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Benyó D, Bató E, Faragó D, Rigó G, Domonkos I, Labhane N, Zsigmond L, Prasad M, Nagy I, Szabados L. The zinc finger protein 3 of Arabidopsis thaliana regulates vegetative growth and root hair development. FRONTIERS IN PLANT SCIENCE 2024; 14:1221519. [PMID: 38250442 PMCID: PMC10796524 DOI: 10.3389/fpls.2023.1221519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024]
Abstract
Introduction Zinc finger protein 3 (ZFP3) and closely related C2H2 zinc finger proteins have been identified as regulators of abscisic acid signals and photomorphogenic responses during germination. Whether ZFP3 and related ZFP factors regulate plant development is, however, not known. Results ZFP3 overexpression reduced plant growth, limited cell expansion in leaves, and compromised root hair development. The T-DNA insertion zfp3 mutant and transgenic lines with silenced ZFP1, ZFP3, ZFP4, and ZFP7 genes were similar to wild-type plants or had only minor differences in plant growth and morphology, probably due to functional redundancy. RNAseq transcript profiling identified ZFP3-controlled gene sets, including targets of ABA signaling with reduced transcript abundance. The largest gene set that was downregulated by ZFP3 encoded regulatory and structural proteins in cell wall biogenesis, cell differentiation, and root hair formation. Chromatin immunoprecipitation confirmed ZFP3 binding to several target promoters. Discussion Our results suggest that ZFP3 and related ZnF proteins can modulate cellular differentiation and plant vegetative development by regulating the expression of genes implicated in cell wall biogenesis.
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Affiliation(s)
- Dániel Benyó
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Emese Bató
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Dóra Faragó
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Gábor Rigó
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Ildikó Domonkos
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Nitin Labhane
- Department of Botany, Bhavan’s College, Mumbai, Maharashtra, India
| | - Laura Zsigmond
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Melvin Prasad
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - István Nagy
- Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- SeqOmics Biotechnology Ltd, Mórahalom, Hungary
| | - László Szabados
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
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Panahabadi R, Ahmadikhah A, Farrokhi N. Genetic dissection of monosaccharides contents in rice whole grain using genome-wide association study. THE PLANT GENOME 2023; 16:e20292. [PMID: 36691363 DOI: 10.1002/tpg2.20292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
The simplest form of carbohydrates are monosaccharides which are the building blocks for the synthesis of polymers or complex carbohydrates. Monosaccharide contents of 197 rice accessions were quantified by HPAEC-PAD in rice (Oryza sativa L.) whole grain (RWG). A genome-wide association study (GWAS) was carried out using 33,812 single nucleotide polymorphisms (SNPs) to identify corresponding genomic regions influencing neutral monosaccharides contents. In total, 49 GWAS signals contained in 17 genomic regions (quantitative trait loci [QTLs]) on seven chromosomes of rice were determined to be associated with monosaccharides contents of whole grain. The QTLs were found for fucose (1), mannose (1), xylose (2), arabinose (2), galactose (4), and rhamnose (7) contents, all of which are novel. Based on co-location of annotated rice genes in the vicinity of GWAS signals, the constituents of the whole grain were associated with the following candidate genes: arabinose content with α-N-arabinofuranosidase, pectinesterase inhibitor, and glucosamine-fructose-6-phosphate aminotransferase 1; xylose content with ZOS1-10 (a C2H2 zinc finger transcription factor [TF]); mannose content with aldose 1-epimerase-like protein and a MYB family TF; galactose content with a GT8 family member (galacturonosyltransferase-like 3), a GRAS family TF, and a GH16 family member (xyloglucan endotransglucosylase/hydrolase xyloglucan 23); fucose content with gibberellin 20 oxidase and a lysine-rich arabinogalactan protein 19, and finally rhamnose content with myo-inositol-1-phosphate synthase, UDP-arabinopyranose mutase, and COBRA-like protein precursor. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in the biosynthesis, regulation, and turnover of monosaccharides in RWG, aiming to enhance the nutritional value of rice grain and impact the related industries.
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Affiliation(s)
- Rahele Panahabadi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
| | | | - Naser Farrokhi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
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Selva C, Yang X, Shirley NJ, Whitford R, Baumann U, Tucker MR. HvSL1 and HvMADS16 promote stamen identity to restrict multiple ovary formation in barley. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5039-5056. [PMID: 37279531 PMCID: PMC10498024 DOI: 10.1093/jxb/erad218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 06/01/2023] [Indexed: 06/08/2023]
Abstract
Correct floral development is the result of a sophisticated balance of molecular cues. Floral mutants provide insight into the main genetic determinants that integrate these cues, as well as providing opportunities to assess functional variation across species. In this study, we characterize the barley (Hordeum vulgare) multiovary mutants mov2.g and mov1, and propose causative gene sequences: a C2H2 zinc-finger gene HvSL1 and a B-class gene HvMADS16, respectively. In the absence of HvSL1, florets lack stamens but exhibit functional supernumerary carpels, resulting in multiple grains per floret. Deletion of HvMADS16 in mov1 causes homeotic conversion of lodicules and stamens into bract-like organs and carpels that contain non-functional ovules. Based on developmental, genetic, and molecular data, we propose a model by which stamen specification in barley is defined by HvSL1 acting upstream of HvMADS16. The present work identifies strong conservation of stamen formation pathways with other cereals, but also reveals intriguing species-specific differences. The findings lay the foundation for a better understanding of floral architecture in Triticeae, a key target for crop improvement.
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Affiliation(s)
- Caterina Selva
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Xiujuan Yang
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Neil J Shirley
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Ryan Whitford
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Ute Baumann
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Matthew R Tucker
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
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Mao X, Zheng X, Chen W, Li C. Characterization and Gene Mapping of an Open-Glume Oryza sativa L. Mutant. Int J Mol Sci 2023; 24:12702. [PMID: 37628883 PMCID: PMC10454609 DOI: 10.3390/ijms241612702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Floral organ development determines agricultural productivity by affecting seed development, seed quality, and final yield. In this study, we described the novel ogl mutant in rice (Oryza sativa L.), which is characterized by an open-glume phenotype, increased pistil number, reduced stamen number, decreased seed setting rate, and smaller rice grains. Genetic analysis showed that the open-glume phenotype might be controlled by a recessive qualitative trait locus. Employing bulked segregant analysis (BSA), one candidate region was identified on rice chromosome 1. The glume opening phenotype cosegregated with SNP (Chr1:1522703), which was located at the start codon of one transcript of OsJAG, resulting in partial loss of OsJAG function. cDNA analysis revealed that OsJAG encodes two transcript variants. Compared to normal plants, the expression of OsJAG.1 was upregulated in open-glume plants. When investigating the glume phenotype, we found that the expression of genes related to floral development changed greatly in open-glume plants. Taken together, this work increases our understanding of the developmental role of OsJAG in rice floral development.
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Affiliation(s)
- Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Xiaoyu Zheng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
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Wang Y, Wang G, Lin D, Luo Q, Xu W, Qu S. QTL mapping and stability analysis of trichome density in zucchini ( Cucurbita pepo L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1232154. [PMID: 37636121 PMCID: PMC10457680 DOI: 10.3389/fpls.2023.1232154] [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: 05/31/2023] [Accepted: 07/06/2023] [Indexed: 08/29/2023]
Abstract
Trichomes provide an excellent model for studying cell differentiation and proliferation. The aboveground tissues of plants with long dense trichomes (LDTs) can cause skin itching in people working in a zucchini field, in which management, pollination, and fruit harvesting are difficult. In this study, an F2 population was constructed with the LDT inbred line "16" and the sparse micro trichome (SMT) inbred line "63" for QTL analysis of type I and II trichome density. Two QTLs were identified on chromosomes 3 and 15 using the QTL-seq method. Additionally, 191 InDel markers were developed on 20 chromosomes, a genetic map was constructed for QTL mapping, and three QTLs were identified on chromosomes 3, 6, and 15. Two QTLs, CpTD3.1 and CpTD15.1, were identified in both QTL-seq and genetic map-based QTL analyses, and CpTD15.1 was the major-effect QTL. The stability of CpTD3.1 and CpTD15.1 was confirmed using data from F2 plants under different environmental conditions. The major-effect QTL CpTD15.1 was located between markers chr15-4991349 and chr15-5766791, with a physical distance of 775.44 kb, and explained 12.71%-29.37% of the phenotypic variation observed in the three environments. CpTD3.1 was located between markers chr3-218350 and chr3-2891236, in a region with a physical distance of 2,672.89 kb, and explained 5.00%-10.64% of the phenotypic variation observed in the three environments. The functional annotations of the genes within the CpTD15.1 region were predicted, and five genes encoding transcription factors regulating trichome development were selected. Cp4.1LG15g04400 encoded zinc finger protein (ZFP) and harbored nonsynonymous SNPs in the conserved ring finger domain between the two parental lines. There were significant differences in Cp4.1LG15g04400 expression between "16" and "63", and a similar pattern was found between germplasm resources of LDT lines and SMT lines. It was presumed that Cp4.1LG15g04400 might regulate trichome density in zucchini. These results lay a foundation for better understanding the density of multicellular nonglandular trichomes and the regulatory mechanism of trichome density in zucchini.
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Affiliation(s)
- Yunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Guichao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Dongjuan Lin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Qinfen Luo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Wenlong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Shuping Qu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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Bobadilla LK, Baek Y, Tranel PJ. Comparative transcriptomic analysis of male and females in the dioecious weeds Amaranthus palmeri and Amaranthus tuberculatus. BMC PLANT BIOLOGY 2023; 23:339. [PMID: 37365527 DOI: 10.1186/s12870-023-04286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and Palmer amaranth (Amaranthus palmeri S. Wats.) are two dioecious and important weed species in the world that can rapidly evolve herbicide-resistance traits. Understanding these two species' dioecious and sex-determination mechanisms could open opportunities for new tools to control them. This study aims to identify the differential expression patterns between males and females in A. tuberculatus and A. palmeri. Multiple analyses, including differential expression, co-expression, and promoter analyses, used RNA-seq data from multiple tissue types to identify putative essential genes for sex determination in both dioecious species. RESULTS Genes were identified as potential key players for sex determination in A. palmeri. Genes PPR247, WEX, and ACD6 were differentially expressed between the sexes and located at scaffold 20 within or near the male-specific Y (MSY) region. Multiple genes involved with flower development were co-expressed with these three genes. For A. tuberculatus, no differentially expressed gene was identified within the MSY region; however, multiple autosomal class B and C genes were identified as differentially expressed and possible candidate genes. CONCLUSIONS This is the first study comparing the global expression profile between males and females in dioecious weedy Amaranthus species. Results narrow down putative essential genes for sex-determination in A. palmeri and A. tuberculatus and also strengthen the hypothesis of two different evolutionary events for dioecy within the genus.
