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Petrella R, Caselli F, Roig-Villanova I, Vignati V, Chiara M, Ezquer I, Tadini L, Kater MM, Gregis V. BPC transcription factors and a Polycomb Group protein confine the expression of the ovule identity gene SEEDSTICK in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:582-599. [PMID: 31909505 DOI: 10.1111/tpj.14673] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 12/05/2019] [Accepted: 12/20/2019] [Indexed: 05/26/2023]
Abstract
The BASIC PENTACYSTEINE (BPC) GAGA (C-box) binding proteins belong to a small plant transcription factor family. We previously reported that class I BPCs bind directly to C-boxes in the SEEDSTICK (STK) promoter and the mutagenesis of these cis-elements affects STK expression in the flower. The MADS-domain factor SHORT VEGETATIVE PHASE (SVP) is another key regulator of STK. Direct binding of SVP to CArG-boxes in the STK promoter are required to repress its expression during the first stages of flower development. Here we show that class II BPCs directly interact with SVP and that MADS-domain binding sites in the STK promoter region are important for the correct spatial and temporal expression of this homeotic gene. Furthermore, we show that class I and class II BPCs act redundantly to repress STK expression in the flower, most likely by recruiting TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 (TFL2/LHP1) and mediating the establishment and the maintenance of H3K27me3 repressive marks on DNA. We investigate the role of LHP1 in the regulation of STK expression. In addition to providing a better understanding of the role of BPC transcription factors in the regulation of STK expression, our results suggest the existence of a more general regulatory complex composed of BPCs, MADS-domain factors and Polycomb Repressive Complexes that co-operate to regulate gene expression in reproductive tissues. We believe that our data along with the molecular model described here could provide significant insights for a more comprehensive understanding of gene regulation in plants.
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Affiliation(s)
- Rosanna Petrella
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Francesca Caselli
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Irma Roig-Villanova
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
- Department of Agri-Food Engineering and Biotechnology, Barcelona School of Agricultural Engineering, UPC, Esteve Terrades 8, Building 4, 08860, Castelldefels, Spain
| | - Valentina Vignati
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Luca Tadini
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Martin M Kater
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
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Karami O, Rahimi A, Khan M, Bemer M, Hazarika RR, Mak P, Compier M, van Noort V, Offringa R. A suppressor of axillary meristem maturation promotes longevity in flowering plants. NATURE PLANTS 2020; 6:368-376. [PMID: 32284551 DOI: 10.1038/s41477-020-0637-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 03/11/2020] [Indexed: 05/27/2023]
Abstract
Post-embryonic development and longevity of flowering plants are, for a large part, determined by the activity and maturation state of stem cell niches formed in the axils of leaves, the so-called axillary meristems (AMs)1,2. The genes that are associated with AM maturation and underlie the differences between monocarpic (reproduce once and die) annual and the longer-lived polycarpic (reproduce more than once) perennial plants are still largely unknown. Here we identify a new role for the Arabidopsis AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15) gene as a suppressor of AM maturation. Loss of AHL15 function accelerates AM maturation, whereas ectopic expression of AHL15 suppresses AM maturation and promotes longevity in monocarpic Arabidopsis and tobacco. Accordingly, in Arabidopsis grown under longevity-promoting short-day conditions, or in polycarpic Arabidopsis lyrata, expression of AHL15 is upregulated in AMs. Together, our results indicate that AHL15 and other AHL clade-A genes play an important role, directly downstream of flowering genes (SOC1, FUL) and upstream of the flowering-promoting hormone gibberellic acid, in suppressing AM maturation and extending the plant's lifespan.
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Affiliation(s)
- Omid Karami
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Arezoo Rahimi
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Majid Khan
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
- Institute of Biotechnology and Genetic Engineering, University of Agriculture Peshawar, Peshawar, Pakistan
| | - Marian Bemer
- Laboratory of Molecular Biology and B.U. Bioscience, Wageningen University and Research, Wageningen, the Netherlands
| | | | - Patrick Mak
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
- Sanquin Plasma Products BV, Department of Product Development, Amsterdam, the Netherlands
| | - Monique Compier
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
- Rijk Zwaan, De Lier, the Netherlands
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Leuven, Belgium
- Bioinformatics and Genomics, Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, the Netherlands.
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53
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Identification of Candidate Genes Involved in Curd Riceyness in Cauliflower. Int J Mol Sci 2020; 21:ijms21061999. [PMID: 32183438 PMCID: PMC7139996 DOI: 10.3390/ijms21061999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 11/23/2022] Open
Abstract
“Riceyness” refers to the precocious development of flower bud initials over the curd surface of cauliflower, and it is regarded as undesirable for the market. The present study aimed to identify the candidate loci and genes responsible for the morphological difference in riceyness between a pair of cauliflower sister lines. Genetic analysis revealed that riceyness is controlled by a single dominant locus. An F2 population derived from the cross between these sister lines was used to construct “riceyness” and “non-riceyness” bulks, and then it was subjected to BSA-seq. On the basis of the results of Δ(SNP-index) analysis, a 4.0 Mb candidate region including 22 putative SNPs was mapped on chromosome C04. Combining the RNA-seq, gene function annotation, and target sequence analysis among two parents and other breeding lines, an orthologous gene of the Arabidopsis gene SOC1, Bo4g024850 was presumed as the candidate gene, and an upstream SNP likely resulted in riceyness phenotype via influencing the expression levels of Bo4g024850. These results are helpful to understand the genetic mechanism regulating riceyness, and to facilitate the molecular improvement on cauliflower curds.
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Sri T, Gupta B, Tyagi S, Singh A. Homeologs of Brassica SOC1, a central regulator of flowering time, are differentially regulated due to partitioning of evolutionarily conserved transcription factor binding sites in promoters. Mol Phylogenet Evol 2020; 147:106777. [PMID: 32126279 DOI: 10.1016/j.ympev.2020.106777] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/03/2020] [Accepted: 02/26/2020] [Indexed: 01/06/2023]
Abstract
Evolution of Brassica genome post-polyploidization reveals asymmetrical genome fractionation and copy number variation. Herein, we describe the impact of promoter divergence among SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) homeologs on expression and function in Brassica spp. SOC1, a regulated floral pathway integrator, is conserved as 3 redundant homeologs in diploid Brassicas. Even with high sequence identity within coding regions (92.8-100%), the spatio-temporal expression patterns of 9 SOC1 homologs in B. juncea and B. nigra indicates regulatory divergence. While LF and MF2 SOC1 homeologs are upregulated during floral transition, MF1 is barely expressed. Also, MF2 homeolog levels do not decline post-flowering, unlike LF. To investigate the underlying source of divergence, we analyzed the sequence and phylogeny of all reported (22) and isolated (21) upstream regions of Brassica SOC1. Full length upstream regions (4712-19189 bp) reveal 5 ubiquitously conserved ancestral Blocks, harboring binding sites of 18 TFs (TFBSs) characterized in Arabidopsis thaliana. The orthologs of these TFBSs are differentially conserved among Brassica SOC1 homeologs, imparting expression divergence. No crucial TFBSs are exclusively lost from LF_SOC1 promoter, while MF1_SOC1 has lost NF-Y binding site crucial for SOC1 activation by CONSTANS. MF2_SOC1 homeologs have lost important TFBSs (SEP3, AP1 and SMZ), responsible for SOC1 repression post-flowering. BjuAALF_SOC1 promoter (proximal 2 kb) shows ubiquitous reporter expression in B. juncea cv. Varuna transgenics, while BjuAAMF1_SOC1 promoter shows absence of reporter expression, validating the impact of TFBS divergence. Conservation of the original primary protein sequence is discovered in B. rapa homeologs (46) of 18 TFs. Co-regulation pattern of these TFs appeared similar for B. rapa LF and MF2 SOC1 homeologs; MF1 shows significant variation. Strong regulatory association is recorded for AP1, AP2, SEP3, FLC and CONSTANS/NF-Y, highlighting their importance in homeolog-specific SOC1 regulation. Correlation of B. juncea AP1, AP2 and FLC expression with SOC1 homeologs also complies with the TFBS differences. We thus conclude that redundant SOC1 loci contribute differentially to cumulative expression of SOC1 due to divergent selection of ancestral TFBSs.
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Affiliation(s)
- Tanu Sri
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi 110070, India
| | - Bharat Gupta
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi 110070, India
| | - Shikha Tyagi
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi 110070, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi 110070, India.
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Zhao H, Zhang W, Zhang T, Lin Y, Hu Y, Fang C, Jiang J. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biol 2020; 21:24. [PMID: 32014062 PMCID: PMC6996174 DOI: 10.1186/s13059-020-1927-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species. RESULTS We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~ 90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to "specific MHSs" (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains. CONCLUSION MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.
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Affiliation(s)
- Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, 210095, Jiangsu, China.
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yaodong Hu
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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Andrés F, Kinoshita A, Kalluri N, Fernández V, Falavigna VS, Cruz TMD, Jang S, Chiba Y, Seo M, Mettler-Altmann T, Huettel B, Coupland G. The sugar transporter SWEET10 acts downstream of FLOWERING LOCUS T during floral transition of Arabidopsis thaliana. BMC PLANT BIOLOGY 2020; 20:53. [PMID: 32013867 PMCID: PMC6998834 DOI: 10.1186/s12870-020-2266-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/27/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Floral transition initiates reproductive development of plants and occurs in response to environmental and endogenous signals. In Arabidopsis thaliana, this process is accelerated by several environmental cues, including exposure to long days. The photoperiod-dependent promotion of flowering involves the transcriptional induction of FLOWERING LOCUS T (FT) in the phloem of the leaf. FT encodes a mobile protein that is transported from the leaves to the shoot apical meristem, where it forms part of a regulatory complex that induces flowering. Whether FT also has biological functions in leaves of wild-type plants remains unclear. RESULTS In order to address this issue, we first studied the leaf transcriptomic changes associated with FT overexpression in the companion cells of the phloem. We found that FT induces the transcription of SWEET10, which encodes a bidirectional sucrose transporter, specifically in the leaf veins. Moreover, SWEET10 is transcriptionally activated by long photoperiods, and this activation depends on FT and one of its earliest target genes SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1). The ectopic expression of SWEET10 causes early flowering and leads to higher levels of transcription of flowering-time related genes in the shoot apex. CONCLUSIONS Collectively, our results suggest that the FT-signaling pathway activates the transcription of a sucrose uptake/efflux carrier during floral transition, indicating that it alters the metabolism of flowering plants as well as reprogramming the transcription of floral regulators in the shoot meristem.
