif, miR156-mediated posttranscriptional regulation, and expression patterns. 14 CpSPLs were clustered into 8 groups, and two distinct expression patterns were revealed for miR156-targeted and nontargeted CpSPLs in different tissues and fruit development stages. The expression changes of CpSPLs in ethephon and 1-MCP treated fruit during ripening suggested that the CpSPLs guided by CpmiR156 play crucial roles in ethylene signaling pathway. This study sheds light on the new function of SPL family in fruit development and ripening, providing insights on understanding evolutionary divergence of the members of SPL family among plant species.
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23
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Wang Z, Zhu T, Ma W, Fan E, Lu N, Ouyang F, Wang N, Yang G, Kong L, Qu G, Zhang S, Wang J. Potential function of CbuSPL and gene encoding its interacting protein during flowering in Catalpa bungei. BMC PLANT BIOLOGY 2020; 20:105. [PMID: 32143577 PMCID: PMC7060540 DOI: 10.1186/s12870-020-2303-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/24/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND "Bairihua", a variety of the Catalpa bungei, has a large amount of flowers and a long flowering period which make it an excellent material for flowering researches in trees. SPL is one of the hub genes that regulate both flowering transition and development. RESULTS SPL homologues CbuSPL9 was cloned using degenerate primers with RACE. Expression studies during flowering transition in "Bairihua" and ectopic expression in Arabidopsis showed that CbuSPL9 was functional similarly with its Arabidopsis homologues. In the next step, we used Y2H to identify the proteins that could interact with CbuSPL9. HMGA, an architectural transcriptional factor, was identified and cloned for further research. BiFC and BLI showed that CbuSPL9 could form a heterodimer with CbuHMGA in the nucleus. The expression analysis showed that CbuHMGA had a similar expression trend to that of CbuSPL9 during flowering in "Bairihua". Intriguingly, ectopic expression of CbuHMGA in Arabidopsis would lead to aberrant flowers, but did not effect flowering time. CONCLUSIONS Our results implied a novel pathway that CbuSPL9 regulated flowering development, but not flowering transition, with the participation of CbuHMGA. Further investments need to be done to verify the details of this pathway.
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Affiliation(s)
- Zhi Wang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Tianqing Zhu
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Wenjun Ma
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Erqin Fan
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
- Present address: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 People’s Republic of China
| | - Nan Lu
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Fangqun Ouyang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Nan Wang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Guijuan Yang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Lisheng Kong
- Present address: Department of Biology Centre for Forest Biology, University of Victoria, Victoria 11, BC Canada
| | - Guanzheng Qu
- Present address: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 People’s Republic of China
| | - Shougong Zhang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Junhui Wang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
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25
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Liu MM, Wang MM, Yang J, Wen J, Guo PC, Wu YW, Ke YZ, Li PF, Li JN, Du H. Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants. Int J Mol Sci 2019; 20:E3591. [PMID: 31340456 PMCID: PMC6679135 DOI: 10.3390/ijms20143591] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants' development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.
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Affiliation(s)
- Ming-Ming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Mang-Mang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Cheng Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Wen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Zhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Feng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jia-Na Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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Wang H, Lu Z, Xu Y, Kong L, Shi J, Liu Y, Fu C, Wang X, Wang ZY, Zhou C, Han L. Genome-wide characterization of SPL family in Medicago truncatula reveals the novel roles of miR156/SPL module in spiky pod development. BMC Genomics 2019; 20:552. [PMID: 31277566 PMCID: PMC6612136 DOI: 10.1186/s12864-019-5937-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 06/26/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND SQUAMOSA Promoter Binding Protein-Likes (SPLs) proteins are plant-specific transcription factors that play many crucial roles in plant growth and development. However, there is little information about SPL family in the model legume Medicago truncatula. RESULTS In this study, a total of 23 MtSPL genes were identified in M. truncatula genome, in which 17 of the MtSPLs contained the putative MtmiR156 binding site at the coding or 3' UTR regions. Tissue-specific expression pattern analysis showed that most MtmiR156-targeted MtSPLs were highly expressed in seed and pod. The observation of MtmiR156B-overexpressing plants reveals that MtmiR156/MtSPL modules are not only involved in the development of leaves and branches, but also in the seed pod development, especially the formation of spine on pod. CONCLUSION The spines on pods are developed in many plant species, which allow pods to adhere to the animals, and then be transported on the outside. This study sheds light on the new function of SPL family in seed dispersal by controlling the formation of spiky pod, and provides insights on understanding evolutionary divergence of the members of SPL gene family among plant species.