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Affiliation(s)
- Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Yousoon Baek
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
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Abiri N, Sinjushin A, Tekdal D, Cetiner S. Evaluation of the Possible Contribution of Various Regulatory Genes to Determination of Carpel Number as a Potential Mechanism for Optimal Agricultural Yield. Int J Mol Sci 2022; 23:ijms23179723. [PMID: 36077121 PMCID: PMC9456115 DOI: 10.3390/ijms23179723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Various regulatory genes encoding transcription factors and miRNAs regulate carpel number. Multicarpelly is normally associated with increased size of the floral meristem, and several genetic factors have been discovered that influence this characteristic. A fundamental understanding of the regulatory genes affecting carpel number can facilitate strategies for agricultural yield improvement, which is crucial, given that the global population is growing rapidly. A multicarpellate plant may provide a significantly higher yield than a plant bearing fewer carpels. Higher yields can be achieved via various means; in this review, we provide an overview of the current knowledge of the various regulatory factors that contribute to multicarpelly and the potential of increasing carpel number to achieve an increased yield.
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Affiliation(s)
- Naghmeh Abiri
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
- Correspondence: ; Tel.: +90-5457874622
| | - Andrey Sinjushin
- Department of Genetics, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119234 Moscow, Russia
| | - Dilek Tekdal
- Faculty of Science and Letters, Department of Biotechnology, Mersin University, 33343 Mersin, Turkey
| | - Selim Cetiner
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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Poulin V, Amesefe D, Gonzalez E, Alexandre H, Joly S. Testing candidate genes linked to corolla shape variation of a pollinator shift in Rhytidophyllum (Gesneriaceae). PLoS One 2022; 17:e0267540. [PMID: 35853078 PMCID: PMC9295946 DOI: 10.1371/journal.pone.0267540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Floral adaptations to specific pollinators like corolla shape variation often result in reproductive isolation and thus speciation. But despite their ecological importance, the genetic bases of corolla shape transitions are still poorly understood, especially outside model species. Hence, our goal was to identify candidate genes potentially involved in corolla shape variation between two closely related species of the Rhytidophyllum genus (Gesneriaceae family) from the Antilles with contrasting pollination strategies. Rhytidophyllum rupincola has a tubular corolla and is strictly pollinated by hummingbirds, whereas R. auriculatum has more open flowers and is pollinated by hummingbirds, bats, and insects. We surveyed the literature and used a comparative transcriptome sequence analysis of synonymous and non-synonymous nucleotide substitutions to obtain a list of genes that could explain floral variation between R. auriculatum and R. rupincola. We then tested their association with corolla shape variation using QTL mapping in a F2 hybrid population. Out of 28 genes tested, three were found to be good candidates because of a strong association with corolla shape: RADIALIS, GLOBOSA, and JAGGED. Although the role of these genes in Rhytidophyllum corolla shape variation remains to be confirmed, these findings are a first step towards identifying the genes that have been under selection by pollinators and thus involved in reproductive isolation and speciation in this genus.
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Affiliation(s)
- Valérie Poulin
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Delase Amesefe
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Emmanuel Gonzalez
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Department of Human Genetics, Canadian Centre for Computational Genomics (C3G), McGill University, Montréal, QC, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
| | - Hermine Alexandre
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Simon Joly
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Montreal Botanical Garden, Montréal, Canada
- * E-mail:
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Hernández MA, Butler JB, Ammitzboll H, Weller JL, Vaillancourt RE, Potts BM. Genetic control of the operculum and capsule morphology of Eucalyptus globulus. ANNALS OF BOTANY 2022; 130:97-108. [PMID: 35652517 PMCID: PMC9295918 DOI: 10.1093/aob/mcac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS The petaline operculum that covers the inner whorls until anthesis and the woody capsule that develops after fertilization are reproductive structures of eucalypts that protect the flower and seeds. Although they are distinct organs, they both develop from flower buds and this common ontogeny suggests shared genetic control. In Eucalyptus globulus their morphology is variable and we aimed to identify the quantitative trait loci (QTL) underlying this variation and determine whether there is common genetic control of these ecologically and taxonomically important reproductive structures. METHODS Samples of opercula and capsules were collected from 206 trees that belong to a large outcrossed F2E. globulus mapping population. The morphological variation in these structures was characterized by measuring six operculum and five capsule traits. QTL analysis was performed using these data and a linkage map consisting of 480 markers. KEY RESULTS A total of 27 QTL were detected for operculum traits and 28 for capsule traits, with the logarithm of odds ranging from 2.8 to 11.8. There were many co-located QTL associated with operculum or capsule traits, generally reflecting allometric relationships. A key finding was five genomic regions where co-located QTL affected both operculum and capsule morphology, and the overall trend for these QTL was to affect elongation of both organs. Some of these QTL appear to have a significant effect on the phenotype, with the strongest QTL explaining 26.4 % of the variation in operculum shape and 16.4 % in capsule shape. Flower bud measurements suggest the expression of these QTL starts during bud development. Several candidate genes were found associated with the QTL and their putative function is discussed. CONCLUSIONS Variation in both operculum and capsule traits in E. globulus is under strong genetic control. Our results suggest that these reproductive structures share a common genetic pathway during flower bud development.
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Affiliation(s)
- Mariano A Hernández
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Route 27 - Km 38.3, Bella Vista, Corrientes 3432, Argentina
| | | | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture
| | - René E Vaillancourt
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Brad M Potts
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
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Han J, Ma Z, Chen L, Wang Z, Wang C, Wang L, Chen C, Ren Z, Cao C. Morphological Characterization and Integrated Transcriptome and Proteome Analysis of Organ Development Defective 1 ( odd1) Mutant in Cucumis sativus L. Int J Mol Sci 2022; 23:ijms23105843. [PMID: 35628653 PMCID: PMC9145247 DOI: 10.3390/ijms23105843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/09/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Cucumber (Cucumis sativus L.) is an economically important vegetable crop with the unique growth habit and typical trailing shoot architecture of Cucurbitaceae. Elucidating the regulatory mechanisms of growth and development is significant for improving quality and productivity in cucumber. Here we isolated a spontaneous cucumber mutant organ development defective 1 (odd1) with multiple morphological changes including root, plant stature, stem, leaf, male and female flowers, as well as fruit. Anatomical and cytological analyses demonstrated that both cell size and number decreased, and the shoot apical meristem (SAM) was smaller in odd1 compared with WT. Pollen vigor and germination assays and cross tests revealed that odd1 is female sterile, which may be caused by the absence of ovules. Genetic analysis showed that odd1 is a recessive single gene mutant. Using the MutMap strategy, the odd1 gene was found to be located on chromosome 5. Integrated profiling of transcriptome and proteome indicated that the different expression genes related to hormones and SAM maintenance might be the reason for the phenotypic changes of odd1. These results expanded the insight into the molecular regulation of organ growth and development and provided a comprehensive reference map for further studies in cucumber.
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Silveira SR, Le Gloanec C, Gómez-Felipe A, Routier-Kierzkowska AL, Kierzkowski D. Live-imaging provides an atlas of cellular growth dynamics in the stamen. PLANT PHYSIOLOGY 2022; 188:769-781. [PMID: 34618064 PMCID: PMC8825458 DOI: 10.1093/plphys/kiab363] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Development of multicellular organisms is a complex process involving precise coordination of growth among individual cells. Understanding organogenesis requires measurements of cellular behaviors over space and time. In plants, such a quantitative approach has been successfully used to dissect organ development in both leaves and external floral organs, such as sepals. However, the observation of floral reproductive organs is hampered as they develop inside tightly closed floral buds, and are therefore difficult to access for imaging. We developed a confocal time-lapse imaging method, applied here to Arabidopsis (Arabidopsis thaliana), which allows full quantitative characterization of the development of stamens, the male reproductive organs. Our lineage tracing reveals the early specification of the filament and the anther. Formation of the anther lobes is associated with a temporal increase of growth at the lobe surface that correlates with intensive growth of the developing locule. Filament development is very dynamic and passes through three distinct phases: (1) initial intense, anisotropic growth, and high cell proliferation; (2) restriction of growth and proliferation to the filament proximal region; and (3) resumption of intense and anisotropic growth, displaced to the distal portion of the filament, without cell proliferation. This quantitative atlas of cellular growth dynamics provides a solid framework for future studies into stamen development.
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Affiliation(s)
- Sylvia R Silveira
- Department of Biological Sciences, IRBV, University of Montréal, Montréal, Quebec, Canada H1X 2B2
| | - Constance Le Gloanec
- Department of Biological Sciences, IRBV, University of Montréal, Montréal, Quebec, Canada H1X 2B2
| | - Andrea Gómez-Felipe
- Department of Biological Sciences, IRBV, University of Montréal, Montréal, Quebec, Canada H1X 2B2
| | | | - Daniel Kierzkowski
- Department of Biological Sciences, IRBV, University of Montréal, Montréal, Quebec, Canada H1X 2B2
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Zheng F, Cui L, Li C, Xie Q, Ai G, Wang J, Yu H, Wang T, Zhang J, Ye Z, Yang C. Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:228-244. [PMID: 34499170 DOI: 10.1093/jxb/erab417] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Trichomes are specialized glandular or non-glandular structures that provide physical or chemical protection against insect and pathogen attack. Trichomes in Arabidopsis have been extensively studied as typical non-glandular structures. By contrast, the molecular mechanism underlying glandular trichome formation and elongation remains largely unknown. We previously demonstrated that Hair is essential for the formation of type I and type VI trichomes. Here, we found that overexpression of Hair increased the density and length of tomato trichomes. Biochemical assays revealed that Hair physically interacts with its close homolog SlZFP8-like (SlZFP8L), and SlZFP8L also directly interacts with Woolly. SlZFP8L-overexpressing plants showed increased trichome density and length. We further found that the expression of SlZFP6, which encodes a C2H2 zinc finger protein, is positively regulated by Hair. Using chromatin immunoprecipitation, yeast one-hybrid, and dual-luciferase assays we identified that SlZFP6 is a direct target of Hair. Similar to Hair and SlZFP8L, the overexpression of SlZFP6 also increased the density and length of tomato trichomes. Taken together, our results suggest that Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato.