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Affiliation(s)
- Fernando Andrés
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
- Present Address: UMR AGAP, Univ. Montpellier, INRAE, CIRAD, INSAAE, Montpellier, France
| | - Atsuko Kinoshita
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
| | - Naveen Kalluri
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
| | - Virginia Fernández
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
- Present Address: BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Vítor S. Falavigna
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
| | - Tiago M. D. Cruz
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
| | - Seonghoe Jang
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
- Present Address: World Vegetable Center Korea Office (WKO), 100 Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jellabuk-do 55365 Republic of Korea
| | - Yasutaka Chiba
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Tabea Mettler-Altmann
- Cluster of Excellence on Plant Sciences and Institute of Plant Biochemistry, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
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Petit J, Salentijn EMJ, Paulo MJ, Denneboom C, Trindade LM. Genetic Architecture of Flowering Time and Sex Determination in Hemp ( Cannabis sativa L.): A Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2020; 11:569958. [PMID: 33250906 PMCID: PMC7672029 DOI: 10.3389/fpls.2020.569958] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/12/2020] [Indexed: 05/13/2023]
Abstract
Flowering time and sex determination in hemp (Cannabis sativa L.) strongly influence fiber quality and seed production of this crop. The control of these traits is paramount for the breeding of new cultivars. Yet, little is known about the genetics underlying such complex traits and a better understanding requires in depth knowledge of the molecular mechanisms responsible for these traits. In this report, the genetic architecture of flowering time and sex determination in hemp was studied using a Genome-Wide Association Studies (GWAS) approach. Association studies were performed on a panel of 123 hemp accessions, tested in three contrasting environments, using a set of 600 K SNP markers. Altogether, eight QTLs were identified across environments; six for flowering time traits and two for sex determination. These QTLs covered genomic regions with 33 transcripts predicted to be involved in flowering and sex determination as well as a microRNA, miR156. Genes related to perception and transduction of light and transcription factors well-known to regulate flowering were identified in QTLs for flowering time traits. Transcription factors and genes involved in regulating the balance of phytohormones, specially auxins and gibberellic acid, were identified in QTLs for sex determination. Sex determination QTLs were associated with the development of male flowers in female plants and thus with the stability of sex determination in monecious plants. The present study elucidates relevant knowledge on the genetic mechanisms of flowering and sex determination traits in hemp, and provides new tools for hemp breeding.
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Affiliation(s)
- Jordi Petit
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Elma M. J. Salentijn
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Maria-João Paulo
- Biometris, Wageningen University and Research, Wageningen, Netherlands
| | - Christel Denneboom
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Luisa M. Trindade
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Luisa M. Trindade,
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Jiao Y, Hu Q, Zhu Y, Zhu L, Ma T, Zeng H, Zang Q, Li X, Lin X. Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens). BMC Bioinformatics 2019; 20:687. [PMID: 31874613 PMCID: PMC6929269 DOI: 10.1186/s12859-019-3261-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is still unclear. RESULTS In this study, three successive stages of flowering buds and the corresponding vegetative buds (non-flowering stage) from Lei bamboo (Phyllostachys violascens) were collected for transcriptome analysis using Illumina RNA-Seq method. We generated about 442 million clean reads from the above samples, and 132,678 unigenes were acquired with N50 of 1080 bp. A total of 7266 differentially expressed genes (DEGs) were determined. According to expression profile and gene function analysis, some environmental stress responsive and plant hormone-related DEGs were highly expressed in the inflorescence meristem formation stage (TF_1) while some floral organ development related genes were up-regulated significantly in floral organs determination stage (TF_2) and floral organs maturation (TF_3) stage, implying the essential roles of these DEGs in flower induction and maturation of Lei bamboo. Additionally, a total of 25 MADS-box unigenes were identified. Based on the expression profile, B, C/D and E clade genes were more related to floral organs development compared with A clade genes in Lei bamboo. CONCLUSIONS This transcriptome data presents fundamental information about the genes and pathways involved in flower induction and development of Lei bamboo. Moreover, a critical sampling method is provided which could be benefit for bamboo flowering mechanism study.
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Affiliation(s)
- Yulian Jiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Lin'an, 311300, Zhejiang, China
| | - Qiutao Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Yan Zhu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Longfei Zhu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Tengfei Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Haiyong Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Qiaolu Zang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China.
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Lin'an, 311300, Zhejiang, China.
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Liang M, Xiao S, Cai J, Ow DW. OXIDATIVE STRESS 3 regulates drought-induced flowering through APETALA 1. Biochem Biophys Res Commun 2019; 519:585-590. [PMID: 31540691 DOI: 10.1016/j.bbrc.2019.08.154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 10/26/2022]
Abstract
Stress-induced regulation of flowering time insures evolutionary fitness. Stress-induced late flowering is thought to result from a plant evoking tolerance mechanism to wait out the stress before initiating reproduction. Stress-induced early flowering, on the other hand, is thought to be a stress-escape response. By shortening their life cycle to produce seeds before severe stress leads to death, this insures survival of the species at the cost of lower seed yield. Previously, we reported that overexpression of OXS3 (OXIDATIVE STRESS 3) could enhance tolerance to cadmium and oxidizing agents in Arabidopsis whereas an oxs3 null mutant was slightly more sensitive to these chemicals. In this study, we found that the absence of OXS3 also causes early flowering under a mild drought stress treatment. This contrasts with the behavior of wild type Ws4 and Col ecotypes that responded to the same condition by delaying flowering time. We tested the hypothesis that OXS3 might ordinarily exert a negative regulatory role on flowering during drought stress, which in its absence, would lead to stress-induced early flowering. In a search of whether OXS3 could interfere with regulators that activate flowering, we found that OXS3 could bind SOC1 in vitro and in vivo. Overexpression of OXS3 in a transient expression assay was found to repress the AP1 promoter, and the full repression effect required SOC1. It is possible that the OXS3/SOC1 interaction serves to prevent precocious flower development and prevent low seed set from a premature stress-induced flowering response.
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Affiliation(s)
- Minting Liang
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shimin Xiao
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jiajia Cai
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - David W Ow
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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60
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Guo ZH, Ma PF, Yang GQ, Hu JY, Liu YL, Xia EH, Zhong MC, Zhao L, Sun GL, Xu YX, Zhao YJ, Zhang YC, Zhang YX, Zhang XM, Zhou MY, Guo Y, Guo C, Liu JX, Ye XY, Chen YM, Yang Y, Han B, Lin CS, Lu Y, Li DZ. Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos. MOLECULAR PLANT 2019; 12:1353-1365. [PMID: 31145999 DOI: 10.1016/j.molp.2019.05.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/01/2019] [Accepted: 05/20/2019] [Indexed: 05/15/2023]
Abstract
Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid). We also constructed a high-density genetic linkage map for a hexaploid species of bamboo, and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids. Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos. Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.
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Affiliation(s)
- Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guo-Qian Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jin-Yong Hu
- Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Mi-Cai Zhong
- Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gui-Ling Sun
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, Henan 475001, China
| | - Yu-Xing Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - You-Jie Zhao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Yi-Chi Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yu-Xiao Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Xue-Mei Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xia-Ying Ye
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yun-Mei Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yang Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Bin Han
- National Center for Gene Research, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei.
| | - Ying Lu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Liu Z, Wu X, Cheng M, Xie Z, Xiong C, Zhang S, Wu J, Wang P. Identification and functional characterization of SOC1-like genes in Pyrus bretschneideri. Genomics 2019; 112:1622-1632. [PMID: 31533070 DOI: 10.1016/j.ygeno.2019.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 12/11/2022]
Abstract
Flowering is a prerequisite for pear fruit production. Therefore, the development of flower buds and the control of flowering time are important for pear trees. However, the molecular mechanism of pear flowering is unclear. SOC1, a member of MADS-box family, is known as a flowering signal integrator in Arabidopsis. We identified eight SOC1-like genes in Pyrus bretschneideri and analyzed their basic information and expression patterns. Some pear SOC1-like genes were regulated by photoperiod in leaves. Moreover, the expression patterns were diverse during the development of pear flower buds. Two members of the pear SOC1-like genes, PbSOC1d and PbSOC1g, could lead to early flowering phenotype when overexpressed in Arabidopsis. PbSOC1d and PbSOC1g were identified as activators of the floral meristem identity genes AtAP1 and AtLFY and promote flowering time. These results suggest that PbSOC1d and PbSOC1g are promoters of flowering time and may be involved in flower bud development in pear.
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Affiliation(s)
- Zhe Liu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoping Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengyu Cheng
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihua Xie
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Changlong Xiong
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Juyou Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Peng Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Qin L, Zhang X, Yan J, Fan L, Rong C, Mo C, Zhang M. Effect of exogenous spermidine on floral induction, endogenous polyamine and hormone production, and expression of related genes in 'Fuji' apple (Malus domestica Borkh.). Sci Rep 2019; 9:12777. [PMID: 31484948 PMCID: PMC6726604 DOI: 10.1038/s41598-019-49280-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022] Open
Abstract
Flower bud formation in ‘Fuji’ apple (Malus domestica Borkh.) is difficult, which severely constrains commercial production. Spermidine (Spd) plays an important role in floral induction, but the mechanism of its action is incompletely understood. To investigate the effect of Spd on flowering, 6-year-old ‘Fuji’ apple trees were treated with 1 × 10−5 mol L−1 Spd to study the responses of polyamines [putrescine (Put), Spd and spermine (Spm)], hormones [gibberellins (GA3) and abscisic acid (ABA)], and polyamine-, hormone- and flowering-related genes. Spd application promoted flowering during floral induction by increasing MdGA2ox2 (gibberellin 2-oxidase) through GA3 reduction and increasing MdNCED1 and MdNCED3 (9-cis-epoxycarotenoid dioxygenase) through ABA enrichment during 60 to 80 days after full bloom. The flowering rate as well as the expressions of flower-related genes, except for MdLEY (LEAFY), also increased, thereby promoting flowering. In addition, spraying with Spd significantly increased the contents of endogenous polyamines except for Spm in terminal buds by increasing the expressions of polyamine-associated genes. We hypothesize that the contribution of Spd to flowering is related to crosstalk among polyamines, hormone signals, and related gene expressions, which suggests that Spd participates in the apple floral induction process.