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Affiliation(s)
- Hongfeng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China.,School of Life Science, Guangzhou University, Guangzhou, 510006, China
| | - Zhichao Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Yiteng Xu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Lingcui Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Jianjun Shi
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Yafei Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Xiaoshan Wang
- Department of Grassland Science, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Zeng-Yu Wang
- Noble Research Institute, LLC, Ardmore, OK, USA.,Present Address: Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, People's Republic of China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China.
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China.
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Herath V. The architecture of the GhD7 promoter reveals the roles of GhD7 in growth, development and the abiotic stress response in rice. Comput Biol Chem 2019; 82:1-8. [PMID: 31247396 DOI: 10.1016/j.compbiolchem.2019.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/09/2019] [Accepted: 06/04/2019] [Indexed: 10/26/2022]
Abstract
Grain number, plant height and heading date 7 (GhD7) is considered to be one of the key yield-related genes in the production of high-yielding and climate-ready super rice varieties. GhD7 delays the plant's flowering under long-day conditions, which ultimately results in increased yield. Recent findings indicate that GhD7 also plays a major role in the abiotic stress response; however, the fine regulatory mechanisms controlling Ghd7 expression have yet to be uncovered. This study was carried out to explore the transcription factor binding site (TFBS) architecture of the GhD7 promoter to identify the regulatory dynamics of GhD7 transcription. The promoter sequence (-2000 to +200 base pairs from the transcription start site) was retrieved from the PlantPAN 2.0 database. Ab initio promoter analysis, DNase I hypersensitive site (DHS) analysis, and methylation analysis were carried out to identify TFBSs. The TFBS diversity among rice varieties was also assessed. In addition to the previously identified 8 cis-elements, 448 novel cis-elements were identified in the GhD7 promoter that provide binding sites for 25 transcription factor families. Furthermore, a DNase I hypersensitive site and a CpG island were also identified. The identified transcription factor families include key transcription factors involved in both development and abiotic stress responses, revealing the regulatory dynamics of GhD7. Comparative analysis of multiple GhD7 promoters identified 31 single-nucleotide polymorphisms that result in TFBS variations among rice accessions. These variations are mostly found in relation to flowering and abiotic stress responsive TFBSs on the promoter. This study supports the model that GhD7 acts as a central regulator of rice growth, development, and the abiotic stress response.
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Affiliation(s)
- Venura Herath
- Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka.
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28
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Zhong H, Kong W, Gong Z, Fang X, Deng X, Liu C, Li Y. Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like ( SPL) Gene Family in Oryza Genus. FRONTIERS IN PLANT SCIENCE 2019; 10:565. [PMID: 31139200 PMCID: PMC6517846 DOI: 10.3389/fpls.2019.00565] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/15/2019] [Indexed: 05/07/2023]
Abstract
The SPL (SQUAMOSA promoter binding protein-like) gene family is one of the plant-specific transcription factor families and controls a considerable number of biological functions, including floral development, phytohormone signaling, and toxin resistance. However, the evolutionary patterns and driving forces of SPL genes in the Oryza genus are still not well-characterized. In this study, we investigated a total of 105 SPL genes from six AA genome Oryza representative species (O. barthii, O. glumipatula, O. nivara, O. rufipogon, O. glaberrima, and O. sativa). Phylogenetic and motif analyses indicated that SPL proteins could be divided into two distinct lineages (I and II), and further studies showed lineage II consisted of three clades (IIA, IIB, and IIC). We found that clade I had comparable structural features with clade IIA, whereas genes in clade IIC displayed intrinsic differences, such as lower exon numbers and the presence of miR156 regulation elements. Nineteen orthologous groups of OsSPLs in Oryza were also identified, and most exons within those genes maintained constant length, whereas length of intron changed relatively. All groups were constrained by stronger purifying selection and diversified continually including alterative gene number, intron length, and miR156 regulation. Subsequently, cis-acting element analyses revealed the potential role of SPLs in wild rice, which might participate in light-responsive, phytohormone response, and plant growth and development. Our results shed light on that different evolutionary rates and duplication events might result in divergent evolutionary patterns in each lineage of SPL genes, providing a guide in exploring diverse function in the rice gene family among six closely related Oryza species.