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Affiliation(s)
- Fangyan Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Long Cui
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Changxing Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Qingmin Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Guo Ai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Junqiang Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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13
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Gonçalves B. Case not closed: the mystery of the origin of the carpel. EvoDevo 2021; 12:14. [PMID: 34911578 PMCID: PMC8672599 DOI: 10.1186/s13227-021-00184-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/05/2021] [Indexed: 11/25/2022] Open
Abstract
The carpel is a fascinating structure that plays a critical role in flowering plant reproduction and contributed greatly to the evolutionary success and diversification of flowering plants. The remarkable feature of the carpel is that it is a closed structure that envelopes the ovules and after fertilization develops into the fruit which protects, helps disperse, and supports seed development into a new plant. Nearly all plant-based foods are either derived from a flowering plant or are a direct product of the carpel. Given its importance it's no surprise that plant and evolutionary biologists have been trying to explain the origin of the carpel for a long time. Before carpel evolution seeds were produced on open leaf-like structures that are exposed to the environment. When the carpel evolved in the stem lineage of flowering plants, seeds became protected within its closed structure. The evolutionary transition from that open precursor to the closed carpel remains one of the greatest mysteries of plant evolution. In recent years, we have begun to complete a picture of what the first carpels might have looked like. On the other hand, there are still many gaps in our understanding of what the precursor of the carpel looked like and what changes to its developmental mechanisms allowed for this evolutionary transition. This review aims to present an overview of existing theories of carpel evolution with a particular emphasis on those that account for the structures that preceded the carpel and/or present testable developmental hypotheses. In the second part insights from the development and evolution of diverse plant organs are gathered to build a developmental hypothesis for the evolutionary transition from a hypothesized laminar open structure to the closed structure of the carpel.
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14
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Li J, Zhang L, Yuan Y, Wang Q, Elbaiomy RG, Zhou W, Wu H, Soaud SA, Abbas M, Chen B, Zhao D, El-Sappah AH. In Silico Functional Prediction and Expression Analysis of C2H2 Zinc-Finger Family Transcription Factor Revealed Regulatory Role of ZmZFP126 in Maize Growth. Front Genet 2021; 12:770427. [PMID: 34804129 PMCID: PMC8602080 DOI: 10.3389/fgene.2021.770427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The C2H2-zinc finger proteins (ZFP) comprise a large family of transcription factors with various functions in biological processes. In maize, the function regulation of C2H2- zine finger (ZF) genes are poorly understood. We conducted an evolution analysis and functional prediction of the maize C2H2-ZF gene family. Furthermore, the ZmZFP126 gene has been cloned and sequenced for further favorable allelic variation discovery. The phylogenetic analysis of the C2H2-ZF domain indicated that the position and sequence of the C2H2-ZF domain of the poly-zinc finger gene are relatively conserved during evolution, and the C2H2-ZF domain with the same position is highly conserved. The expression analysis of the C2H2-ZF gene family in 11 tissues at different growth stages of B73 inbred lines showed that genes with multiple transcripts were endowed with more functions. The expression analysis of the C2H2-ZF gene in P1 and P2 inbred lines under drought conditions showed that the C2H2-ZF genes were mainly subjected to negative regulation under drought stress. Functional prediction indicated that the maize C2H2-ZF gene is mainly involved in reproduction and development, especially concerning the formation of important agronomic traits in maize yield. Furthermore, sequencing and correlation analysis of the ZmZFP126 gene indicated that this gene was significantly associated with the SDW-NAP and TDW-NAP. The analysis of the relationship between maize C2H2-ZF genes and C2H2-ZF genes with known functions indicated that the functions of some C2H2-ZF genes are relatively conservative, and the functions of homologous genes in different species are similar.
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Affiliation(s)
- Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Litian Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining, China
| | - Yibing Yuan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | | | - Wanhai Zhou
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Hui Wu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Bo Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Deming Zhao
- Yibin Academy of Agricultural Sciences, Yibin, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
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15
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Coordination of biradial-to-radial symmetry and tissue polarity by HD-ZIP II proteins. Nat Commun 2021; 12:4321. [PMID: 34262040 PMCID: PMC8280177 DOI: 10.1038/s41467-021-24550-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 06/21/2021] [Indexed: 11/15/2022] Open
Abstract
Symmetry establishment is a critical process in the development of multicellular organs and requires careful coordination of polarity axes while cells actively divide within tissues. Formation of the apical style in the Arabidopsis gynoecium involves a bilateral-to-radial symmetry transition, a stepwise process underpinned by the dynamic distribution of the plant morphogen auxin. Here we show that SPATULA (SPT) and the HECATE (HEC) bHLH proteins mediate the final step in the style radialisation process and synergistically control the expression of adaxial-identity genes, HOMEOBOX ARABIDOPSIS THALIANA 3 (HAT3) and ARABIDOPSIS THALIANA HOMEOBOX 4 (ATHB4). HAT3/ATHB4 module drives radialisation of the apical style by promoting basal-to-apical auxin flow and via a negative feedback mechanism that finetune auxin distribution through repression of SPT expression and cytokinin sensitivity. Thus, this work reveals the molecular basis of axes-coordination and hormonal cross-talk during the sequential steps of symmetry transition in the Arabidopsis style. The apical style in Arabidopsis is formed following a bilateral-to-radial symmetry transition in the gynoecium. Here the authors show that the final step in style radialization is coordinated by the adaxial regulators HAT3 and ATHB4, which are induced by the SPT and HEC transcription factors.
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16
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Genome-Wide Identification and Expression Patterns of the C2H2-Zinc Finger Gene Family Related to Stress Responses and Catechins Accumulation in Camellia sinensis [L.] O. Kuntze. Int J Mol Sci 2021; 22:ijms22084197. [PMID: 33919599 PMCID: PMC8074030 DOI: 10.3390/ijms22084197] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 11/18/2022] Open
Abstract
The C2H2-zinc finger protein (C2H2-ZFP) is essential for the regulation of plant development and widely responsive to diverse stresses including drought, cold and salt stress, further affecting the late flavonoid accumulation in higher plants. Tea is known as a popular beverage worldwide and its quality is greatly dependent on the physiological status and growing environment of the tea plant. To date, the understanding of C2H2-ZFP gene family in Camellia sinensis [L.] O. Kuntze is not yet available. In the present study, 134 CsC2H2-ZFP genes were identified and randomly distributed on 15 chromosomes. The CsC2H2-ZFP gene family was classified into four clades and gene structures and motif compositions of CsC2H2-ZFPs were similar within the same clade. Segmental duplication and negative selection were the main forces driving the expansion of the CsC2H2-ZFP gene family. Expression patterns suggested that CsC2H2-ZFPs were responsive to different stresses including drought, salt, cold and methyl jasmonate (MeJA) treatment. Specially, several C2H2-ZFPs showed a significant correlation with the catechins content and responded to the MeJA treatment, which might contribute to the tea quality and specialized astringent taste. This study will lay the foundations for further research of C2H2-type zinc finger proteins on the stress responses and quality-related metabolites accumulation in C. sinensis.
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17
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Kivivirta KI, Herbert D, Roessner C, de Folter S, Marsch-Martinez N, Becker A. Transcriptome analysis of gynoecium morphogenesis uncovers the chronology of gene regulatory network activity. PLANT PHYSIOLOGY 2021; 185:1076-1090. [PMID: 33793890 PMCID: PMC8133673 DOI: 10.1093/plphys/kiaa090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/04/2020] [Indexed: 05/12/2023]
Abstract
The gynoecium is the most complex organ formed by the flowering plants. It encloses the ovules, provides a surface for pollen contact and self-incompatibility reactions, allows pollen tube growth, and, post fertilization, develops into the fruit. Consequently, the regulation of gynoecium morphogenesis is complex and appropriate timing of this process in part determines reproductive success. However, little is known about the global control of gynoecium development, even though many regulatory genes have been characterized. Here, we characterized dynamic gene expression changes using laser-microdissected gynoecium tissue from four developmental stages in Arabidopsis. We provide a high-resolution map of global expression dynamics during gynoecium morphogenesis and link these to the gynoecium interactome. We reveal groups of genes acting together early and others acting late in morphogenesis. Clustering of co-expressed genes enables comparisons between the leaf, shoot apex, and gynoecium transcriptomes, allowing the dissection of common and distinct regulators. Furthermore, our results lead to the discovery of genes with putative transcription factor activity (B3LF1, -2, DOFLF1), which, when mutated, lead to impaired gynoecium expansion, illustrating that global transcriptome analyses reveal yet unknown developmental regulators. Our data show that genes encoding highly interacting proteins, such as SEPALLATA3, AGAMOUS, and TOPLESS, are expressed evenly during development but switch interactors over time, whereas stage-specific proteins tend to have fewer interactors. Our analysis connects specific transcriptional regulator activities, protein interactions, and underlying metabolic processes, contributing toward a dynamic network model for gynoecium development.
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Affiliation(s)
- Kimmo I Kivivirta
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Heinrich-Buff-Ring 38, 35392 Gießen, Germany
| | - Denise Herbert
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Heinrich-Buff-Ring 38, 35392 Gießen, Germany
| | - Clemens Roessner
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Heinrich-Buff-Ring 38, 35392 Gießen, Germany
| | - Stefan de Folter
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Unidad de Genómica Avanzada (UGA-LANGEBIO), CP 36824 Irapuato, Mexico
| | | | - Annette Becker
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Heinrich-Buff-Ring 38, 35392 Gießen, Germany
- Author for communication:
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18
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Ma H, Xu L, Fu Y, Zhu L. Arabidopsis QWRF1 and QWRF2 Redundantly Modulate Cortical Microtubule Arrangement in Floral Organ Growth and Fertility. Front Cell Dev Biol 2021; 9:634218. [PMID: 33634133 PMCID: PMC7901996 DOI: 10.3389/fcell.2021.634218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/15/2021] [Indexed: 11/13/2022] Open
Abstract
Floral organ development is fundamental to sexual reproduction in angiosperms. Many key floral regulators (most of which are transcription factors) have been identified and shown to modulate floral meristem determinacy and floral organ identity, but not much is known about the regulation of floral organ growth, which is a critical process by which organs to achieve appropriate morphologies and fulfill their functions. Spatial and temporal control of anisotropic cell expansion following initial cell proliferation is important for organ growth. Cortical microtubules are well known to have important roles in plant cell polar growth/expansion and have been reported to guide the growth and shape of sepals and petals. In this study, we identified two homolog proteins, QWRF1 and QWRF2, which are essential for floral organ growth and plant fertility. We found severely deformed morphologies and symmetries of various floral organs as well as a significant reduction in the seed setting rate in the qwrf1qwrf2 double mutant, although few flower development defects were seen in qwrf1 or qwrf2 single mutants. QWRF1 and QWRF2 display similar expression patterns and are both localized to microtubules in vitro and in vivo. Furthermore, we found altered cortical microtubule organization and arrangements in qwrf1qwrf2 cells, consistent with abnormal cell expansion in different floral organs, which eventually led to poor fertility. Our results suggest that QWRF1 and QWRF2 are likely microtubule-associated proteins with functional redundancy in fertility and floral organ development, which probably exert their effects via regulation of cortical microtubules and anisotropic cell expansion.