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Affiliation(s)
- Ling Qin
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jie Yan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lu Fan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chunxiao Rong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chuanyuan Mo
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Manrang Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Lai X, Daher H, Galien A, Hugouvieux V, Zubieta C. Structural Basis for Plant MADS Transcription Factor Oligomerization. Comput Struct Biotechnol J 2019; 17:946-953. [PMID: 31360333 PMCID: PMC6639411 DOI: 10.1016/j.csbj.2019.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022] Open
Abstract
MADS transcription factors (TFs) are DNA binding proteins found in almost all eukaryotes that play essential roles in diverse biological processes. While present in animals and fungi as a small TF family, the family has dramatically expanded in plants over the course of evolution, with the model flowering plant, Arabidopsis thaliana, possessing over 100 type I and type II MADS TFs. All MADS TFs contain a core and highly conserved DNA binding domain called the MADS or M domain. Plant MADS TFs have diversified this domain with plant-specific auxiliary domains. Plant type I MADS TFs have a highly diverse and largely unstructured Carboxy-terminal (C domain), whereas type II MADS have added oligomerization domains, called Intervening (I domain) and Keratin-like (K domain), in addition to the C domain. In this mini review, we describe the overall structure of the type II "MIKC" type MADS TFs in plants, with a focus on the K domain, a critical oligomerization module. We summarize the determining factors for oligomerization and provide mechanistic insights on how secondary structural elements are required for oligomerization capability and specificity. Using MADS TFs that are involved in flower organ specification as an example, we provide case studies and homology modeling of MADS TFs complex formation. Finally, we highlight outstanding questions in the field.
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Affiliation(s)
- Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Hussein Daher
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Antonin Galien
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Veronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
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Zhou B, Wang J, Lou H, Wang H, Xu Q. Comparative transcriptome analysis of dioecious, unisexual floral development in Ribes diacanthum pall. Gene 2019; 699:43-53. [DOI: 10.1016/j.gene.2019.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 01/09/2023]
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Del Prete S, Molitor A, Charif D, Bessoltane N, Soubigou-Taconnat L, Guichard C, Brunaud V, Granier F, Fransz P, Gaudin V. Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction. BMC PLANT BIOLOGY 2019; 19:135. [PMID: 30971226 PMCID: PMC6458719 DOI: 10.1186/s12870-019-1738-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/24/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The floral transition is a complex developmental event, fine-tuned by various environmental and endogenous cues to ensure the success of offspring production. Leaves are key organs in sensing floral inductive signals, such as a change in light regime, and in the production of the mobile florigen. CONSTANS and FLOWERING LOCUS T are major players in leaves in response to photoperiod. Morphological and molecular events during the floral transition have been intensively studied in the shoot apical meristem. To better understand the concomitant processes in leaves, which are less described, we investigated the nuclear changes in fully developed leaves during the time course of the floral transition. RESULTS We highlighted new putative regulatory candidates of flowering in leaves. We observed differential expression profiles of genes related to cellular, hormonal and metabolic actions, but also of genes encoding long non-coding RNAs and new natural antisense transcripts. In addition, we detected a significant increase in ploidy level during the floral transition, indicating endoreduplication. CONCLUSIONS Our data indicate that differentiated mature leaves, possess physiological plasticity and undergo extensive nuclear reprogramming during the floral transition. The dynamic events point at functionally related networks of transcription factors and novel regulatory motifs, but also complex hormonal and metabolic changes.
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Affiliation(s)
- Stefania Del Prete
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Anne Molitor
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Delphine Charif
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Nadia Bessoltane
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Cécile Guichard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Fabienne Granier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
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Floral regulators FLC and SOC1 directly regulate expression of the B3-type transcription factor TARGET OF FLC AND SVP 1 at the Arabidopsis shoot apex via antagonistic chromatin modifications. PLoS Genet 2019; 15:e1008065. [PMID: 30946745 PMCID: PMC6467423 DOI: 10.1371/journal.pgen.1008065] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/16/2019] [Accepted: 03/04/2019] [Indexed: 11/23/2022] Open
Abstract
Integration of environmental and endogenous cues at plant shoot meristems determines the timing of flowering and reproductive development. The MADS box transcription factor FLOWERING LOCUS C (FLC) of Arabidopsis thaliana is an important repressor of floral transition, which blocks flowering until plants are exposed to winter cold. However, the target genes of FLC have not been thoroughly described, and our understanding of the mechanisms by which FLC represses transcription of these targets and how this repression is overcome during floral transition is still fragmentary. Here, we identify and characterize TARGET OF FLC AND SVP1 (TFS1), a novel target gene of FLC and its interacting protein SHORT VEGETATIVE PHASE (SVP). TFS1 encodes a B3-type transcription factor, and we show that tfs1 mutants are later flowering than wild-type, particularly under short days. FLC and SVP repress TFS1 transcription leading to deposition of trimethylation of Iysine 27 of histone 3 (H3K27me3) by the Polycomb Repressive Complex 2 at the TFS1 locus. During floral transition, after downregulation of FLC by cold, TFS1 transcription is promoted by SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), a MADS box protein encoded by another target of FLC/SVP. SOC1 opposes PRC function at TFS1 through recruitment of the histone demethylase RELATIVE OF EARLY FLOWERING 6 (REF6) and the SWI/SNF chromatin remodeler ATPase BRAHMA (BRM). This recruitment of BRM is also strictly required for SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9) binding at TFS1 to coordinate RNAPII recruitment through the Mediator complex. Thus, we show that antagonistic chromatin modifications mediated by different MADS box transcription factor complexes play a crucial role in defining the temporal and spatial patterns of transcription of genes within a network of interactions downstream of FLC/SVP during floral transition. The initiation of flowering in plants is exquisitely sensitive to environmental signals, ensuring that reproduction occurs at the appropriate time of year. The sensitivity of these responses depends upon strong repression of flowering under inappropriate conditions. FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are related transcription factors that act in concert to strongly inhibit flowering in crucifer plants through repressing transcription of their target genes. Many direct FLC/ SVP targets have been identified in genome-wide studies, however few of these genes have been characterized for their roles in regulating flowering time or other aspects of reproductive development. Here, we characterize TARGET OF FLC AND SVP1 (TFS1) as a novel target of FLC and SVP, and demonstrate that TFS1 contributes to proper flowering-time control. Moreover, we provide a detailed mechanistic view of how TFS1 transcription is controlled during reproductive development through the repressive activity of FLC/SVP being overcome by the transcriptional activator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1. Thus we further elucidate the network of genes repressed by FLC/SVP to block flowering and determine mechanisms by which their repressive activity is overcome during the initiation of flowering.
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Hwang K, Susila H, Nasim Z, Jung JY, Ahn JH. Arabidopsis ABF3 and ABF4 Transcription Factors Act with the NF-YC Complex to Regulate SOC1 Expression and Mediate Drought-Accelerated Flowering. MOLECULAR PLANT 2019; 12:489-505. [PMID: 30639313 DOI: 10.1016/j.molp.2019.01.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 05/19/2023]
Abstract
The drought-escape response accelerates flowering in response to drought stress, allowing plants to adaptively shorten their life cycles. Abscisic acid (ABA) mediates plant responses to drought, but the role of ABA-responsive element (ABRE)-binding factors (ABFs) in the drought-escape response is poorly understood. Here, we show that Arabidopsis thaliana ABF3 and ABF4 regulate flowering in response to drought through transcriptional regulation of the floral integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The abf3 abf4 mutant displayed ABA-insensitive late flowering under long-day conditions. Ectopic expression of ABF3 or ABF4 in the vasculature, but not in the shoot apex, induced early flowering, whereas expression of ABF3 fused with the SRDX transcriptional repressor domain delayed flowering. We identified SOC1 as a direct downstream target of ABF3/4, and found that SOC1 mRNA levels were lower in abf3 abf4 than in wild-type plants. Moreover, induction of SOC1 by ABA was hampered in abf3 abf4 mutants. ABF3 and ABF4 were enriched at the -1028- to -657-bp region of the SOC1 promoter, which does not contain canonical ABF-ABRE-binding motifs but has the NF-Y binding element. We found that ABF3 and ABF4 interact with nuclear factor Y subunit C (NF-YC) 3/4/9 in vitro and in planta, and induction of SOC1 by ABA was hampered in nf-yc3 yc4 yc9 mutants. Interestingly, the abf3 abf4, nf-yc3 yc4 yc9, and soc1 mutants displayed a reduced drought-escape response. Taken together, these results suggest that ABF3 and ABF4 act with NF-YCs to promote flowering by inducing SOC1 transcription under drought conditions. This mechanism might contribute to adaptation by enabling plants to complete their life cycles under drought stress.
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Affiliation(s)
- Keumbi Hwang
- Department of Life Sciences, Korea University, Anamro 145, Seongbuk-Gu, Seoul 02841, South Korea
| | - Hendry Susila
- Department of Life Sciences, Korea University, Anamro 145, Seongbuk-Gu, Seoul 02841, South Korea
| | - Zeeshan Nasim
- Department of Life Sciences, Korea University, Anamro 145, Seongbuk-Gu, Seoul 02841, South Korea
| | - Ji-Yul Jung
- Department of Life Sciences, Korea University, Anamro 145, Seongbuk-Gu, Seoul 02841, South Korea
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Anamro 145, Seongbuk-Gu, Seoul 02841, South Korea.