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Wang P, Chen D, Zheng Y, Jin S, Yang J, Ye N. Identification and Expression Analyses of SBP-Box Genes Reveal Their Involvement in Abiotic Stress and Hormone Response in Tea Plant ( Camellia sinensis). Int J Mol Sci 2018; 19:ijms19113404. [PMID: 30380795 PMCID: PMC6274802 DOI: 10.3390/ijms19113404] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/26/2018] [Accepted: 10/28/2018] [Indexed: 11/23/2022] Open
Abstract
The SQUAMOSA promoter binding protein (SBP)-box gene family is a plant-specific transcription factor family. This family plays a crucial role in plant growth and development. In this study, 20 SBP-box genes were identified in the tea plant genome and classified into six groups. The genes in each group shared similar exon-intron structures and motif positions. Expression pattern analyses in five different tissues demonstrated that expression in the buds and leaves was higher than that in other tissues. The cis-elements and expression patterns of the CsSBP genes suggested that the CsSBP genes play active roles in abiotic stress responses; these responses may depend on the abscisic acid (ABA), gibberellic acid (GA), and methyl jasmonate (MeJA) signaling pathways. Our work provides a comprehensive understanding of the CsSBP family and will aid in genetically improving tea plants.
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Affiliation(s)
- Pengjie Wang
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Di Chen
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yucheng Zheng
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shan Jin
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Jiangfan Yang
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Naixing Ye
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Zhou Q, Zhang S, Chen F, Liu B, Wu L, Li F, Zhang J, Bao M, Liu G. Genome-wide identification and characterization of the SBP-box gene family in Petunia. BMC Genomics 2018; 19:193. [PMID: 29703141 PMCID: PMC6389188 DOI: 10.1186/s12864-018-4537-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/08/2018] [Indexed: 11/29/2022] Open
Abstract
Background SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box genes encode a family of plant-specific transcription factors (TFs) that play important roles in many growth and development processes including phase transition, leaf initiation, shoot and inflorescence branching, fruit development and ripening etc. The SBP-box gene family has been identified and characterized in many species, but has not been well studied in Petunia, an important ornamental genus. Results We identified 21 putative SPL genes of Petunia axillaris and P. inflata from the reference genome of P. axillaris N and P. inflata S6, respectively, which were supported by the transcriptome data. For further confirmation, all the 21 genes were also cloned from P. hybrida line W115 (Mitchel diploid). Phylogenetic analysis based on the highly conserved SBP domains arranged PhSPLs in eight groups, analogous to those from Arabidopsis and tomato. Furthermore, the Petunia SPL genes had similar exon-intron structure and the deduced proteins contained very similar conserved motifs within the same subgroup. Out of 21 PhSPL genes, fourteen were predicted to be potential targets of PhmiR156/157, and the putative miR156/157 response elements (MREs) were located in the coding region of group IV, V, VII and VIII genes, but in the 3’-UTR regions of group VI genes. SPL genes were also identified from another two wild Petunia species, P. integrifolia and P. exserta, based on their transcriptome databases to investigate the origin of PhSPLs. Phylogenetic analysis and multiple alignments of the coding sequences of PhSPLs and their orthologs from wild species indicated that PhSPLs were originated mainly from P. axillaris. qRT-PCR analysis demonstrated differential spatiotemperal expression patterns of PhSPL genes in petunia and many were expressed predominantly in the axillary buds and/or inflorescences. In addition, overexpression of PhSPL9a and PhSPL9b in Arabidopsis suggested that these genes play a conserved role in promoting the vegetative-to-reproductive phase transition. Conclusion Petunia genome contains at least 21 SPL genes, and most of the genes are expressed in different tissues. The PhSPL genes may play conserved and diverse roles in plant growth and development, including flowering regulation, leaf initiation, axillary bud and inflorescence development. This work provides a comprehensive understanding of the SBP-box gene family in Petunia and lays a significant foundation for future studies on the function and evolution of SPL genes in petunia. Electronic supplementary material The online version of this article (10.1186/s12864-018-4537-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qin Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Sisi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China.,Wuhan Institute of Landscape Architecture, Peace Avenue No. 1240, Wuhan, 430081, China
| | - Feng Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Baojun Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Lan Wu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Fei Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Guofeng Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China.