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Affiliation(s)
- Huifang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liyuan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
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19
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Osnato M, Lacchini E, Pilatone A, Dreni L, Grioni A, Chiara M, Horner D, Pelaz S, Kater MM. Transcriptome analysis reveals rice MADS13 as an important repressor of the carpel development pathway in ovules. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:398-414. [PMID: 33035313 DOI: 10.1093/jxb/eraa460] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
In angiosperms, floral homeotic genes encoding MADS-domain transcription factors regulate the development of floral organs. Specifically, members of the SEPALLATA (SEP) and AGAMOUS (AG) subfamilies form higher-order protein complexes to control floral meristem determinacy and to specify the identity of female reproductive organs. In rice, the AG subfamily gene OsMADS13 is intimately involved in the determination of ovule identity, since knock-out mutant plants develop carpel-like structures in place of ovules, resulting in female sterility. Little is known about the regulatory pathways at the base of rice gynoecium development. To investigate molecular mechanisms acting downstream of OsMADS13, we obtained transcriptomes of immature inflorescences from wild-type and Osmads13 mutant plants. Among a total of 476 differentially expressed genes (DEGs), a substantial overlap with DEGs from the SEP-family Osmads1 mutant was found, suggesting that OsMADS1 and OsMADS13 may act on a common set of target genes. Expression studies and preliminary analyses of two up-regulated genes encoding Zinc-finger transcription factors indicated that our dataset represents a valuable resource for the identification of both OsMADS13 target genes and novel players in rice ovule development. Taken together, our study suggests that OsMADS13 is an important repressor of the carpel pathway during ovule development.
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Affiliation(s)
- Michela Osnato
- Department of Biosciences, University of Milan, Milano, Italy
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Elia Lacchini
- Department of Biosciences, University of Milan, Milano, Italy
- VIB Center for Plant System Biology, Ghent, BELGIUM
| | | | - Ludovico Dreni
- Department of Biosciences, University of Milan, Milano, Italy
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Andrea Grioni
- Department of Biosciences, University of Milan, Milano, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Milano, Italy
| | - David Horner
- Department of Biosciences, University of Milan, Milano, Italy
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Martin M Kater
- Department of Biosciences, University of Milan, Milano, Italy
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20
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Huang M, Zhang L, Zhou L, Wang M, Yung WS, Wang Z, Duan S, Xiao Z, Wang Q, Wang X, Li MW, Lam HM. An expedient survey and characterization of the soybean JAGGED 1 (GmJAG1) transcription factor binding preference in the soybean genome by modified ChIPmentation on soybean protoplasts. Genomics 2021; 113:344-355. [PMID: 33338631 DOI: 10.1016/j.ygeno.2020.12.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/11/2020] [Accepted: 12/13/2020] [Indexed: 12/21/2022]
Abstract
ChIP-seq is widely used for mapping the transcription factor (TF) binding sites throughout the genome in vivo. In this study, we adopted and modified ChIPmentation, a fast, robust, low-input requirement ChIP-seq method, to a transient expression system using soybean protoplasts to expedite the exploration of TF binding sites. To test this new protocol, we expressed a tagged version of a C2H2-type zinc finger TF, JAGGED1 (GmJAG1), in soybean protoplasts and successfully identified its binding sites in the soybean genome. Furthermore, valuable genomic features such as a novel GmJAG1-binding motif, and the epigenetic characteristics as well as an enhancer-like function of GmJBSs were also found via coupling ATAC-seq and H3K27me3 ChIP-seq data. The application of the modified ChIPmentation protocol in this study using soybean protoplasts provided a new approach for rapid elucidation of how a TF binds to the various target genes in the soybean genome, as illustrated here using GmJAG1.
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Affiliation(s)
- Mingkun Huang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Ling Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518055, PR China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518055, PR China
| | - Limeng Zhou
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Mozhu Wang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Wai-Shing Yung
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Zhili Wang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Shaowei Duan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Zhixia Xiao
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Qianwen Wang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Xin Wang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Man-Wah Li
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China.
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21
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Liao X, Wang L, Zhu S, Zheng F, Yang C. Identification, genomic organization, and expression profiles of single C2H2 zinc finger transcription factors in tomato (Solanum lycopersicum). J Appl Genet 2020; 62:1-15. [PMID: 33034011 DOI: 10.1007/s13353-020-00587-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/20/2020] [Accepted: 09/09/2020] [Indexed: 01/22/2023]
Abstract
C2H2 zinc finger proteins (ZFPs) play essential roles in leaf morphogenesis and floral development, as well as heat stress response and trichome formation, which activate or inhibit gene transcription mainly through interactions with nucleic acids, such as single-strand DNA, RNA binding or RNA/DNA bidirectional binding, and protein interaction. Single C2H2 ZFPs is the subfamily of ZFPs, but little of single C2H2 ZFP family is known in tomato. In this study, we identified 30 single ZFP genes in tomato using bioinformatics-based methods. Gene structures, phylogeny, conserved motifs, cis-element of promoter, chromosomal localization, gene duplication, and expression patterns of these single C2H2 ZFP genes were analyzed. Sequence analysis showed that most single C2H2 ZFP genes possessed only one exon, except for SlC1-liZFP1 and SlC1-liZFP2. These single C2H2 ZFP genes were asymmetrically distributed on 10 chromosomes, excluding 2 and 12 chromosomes. In addition, 24 of these genes were predicated to have experienced segmental duplication. Cis-element prediction indicated that many important elements were located in the putative promoter regions, like light and gibberellic acid (GA)-responsive elements. The expression profiles of these genes in different tissues and various hormones and stress treatment were further analyzed. Many genes were lowly expressed in all tissues, whereas some were specifically expressed in certain tissues, like SlC1-liZFP2 in young leaves, and SlC1-liZFP15 in fruits. Furthermore, these genes could also be induced by several hormones and stresses, including IAA, ETH, GA, cold, and drought. This study sets a good foundation for further characterizing the biological roles of single C2H2 ZFP genes in tomato.
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Affiliation(s)
- Xiaoli Liao
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Wang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shunhua Zhu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangyan Zheng
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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22
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Spurney RJ, Van den Broeck L, Clark NM, Fisher AP, de Luis Balaguer MA, Sozzani R. tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:716-730. [PMID: 31571287 DOI: 10.1111/tpj.14558] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/20/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Predicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA-sequencing data analysis, are not automated or are restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet, a user-friendly platform that can process raw RNA-sequencing data from any organism with an existing reference genome using a modified tuxedo pipeline (hisat 2 + cufflinks package) and infer GRNs from these processed data. tuxnet is implemented as a graphical user interface and can mine gene regulations, either by applying a dynamic Bayesian network (DBN) inference algorithm, genist, or a regression tree-based pipeline, rtp-star. We obtained time-course expression data of a PERIANTHIA (PAN) inducible line and inferred a GRN using genist to illustrate the use of tuxnet while gaining insight into the regulations downstream of the Arabidopsis root stem cell regulator PAN. Using rtp-star, we inferred the network of ATHB13, a downstream gene of PAN, for which we obtained wild-type and mutant expression profiles. Additionally, we generated two networks using temporal data from developmental leaf data and spatial data from root cell-type data to highlight the use of tuxnet to form new testable hypotheses from previously explored data. Our case studies feature the versatility of tuxnet when using different types of gene expression data to infer networks and its accessibility as a pipeline for non-bioinformaticians to analyze transcriptome data, predict causal regulations, assess network topology and identify key regulators.
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Affiliation(s)
- Ryan J Spurney
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Lisa Van den Broeck
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Natalie M Clark
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA
- Biomathematics Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, 50010, USA
| | - Adam P Fisher
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Maria A de Luis Balaguer
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA
- Elo Life Systems, Durham, NC, 27709, USA
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA
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Lyu T, Liu W, Hu Z, Xiang X, Liu T, Xiong X, Cao J. Molecular characterization and expression analysis reveal the roles of Cys 2/His 2 zinc-finger transcription factors during flower development of Brassica rapa subsp. chinensis. PLANT MOLECULAR BIOLOGY 2020; 102:123-141. [PMID: 31776846 DOI: 10.1007/s11103-019-00935-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
Conserved motif, gene structure, expression and interaction analysis of C2H2-ZFPs in Brassica rapa, and identified types of genes may play essential roles in flower development, and BrZFP38 was proved to function in flower development by affecting pollen formation. Flower development plays a central role in determining the reproduction of higher plants, and Cys2/His2 zinc-finger proteins (C2H2-ZFPs) widely participate in the transcriptional regulation of flower development. C2H2-ZFPs with various structures are the most widespread DNA-binding transcription factors in plants. In this study, conserved protein motif and gene structures were analyzed to investigate systematically the molecular features of Brassica rapa C2H2-ZFP genes. Expression of B. rapa C2H2-ZFPs in multiple tissues showed that more than half of the family members with different types ZFs were expressed in flowers. The specific expression profiles of these C2H2-ZFPs in different B. rapa floral bud stages were further evaluated to identify their potential roles in flower development. Interaction networks were constructed in B. rapa based on the orthology of flower-related C2H2-ZFP genes in Arabidopsis. The putative cis-regulatory elements in the promoter regions of these C2H2-ZFP genes were thoroughly analyzed to elucidate their transcriptional regulation. Results showed that the orthologs of known-function flower-related C2H2-ZFP genes were conserved and differentiated in B. rapa. A C2H2-ZFP was proved to function in B. rapa flower development. Our study provides a systematic investigation of the molecular characteristics and expression profiles of C2H2-ZFPs in B. rapa and promotes further work in function and transcriptional regulation of flower development.