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Wu R, Wang T, Richardson AC, Allan AC, Macknight RC, Varkonyi-Gasic E. Histone modification and activation by SOC1-like and drought stress-related transcription factors may regulate AcSVP2 expression during kiwifruit winter dormancy. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:242-250. [PMID: 30824057 DOI: 10.1016/j.plantsci.2018.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 05/03/2023]
Abstract
The SHORT VEGETATIVE PHASE (SVP)-like and DORMANCY ASSOCIATED MADS-BOX (DAM) genes have been shown to regulate winter dormancy in woody perennials. In kiwifruit, AcSVP2 affects the duration of dormancy in cultivars that require high chill for dormancy release. In this study, we used a low-chill kiwifruit Actinidia chinensis 'Hort16A' to further study the function and regulation of AcSVP2. Overexpression of AcSVP2 in transgenic A. chinensis delayed budbreak in spring. A reduction in the active trimethylation histone marks of the histone H3K4 and acetylation of histone H3 contributed to the reduction of AcSVP2 expression towards dormancy release, while the inactive histone marks of trimethylation of the histone H3K27 and H3K9 in AcSVP2 locus did not show significant enrichment at the end of winter dormancy. Analysis of expression in shoot buds showed that AcSVP2 transcript was elevated in dormant buds during winter months and declined prior to budbreak, which was coordinated with expression of some of kiwifruit SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)-like genes. Screening of 101 transcription factors in an assay with a 2.3 kb promoter region of AcSVP2 found that kiwifruit SOC1-like genes are able to activate the AcSVP2 promoter. We further identified additional transcription factors associated with drought/osmotic stress and dormancy which may regulate AcSVP2 expression.
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Affiliation(s)
- Rongmei Wu
- The New Zealand Institute for Plant & Food Research Limited (PFR) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant & Food Research Limited (PFR) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Annette C Richardson
- The New Zealand Institute for Plant & Food Research Limited (PFR) Kerikeri, 121 Keri Downs Road, RD1, Kerikeri 0294, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited (PFR) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Richard C Macknight
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Limited (PFR) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
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Xiao D, Shen HR, Zhao JJ, Wei YP, Liu DR, Hou XL, Bonnema G. Genetic dissection of flowering time in Brassica rapa responses to temperature and photoperiod. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:110-119. [PMID: 30823988 DOI: 10.1016/j.plantsci.2018.10.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/19/2018] [Accepted: 10/31/2018] [Indexed: 06/09/2023]
Abstract
The Brassica rapa (B. rapa) species displays enormous phenotypic diversity, with leafy vegetables, storage root vegetables and oil crops. These different crops all have different flowering time, which determine their growing season and cultivation area. Little is known about the effects of diverse temperature and day-lengths on flowering time QTL associated with FLC paralogues. We phenotyped the flowering time of a doubled haploid population, established from a cross between Yellow sarson and Pak choi under diverse environmental conditions. We identified flowering-time QTL (fQTL) in different photoperiod and temperature regimes in the greenhouse, and studied their colocation with known flowering time genes. As several fQTL colocalized with FLC paralogues, we studied the expression patterns of four FLC paralogues during the course of vernalization in parental lines. Under all environmental conditions tested the major fQTL that mapped to the BrFLC2_A02 locus was detected, however its effect decreased when plants were grown at low temperatures. Another fQTL that mapped to the FLC paralogue, BrFLC5_A03 was also identified under all tested environments, while no fQTL colocated with BrFLC1_A10 or BrFLC3_A03. Furthermore, the vernalization treatment decreased expression of all BrFLC paralogues in the parental lines, and showed the lowest transcript level after 28 days of vernalization. Transcript abundance stayed low after returning the plants for seven days to normal growth temperature. Interestingly, transcript abundance of BrFLC3_A03 and BrFLC5_A03 was repressed much stronger and already reached lowest levels after 14d in the early-flowering type YS-143. This study improves understanding of the effects of daylength and vernalization on flowering time in B. rapa and the role of the different BrFLC paralogues therein.
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Affiliation(s)
- Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao-Ran Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Jun Zhao
- Horticultural College, Agricultural University of Hebei, Baoding, 071001, China
| | - Yan-Ping Wei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong-Rang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, the Netherlands.
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70
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Chow CN, Lee TY, Hung YC, Li GZ, Tseng KC, Liu YH, Kuo PL, Zheng HQ, Chang WC. PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic Acids Res 2019. [PMID: 30395277 DOI: 10.1093/nar/gky1081chu] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional regulatory networks for plant genes. In this release (PlantPAN 3.0), 17 230 TFs were collected from 78 plant species. To explore regulatory landscapes, genomic locations of TFBSs have been captured from 662 public ChIP-seq samples using standard data processing. A total of 1 233 999 regulatory linkages were identified from 99 regulatory factors (TFs, histones and other DNA-binding proteins) and their target genes across seven species. Additionally, this new version added 2449 matrices extracted from ChIP-seq peaks for cis-regulatory element prediction. In addition to integrated ChIP-seq data, four major improvements were provided for more comprehensive information of TF binding events, including (i) 1107 experimentally verified TF matrices from the literature, (ii) gene regulation network comparison between two species, (iii) 3D structures of TFs and TF-DNA complexes and (iv) condition-specific co-expression networks of TFs and their target genes extended to four species. The PlantPAN 3.0 can not only be efficiently used to investigate critical cis- and trans-regulatory elements in plant promoters, but also to reconstruct high-confidence relationships among TF-targets under specific conditions.
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Affiliation(s)
- Chi-Nga Chow
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan
| | - Tzong-Yi Lee
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China
| | - Yu-Cheng Hung
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Guan-Zhen Li
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Kuan-Chieh Tseng
- Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ya-Hsin Liu
- Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Po-Li Kuo
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Han-Qin Zheng
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wen-Chi Chang
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
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71
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Salentijn EMJ, Petit J, Trindade LM. The Complex Interactions Between Flowering Behavior and Fiber Quality in Hemp. FRONTIERS IN PLANT SCIENCE 2019; 10:614. [PMID: 31156677 PMCID: PMC6532435 DOI: 10.3389/fpls.2019.00614] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/25/2019] [Indexed: 05/05/2023]
Abstract
Hemp, Cannabis sativa L., is a sustainable multipurpose fiber crop with high nutrient and water use efficiency and with biomass of excellent quality for textile fibers and construction materials. The yield and quality of hemp biomass are largely determined by the genetic background of the hemp cultivar but are also strongly affected by environmental factors, such as temperature and photoperiod. Hemp is a facultative short-day plant, characterized by a strong adaptation to photoperiod and a great influence of environmental factors on important agronomic traits such as "flowering-time" and "sex determination." This sensitivity of hemp can cause a considerable degree of heterogeneity, leading to unforeseen yield reductions. Fiber quality for instance is influenced by the developmental stage of hemp at harvest. Also, male and female plants differ in stature and produce fibers with different properties and quality. Next to these causes, there is evidence for specific genotypic variation in fiber quality among hemp accessions. Before improved hemp cultivars can be developed, with specific flowering-times and fiber qualities, and adapted to different geographical regions, a better understanding of the molecular mechanisms controlling important phenological traits such as "flowering-time" and "sex determination" in relation to fiber quality in hemp is required. It is well known that genetic factors play a major role in the outcome of both phenological traits, but the major molecular factors involved in this mechanism are not characterized in hemp. Genome sequences and transcriptome data are available but their analysis mainly focused on the cannabinoid pathway for medical purposes. Herein, we review the current knowledge of phenotypic and genetic data available for "flowering-time," "sex determination," and "fiber quality" in short-day and dioecious crops, respectively, and compare them with the situation in hemp. A picture emerges for several controlling key genes, for which natural genetic variation may lead to desired flowering behavior, including examples of pleiotropic effects on yield quality and on carbon partitioning. Finally, we discuss the prospects for using this knowledge for the molecular breeding of this sustainable crop via a candidate gene approach.
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72
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Yan K, Li CC, Wang Y, Wang XQ, Wang ZM, Wei DY, Tang QL. AGL18-1 delays flowering time through affecting expression of flowering-related genes in Brassica juncea. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:357-363. [PMID: 31892823 PMCID: PMC6905224 DOI: 10.5511/plantbiotechnology.18.0824a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Brassica juncea is an important vegetable and condiment crop widely grown in Asia, and the yield and quality of its product organs are affected by flowering time. AGAMOUS-LIKE18-1 (AGL18-1) belongs to a member of MADS-domain transcription factors, which play vital roles in flowering time control, but the biological role of AGL18-1 in B. juncea (BjuAGL18-1) has not been thoroughly revealed in flowering regulatory network. In this study, BjuAGL18-1 expressed highly in inflorescence and flower, but slightly in root, stem and leaf. The sense and anti-sense transgenic lines of BjuAGL18-1 were generated and showed that BjuAGL18-1 functioned as a flowering inhibitor and depressed growth of lateral branching. During the vegetative phase, BjuAGL18-1 induced another flowering repressor AGAMOUS-LIKE15 (BjuAGL15) but inhibited the flowering signal integrator of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (BjuSOC1) in Brassica juncea. Whereas, during the flower developmental phase, both SOC1 and AGAMOUS-LIKE24 (AGL24) were down-regulated by BjuAGL18-1. By contrast, AGL15 was promoted by BjuAGL18-1, while SHORT VEGETATIVE PHASE (SVP) was independent of BjuAGL18-1. Additionally, HISTONE DEACETYLASE 9 (HDA9) was highly induced by BjuAGL18-1. These results will provide valuable information for clarifying the molecular mechanism of BjuAGL18-1 in mediating flowering time.
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Affiliation(s)
- Kai Yan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Chao-Chuang Li
- College of Biotechnology, Chongqing University, Chongqing 401331, China
| | - Yu Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Xiao-Quan Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Zhi-Min Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Da-Yong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
- E-mail: Tel: +86-23-6825-0974 Fax: +86-6825-1274
| | - Qing-Lin Tang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
- E-mail: Tel: +86-23-6825-0974 Fax: +86-6825-1274
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73
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Chen D, Yan W, Fu LY, Kaufmann K. Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana. Nat Commun 2018; 9:4534. [PMID: 30382087 PMCID: PMC6208445 DOI: 10.1038/s41467-018-06772-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 09/26/2018] [Indexed: 11/29/2022] Open
Abstract
Floral homeotic transcription factors (TFs) act in a combinatorial manner to specify the organ identities in the flower. However, the architecture and the function of the gene regulatory network (GRN) controlling floral organ specification is still poorly understood. In particular, the interconnections of homeotic TFs, microRNAs (miRNAs) and other factors controlling organ initiation and growth have not been studied systematically so far. Here, using a combination of genome-wide TF binding, mRNA and miRNA expression data, we reconstruct the dynamic GRN controlling floral meristem development and organ differentiation. We identify prevalent feed-forward loops (FFLs) mediated by floral homeotic TFs and miRNAs that regulate common targets. Experimental validation of a coherent FFL shows that petal size is controlled by the SEPALLATA3-regulated miR319/TCP4 module. We further show that combinatorial DNA-binding of homeotic factors and selected other TFs is predictive of organ-specific patterns of gene expression. Our results provide a valuable resource for studying molecular regulatory processes underlying floral organ specification in plants. Homeotic transcription factors and miRNAs promote floral organ specification. Here Chen et al. reconstruct gene regulatory networks in Arabidopsis flowers and find evidence for feed forward loops between transcription factors, miRNAs and their targets that determine organ-specific gene expression.