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Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus. Heredity (Edinb) 2018. [PMID: 29523839 DOI: 10.1038/s41437-018-0058-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Terpenes are economically and ecologically important phytochemicals. Their synthesis is controlled by the terpene synthase (TPS) gene family, which is highly diversified throughout the plant kingdom. The plant family Myrtaceae are characterised by especially high terpene concentrations, and considerable variation in terpene profiles. Many Myrtaceae are grown commercially for terpene products including the eucalypts Corymbia and Eucalyptus. Eucalyptus grandis has the largest TPS gene family of plants currently sequenced, which is largely conserved in the closely related E. globulus. However, the TPS gene family has been well studied only in these two eucalypt species. The recent assembly of two Corymbia citriodora subsp. variegata genomes presents an opportunity to examine the conservation of this important gene family across more divergent eucalypt lineages. Manual annotation of the TPS gene family in C. citriodora subsp. variegata revealed a similar overall number, and relative subfamily representation, to that previously reported in E. grandis and E. globulus. Many of the TPS genes were in physical clusters that varied considerably between Eucalyptus and Corymbia, with several instances of translocation, expansion/contraction and loss. Notably, there was greater conservation in the subfamilies involved in primary metabolism than those involved in secondary metabolism, likely reflecting different selective constraints. The variation in cluster size within subfamilies and the broad conservation between the eucalypts in the face of this variation are discussed, highlighting the potential contribution of selection, concerted evolution and stochastic processes. These findings provide the foundation to better understand terpene evolution within the ecologically and economically important Myrtaceae.
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Huo W, Li B, Kuang J, He P, Xu Z, Wang J. Functional Characterization of the Steroid Reductase Genes GmDET2a and GmDET2b form Glycine max. Int J Mol Sci 2018; 19:E726. [PMID: 29510512 PMCID: PMC5877587 DOI: 10.3390/ijms19030726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 12/02/2022] Open
Abstract
Brassinosteroids are important phytohormones for plant growth and development. In soybean (Glycine max), BR receptors have been identified, but the genes encoding BR biosynthesis-related enzymes remain poorly understood. Here, we found that the soybean genome encodes eight steroid reductases (GmDET2a to GmDET2h). Phylogenetic analysis grouped 105 steroid reductases from moss, fern and higher plants into five subgroups and indicated that the steroid reductase family has experienced purifying selection. GmDET2a and GmDET2b, homologs of the Arabidopsis thaliana steroid 5 α -reductase AtDET2, are proteins of 263 amino acids. Ectopic expression of GmDET2a and GmDET2b rescued the defects of the Atdet2-1 mutant in both darkness and light. Compared to the mutant, the hypocotyl length and plant height of the transgenic lines GmDET2a and GmDET2b increased significantly, in both darkness and light, and the transcript levels of the BR biosynthesis-related genes CPD, DWF4, BR6ox-1 and BR6ox-2 were downregulated in GmDET2aOX-23 and GmDET2bOX-16 lines compared to that in Atdet2-1. Quantitative real-time PCR revealed that GmDET2a and GmDET2b are ubiquitously expressed in all tested soybean organs, including roots, leaves and hypocotyls. Moreover, epibrassinosteroid negatively regulated GmDET2a and GmDET2b expression. Sulfate deficiency downregulated GmDET2a in leaves and GmDET2b in leaves and roots; by contrast, phosphate deficiency upregulated GmDET2b in roots and leaves. Taken together, our results revealed that GmDET2a and GmDET2b function as steroid reductases.