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Affiliation(s)
- Tianqi Lyu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
| | - Weimiao Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
| | - Ziwei Hu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
| | - Xun Xiang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
| | - Tingting Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
| | - Xingpeng Xiong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
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Zaman QU, Chu W, Hao M, Shi Y, Sun M, Sang SF, Mei D, Cheng H, Liu J, Li C, Hu Q. CRISPR/Cas9-Mediated Multiplex Genome Editing of JAGGED Gene in Brassica napus L. Biomolecules 2019; 9:biom9110725. [PMID: 31726660 PMCID: PMC6921047 DOI: 10.3390/biom9110725] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 11/16/2022] Open
Abstract
Pod shattering resistance is an essential component to achieving a high yield, which is a substantial objective in polyploid rapeseed cultivation. Previous studies have suggested that the Arabidopsis JAGGED (JAG) gene is a key factor implicated in the regulatory web of dehiscence fruit. However, its role in controlling pod shattering resistance in oilseed rape is still unknown. In this study, multiplex genome editing was carried out by the CRISPR/Cas9 system on five homoeologs (BnJAG.A02, BnJAG.C02, BnJAG.C06, BnJAG.A07, and BnJAG.A08) of the JAG gene. Knockout mutagenesis of all homoeologs drastically affected the development of the lateral organs in organizing pod shape and size. The cylindrical body of the pod comprised a number of undifferentiated cells like a callus, without distinctive valves, replum, septum, and valve margins. Pseudoseeds were produced, which were divided into two halves with an incomplete layer of cells (probably septum) that separated the undifferentiated cells. These mutants were not capable of generating any productive seeds for further generations. However, one mutant line was identified in which only a BnJAG.A08-NUB-Like paralog of the JAG gene was mutated. Knockout mutagenesis in BnJAG.A08-NUB gene caused significant changes in the pod dehiscence zone. The replum region of the mutant was increased to a great extent, resulting in enlarged cell size, bumpy fruit, and reduced length compared with the wild type. A higher replum-valve joint area may have increased the resistance to pod shattering by ~2-fold in JAG mutants compared with wild type. Our results offer a basis for understanding variations in Brassica napus fruit by mutating JAG genes and providing a way forward for other Brassicaceae species.
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Affiliation(s)
- Qamar U Zaman
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen Chu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Mengyu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Yuqin Shi
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Mengdan Sun
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Shi-Fei Sang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Desheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Chao Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
- Correspondence: (C.L.); (Q.H.)
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
- Correspondence: (C.L.); (Q.H.)
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Coito JL, Silva HG, Ramos MJ, Cunha J, Eiras-Dias J, Amâncio S, Costa MM, Rocheta M. Vitis flower types: from the wild to crop plants. PeerJ 2019; 7:e7879. [PMID: 31737441 PMCID: PMC6855205 DOI: 10.7717/peerj.7879] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/12/2019] [Indexed: 01/27/2023] Open
Abstract
Vitis vinifera can be divided into two subspecies, V. vinifera subsp. vinifera, one of the most important agricultural crops in the world, and its wild ancestor, V. vinifera subsp. sylvestris. Three flower types can be observed: hermaphrodite and female (on some varieties) in vinifera, and male or female flowers in sylvestris. It is assumed that the different flower types in the wild ancestor arose through specific floral patterns of organ abortion. A considerable amount of data about the diversity of sexual systems in grapevines has been collected over the past century. Several grapevine breeding studies led to the hypothesis that dioecy in vinifera is derived from a hermaphrodite ancestor and could be controlled by either, one or two linked genetic determinants following Mendelian inherence. More recently, experiments using molecular approaches suggested that these loci were located in a specific region of the chromosome 2 of vinifera. Based on the works published so far, its seems evident that a putative sex locus is present in chromosome 2. However, it is still not fully elucidated whether flower types are regulated by two linked loci or by one locus with three alleles. Nevertheless, several genes could contribute to sex determination in grapevine. This review presents the results from early studies, combined with the recent molecular approaches, which may contribute to the design of new experiments towards a better understanding of the sex inheritance in grapevine.
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Affiliation(s)
- João L. Coito
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Helena G. Silva
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Miguel J.N. Ramos
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, Quinta d’Almoinha, Dois Portos, Portugal
| | - José Eiras-Dias
- Instituto Nacional de Investigação Agrária e Veterinária, Quinta d’Almoinha, Dois Portos, Portugal
| | - Sara Amâncio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Maria M.R. Costa
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Margarida Rocheta
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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Mahapatra M, Mahanty B, Joshi RK. Genome wide identification and functional assignments of C 2H 2 Zinc-finger family transcription factors in Dichanthelium oligosanthes. Bioinformation 2019; 15:689-696. [PMID: 31787818 PMCID: PMC6859702 DOI: 10.6026/97320630015689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/23/2022] Open
Abstract
Transcription factors (TFs) are biological regulators of gene function in response to various internal and external stimuli. C2H2 zinc finger proteins (C2H2-ZFPs) are a large family of TFs that play crucial roles in plant growth and development, hormone signalling and response to biotic and abiotic stresses. While C2H2-ZFPs have been well characterized in many model and crop plants, they are yet to be ascertained in the evolutionarily important C3 plant Dichanthelium oligosanthes (Heller's rosette grass). In the present study, we report 32 C2H2-ZF genes (DoZFs) belonging to three different classes-Q type, C-type and Z-type based on structural elucidation and phylogenetic analysis. Sequence comparisons revealed paralogs within the DoZFs and orthologs among with rice ZF genes. Motif assignment showed the presence of the distinctive C2H2-ZF conserved domain "QALGGH" in these proteins. Cis-element analysis indicated that majority of the predicted C2H2-ZFPs are associated with hormone signalling and abiotic stress responses. Further, their role in nucleic acid binding and transcriptional regulation was also observed using predicted functional assignment. Thus, we report an overview of the C2H2-ZF gene family in D. oligosanthes that could serve as the basis for future experimental studies on isolation and functional implication of these genes in different biological mechanism of C3 plants.
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Affiliation(s)
- Manisha Mahapatra
- Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, INDIA
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, INDIA
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, INDIA
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Salih H, Odongo MR, Gong W, He S, Du X. Genome-wide analysis of cotton C2H2-zinc finger transcription factor family and their expression analysis during fiber development. BMC PLANT BIOLOGY 2019; 19:400. [PMID: 31510939 PMCID: PMC6739942 DOI: 10.1186/s12870-019-2003-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/30/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND C2H2-zinc finger protein family is commonly found in the plant, and it is known as the key actors in the regulation of transcription and vital component of chromatin structure. A large number of the C2H2-zinc finger gene members have not been well characterized based on their functions and structure in cotton. However, in other plants, only a few C2H2-zinc finger genes have been studied. RESULTS In this work, we performed a comprehensive analysis and identified 386, 196 and 195 C2H2-zinc finger genes in Gossypium hirsutum (upland cotton), Gossypium arboreum and Gossypium raimondii, respectively. Phylogenetic tree analysis of the C2H2-zinc finger proteins encoding the C2H2-zinc finger genes were classified into seven (7) subgroups. Moreover, the C2H2-zinc finger gene members were distributed in all cotton chromosomes though with asymmetrical distribution patterns. All the orthologous genes were detected between tetraploid and the diploid cotton, with 154 orthologous genes pair detected between upland cotton and Gossypium arboreum while 165 orthologous genes were found between upland cotton and Gossypium raimondii. Synonymous (Ks) and non-synonymous (Ka) nucleotide substitution rates (Ka/Ks) analysis indicated that the cotton C2H2-zinc finger genes were highly influenced mainly by negative selection, which maintained their protein levels after the duplication events. RNA-seq data and RT-qPCR validation of the RNA seq result revealed differential expression pattern of some the C2H2-zinc finger genes at different stages of cotton fiber development, an indication that the C2H2-zinc finger genes play an important role in initiating and regulating fiber development in cotton. CONCLUSIONS This study provides a strong foundation for future practical genome research on C2H2-zinc finger genes in upland cotton. The expression levels of C2H2-zinc finger genes family is a pointer of their involvement in various biochemical and physiological functions which are directly related to cotton fiber development during initiation and elongation stages. This work not only provides a basis for determining the nominal role of the C2H2-zinc finger genes in fiber development but also provide valuable information for characterization of potential candidate genes involved in regulation of cotton fiber development.
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Affiliation(s)
- Haron Salih
- College of life sciences, Huazhong Agricultural University, Wuhan, 430070 Hubei China
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
- Zalingei University, Central Darfur, Sudan
| | - Magwanga Richard Odongo
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Shoupu He
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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The Roles of Arabidopsis C1-2i Subclass of C2H2-type Zinc-Finger Transcription Factors. Genes (Basel) 2019; 10:genes10090653. [PMID: 31466344 PMCID: PMC6770587 DOI: 10.3390/genes10090653] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 01/07/2023] Open
Abstract
The Cys2His2 (C2H2)-type zinc-finger protein (ZFP) family, which includes 176 members in Arabidopsis thaliana, is one of the largest families of putative transcription factors in plants. Of the Arabidopsis ZFP members, only 33 members are conserved in other eukaryotes, with 143 considered to be plant specific. C2H2-type ZFPs have been extensively studied and have been shown to play important roles in plant development and environmental stress responses by transcriptional regulation. The ethylene-responsive element binding-factor-associated amphiphilic repression (EAR) domain (GCC box) has been found to have a critical role in the tolerance response to abiotic stress. Many of the plant ZFPs containing the EAR domain, such as AZF1/2/3, ZAT7, ZAT10, and ZAT12, have been shown to function as transcriptional repressors. In this review, we mainly focus on the C1-2i subclass of C2H2 ZFPs and summarize the latest research into their roles in various stress responses. The role of C2H2-type ZFPs in response to the abiotic and biotic stress signaling network is not well explained, and amongst them, C1-2i is one of the better-characterized classifications in response to environmental stresses. These studies of the C1-2i subclass ought to furnish the basis for future studies to discover the pathways and receptors concerned in stress defense. Research has implied possible protein-protein interactions between members of C1-2i under various stresses, for which we have proposed a hypothetical model.
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Lyu T, Hu Z, Liu W, Cao J. Arabidopsis Cys 2/His 2 zinc-finger protein MAZ1 is essential for intine formation and exine pattern. Biochem Biophys Res Commun 2019; 518:299-305. [PMID: 31427085 DOI: 10.1016/j.bbrc.2019.08.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 11/25/2022]
Abstract
Cys2/His2 zinc-finger protein (C2H2-ZFP) is widely involved in the reproductive development of plants, but its role in pollen development is still elusive. Here, we identified a pollen-related C2H2-ZFP gene named as MALE FERTILITY-ASSOCIATED ZINC FINGER PROTEIN 1 (MAZ1), which was first isolated from Arabidopsis thaliana. MAZ1 showed a preferential expression pattern in early anther development. Its mutation resulted in aberrant primexine deposition at the tetrad stage, followed by a defective multiple-layer pattern of exine with irregular baculum and no tectum. Furthermore, microspore development was arrested, and no intine layer was formed. These developmental defects led to fertility reduction and pollen abortion. This study reveals the essential role of MAZ1 in pollen wall development.