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Affiliation(s)
- Dijun Chen
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Wenhao Yan
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Liang-Yu Fu
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Kerstin Kaufmann
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
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74
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Jaudal M, Zhang L, Che C, Li G, Tang Y, Wen J, Mysore KS, Putterill J. A SOC1-like gene MtSOC1a promotes flowering and primary stem elongation in Medicago. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4867-4880. [PMID: 30295903 PMCID: PMC6137972 DOI: 10.1093/jxb/ery284] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/10/2018] [Indexed: 05/19/2023]
Abstract
Medicago flowering, like that of Arabidopsis, is promoted by vernalization and long days, but alternative mechanisms are predicted because Medicago lacks the key regulators CO and FLC. Three Medicago SOC1-like genes, including MtSOC1a, were previously implicated in flowering control, but no legume soc1 mutants with altered flowering were reported. Here, reverse transciption-quantitative PCR (RT-qPCR) indicated that the timing and magnitude of MtSOC1a expression was regulated by the flowering promoter FTa1, while in situ hybridization indicated that MtSOC1a expression increased in the shoot apical meristem during the floral transition. A Mtsoc1a mutant showed delayed flowering and short primary stems. Overexpression of MtSOC1a partially rescued the flowering of Mtsoc1a, but caused a dramatic increase in primary stem height, well before the transition to flowering. Internode cell length correlated with stem height, indicating that MtSOC1a promotes cell elongation in the primary stem. However, application of gibberellin (GA3) caused stem elongation in both the wild type and Mtsoc1a, indicating that the mutant was not defective in gibberellin responsiveness. These results indicate that MtSOC1a may function as a floral integrator gene and promotes primary stem elongation. Overall, this study suggests that apart from some conservation with the Arabidopsis flowering network, MtSOC1a has a novel role in regulating aspects of shoot architecture.
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Affiliation(s)
- Mauren Jaudal
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lulu Zhang
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Chong Che
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Guifen Li
- Noble Research Institute, LLC, Ardmore, OK, USA
| | - Yuhong Tang
- Noble Research Institute, LLC, Ardmore, OK, USA
| | - Jiangqi Wen
- Noble Research Institute, LLC, Ardmore, OK, USA
| | | | - Joanna Putterill
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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75
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Yan W, Chen D, Smaczniak C, Engelhorn J, Liu H, Yang W, Graf A, Carles CC, Zhou DX, Kaufmann K. Dynamic and spatial restriction of Polycomb activity by plant histone demethylases. NATURE PLANTS 2018; 4:681-689. [PMID: 30104650 DOI: 10.1038/s41477-018-0219-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 07/12/2018] [Indexed: 05/23/2023]
Abstract
Targeted changes in chromatin state at thousands of genes are central to eukaryotic development. RELATIVE OF EARLY FLOWERING 6 (REF6) is a Jumonji-type histone demethylase that counteracts Polycomb repressive complex 2 (PRC2)-mediated gene silencing in plants and was reported to select its binding sites in a direct, sequence-specific manner1-3. Here we show that REF6 and its two close paralogues determine spatial 'boundaries' of the repressive histone H3K27me3 mark in the genome and control the tissue-specific release from PRC2-mediated gene repression. Targeted mutagenesis revealed that these histone demethylases display pleiotropic, redundant functions in plant development, several of which depend on trans factor-mediated recruitment. Thus, Jumonji-type histone demethylases restrict repressive chromatin domains and contribute to tissue-specific gene activation via complementary targeting mechanisms.
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Affiliation(s)
- Wenhao Yan
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Dijun Chen
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cezary Smaczniak
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia Engelhorn
- LPCV, CNRS, CEA, INRA, Université Grenoble Alpes, Grenoble, France
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Haiyang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenjing Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Alexander Graf
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Cristel C Carles
- LPCV, CNRS, CEA, INRA, Université Grenoble Alpes, Grenoble, France
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Institute Plant Science Paris-Saclay (IPS2), CNRS, INRA, Université Paris-sud 11, Université Paris-Saclay, Orsay, France
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
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Chen Z, Zhao W, Ge D, Han Y, Ning K, Luo C, Wang S, Liu R, Zhang X, Wang Q. LCM-seq reveals the crucial role of LsSOC1 in heat-promoted bolting of lettuce (Lactuca sativa L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:516-528. [PMID: 29772090 DOI: 10.1111/tpj.13968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/26/2018] [Accepted: 05/02/2018] [Indexed: 05/08/2023]
Abstract
Lettuce (Lactuca sativa L.) is one of the most economically important vegetables. The floral transition in lettuce is accelerated under high temperatures, which can significantly decrease yields. However, the molecular mechanism underlying the floral transition in lettuce is poorly known. Using laser capture microdissection coupled with RNA sequencing, we isolated shoot apical meristem cells from the bolting-sensitive lettuce line S39 at four critical stages of development. Subsequently, we screened specifically for the flowering-related gene LsSOC1 during the floral transition through comparative transcriptomic analysis. Molecular biology, developmental biology, and biochemical tools were combined to investigate the biological function of LsSOC1 in lettuce. LsSOC1 knockdown by RNA interference resulted in a significant delay in the timing of bolting and insensitivity to high temperature, which indicated that LsSOC1 functions as an activator during heat-promoted bolting in lettuce. We determined that two heat shock transcription factors, HsfA1e and HsfA4c, bound to the promoter of LsSOC1 to confirm that LsSOC1 played an important role in heat-promoted bolting. This study indicates that LsSOC1 plays a crucial role in the heat-promoted bolting process in lettuce. Further investigation of LsSOC1 may be useful for clarification of the bolting mechanism in lettuce.
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Affiliation(s)
- Zijing Chen
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Wensheng Zhao
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Danfeng Ge
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100094, China
| | - Yingyan Han
- Plant Science and Technology College, Beijing University of Agriculture/New Technological Laboratory in Agriculture Application in Beijing, Beijing, 102206, China
| | - Kang Ning
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Chen Luo
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Shenglin Wang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Renyi Liu
- College of Horticulture and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaolan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Qian Wang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
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77
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Severing E, Faino L, Jamge S, Busscher M, Kuijer-Zhang Y, Bellinazzo F, Busscher-Lange J, Fernández V, Angenent GC, Immink RGH, Pajoro A. Arabidopsis thaliana ambient temperature responsive lncRNAs. BMC PLANT BIOLOGY 2018; 18:145. [PMID: 30005624 PMCID: PMC6045843 DOI: 10.1186/s12870-018-1362-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/04/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level. Recent studies also identified lncRNAs in plant genomes, revealing a new level of transcriptional complexity in plants. Thousands of lncRNAs have been predicted in the Arabidopsis thaliana genome, but only a few have been studied in depth. RESULTS Here we report the identification of Arabidopsis lncRNAs that are expressed during the vegetative stage of development in either the shoot apical meristem or in leaves. We found that hundreds of lncRNAs are expressed in these tissues, of which 50 show differential expression upon an increase in ambient temperature. One of these lncRNAs, FLINC, is down-regulated at higher ambient temperature and affects ambient temperature-mediated flowering in Arabidopsis. CONCLUSION A number of ambient temperature responsive lncRNAs were identified with potential roles in the regulation of temperature-dependent developmental changes, such as the transition from the vegetative to the reproductive (flowering) phase. The challenge for the future is to characterize the biological function and molecular mode of action of the large number of ambient temperature-regulated lncRNAs that have been identified in this study.
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Affiliation(s)
- Edouard Severing
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Suraj Jamge
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Marco Busscher
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Yang Kuijer-Zhang
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Francesca Bellinazzo
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | | | | | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Richard G. H. Immink
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Alice Pajoro
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
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78
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Tyagi S, Sri T, Singh A, Mayee P, Shivaraj SM, Sharma P, Singh A. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 influences flowering time, lateral branching, oil quality, and seed yield in Brassica juncea cv. Varuna. Funct Integr Genomics 2018; 19:43-60. [DOI: 10.1007/s10142-018-0626-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 01/18/2023]
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79
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Aerts N, de Bruijn S, van Mourik H, Angenent GC, van Dijk ADJ. Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana. BMC PLANT BIOLOGY 2018; 18:131. [PMID: 29940855 PMCID: PMC6019531 DOI: 10.1186/s12870-018-1348-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 06/11/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Correct flower formation requires highly specific temporal and spatial regulation of gene expression. In Arabidopsis thaliana the majority of the master regulators that determine flower organ identity belong to the MADS-domain transcription factor family. The canonical DNA binding motif for this transcription factor family is the CArG-box, which has the consensus CC(A/T)6GG. However, so far, a comprehensive analysis of MADS-domain binding patterns has not yet been performed. RESULTS Eight publicly available ChIP-seq datasets of MADS-domain proteins that regulate the floral transition and flower formation were analyzed. Surprisingly, the preferred DNA binding motif of each protein was a CArG-box with an NAA extension. Furthermore, motifs of other transcription factors were found in the vicinity of binding sites of MADS-domain transcription factors, suggesting that interaction of MADS-domain proteins with other transcription factors is important for target gene regulation. Finally, conservation of CArG-boxes between Arabidopsis ecotypes was assessed to obtain information about their evolutionary importance. CArG-boxes that fully matched the consensus were more conserved than other CArG-boxes, suggesting that the perfect CArG-box is evolutionary more important than other CArG-box variants. CONCLUSION Our analysis provides detailed insight into MADS-domain protein binding patterns. The results underline the importance of an extended version of the CArG-box and provide a first view on evolutionary conservation of MADS-domain protein binding sites in Arabidopsis ecotypes.