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Affiliation(s)
- Weige Huo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Bodi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Jiebing Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Pingan He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Zhihao Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Jinxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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Abdullah M, Cao Y, Cheng X, Shakoor A, Su X, Gao J, Cai Y. Genome-Wide Analysis Characterization and Evolution of SBP Genes in Fragaria vesca, Pyrus bretschneideri, Prunus persica and Prunus mume. Front Genet 2018; 9:64. [PMID: 29552026 PMCID: PMC5841269 DOI: 10.3389/fgene.2018.00064] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/12/2018] [Indexed: 12/04/2022] Open
Abstract
The SQUAMOSA promoter binding protein (SBP)-box proteins are plant-specific transcriptional factors in plants. SBP TFs are known to play important functions in a diverse development process and also related in the process of evolutionary novelties. SBP gene family has been characterized in several plant species, but little is known about molecular evolution, functional divergence and comprehensive study of SBP gene family in Rosacea. We carried out genome-wide investigations and identified 14, 32, 17, and 17 SBP genes from four Rosacea species (Fragaria vesca, Pyrus bretschneideri, Prunus persica and Prunus mume, respectively). According to phylogenetic analysis arranged the SBP protein sequences in seven groups. Localization of SBP genes presented an uneven distribution on corresponding chromosomes of Rosacea species. Our analyses designated that the SBP genes duplication events (segmental and tandem) and divergence. In addition, due to highly conserved structure pattern of SBP genes, recommended that highly conserved region of microsyneteny in the Rosacea species. Type I and II functional divergence was detected among various amino acids in SBP proteins, while there was no positive selection according to substitutional model analysis using PMAL software. These results recommended that the purifying selection might be leading force during the evolution process and dominate conservation of SBP genes in Rosacea species according to environmental selection pressure analysis. Our results will provide basic understanding and foundation for future research insights on the evolution of the SBP genes in Rosacea.
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Affiliation(s)
- Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yunpeng Cao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Awais Shakoor
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Xueqiang Su
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Junshan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
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Zhang J, Chen K, Pang Y, Naveed SA, Zhao X, Wang X, Wang Y, Dingkuhn M, Pasuquin J, Li Z, Xu J. QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study. BMC Genomics 2017; 18:828. [PMID: 29078746 PMCID: PMC5658907 DOI: 10.1186/s12864-017-4221-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 10/17/2017] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity and greatly affect rice yield and quality. To improve rice production, understanding the genetic and molecular resistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is an effective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the genetic relationship between them in a genetically diverse population. RESULTS A total of 29 and 31 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW), shoot water content (SWC) and shoot ion concentrations (SFe or SZn) were identified at seedling stage in Fe and Zn experiments, respectively. Five toxicity tolerance QTL (qSdw3a, qSdw3b, qSdw12 and qSFe5 / qSZn5) were detected in the same genomic regions under the two stress conditions and 22 candidate genes for 10 important QTL regions were also determined by haplotype analyses. CONCLUSION Rice plants share partial genetic overlaps of Fe and Zn toxicity tolerance at seedling stage. Candidate genes putatively affecting Fe and Zn toxicity tolerance identified in this study provide valuable information for future functional characterization and improvement of rice tolerance to Fe and Zn toxicity by marker-assisted selection or designed QTL pyramiding.