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Affiliation(s)
- Tianqi Lyu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China.
| | - Ziwei Hu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China.
| | - Weimiao Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China.
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
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Lantican DV, Strickler SR, Canama AO, Gardoce RR, Mueller LA, Galvez HF. De Novo Genome Sequence Assembly of Dwarf Coconut ( Cocos nucifera L. 'Catigan Green Dwarf') Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species. G3 (BETHESDA, MD.) 2019; 9:2377-2393. [PMID: 31167834 PMCID: PMC6686914 DOI: 10.1534/g3.119.400215] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/31/2019] [Indexed: 11/23/2022]
Abstract
We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The genome sequence was generated using the PacBio SMRT sequencing platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. The draft genome was improved through Chicago sequencing to generate a scaffold assembly that results in a total genome size of 2.1 Gbp consisting of 7,998 scaffolds with N50 of 570,487 bp. The final assembly covers around 97.6% of the estimated genome size of coconut 'CATD' based on homozygous k-mer peak analysis. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. The gene markers and genome-wide SSR markers established here will facilitate the development of varieties with resilience to climate change, resistance to pests and diseases, and improved oil yield and quality.
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Affiliation(s)
- Darlon V Lantican
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
| | | | - Alma O Canama
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | - Roanne R Gardoce
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | | | - Hayde F Galvez
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
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Lyu T, Cao J. Cys₂/His₂ Zinc-Finger Proteins in Transcriptional Regulation of Flower Development. Int J Mol Sci 2018; 19:E2589. [PMID: 30200325 PMCID: PMC6164605 DOI: 10.3390/ijms19092589] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 11/17/2022] Open
Abstract
Flower development is the core of higher-plant ontogenesis and is controlled by complex gene regulatory networks. Cys₂/His₂ zinc-finger proteins (C2H2-ZFPs) constitute one of the largest transcription factor families and are highly involved in transcriptional regulation of flowering induction, floral organ morphogenesis, and pollen and pistil maturation. Nevertheless, the molecular mechanism of C2H2-ZFPs has been gradually revealed only in recent years. During flowering induction, C2H2-ZFPs can modify the chromatin of FLOWERING LOCUS C, thereby providing additional insights into the quantification of transcriptional regulation caused by chromatin regulation. C2H2-ZFPs are involved in cell division and proliferation in floral organ development and are associated with hormonal regulation, thereby revealing how a flower is partitioned into four developmentally distinct whorls. The studies reviewed in this work integrate the information from the endogenous, hormonal, and environmental regulation of flower development. The structure of C2H2-ZFPs determines their function as transcriptional regulators. The findings indicate that C2H2-ZFPs play a crucial role in flower development. In this review, we summarize the current understanding of the structure, expression, and function of C2H2-ZFPs and discuss their molecular mechanism in flower development.
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Affiliation(s)
- Tianqi Lyu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
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Abstract
The angiosperm flower develops through a modular programme which, although ancient and conserved, provides the flexibility that has allowed an almost infinite variety of floral forms to emerge. In this review, we explore the evolution of floral diversity, focusing on our recent understanding of the mechanistic basis of evolutionary change. We discuss the various ways in which flower size and floral organ size can be modified, the means by which flower shape and symmetry can change, and the ways in which floral organ position can be varied. We conclude that many challenges remain before we fully understand the ecological and molecular processes that facilitate the diversification of flower structure.
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Brinton J, Simmonds J, Uauy C. Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat. BMC PLANT BIOLOGY 2018; 18:22. [PMID: 29370763 PMCID: PMC5784548 DOI: 10.1186/s12870-018-1241-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/17/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND There is an urgent need to increase global crop production. Identifying and combining specific genes controlling distinct biological processes holds the potential to enhance crop yields. Transcriptomics is a powerful tool to gain insights into the complex gene regulatory networks that underlie such traits, but relies on the availability of a high-quality reference sequence and accurate gene models. Previously, we identified a grain weight QTL on wheat chromosome 5A (5A QTL) which acts during early grain development to increase grain length through cell expansion in the pericarp. In this study, we performed RNA-sequencing on near isogenic lines (NILs) segregating for the 5A QTL and used the latest gene models to identify differentially regulated genes and pathways that potentially influence pericarp cell size and grain weight in wheat. RESULTS We sampled grains at 4 and 8 days post anthesis and found that genes associated with metabolism, biosynthesis, proteolysis and the defence response are upregulated during this stage of grain development in both NILs. We identified a specific set of 112 transcripts differentially expressed (DE) between 5A NILs at either time point, including eight potential candidates for the causal 5A gene and its downstream targets. The 112 DE transcripts had functional annotations including non-coding RNA, transposon-associated, cell-cycle control, ubiquitin-related, heat-shock, transcription and histone-related. Many of the genes identified belong to families that have been previously associated with seed/grain development in other species. Notably, we identified DE transcripts at almost all steps of the pathway associated with ubiquitin-mediated protein degradation. In the promoters of a subset of DE transcripts we identified enrichment of binding sites associated with C2H2, MYB/SANT, YABBY, AT-HOOK and Trihelix transcription factor families. CONCLUSIONS In this study, we identified DE transcripts with a diverse range of predicted biological functions, reflecting the complex nature of the pathways that control early grain development. Few of these are the direct orthologues of grain size genes in other species and none have been previously characterised in wheat. Further functional characterisation of these candidates and how they interact will provide novel insights into the control of grain size in cereals.
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Durán-Medina Y, Serwatowska J, Reyes-Olalde JI, de Folter S, Marsch-Martínez N. The AP2/ERF Transcription Factor DRNL Modulates Gynoecium Development and Affects Its Response to Cytokinin. FRONTIERS IN PLANT SCIENCE 2017; 8:1841. [PMID: 29123539 PMCID: PMC5662920 DOI: 10.3389/fpls.2017.01841] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/10/2017] [Indexed: 05/29/2023]
Abstract
The gynoecium is the female reproductive system in flowering plants. It is a complex structure formed by different tissues, some that are essential for reproduction and others that facilitate the fertilization process and nurture and protect the developing seeds. The coordinated development of these different tissues during the formation of the gynoecium is important for reproductive success. Both hormones and genetic regulators guide the development of the different tissues. Auxin and cytokinin in particular have been found to play important roles in this process. On the other hand, the AP2/ERF2 transcription factor BOL/DRNL/ESR2/SOB is expressed at very early stages of aerial organ formation and has been proposed to be a marker for organ founder cells. In this work, we found that this gene is also expressed at later stages during gynoecium development, particularly at the lateral regions (the region related to the valves of the ovary). The loss of DRNL function affects gynoecium development. Some of the mutant phenotypes present similarities to those observed in plants treated with exogenous cytokinins, and AHP6 has been previously proposed to be a target of DRNL. Therefore, we explored the response of drnl-2 developing gynoecia to cytokinins, and found that the loss of DRNL function affects the response of the gynoecium to exogenously applied cytokinins in a developmental-stage-dependent manner. In summary, this gene participates during gynoecium development, possibly through the dynamic modulation of cytokinin homeostasis and response.
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Affiliation(s)
- Yolanda Durán-Medina
- Laboratorio de Identidad Celular de Plantas, Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Joanna Serwatowska
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - J. Irepan Reyes-Olalde
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Nayelli Marsch-Martínez
- Laboratorio de Identidad Celular de Plantas, Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
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Min Y, Kramer EM. The Aquilegia JAGGED homolog promotes proliferation of adaxial cell types in both leaves and stems. THE NEW PHYTOLOGIST 2017; 216:536-548. [PMID: 27864962 DOI: 10.1111/nph.14282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/14/2016] [Indexed: 06/06/2023]
Abstract
In order to explore the functional conservation of JAGGED, a key gene involved in the sculpting of lateral organs in several model species, we identified its ortholog AqJAG in the lower eudicot species Aquilegia coerulea. We analyzed the expression patterns of AqJAG in various tissues and developmental stages, and used RNAi-based methods to generate knockdown phenotypes of AqJAG. AqJAG was strongly expressed in shoot apices, floral meristems, lateral root primordia and all lateral organ primordia. Silencing of AqJAG revealed a wide range of defects in the developing stems, leaves and flowers; strongest phenotypes include severe reduction of leaflet laminae due to a decrease in cell size and number, change of adaxial cell identity, outgrowth of laminar-like tissue on the inflorescence stem, and early arrest of floral meristems and floral organ primordia. Our results indicate that AqJAG plays a critical role in controlling primordia initiation and distal growth of floral organs, and laminar development of leaflets. Most strikingly, we demonstrated that AqJAG disproportionally controls the behavior of cells with adaxial identity in vegetative tissues, providing evidence of how cell proliferation is controlled in an identity-specific manner.
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Affiliation(s)
- Ya Min
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
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Global gene expression defines faded whorl specification of double flower domestication in Camellia. Sci Rep 2017; 7:3197. [PMID: 28600507 PMCID: PMC5466612 DOI: 10.1038/s41598-017-03575-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/28/2017] [Indexed: 12/03/2022] Open
Abstract
Double flowers in cultivated camellias are divergent in floral patterns which present a rich resource for demonstrating molecular modifications influenced by the human demands. Despite the key principle of ABCE model in whorl specification, the underlying mechanism of fine-tuning double flower formation remains largely unclear. Here a comprehensive comparative transcriptomics interrogation of gene expression among floral organs of wild type and “formal double” and “anemone double” is presented. Through a combination of transcriptome, small RNA and “degradome” sequencing, we studied the regulatory gene expression network underlying the double flower formation. We obtained the differentially expressed genes between whorls in wild and cultivated Camellia. We showed that the formation of double flowers tends to demolish gene expression canalization of key functions; the faded whorl specification mechanism was fundamental under the diverse patterns of double flowers. Furthermore, we identified conserved miRNA-targets regulations in the control of double flowers, and we found that miR172-AP2, miR156-SPLs were critical regulatory nodes contributing to the diversity of double flower forms. This work highlights the hierarchical patterning of global gene expression in floral development, and supports the roles of “faded ABC model” mechanism and miRNA-targets regulations underlying the double flower domestication.