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Affiliation(s)
- Niels Aerts
- Bioscience, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands
- Plant-Microbe Interactions, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Suzanne de Bruijn
- Bioscience, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Hilda van Mourik
- Bioscience, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Gerco C. Angenent
- Bioscience, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Aalt D. J. van Dijk
- Bioscience, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands
- Biometris, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands
- Bioinformatics, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands
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80
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Cheng Y, Zhang Y, Liu C, Ai P, Liu J. Identification of genes regulating ovary differentiation after pollination in hazel by comparative transcriptome analysis. BMC PLANT BIOLOGY 2018; 18:84. [PMID: 29739322 PMCID: PMC5941469 DOI: 10.1186/s12870-018-1296-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/26/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Hazel (Corylus spp.) exhibits ovary differentiation and development that is initiated from the ovary primordium after pollination, conferring the plant with a unique delayed fertilization. Failure of development of the ovary and ovule after pollination can lead to ovary abortion and blank fruit formation, respectively, with consequent yield loss. However, the genes involved in ovary and ovule differentiation and development are largely unknown. RESULTS In unpollinated pistillate inflorescences (stage F), the stigma shows an extension growth pattern. After pollination, a rudimentary ovary begins to form (stage S), followed by ovule differentiation (stage T) and growth (stage FO). Total RNA was obtained from pistillate inflorescences or young ovaries at stage F, S, T and FO, and sequencing was carried out on a HiSeq 4000 system. De novo assembly of sequencing data yielded 62.58 Gb of nucleotides and 90,726 unigenes; 5524, 3468, and 8714 differentially expressed transcripts were identified in F-vs-S, S-vs-T, and T-vs-FO paired comparisons, respectively. An analysis of F-vs-S, S-vs-T, and T-vs-FO paired comparisons based on annotations in the Kyoto Encyclopedia of Genes and Genomes revealed six pathways that were significantly enriched during ovary differentiation, including ko04075 (Plant hormone signal transduction). Auxin level increased after pollination, and an immunohistochemical analysis indicated that auxin was enriched at the growth center of pistillate inflorescences and young ovaries. These results indicate that genes related to auxin biosynthesis, transport, signaling, the floral quartet model, and flower development may regulate ovary and ovule differentiation and development in hazel. CONCLUSIONS Our findings provide insight into the molecular mechanisms of ovary differentiation and development after pollination in this economically valuable plant.
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Affiliation(s)
- Yunqing Cheng
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, Jilin Province, China
| | - Yuchu Zhang
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, Jilin Province, China
| | - Chunming Liu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, Jilin Province, China
| | - Pengfei Ai
- College of Bioscience & Bioengineering, Hebei University of Science and Technology, Shijiazhuang, 050080, Hebei Province, China
| | - Jianfeng Liu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, Jilin Province, China.
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81
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Zeng X, Liu H, Du H, Wang S, Yang W, Chi Y, Wang J, Huang F, Yu D. Soybean MADS-box gene GmAGL1 promotes flowering via the photoperiod pathway. BMC Genomics 2018; 19:51. [PMID: 29338682 PMCID: PMC5769455 DOI: 10.1186/s12864-017-4402-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/19/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The MADS-box transcription factors are an ancient family of genes that regulate numerous physiological and biochemical processes in plants and facilitate the development of floral organs. However, the functions of most of these transcription factors in soybean remain unknown. RESULTS In this work, a MADS-box gene, GmAGL1, was overexpressed in soybean. Phenotypic analysis showed that GmAGL1 overexpression not only resulted in early maturation but also promoted flowering and affected petal development. Furthermore, the GmAGL1 was much more effective at promoting flowering under long-day conditions than under short-day conditions. Transcriptome sequencing analysis showed that before flowering, the photoperiod pathway photoreceptor CRY2 and several circadian rhythm genes, such as SPA1, were significantly down-regulated, while some other flowering-promoting circadian genes, such as GI and LHY, and downstream genes related to flower development, such as FT, LEAFY, SEP1, SEP3, FUL, and AP1, were up-regulated compared with the control. Other genes related to the flowering pathway were not noticeably affected. CONCLUSIONS The findings reported herein indicate that GmAGL1 may promote flowering mainly through the photoperiod pathway. Interestingly, while overexpression of GmAGL1 promoted plant maturity, no reduction in seed production or oil and protein contents was observed.
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Affiliation(s)
- Xuanrui Zeng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Hailun Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Hongyang Du
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Sujing Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Wenming Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Yingjun Chi
- College of Agro-grass-land Science, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Jiao Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Fang Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
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82
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Fudge JB, Lee RH, Laurie RE, Mysore KS, Wen J, Weller JL, Macknight RC. Medicago truncatula SOC1 Genes Are Up-regulated by Environmental Cues That Promote Flowering. FRONTIERS IN PLANT SCIENCE 2018; 9:496. [PMID: 29755488 PMCID: PMC5934494 DOI: 10.3389/fpls.2018.00496] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/03/2018] [Indexed: 05/20/2023]
Abstract
Like Arabidopsis thaliana, the flowering of the legume Medicago truncatula is promoted by long day (LD) photoperiod and vernalization. However, there are differences in the molecular mechanisms involved, with orthologs of two key Arabidopsis thaliana regulators, FLOWERING LOCUS C (FLC) and CONSTANS (CO), being absent or not having a role in flowering time function in Medicago. In Arabidopsis, the MADS-box transcription factor gene, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (AtSOC1), plays a key role in integrating the photoperiodic and vernalization pathways. In this study, we set out to investigate whether the Medicago SOC1 genes play a role in regulating flowering time. Three Medicago SOC1 genes were identified and characterized (MtSOC1a-MtSOC1c). All three MtSOC1 genes, when heterologously expressed, were able to promote earlier flowering of the late-flowering Arabidopsis soc1-2 mutant. The three MtSOC1 genes have different patterns of expression. However, consistent with a potential role in flowering time regulation, all three MtSOC1 genes are expressed in the shoot apex and are up-regulated in the shoot apex of plants in response to LD photoperiods and vernalization. The up-regulation of MtSOC1 genes was reduced in Medicago fta1-1 mutants, indicating that they are downstream of MtFTa1. Insertion mutant alleles of Medicago soc1b do not flower late, suggestive of functional redundancy among Medicago SOC1 genes in promoting flowering.
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Affiliation(s)
- Jared B. Fudge
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Robyn H. Lee
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Rebecca E. Laurie
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Kirankumar S. Mysore
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, United States
| | - Jiangqi Wen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, United States
| | - James L. Weller
- School of Biological Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Richard C. Macknight
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- New Zealand Institute for Plant and Food Research Ltd., University of Otago, Dunedin, New Zealand
- *Correspondence: Richard C. Macknight,
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83
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Abstract
Transcription factors that trigger major developmental decisions in plants and animals are termed "master regulators". Such master regulators are classically seen as acting on the top of a regulatory hierarchy that determines a complete developmental program, and they usually encode transcription factors. Here, we introduce master regulators of flowering time and flower development as examples to show how analysis of molecular interactions and gene-regulatory networks in plants has changed our view on the molecular mechanisms by which these factors control developmental processes. A picture has emerged that emphasizes a complex combinatorial interplay in determining cell-type transcriptional programs, and a high level of feedback control. The expression of master regulators themselves is usually regulated by multiple factors integrating environmental and endogenous spatiotemporal cues. Master regulatory transcription factors regulate gene expression by different mechanisms, including modifications in chromatin status in the bound regions. A poorly understood phenomenon is how developmental master regulators exert functions in different cell- and organ types. This is especially relevant for those factors that have important functions in several developmental processes.
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84
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Lucero LE, Manavella PA, Gras DE, Ariel FD, Gonzalez DH. Class I and Class II TCP Transcription Factors Modulate SOC1-Dependent Flowering at Multiple Levels. MOLECULAR PLANT 2017; 10:1571-1574. [PMID: 28893715 DOI: 10.1016/j.molp.2017.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/28/2017] [Accepted: 09/01/2017] [Indexed: 05/18/2023]
Affiliation(s)
- Leandro E Lucero
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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85
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Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species. Proc Natl Acad Sci U S A 2017; 114:E11037-E11046. [PMID: 29203652 PMCID: PMC5754749 DOI: 10.1073/pnas.1618075114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared with WT, and this correlated with reduced growth in pep1-1 Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.
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86
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Jamge S, Stam M, Angenent GC, Immink RGH. A cautionary note on the use of chromosome conformation capture in plants. PLANT METHODS 2017; 13:101. [PMID: 29177001 PMCID: PMC5691870 DOI: 10.1186/s13007-017-0251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The chromosome conformation capture (3C) technique is a method to study chromatin interactions at specific genomic loci. Initially established for yeast the 3C technique has been adapted to plants in recent years in order to study chromatin interactions and their role in transcriptional gene regulation. As the plant scientific community continues to implement this technology, a discussion on critical controls, validations steps and interpretation of 3C data is essential to fully benefit from 3C in plants. RESULTS Here we assess the reliability and robustness of the 3C technique for the detection of chromatin interactions in Arabidopsis. As a case study, we applied this methodology to the genomic locus of a floral integrator gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), and demonstrate the need of several controls and standard validation steps to allow a meaningful interpretation of 3C data. The intricacies of this promising but challenging technique are discussed in depth. CONCLUSIONS The 3C technique offers an interesting opportunity to study chromatin interactions at a resolution infeasible by microscopy. However, for interpretation of 3C interaction data and identification of true interactions, 3C technology demands a stringent experimental setup and extreme caution.
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Affiliation(s)
- Suraj Jamge
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Plant Research, Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G. H. Immink
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Plant Research, Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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87
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Smaczniak C, Muiño JM, Chen D, Angenent GC, Kaufmann K. Differences in DNA Binding Specificity of Floral Homeotic Protein Complexes Predict Organ-Specific Target Genes. THE PLANT CELL 2017; 29:1822-1835. [PMID: 28733422 PMCID: PMC5590503 DOI: 10.1105/tpc.17.00145] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/30/2017] [Accepted: 07/18/2017] [Indexed: 05/20/2023]
Abstract
Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors. However, how these factors achieve their regulatory specificities is still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high-throughput DNA sequencing (SELEX-seq) on several floral MADS domain protein homo- and heterodimers to measure their DNA binding specificities. We show that specification of reproductive organs is associated with distinct binding preferences of a complex formed by SEPALLATA3 and AGAMOUS. Binding specificity is further modulated by different binding site spacing preferences. Combination of SELEX-seq and genome-wide DNA binding data allows differentiation between targets in specification of reproductive versus perianth organs in the flower. We validate the importance of DNA binding specificity for organ-specific gene regulation by modulating promoter activity through targeted mutagenesis. Our study shows that intrafamily protein interactions affect DNA binding specificity of floral MADS domain proteins. Differential DNA binding of MADS domain protein complexes plays a role in the specificity of target gene regulation.