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Affiliation(s)
- Jian Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Kai Chen
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Yunlong Pang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shahzad Amir Naveed
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaoqian Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yun Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Michael Dingkuhn
- Cirad, Umr AGAP (Dept. BIOS) and Upr AIDA (Dept. ES), F-34398 Montpellier, France
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
| | - Julie Pasuquin
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
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Zhang B, Xu W, Liu X, Mao X, Li A, Wang J, Chang X, Zhang X, Jing R. Functional Conservation and Divergence among Homoeologs of TaSPL20 and TaSPL21, Two SBP-Box Genes Governing Yield-Related Traits in Hexaploid Wheat. PLANT PHYSIOLOGY 2017; 174:1177-1191. [PMID: 28424214 PMCID: PMC5462027 DOI: 10.1104/pp.17.00113] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/15/2017] [Indexed: 05/20/2023]
Abstract
Maintaining high and stable yields has become an increasing challenge in wheat breeding due to climate change. Although Squamosa-promoter binding protein (SBP)-box genes have important roles in plant development, very little is known about the actual biological functions of wheat SBP-box family members. Here, we dissect the functional conservation, divergence, and exploitation of homoeologs of two paralogous TaSPL wheat loci during domestication and breeding. TaSPL20 and TaSPL21 were highly expressed in the lemma and palea. Ectopic expressions of TaSPL20/21 in rice exhibited similar functions in terms of promoting panicle branching but had different functions during seed development. We characterized all six TaSPL20/21 genes located across the three homoeologous (A, B, and D) genomes. According to the functional analysis of naturally occurring variants in 20 environments, four favorable haplotypes were identified. Together, they reduced plant height by up to 27.5%, and TaSPL21-6D-HapII increased 1000-grain weight by 9.73%. Our study suggests that TaSPL20 and TaSPL21 homoeologs underwent diversification in function with each evolving its own distinctive characteristics. During domestication and breeding of wheat in China, favorable haplotypes of each set were selected and exploited to varying degrees due to their large effects on plant height and 1000-grain weight.
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Affiliation(s)
- Bin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China (B.Z., W.X., X.L., A.L., J.W., X.C., X.Z., R.J.); and
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China (X.L.)
| | - Weina Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China (B.Z., W.X., X.L., A.L., J.W., X.C., X.Z., R.J.); and
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China (X.L.)
| | - Xia Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China (B.Z., W.X., X.L., A.L., J.W., X.C., X.Z., R.J.); and
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China (X.L.)
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China (B.Z., W.X., X.L., A.L., J.W., X.C., X.Z., R.J.); and
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China (X.L.)
| | - Ang Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China (B.Z., W.X., X.L., A.L., J.W., X.C., X.Z., R.J.); and
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China (X.L.)
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China (B.Z., W.X., X.L., A.L., J.W., X.C., X.Z., R.J.); and
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China (X.L.)
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China (B.Z., W.X., X.L., A.L., J.W., X.C., X.Z., R.J.); and
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China (X.L.)
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China (B.Z., W.X., X.L., A.L., J.W., X.C., X.Z., R.J.); and
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China (X.L.)
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China (B.Z., W.X., X.L., A.L., J.W., X.C., X.Z., R.J.); and
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China (X.L.)
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Ling LZ, Zhang SD, Zhao F, Yang JL, Song WH, Guan SM, Li XS, Huang ZJ, Cheng L. Transcriptome-Wide Identification and Prediction of miRNAs and Their Targets in Paris polyphylla var. yunnanensis by High-Throughput Sequencing Analysis. Int J Mol Sci 2017; 18:ijms18010219. [PMID: 28117746 PMCID: PMC5297848 DOI: 10.3390/ijms18010219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/17/2017] [Accepted: 01/17/2017] [Indexed: 01/08/2023] Open
Abstract
Long dormancy period of seeds limits the large-scale artificial cultivation of the scarce Paris polyphylla var. yunnanensis, an important traditional Chinese medicine. Characterizing miRNAs and their targets is crucial to understanding the role of miRNAs during seed dormancy in this species. Considering the limited genome information of this species, we first sequenced and assembled the transcriptome data of dormant seeds and their seed coats as the reference genome. A total of 146,671 unigenes with an average length of 923 bp were identified and showed functional diversity based on different annotation methods. Two small RNA libraries from respective seeds and seed coats were sequenced and the combining data indicates that 263 conserved miRNAs belonging to at least 83 families and 768 novel miRNAs in 1174 transcripts were found. The annotations of the predicted putative targets of miRNAs suggest that these miRNAs were mainly involved in the cell, metabolism and genetic information processing by direct and indirect regulation patterns in dormant seeds of P. polyphylla var. yunnanensis. Therefore, we provide the first known miRNA profiles and their targets, which will assist with further study of the molecular mechanism of seed dormancy in P. polyphylla var. yunnanensis.