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Frerichs A, Thoma R, Abdallah AT, Frommolt P, Werr W, Chandler JW. The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem. BMC Genomics 2016; 17:855. [PMID: 27809788 PMCID: PMC5093967 DOI: 10.1186/s12864-016-3189-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 10/22/2016] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem flanks where they differentiate, remains largely unknown. We have combined fluorescence-activated cell sorting and RNA-seq to characterise the cell-type-specific transcriptome at the earliest developmental time-point of lateral organ formation using DORNRÖSCHEN-LIKE::GFP to mark founder-cell populations at the periphery of the inflorescence meristem (IM) in apetala1 cauliflower double mutants, which overproliferate IMs. RESULTS Within the lateral organ founder-cell population at the inflorescence meristem, floral primordium identity genes are upregulated and stem-cell identity markers are downregulated. Additional differentially expressed transcripts are involved in polarity generation and boundary formation, and in epigenetic and post-translational changes. However, only subtle transcriptional reprogramming within the global auxin network was observed. CONCLUSIONS The transcriptional network of differentially expressed genes supports the hypothesis that lateral organ founder-cell specification involves the creation of polarity from the centre to the periphery of the IM and the establishment of a boundary from surrounding cells, consistent with bract initiation. However, contrary to the established paradigm that sites of auxin response maxima pre-pattern lateral organ initiation in the IM, auxin response might play a minor role in the earliest stages of lateral floral initiation.
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Affiliation(s)
- Anneke Frerichs
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, D-50674, Cologne, Germany
| | - Rahere Thoma
- Present address: Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829, Cologne, Germany
| | - Ali Taleb Abdallah
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Peter Frommolt
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Wolfgang Werr
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, D-50674, Cologne, Germany
| | - John William Chandler
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, D-50674, Cologne, Germany.
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Ding W, Wang Y, Fang W, Gao S, Li X, Xiao K. TaZAT8, a C2H2-ZFP type transcription factor gene in wheat, plays critical roles in mediating tolerance to Pi deprivation through regulating P acquisition, ROS homeostasis and root system establishment. PHYSIOLOGIA PLANTARUM 2016; 158:297-311. [PMID: 27194419 DOI: 10.1111/ppl.12467] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/07/2016] [Accepted: 04/12/2016] [Indexed: 06/05/2023]
Abstract
Transcription factors (TFs) play critical roles in mediating defense of plants to abiotic stresses through regulating downstream defensive genes. In this study, a wheat C2H2-ZFP (zinc finger protein) type TF gene designated as TaZAT8 was functionally characterized in mediating tolerance to the inorganic phosphate (Pi)-starvation stress. TaZAT8 bears conserved motifs harboring in the C2H2-ZFP type counterparts across vascular plant species. The expression of TaZAT8 was shown to be induced in roots upon Pi deprivation, with a Pi concentration- and temporal-dependent manner. Overexpression of TaZAT8 in tobacco conferred plants improved tolerance to Pi deprivation; the transgenic lines exhibited enlarged phenotype and elevated biomass and phosphorus (P) accumulation relative to wild-type (WT) after Pi-starvation treatment. NtPT1 and NtPT2, the tobacco phosphate transporter (PT) genes, showed increased transcripts in the Pi-deprived transgenic lines, indicative of their transcriptional regulation by TaZAT8. Overexpression analysis of these PT genes validated their function in mediating Pi acquisition under the Pi deprivation conditions. Additionally, the TaZAT8-overexpressing lines also behaved enhanced antioxidant enzyme (AE) activities and enlarged root system architecture (RSA) with respect to WT. Evaluation of the transcript abundance of tobacco genes encoding AE and PIN proteins, including NtMnSOD1, NtSOD1, NtPOD1;2, NtPOD1;5, NtPOD1;6, and NtPOD1;9, and NtPIN1 and NtPIN4 are upregulated in the TaZAT8-overexpressing lines. Overexpression of NtPIN1 and NtPIN4 conferred plants to enlarged RSA and elevated biomass under the Pi-starvation stress conditions. Our investigation provides insights into plant adaptation to the Pi-starvation stress mediated by distinct ZFP TFs through modulation of Pi acquisition and cellular ROS detoxicity.
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Affiliation(s)
- Weiwei Ding
- College of Life Sciences, Agricultural University of Hebei, Baoding 071001, China
- Key Laboratory of Hebei Province for Molecular Plant-Microbe Interaction, Agricultural University of Hebei, Baoding 071001, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang 050041, China
| | - Weibo Fang
- College of Life Sciences, Agricultural University of Hebei, Baoding 071001, China
- College of Agronomy, Agricultural University of Hebei, Baoding 071001, China
| | - Si Gao
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang 050041, China
- College of Agronomy, Agricultural University of Hebei, Baoding 071001, China
| | - Xiaojuan Li
- College of Life Sciences, Agricultural University of Hebei, Baoding 071001, China.
- Key Laboratory of Hebei Province for Molecular Plant-Microbe Interaction, Agricultural University of Hebei, Baoding 071001, China.
| | - Kai Xiao
- College of Agronomy, Agricultural University of Hebei, Baoding 071001, China.
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Shwartz I, Levy M, Ori N, Bar M. Hormones in tomato leaf development. Dev Biol 2016; 419:132-142. [PMID: 27339291 DOI: 10.1016/j.ydbio.2016.06.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/16/2016] [Accepted: 06/17/2016] [Indexed: 11/19/2022]
Abstract
Leaf development serves as a model for plant developmental flexibility. Flexible balancing of morphogenesis and differentiation during leaf development results in a large diversity of leaf forms, both between different species and within the same species. This diversity is particularly evident in compound leaves. Hormones are prominent regulators of leaf development. Here we discuss some of the roles of plant hormones and the cross-talk between different hormones in tomato compound-leaf development.
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Affiliation(s)
- Ido Shwartz
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel
| | - Matan Levy
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel.
| | - Maya Bar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel.
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Seeliger I, Frerichs A, Glowa D, Velo L, Comelli P, Chandler JW, Werr W. The AP2-type transcription factors DORNRÖSCHEN and DORNRÖSCHEN-LIKE promote G1/S transition. Mol Genet Genomics 2016; 291:1835-49. [PMID: 27277595 DOI: 10.1007/s00438-016-1224-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/03/2016] [Indexed: 11/30/2022]
Abstract
The paralogous genes DORNRÖSCHEN (DRN) and DORNRÖSCHEN-LIKE (DRNL) encode AP2-type transcription factors that are expressed and act cell-autonomously in the central stem-cell zone or lateral organ founder cells (LOFCs) in the peripheral zone of the Arabidopsis shoot meristem (SAM), but their molecular contribution is unknown. Here, we show using the Arabidopsis thaliana MERISTEM LAYER 1 promoter that DRN and DRNL share a common function in cell cycle progression and potentially provide local competence for G1-S transitions in the SAM. Analysis of double transgenic DRN::erGFP and DRNL::erCERULEAN promoter fusion lines suggests that the trajectory of this cellular competence starts with DRN activity in the central stem-cell zone and extends locally via DRNL activity into groups of founder cells at the IM or FM periphery. Our data support the scenario that after gene duplication, DRN and DRNL acquired different transcription domains within the shoot meristem, but retained protein function that affects cell cycle progression, either centrally in stem cells or peripherally in primordial founder cells, a finding that is of general relevance for meristem function.
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Affiliation(s)
- Ingo Seeliger
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674, Cologne, Germany
| | - Anneke Frerichs
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674, Cologne, Germany
| | - Dorothea Glowa
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674, Cologne, Germany
| | - Laura Velo
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674, Cologne, Germany.,Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674, Cologne, Germany
| | - Petra Comelli
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674, Cologne, Germany
| | - John W Chandler
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674, Cologne, Germany
| | - Wolfgang Werr
- Institute of Developmental Biology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674, Cologne, Germany.
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Walbot V, Egger RL. Pre-Meiotic Anther Development: Cell Fate Specification and Differentiation. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:365-95. [PMID: 26735065 DOI: 10.1146/annurev-arplant-043015-111804] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Research into anther ontogeny has been an active and developing field, transitioning from a strictly lineage-based view of cellular differentiation events to a more complex understanding of cell fate specification. Here we describe the modern interpretation of pre-meiotic anther development, from the earliest cell specifications within the anther lobes through SPL/NZZ-, MSP1-, and MEL1-dependent pathways as well as the initial setup of the abaxial and adaxial axes and outgrowth of the anther lobes. We then continue with a look at the known information regarding further differentiation of the somatic layers of the anther (the epidermis, endothecium, middle layer, and tapetum), with an emphasis on male-sterile mutants identified as defective in somatic cell specification. We also describe the differences in developmental stages among species and use this information to discuss molecular studies that have analyzed transcriptome, proteome, and small-RNA information in the anther.
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Affiliation(s)
- Virginia Walbot
- Department of Biology, Stanford University, Stanford, California 94305-5020; ,
| | - Rachel L Egger
- Department of Biology, Stanford University, Stanford, California 94305-5020; ,
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Ding L, Yan S, Jiang L, Zhao W, Ning K, Zhao J, Liu X, Zhang J, Wang Q, Zhang X. HANABA TARANU (HAN) Bridges Meristem and Organ Primordia Boundaries through PINHEAD, JAGGED, BLADE-ON-PETIOLE2 and CYTOKININ OXIDASE 3 during Flower Development in Arabidopsis. PLoS Genet 2015; 11:e1005479. [PMID: 26390296 PMCID: PMC4577084 DOI: 10.1371/journal.pgen.1005479] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/31/2015] [Indexed: 01/02/2023] Open
Abstract
Shoot organ primordia are initiated from the shoot apical meristem and develop into leaves during the vegetative stage, and into flowers during the reproductive phase. Between the meristem and the newly formed organ primordia, a boundary with specialized cells is formed that separates meristematic activity from determinate organ growth. Despite interactions that have been found between boundary regulators with genes controlling meristem maintenance or primordial development, most boundary studies were performed during embryogenesis or vegetative growth, hence little is known about whether and how boundaries communicate with meristem and organ primordia during the reproductive stage. We combined genetic, molecular and biochemical tools to explore interactions between the boundary gene HANABA TARANU (HAN) and two meristem regulators BREVIPEDICELLUS (BP) and PINHEAD (PNH), and three primordia-specific genes PETAL LOSS (PTL), JAGGED (JAG) and BLADE-ON-PETIOLE (BOP) during flower development. We demonstrated the key role of HAN in determining petal number, as part of a set of complex genetic interactions. HAN and PNH transcriptionally promote each other, and biochemically interact to regulate meristem organization. HAN physically interacts with JAG, and directly stimulates the expression of JAG and BOP2 to regulate floral organ development. Further, HAN directly binds to the promoter and intron of CYTOKININ OXIDASE 3 (CKX3) to modulate cytokinin homeostasis in the boundary. Our data suggest that boundary-expressing HAN communicates with the meristem through the PNH, regulates floral organ development via JAG and BOP2, and maintains boundary morphology through CKX3 during flower development in Arabidopsis.