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Affiliation(s)
- Cezary Smaczniak
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708PB, The Netherlands
- Institute for Biochemistry and Biology, Potsdam University, Potsdam 14476, Germany
| | - Jose M Muiño
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Dijun Chen
- Institute for Biochemistry and Biology, Potsdam University, Potsdam 14476, Germany
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708PB, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen 6708PB, The Netherlands
| | - Kerstin Kaufmann
- Institute for Biochemistry and Biology, Potsdam University, Potsdam 14476, Germany
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88
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Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1020008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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89
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You Y, Sawikowska A, Neumann M, Posé D, Capovilla G, Langenecker T, Neher RA, Krajewski P, Schmid M. Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering. Nat Commun 2017; 8:15120. [PMID: 28513600 PMCID: PMC5442315 DOI: 10.1038/ncomms15120] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 03/01/2017] [Indexed: 02/04/2023] Open
Abstract
Plants can produce organs throughout their entire life from pluripotent stem cells located at their growing tip, the shoot apical meristem (SAM). At the time of flowering, the SAM of Arabidopsis thaliana switches fate and starts producing flowers instead of leaves. Correct timing of flowering in part determines reproductive success, and is therefore under environmental and endogenous control. How epigenetic regulation contributes to the floral transition has eluded analysis so far, mostly because of the poor accessibility of the SAM. Here we report the temporal dynamics of the chromatin modifications H3K4me3 and H3K27me3 and their correlation with transcriptional changes at the SAM in response to photoperiod-induced flowering. Emphasizing the importance of tissue-specific epigenomic analyses we detect enrichments of chromatin states in the SAM that were not apparent in whole seedlings. Furthermore, our results suggest that regulation of translation might be involved in adjusting meristem function during the induction of flowering. When plants flower, the shoot apical meristem switches fate to produce floral organs instead of leaves. Here You et al. perform tissue-specific epigenome profiling and show that during this transition changes in histone methylation are correlated with transcriptional responses in the meristem.
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Affiliation(s)
- Yuan You
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Aneta Sawikowska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - David Posé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Giovanna Capovilla
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Tobias Langenecker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Richard A Neher
- Evolutionary Dynamics and Biophysics Group, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.,Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
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90
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van Dijk ADJ, Molenaar J. Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time. PeerJ 2017; 5:e3197. [PMID: 28439467 PMCID: PMC5399868 DOI: 10.7717/peerj.3197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/17/2017] [Indexed: 11/20/2022] Open
Abstract
The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral pathway integrator genes. At a quantitative level, it is currently unclear how the impact of genetic variation in signaling pathways on flowering time is mediated by floral pathway integrator genes. Here, using datasets available from literature, we connect Arabidopsis thaliana flowering time in genetic backgrounds varying in upstream signalling components with the expression levels of floral pathway integrator genes in these genetic backgrounds. Our modelling results indicate that flowering time depends in a quite linear way on expression levels of floral pathway integrator genes. This gradual, proportional response of flowering time to upstream changes enables a gradual adaptation to changing environmental factors such as temperature and light.
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Affiliation(s)
- Aalt D J van Dijk
- Biometris, Department for Mathematical and Statistical Methods, Wageningen University, Wageningen, The Netherlands.,Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands.,Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Jaap Molenaar
- Biometris, Department for Mathematical and Statistical Methods, Wageningen University, Wageningen, The Netherlands
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91
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Aghamirzaie D, Raja Velmurugan K, Wu S, Altarawy D, Heath LS, Grene R. Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data. F1000Res 2017; 6:372. [PMID: 28529706 PMCID: PMC5414811 DOI: 10.12688/f1000research.10041.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 11/20/2022] Open
Abstract
Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though
in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential. Results: We present Expresso (database and webserver) as a tool for the collection and integration of available
Arabidopsis ChIP-Seq peak data, which in turn can be linked to a user’s gene expression data. Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets. Expresso currently provides three services: 1) Identification of target genes of a given transcription factor; 2) Identification of transcription factors that regulate a gene of interest; 3) Computation of correlation between the gene expression of transcription factors and their target genes. Availability: Expresso is freely available at
http://bioinformatics.cs.vt.edu/expresso/
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Affiliation(s)
- Delasa Aghamirzaie
- Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA, 24061, USA
| | - Karthik Raja Velmurugan
- Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA, 24061, USA.,Center for Bioinformatics and Genetics and the Primary Care Research Network, Edward Via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA
| | - Shuchi Wu
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Doaa Altarawy
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
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92
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Ou CG, Mao JH, Liu LJ, Li CJ, Ren HF, Zhao ZW, Zhuang FY. Characterising genes associated with flowering time in carrot (Daucus carota L.) using transcriptome analysis. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:286-297. [PMID: 27775866 DOI: 10.1111/plb.12519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/19/2016] [Indexed: 05/24/2023]
Abstract
Carrot is generally regarded as a biennial plant with an obligatory vernalization requirement. Early spring cultivation makes plants vulnerable to premature bolting, which results in a loss of commercial value. However, our knowledge of flowering time genes and flowering mechanisms in carrot remain limited. Bolting behavior of D. carota ssp. carota 'Songzi', a wild species sensitive to flower induction by vernalization and photoperiod, and orange cultivar 'Amsterdam forcing', and their offspring were investigated in different growing conditions. We performed RNA-seq to identify the flowering time genes, and digital gene expression (DGE) analysis to examine their expression levels. The circadian patterns of related genes were identified by qPCR. The results showed bolting behavior of carrot was influenced by low temperature, illumination intensity and photoperiod. A total of 45 flowering time-related unigenes were identified, which were classified into five categories including photoperiod, vernalization, autonomous and gibberellin pathway, and floral integrators. Homologs of LATE ELONGATED HYPOCOTYL (LHY) and CONSTANS-LIKE 2 (COL2) were more highly expressed under short day condition than under long day condition. Homologs of COL2, CONSTANS-LIKE 5 (COL5), SUPPRESSION OF OVEREXPRESSION OF CONSTANS 1 (SOC1), FLOWERING LOCUS C (FLC) and GIBBERELLIC ACID INSENSITIVE (GAI) were differentially expressed between 'Songzi' and 'Amsterdam forcing'. The homolog of COL2 (Dct43207) was repressed by light, but that of COL5 (Dct20940) was induced. A preliminary model of genetic network controlling flowering time was constructed by associating the results of DGE analysis with correlation coefficients between genes. This study provides useful information for further investigating the genetic mechanism of flowering in carrot.
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Affiliation(s)
- C-G Ou
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - J-H Mao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - L-J Liu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - C-J Li
- Suzhou Academy of Agricultural Science, Suzhou, Anhui, China
| | - H-F Ren
- Suzhou Academy of Agricultural Science, Suzhou, Anhui, China
| | - Z-W Zhao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - F-Y Zhuang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
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93
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Chen J, Zhu X, Ren J, Qiu K, Li Z, Xie Z, Gao J, Zhou X, Kuai B. Suppressor of Overexpression of CO 1 Negatively Regulates Dark-Induced Leaf Degreening and Senescence by Directly Repressing Pheophytinase and Other Senescence-Associated Genes in Arabidopsis. PLANT PHYSIOLOGY 2017; 173:1881-1891. [PMID: 28096189 PMCID: PMC5338665 DOI: 10.1104/pp.16.01457] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/16/2017] [Indexed: 05/22/2023]
Abstract
Although the biochemical pathway of chlorophyll (Chl) degradation has been largely elucidated, how Chl is rapidly yet coordinately degraded during leaf senescence remains elusive. Pheophytinase (PPH) is the enzyme for catalyzing the removal of the phytol group from pheophytin a, and PPH expression is significantly induced during leaf senescence. To elucidate the transcriptional regulation of PPH, we used a yeast (Saccharomyces cerevisiae) one-hybrid system to screen for its trans-regulators. SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), a key flowering pathway integrator, was initially identified as one of the putative trans-regulators of PPH After dark treatment, leaves of an SOC1 knockdown mutant (soc1-6) showed an accelerated yellowing phenotype, whereas those of SOC1-overexpressing lines exhibited a partial stay-green phenotype. SOC1 and PPH expression showed a negative correlation during leaf senescence. Substantially, SOC1 protein could bind specifically to the CArG box of the PPH promoter in vitro and in vivo, and overexpression of SOC1 significantly inhibited the transcriptional activity of the PPH promoter in Arabidopsis (Arabidopsis thaliana) protoplasts. Importantly, soc1-6 pph-1 (a PPH knockout mutant) double mutant displayed a stay-green phenotype similar to that of pph-1 during dark treatment. These results demonstrated that SOC1 inhibits Chl degradation via negatively regulating PPH expression. In addition, measurement of the Chl content and the maximum photochemical efficiency of photosystem II of soc1-6 and SOC1-OE leaves after dark treatment suggested that SOC1 also negatively regulates the general senescence process. Seven SENESCENCE-ASSOCIATED GENES (SAGs) were thereafter identified as its potential target genes, and NONYELLOWING1 and SAG113 were experimentally confirmed. Together, we reveal that SOC1 represses dark-induced leaf Chl degradation and senescence in general in Arabidopsis.