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Affiliation(s)
- Li-Zhen Ling
- BGI-Yunnan, Kunming 650106, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
| | - Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Fan Zhao
- BGI-Yunnan, Kunming 650106, China.
| | | | | | | | | | | | - Le Cheng
- BGI-Yunnan, Kunming 650106, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
- College of Clinical Medicine, College of Basic Medical Sciences, Dali University, Dali 671000, China.
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Kavas M, Kızıldoğan AK, Abanoz B. Comparative genome-wide phylogenetic and expression analysis of SBP genes from potato (Solanum tuberosum). Comput Biol Chem 2017; 67:131-140. [PMID: 28081487 DOI: 10.1016/j.compbiolchem.2017.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/27/2016] [Accepted: 01/03/2017] [Indexed: 11/28/2022]
Abstract
Flowering time is a very important phase in transition to reproductive stage of life in higher plants. SQUAMOSA promoter-binding protein (SBP) gene family encodes plant-specific transcription factors that are involved in regulation of several developmental processes, especially flowering. Although SBP-box genes have been identified in different plants, there have been no study indicating the regulatory effect of SBP box in potato flowering. Here, we report for the first time the identification and characterization of SBP-box transcription factors as well as determination of expression level of SBP-box genes in Solanum tuberosum L. an important crop worldwide. Fifteen different SBP-box transcription factor genes were identified in potato genome. They were found to be distributed in nine chromosomes and eight of them included miR156 and miRNA157 target sites. Characterization of amino acid sequences were performed and protein interactions were predicted. In addition, expression levels of five S. tuberosum SBP-box genes were analysed by both in silico and qRT-PCR. All these results provide a better understanding of functional role of SBP-box gene family members in flowering time in potato.
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Affiliation(s)
- Musa Kavas
- Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey.
| | - Aslıhan Kurt Kızıldoğan
- Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
| | - Büşra Abanoz
- Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
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Cheng H, Hao M, Wang W, Mei D, Tong C, Wang H, Liu J, Fu L, Hu Q. Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus. BMC PLANT BIOLOGY 2016; 16:196. [PMID: 27608922 PMCID: PMC5017063 DOI: 10.1186/s12870-016-0852-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/11/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined. RESULTS In the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3'UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle. CONCLUSIONS Taken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for understanding the crucial roles of BnaSBP genes in plant development and other biological processes.
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Affiliation(s)
- Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Mengyu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Wenxiang Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Desheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Chaobo Tong
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Li Fu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062 People’s Republic of China
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Peng S, Tao P, Xu F, Wu A, Huo W, Wang J. Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors. Int J Mol Sci 2016; 17:E897. [PMID: 27338344 PMCID: PMC4926431 DOI: 10.3390/ijms17060897] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 11/29/2022] Open
Abstract
Brassinosteroids (BR) play important roles in plant growth and development. Although BR receptors have been intensively studied in Arabidopsis, the BR receptors in soybean remain largely unknown. Here, in addition to the known receptor gene Glyma06g15270 (GmBRI1a), we identified five putative BR receptor genes in the soybean genome: GmBRI1b, GmBRL1a, GmBRL1b, GmBRL2a, and GmBRL2b. Analysis of their expression patterns by quantitative real-time PCR showed that they are ubiquitously expressed in primary roots, lateral roots, stems, leaves, and hypocotyls. We used rapid amplification of cDNA ends (RACE) to clone GmBRI1b (Glyma04g39160), and found that the predicted amino acid sequence of GmBRI1b showed high similarity to those of AtBRI1 and pea PsBRI1. Structural modeling of the ectodomain also demonstrated similarities between the BR receptors of soybean and Arabidopsis. GFP-fusion experiments verified that GmBRI1b localizes to the cell membrane. We also explored GmBRI1b function in Arabidopsis through complementation experiments. Ectopic over-expression of GmBRI1b in Arabidopsis BR receptor loss-of-function mutant (bri1-5 bak1-1D) restored hypocotyl growth in etiolated seedlings; increased the growth of stems, leaves, and siliques in light; and rescued the developmental defects in leaves of the bri1-6 mutant, and complemented the responses of BR biosynthesis-related genes in the bri1-5 bak1-D mutant grown in light. Bioinformatics analysis demonstrated that the six BR receptor genes in soybean resulted from three gene duplication events during evolution. Phylogenetic analysis classified the BR receptors in dicots and monocots into three subclades. Estimation of the synonymous (Ks) and the nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) revealed that the Ka/Ks of BR receptor genes from dicots and monocots were less than 1.0, indicating that BR receptor genes in plants experienced purifying selection during evolution.