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Affiliation(s)
- Lian Ding
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Shuangshuang Yan
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Li Jiang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Wensheng Zhao
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Kang Ning
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Jianyu Zhao
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaofeng Liu
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Juan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Qian Wang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaolan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
- * E-mail:
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Liu Q, Wang Z, Xu X, Zhang H, Li C. Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa). PLoS One 2015; 10:e0134753. [PMID: 26237514 PMCID: PMC4523194 DOI: 10.1371/journal.pone.0134753] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/13/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND C2H2 zinc-finger (C2H2-ZF) proteins are a large gene family in plants that participate in various aspects of normal plant growth and development, as well as in biotic and abiotic stress responses. To date, no overall analysis incorporating evolutionary history and expression profiling of the C2H2-ZF gene family in model tree species poplar (Populus trichocarpa) has been reported. PRINCIPAL FINDINGS Here, we identified 109 full-length C2H2-ZF genes in P. trichocarpa, and classified them into four groups, based on phylogenetic analysis. The 109 C2H2-ZF genes were distributed unequally on 19 P. trichocarpa linkage groups (LGs), with 39 segmental duplication events, indicating that segmental duplication has been important in the expansion of the C2H2-ZF gene family. Promoter cis-element analysis indicated that most of the C2H2-ZF genes contain phytohormone or abiotic stress-related cis-elements. The expression patterns of C2H2-ZF genes, based on heatmap analysis, suggested that C2H2-ZF genes are involved in tissue and organ development, especially root and floral development. Expression analysis based on quantitative real-time reverse transcription polymerase chain reaction indicated that C2H2-ZF genes are significantly involved in drought, heat and salt response, possibly via different mechanisms. CONCLUSIONS This study provides a thorough overview of the P. trichocarpa C2H2-ZF gene family and presents a new perspective on the evolution of this gene family. In particular, some C2H2-ZF genes may be involved in environmental stress tolerance regulation. PtrZFP2, 19 and 95 showed high expression levels in leaves and/or roots under environmental stresses. Additionally, this study provided a solid foundation for studying the biological roles of C2H2-ZF genes in Populus growth and development. These results form the basis for further investigation of the roles of these candidate genes and for future genetic engineering and gene functional studies in Populus.
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Affiliation(s)
- Quangang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Zhanchao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Xuemei Xu
- Library of Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Haizhen Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
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Chawla A, Stobdan T, Srivastava RB, Jaiswal V, Chauhan RS, Kant A. Sex-Biased Temporal Gene Expression in Male and Female Floral Buds of Seabuckthorn (Hippophae rhamnoides). PLoS One 2015; 10:e0124890. [PMID: 25915052 PMCID: PMC4410991 DOI: 10.1371/journal.pone.0124890] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 03/18/2015] [Indexed: 12/29/2022] Open
Abstract
Seabuckthorn is an economically important dioecious plant in which mechanism of sex determination is unknown. The study was conducted to identify seabuckthorn homologous genes involved in floral development which may have role in sex determination. Forty four putative Genes involved in sex determination (GISD) reported in model plants were shortlisted from literature survey, and twenty nine seabuckthorn homologous sequences were identified from available seabuckthorn genomic resources. Of these, 21 genes were found to differentially express in either male or female flower bud stages. HrCRY2 was significantly expressed in female flower buds only while HrCO had significant expression in male flowers only. Among the three male and female floral development stages (FDS), male stage II had significant expression of most of the GISD. Information on these sex-specific expressed genes will help in elucidating sex determination mechanism in seabuckthorn.
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Affiliation(s)
- Aseem Chawla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Tsering Stobdan
- Defence Institute of High Altitude Research, Defence R & D Organisation, Leh, Jammu, and Kashmir, India
| | - Ravi B. Srivastava
- Defence Institute of High Altitude Research, Defence R & D Organisation, Leh, Jammu, and Kashmir, India
| | - Varun Jaiswal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Rajinder S. Chauhan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Anil Kant
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
- * E-mail:
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Sun L, Zhang A, Zhou Z, Zhao Y, Yan A, Bao S, Yu H, Gan Y. GLABROUS INFLORESCENCE STEMS3 (GIS3) regulates trichome initiation and development in Arabidopsis. THE NEW PHYTOLOGIST 2015; 206:220-230. [PMID: 25640859 DOI: 10.1111/nph.13218] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/07/2014] [Indexed: 05/24/2023]
Abstract
Arabidopsis trichome formation is an excellent model for studying various aspects of plant cell development and cell differentiation. Our previous works have demonstrated that several C2H2 zinc finger proteins, including GIS, GIS2, ZFP5, ZFP6 and ZFP8, control trichome cell development through GA and cytokinin signalling in Arabidopsis. We identified a novel C2H2 zinc finger protein, GLABROUS INFLORESCENCE STEMS 3 (GIS3), which is a key factor in regulating trichome development in Arabidopsis. In comparison with wild-type plants, loss-of-function of GIS3 mutants exhibited a significantly decreased number of trichomes in cauline leaves, lateral branches, sepals of flowers, and main stems. Overexpression of GIS3 resulted in increased trichome densities in sepal, cauline leaves, lateral branches, main inflorescence stems and in the appearance of ectopic trichomes on carpels. The molecular and genetic analyses show that GIS3 acts upstream of GIS, GIS2, ZFP8 and the key trichome initiation factors, GL1 and GL3. Steroid-inducible gene expression analyses and chromatin immunoprecipitation (ChIP) experiments suggest that GIS and GIS2 are the direct target genes of GIS3.
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Affiliation(s)
- Lili Sun
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
| | - Aidong Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
| | - Zhongjing Zhou
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Rd, Hangzhou, 310058, China
| | - Yongqin Zhao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
| | - An Yan
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
| | - Shengjie Bao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore, Singapore
| | - Yinbo Gan
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
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Sablowski R. Control of patterning, growth, and differentiation by floral organ identity genes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1065-73. [PMID: 25609826 DOI: 10.1093/jxb/eru514] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In spite of the different morphologies of sepals, petals, stamens, and carpels, all these floral organs are believed to be modified versions of a ground-state organ similar to the leaf. Modifications of the ground-state developmental programme are orchestrated by different combinations of MADS-domain transcription factors encoded by floral organ identity genes. In recent years, much has been revealed about the gene regulatory networks controlled by the floral organ identity genes and about the genetic pathways that control leaf development. This review examines how floral organ identity is connected with the control of morphogenesis and differentiation of shoot organs, focusing on the model species Arabidopsis thaliana. Direct links have emerged between floral organ identity genes and genes involved in abaxial-adaxial patterning, organ boundary formation, tissue growth, and cell differentiation. In parallel, predictive models have been developed to explain how the activity of regulatory genes can be coordinated by intercellular signalling and constrained by tissue mechanics. When combined, these advances provide a unique opportunity for revealing exactly how leaf-like organs have been 'metamorphosed' into floral organs during evolution and showing crucial regulatory points in the generation of plant form.
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Affiliation(s)
- Robert Sablowski
- Cell and Developmental Biology Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Crawford BCW, Sewell J, Golembeski G, Roshan C, Long JA, Yanofsky MF. Plant development. Genetic control of distal stem cell fate within root and embryonic meristems. Science 2015; 347:655-9. [PMID: 25612610 DOI: 10.1126/science.aaa0196] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The root meristem consists of populations of distal and proximal stem cells and an organizing center known as the quiescent center. During embryogenesis, initiation of the root meristem occurs when an asymmetric cell division of the hypophysis forms the distal stem cells and quiescent center. We have identified NO TRANSMITTING TRACT (NTT) and two closely related paralogs as being required for the initiation of the root meristem. All three genes are expressed in the hypophysis, and their expression is dependent on the auxin-signaling pathway. Expression of these genes is necessary for distal stem cell fate within the root meristem, whereas misexpression is sufficient to transform other stem cell populations to a distal stem cell fate in both the embryo and mature roots.
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Affiliation(s)
- Brian C W Crawford
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jared Sewell
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Greg Golembeski
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Carmel Roshan
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff A Long
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Martin F Yanofsky
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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Abstract
The development of plant leaves follows a common basic program that is flexible and is adjusted according to species, developmental stage and environmental circumstances. Leaves initiate from the flanks of the shoot apical meristem and develop into flat structures of variable sizes and forms. This process is regulated by plant hormones, transcriptional regulators and mechanical properties of the tissue. Here, we review recent advances in the understanding of how these factors modulate leaf development to yield a substantial diversity of leaf forms. We discuss these issues in the context of leaf initiation, the balance between morphogenesis and differentiation, and patterning of the leaf margin.
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Affiliation(s)
- Maya Bar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel
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Characterization of the global transcriptome for cotton (Gossypium hirsutum L.) anther and development of SSR marker. Gene 2014; 551:206-13. [PMID: 25178523 DOI: 10.1016/j.gene.2014.08.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 08/26/2014] [Accepted: 08/29/2014] [Indexed: 11/20/2022]
Abstract
Cotton is an important fiber plant, and it's attractive to elucidate the molecular mechanism of anther development due to the close relationship between the anther fertility and boll-setting, and also fiber yield. In the present paper, 47.2 million paired-end reads with average length of 82.87 bp from the anthers of TM-1 (Gossypium hirsutum L.), a genetic standard line, were generated through transcriptome sequencing, and 210,965 unigenes of more than 100 bp were obtained. BLAST, KEGG, COG, and GO analyses showed that the genes were enriched in the processes of transcription, translation, and post-translation as well as hormone signal transduction, the transcription factor families, and cell wall-related genes mainly participating in cell expansion and carbohydrate metabolism. Further analysis identified 11,153 potential SSRs. A suit of 5122 primer pair sequences were designed, and 82 of 300 randomly selected primer pairs produced reproducible amplicons that were polymorphic among 22 cotton accessions from G. hirsutum, Gossypium barbadense and Gossypium arboreum. The UPGMA clustering analysis further confirmed high quality and effectiveness of these novel SSR markers. The present study provided insights into the transcriptome profile of the cotton and established a public information platform for functional genomics and molecular breeding.
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