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Affiliation(s)
- Junyi Chen
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoyu Zhu
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Ren
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Kai Qiu
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhongpeng Li
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zuokun Xie
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiong Gao
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin Zhou
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Benke Kuai
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
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94
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Khanday I, Das S, Chongloi GL, Bansal M, Grossniklaus U, Vijayraghavan U. Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties. PLANT PHYSIOLOGY 2016; 172:372-88. [PMID: 27457124 PMCID: PMC5074623 DOI: 10.1104/pp.16.00789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/23/2016] [Indexed: 05/04/2023]
Abstract
OsMADS1 controls rice (Oryza sativa) floral fate and organ development. Yet, its genome-wide targets and the mechanisms underlying its role as a transcription regulator controlling developmental gene expression are unknown. We identify 3112 gene-associated OsMADS1-bound sites in the floret genome. These occur in the vicinity of transcription start sites, within gene bodies, and in intergenic regions. Majority of the bound DNA contained CArG motif variants or, in several cases, only A-tracts. Sequences flanking the binding peak had a higher AT nucleotide content, implying that broader DNA structural features may define in planta binding. Sequences for binding by other transcription factor families like MYC, AP2/ERF, bZIP, etc. are enriched in OsMADS1-bound DNAs. Target genes implicated in transcription, chromatin remodeling, cellular processes, and hormone metabolism were enriched. Combining expression data from OsMADS1 knockdown florets with these DNA binding data, a snapshot of a gene regulatory network was deduced where targets, such as AP2/ERF and bHLH transcription factors and chromatin remodelers form nodes. We show that the expression status of these nodal factors can be altered by inducing the OsMADS1-GR fusion protein and present a model for a regulatory cascade where the direct targets of OsMADS1, OsbHLH108/SPT, OsERF034, and OsHSF24, in turn control genes such as OsMADS32 and OsYABBY5 This cascade, with other similar relationships, cumulatively contributes to floral organ development. Overall, OsMADS1 binds to several regulatory genes and, probably in combination with other factors, controls a gene regulatory network that ensures rice floret development.
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Affiliation(s)
- Imtiyaz Khanday
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Sanjukta Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Grace L Chongloi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Manju Bansal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Ueli Grossniklaus
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
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95
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Integrative effect of drought and low temperature on litchi (Litchi chinensis Sonn.) floral initiation revealed by dynamic genome-wide transcriptome analysis. Sci Rep 2016; 6:32005. [PMID: 27557749 PMCID: PMC4997319 DOI: 10.1038/srep32005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/01/2016] [Indexed: 12/23/2022] Open
Abstract
Floral induction in litchi is influenced by multiple environment cues including temperature and soil water condition. In the present study, we determined that a combined treatment consisting of 14-day drought imposed prior to exposure to 35-day low temperature (T3) significantly promoted litchi flowering relative to the low temperature alone (T2), suggesting an integrative effect of drought and low temperature on litchi floral initiation. Analysis of transcriptomic changes in leaves from different treatments showed that 2,198 and 4,407 unigenes were differentially expressed in response to drought and low temperature, respectively. 1,227 of these unigenes were expressed in response to both treatments, implying an interaction of drought and low temperature on expression of genes involved in litchi floral initiation. Additionally, 932 unigenes were consistently differentially expressed during floral induction between T2 and T3 plants, which potentially accounts for the difference of flowering time. Thirty-eight transcription factors out of these 932 unigenes were identified as hub genes with central roles in regulation of litchi floral induction. The expression of litchi homologs of well-known flowering genes was also investigated, and one Flowering Locus T (FT) homolog may play a crucial role in litchi flowering in responses to drought and low temperature.
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96
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Abstract
One of the central goals in biology is to understand how and how much of the phenotype of an organism is encoded in its genome. Although many genes that are crucial for organismal processes have been identified, much less is known about the genetic bases underlying quantitative phenotypic differences in natural populations. We discuss the fundamental gap between the large body of knowledge generated over the past decades by experimental genetics in the laboratory and what is needed to understand the genotype-to-phenotype problem on a broader scale. We argue that systems genetics, a combination of systems biology and the study of natural variation using quantitative genetics, will help to address this problem. We present major advances in these two mostly disconnected areas that have increased our understanding of the developmental processes of flowering time control and root growth. We conclude by illustrating and discussing the efforts that have been made toward systems genetics specifically in plants.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
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97
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Beydler B, Osadchuk K, Cheng CL, Manak JR, Irish EE. The Juvenile Phase of Maize Sees Upregulation of Stress-Response Genes and Is Extended by Exogenous Jasmonic Acid. PLANT PHYSIOLOGY 2016; 171:2648-58. [PMID: 27307257 PMCID: PMC4972259 DOI: 10.1104/pp.15.01707] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 06/08/2016] [Indexed: 05/05/2023]
Abstract
As maize (Zea mays) plants undergo vegetative phase change from juvenile to adult, they both exhibit heteroblasty, an abrupt change in patterns of leaf morphogenesis, and gain the ability to produce flowers. Both processes are under the control of microRNA156 (miR156), whose levels decline at the end of the juvenile phase. Gain of the ability to flower is conferred by the expression of miR156 targets that encode SQUAMOSA PROMOTER-BINDING transcription factors, which, when derepressed in the adult phase, induce the expression of MADS box transcription factors that promote maturation and flowering. How gene expression, including targets of those microRNAs, differs between the two phases remains an open question. Here, we compare transcript levels in primordia that will develop into juvenile or adult leaves to identify genes that define these two developmental states and may influence vegetative phase change. In comparisons among successive leaves at the same developmental stage, plastochron 6, three-fourths of approximately 1,100 differentially expressed genes were more highly expressed in primordia of juvenile leaves. This juvenile set was enriched in photosynthetic genes, particularly those associated with cyclic electron flow at photosystem I, and in genes involved in oxidative stress and retrograde redox signaling. Pathogen- and herbivory-responsive pathways including salicylic acid and jasmonic acid also were up-regulated in juvenile primordia; indeed, exogenous application of jasmonic acid delayed both the appearance of adult traits and the decline in the expression of miR156-encoding loci in maize seedlings. We hypothesize that the stresses associated with germination promote juvenile patterns of differentiation in maize.
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Affiliation(s)
- Benjamin Beydler
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Krista Osadchuk
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Chi-Lien Cheng
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - J Robert Manak
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Erin E Irish
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
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98
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Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:95-105. [PMID: 27487457 DOI: 10.1016/j.bbagrm.2016.07.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/23/2022]
Abstract
Reproductive development in plants is controlled by complex and intricate gene-regulatory networks of transcription factors. These networks integrate the information from endogenous, hormonal and environmental regulatory pathways. Many of the key players have been identified in Arabidopsis and other flowering plant species, and their interactions and molecular modes of action are being elucidated. An emerging theme is that there is extensive crosstalk between different pathways, which can be accomplished at the molecular level by modulation of transcription factor activity or of their downstream targets. In this review, we aim to summarize current knowledge on transcription factors and epigenetic regulators that control basic developmental programs during inflorescence and flower morphogenesis in the model plant Arabidopsis thaliana. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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99
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Margaritopoulou T, Kryovrysanaki N, Megkoula P, Prassinos C, Samakovli D, Milioni D, Hatzopoulos P. HSP90 canonical content organizes a molecular scaffold mechanism to progress flowering. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:174-87. [PMID: 27121421 DOI: 10.1111/tpj.13191] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 05/28/2023]
Abstract
Highly interactive signaling processes constitute a set of parameters intertwining in a continuum mode to shape body formation and development. A sophisticated gene network is required to integrate environmental and endogenous cues in order to modulate flowering. However, the molecular mechanisms that coordinate the circuitries of flowering genes remain unclear. Here using complemented experimental approaches, we uncover the decisive and essential role of HEAT SHOCK PROTEIN 90 (HSP90) in restraining developmental noise to an acceptable limit. Localized depletion of HSP90 mRNAs in the shoot apex resulted in low penetrance of vegetative-to-reproductive phase transition and completely abolished flower formation. Extreme variation in expression of flowering genes was also observed in HSP90 mRNA-depleted transformed plants. Transient heat-shock treatments moderately increased HSP90 mRNA levels and rescued flower arrest. The offspring had a low, nevertheless noticeable failure to promote transition from vegetative into the reproductive phase and showed flower morphological heterogeneity. In floral tissues a moderate variation in HSP90 transcript levels and in the expression of flowering genes was detected. Key flowering proteins comprised clientele of the molecular chaperone demonstrating that the HSP90 is essential during vegetative-to-reproductive phase transition and flower development. Our results uncover that HSP90 consolidates a molecular scaffold able to arrange and organize flowering gene network and protein circuitry, and effectively counterbalance the extent to which developmental noise perturbs phenotypic traits.
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Affiliation(s)
- Theoni Margaritopoulou
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Nikoleta Kryovrysanaki
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Panagiota Megkoula
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Constantinos Prassinos
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Despoina Samakovli
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Dimitra Milioni
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Polydefkis Hatzopoulos
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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100
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Ye L, Wang B, Zhang W, Shan H, Kong H. Gains and Losses of Cis-regulatory Elements Led to Divergence of the Arabidopsis APETALA1 and CAULIFLOWER Duplicate Genes in the Time, Space, and Level of Expression and Regulation of One Paralog by the Other. PLANT PHYSIOLOGY 2016; 171:1055-69. [PMID: 27208240 PMCID: PMC4902614 DOI: 10.1104/pp.16.00320] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/04/2016] [Indexed: 05/05/2023]
Abstract
How genes change their expression patterns over time is still poorly understood. Here, by conducting expression, functional, bioinformatic, and evolutionary analyses, we demonstrate that the differences between the Arabidopsis (Arabidopsis thaliana) APETALA1 (AP1) and CAULIFLOWER (CAL) duplicate genes in the time, space, and level of expression were determined by the presence or absence of functionally important transcription factor-binding sites (TFBSs) in regulatory regions. In particular, a CArG box, which is the autoregulatory site of AP1 that can also be bound by the CAL protein, is a key determinant of the expression differences. Because of the CArG box, AP1 is both autoregulated and cross-regulated (by AP1 and CAL, respectively), and its relatively high-level expression is maintained till to the late stages of sepal and petal development. The observation that the CArG box was gained recently further suggests that the autoregulation and cross-regulation of AP1, as well as its function in sepal and petal development, are derived features. By comparing the evolutionary histories of this and other TFBSs, we further indicate that the divergence of AP1 and CAL in regulatory regions has been markedly asymmetric and can be divided into several stages. Specifically, shortly after duplication, when AP1 happened to be the paralog that maintained the function of the ancestral gene, CAL experienced certain degrees of degenerate evolution, in which several functionally important TFBSs were lost. Later, when functional divergence allowed the survival of both paralogs, CAL remained largely unchanged in expression, whereas the functions of AP1 were gradually reinforced by gains of the CArG box and other TFBSs.
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Affiliation(s)
- Lingling Ye
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
| | - Bin Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
| | - Wengen Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
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