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Affiliation(s)
- Suna Peng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agriculture University, Guangzhou 510642, China.
- College of Agriculture & Root Biology Center, South China Agricultural University, Guangzhou 510642, China.
| | - Ping Tao
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agriculture University, Guangzhou 510642, China.
- College of Agriculture & Root Biology Center, South China Agricultural University, Guangzhou 510642, China.
| | - Feng Xu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agriculture University, Guangzhou 510642, China.
- College of Agriculture & Root Biology Center, South China Agricultural University, Guangzhou 510642, China.
| | - Aiping Wu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agriculture University, Guangzhou 510642, China.
- College of Agriculture & Root Biology Center, South China Agricultural University, Guangzhou 510642, China.
| | - Weige Huo
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agriculture University, Guangzhou 510642, China.
- College of Agriculture & Root Biology Center, South China Agricultural University, Guangzhou 510642, China.
| | - Jinxiang Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agriculture University, Guangzhou 510642, China.
- College of Agriculture & Root Biology Center, South China Agricultural University, Guangzhou 510642, China.
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Bajaj D, Srivastava R, Nath M, Tripathi S, Bharadwaj C, Upadhyaya HD, Tyagi AK, Parida SK. EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea. FRONTIERS IN PLANT SCIENCE 2016; 7:450. [PMID: 27148286 PMCID: PMC4835497 DOI: 10.3389/fpls.2016.00450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/22/2016] [Indexed: 05/22/2023]
Abstract
The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.
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Affiliation(s)
- Deepak Bajaj
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Rishi Srivastava
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Manoj Nath
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | | | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Akhilesh K. Tyagi
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Swarup K. Parida
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
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Wu Z, Cao Y, Yang R, Qi T, Hang Y, Lin H, Zhou G, Wang ZY, Fu C. Switchgrass SBP-box transcription factors PvSPL1 and 2 function redundantly to initiate side tillers and affect biomass yield of energy crop. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:101. [PMID: 27158262 PMCID: PMC4858904 DOI: 10.1186/s13068-016-0516-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/25/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a dedicated lignocellulosic feedstock for bioenergy production. The SQUAMOSA PROMOTER-BINDING PROTEIN (SBP-box)-LIKE transcription factors (SPLs) change plant architecture and vegetative-to-reproductive phase transition significantly, and as such, they are promising candidates for genetic improvement of switchgrass biomass yield. However, the genome-wide identification and functional characterization of SPL genes have yet to be investigated in herbaceous energy crops. RESULTS We identified 35 full-length SPL genes in the switchgrass genome. The phylogenetic relationship and expression pattern of PvSPLs provided baseline information for their function characterization. Based on the global overview of PvSPLs, we explored the biological function of miR156-targeted PvSPL1 and PvSPL2, which are closely related members of SPL family in switchgrass. Our results showed that PvSPL1 and PvSPL2 acted redundantly to modulate side tiller initiation, whereas they did not affect phase transition and internode initiation. Consistently, overexpression of the miR156-resistant rPvSPL2 in the miR156-overexpressing transgenic plants greatly reduced tiller initiation, but did not rescue the delayed flowering and increased internode numbers. Furthermore, suppression of PvSPL2 activity in switchgrass increased biomass yield and reduced lignin accumulation, which thereby elevated the total amount of solubilized sugars. CONCLUSIONS Our results indicate that different miR156-targeted PvSPL subfamily genes function predominantly in certain biological processes in switchgrass. We suggest that PvSPL2 and its paralogs can be utilized as the valuable targets in molecular breeding of energy crops for developing novel germplasms with high biofuel production.
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Affiliation(s)
- Zhenying Wu
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Yingping Cao
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Ruijuan Yang
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Tianxiong Qi
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Yuqing Hang
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Hao Lin
- />Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Gongke Zhou
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Zeng-Yu Wang
- />Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Chunxiang Fu
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
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