1
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Fichtner F, Humphreys JL, Barbier FF, Feil R, Westhoff P, Moseler A, Lunn JE, Smith SM, Beveridge CA. Strigolactone signalling inhibits trehalose 6-phosphate signalling independently of BRC1 to suppress shoot branching. THE NEW PHYTOLOGIST 2024; 244:900-913. [PMID: 39187924 DOI: 10.1111/nph.20072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 08/03/2024] [Indexed: 08/28/2024]
Abstract
The phytohormone strigolactone (SL) inhibits shoot branching, whereas the signalling metabolite trehalose 6-phosphate (Tre6P) promotes branching. How Tre6P and SL signalling may interact and which molecular mechanisms might be involved remains largely unknown. Transcript profiling of Arabidopsis SL mutants revealed a cluster of differentially expressed genes highly enriched in the Tre6P pathway compared with wild-type (WT) plants or brc1 mutants. Tre6P-related genes were also differentially expressed in axillary buds of garden pea (Pisum sativum) SL mutants. Tre6P levels were elevated in the SL signalling mutant more axillary (max) growth 2 compared with other SL mutants or WT plants indicating a role of MAX2-dependent SL signalling in regulating Tre6P levels. A transgenic approach to increase Tre6P levels demonstrated that all SL mutant lines and brc1 flowered earlier, showing all of these mutants were responsive to Tre6P. Elevated Tre6P led to increased branching in WT plants but not in max2 and max4 mutants, indicating some dependency between the SL pathway and Tre6P regulation of shoot branching. By contrast, elevated Tre6P led to an enhanced branching phenotype in brc1 mutants indicating independence between BRC1 and Tre6P. A model is proposed whereby SL signalling represses branching via Tre6P and independently of the BRC1 pathway.
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Affiliation(s)
- Franziska Fichtner
- School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
- Faculty of Mathematics and Natural Sciences, Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Cluster of Excellence in Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Jazmine L Humphreys
- ARC Centre for Plant Success in Nature and Agriculture, School of Natural Sciences, University of Tasmania, Hobart, TAS, 7001, Australia
| | - Francois F Barbier
- School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
- Institute for Plant Sciences of Montpellier, University of Montpellier, CNRS, INRAe, Institut Agro, Montpellier, 34060, France
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Philipp Westhoff
- Cluster of Excellence in Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Anna Moseler
- INRES-Chemical Signalling, University of Bonn, Bonn, 53113, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Steven M Smith
- ARC Centre for Plant Success in Nature and Agriculture, School of Natural Sciences, University of Tasmania, Hobart, TAS, 7001, Australia
| | - Christine A Beveridge
- School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
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2
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Li J, Yao X, Lai H, Zhang X, Zhong J. The diversification of the shoot branching system: A quantitative and comparative perspective in meristem determinacy. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102574. [PMID: 38917775 DOI: 10.1016/j.pbi.2024.102574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
Reiterative shoot branching largely defines important yield components of crops and is essentially controlled by programs that direct the initiation, dormancy release, and differentiation of meristems in the axils of leaves. Here, we focus on meristem determinacy, defining the number of reiterations that shape the shoot architectures and exhibit enormous diversity in a wide range of species. The meristem determinacy per se is hierarchically complex and context-dependent for the successively emerged meristems, representing a crucial mechanism in shaping the complexity of the shoot branching. In addition, we have highlighted that two key components of axillary meristem developmental programs may have been co-opted in controlling flower/ear number of an axillary inflorescence in legumes/maize, hinting at the diversification of axillary-meristem-patterning programs in different lineages. This begs the question how axillary meristem patterning programs may have diversified during plant evolution and hence helped shape the rich variation in shoot branching systems.
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Affiliation(s)
- Jiajia Li
- Guangdong Laboratory for Lingnan Modern Agriculture & the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources & College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Xiani Yao
- Guangdong Laboratory for Lingnan Modern Agriculture & the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources & College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Huan Lai
- Guangdong Laboratory for Lingnan Modern Agriculture & the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources & College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Xuelian Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture & the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources & College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jinshun Zhong
- Guangdong Laboratory for Lingnan Modern Agriculture & the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources & College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Laboratory of the Developmental Biology and Environmental Adaptation of Agricultural Organisms, South China Agricultural University, Guangzhou 510642, Guangdong, China; South China Institute for Soybean Innovation Research, South China Agricultural University, Guangzhou 510642, Guangdong, China.
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3
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Ou S, Scheben A, Collins T, Qiu Y, Seetharam AS, Menard CC, Manchanda N, Gent JI, Schatz MC, Anderson SN, Hufford MB, Hirsch CN. Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Res 2024:gr.278131.123. [PMID: 39251347 PMCID: PMC11444183 DOI: 10.1101/gr.278131.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/12/2024] [Indexed: 09/11/2024]
Abstract
Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (n = 216) of TE families, mainly LTR retrotransposons, drive these differences. Evidence from the methylome, transcriptome, LTR age distribution, and LTR insertional polymorphisms reveals that 64.7% of the variability is contributed by LTR families that are young, less methylated, and more expressed in tropical maize, whereas 18.5% is driven by LTR families with removal or loss in temperate maize. Additionally, we find enrichment for Young LTR families adjacent to nucleotide-binding and leucine-rich repeat (NLR) clusters of varying copy number across lines, suggesting TE activity may be associated with disease resistance in maize.
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Affiliation(s)
- Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Tyler Collins
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Claire C Menard
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Sarah N Anderson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA;
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA;
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Yang H, Zhou K, Wu Q, Jia X, Wang H, Yang W, Lin L, Hu X, Pan B, Li P, Huang T, Xu X, Li J, Jiang J, Du M. The tomato WRKY-B transcription factor modulates lateral branching by targeting BLIND, PIN4, and IAA15. HORTICULTURE RESEARCH 2024; 11:uhae193. [PMID: 39257542 PMCID: PMC11384121 DOI: 10.1093/hr/uhae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/05/2024] [Indexed: 09/12/2024]
Abstract
Lateral branching is a crucial agronomic trait that impacts crop yield. In tomato ( Solanum lycopersicum ), excessive lateral branching is unfavorable and results in substantial labor and management costs. Therefore, optimizing lateral branching is a primary objective in tomato breeding. Although many genes related to lateral branching have been reported in tomato, the molecular mechanism underlying their network remains elusive. In this study, we found that the expression profile of a WRKY gene, WRKY-B (for WRKY-BRANCING), was associated with the auxin-dependent axillary bud development process. Wrky-b mutants generated by the CRISPR/Cas9 editing system presented fewer lateral branches, while WRKY-B overexpression lines presented more lateral branches than did wild-type plants. Furthermore, WRKY-B can directly target the well-known branching gene BLIND (BL) and the auxin efflux carrier gene PIN4 to activate their expression. Both the bl and pin4 mutants exhibited reduced lateral branching, similar to the wrky-b mutant. The IAA contents in the axillary buds of the wrky-b, bl, and pin4 mutant plants were significantly higher than those in the wild-type plants. In addition, WRKY-B can also directly target the AUX/IAA gene IAA15 and repress its expression. In summary, WRKY-B works upstream of BL, PIN4, and IAA15 to regulate the development of lateral branches in tomato.
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Affiliation(s)
- Huanhuan Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Ke Zhou
- College of Horticulture, China Agricultural University, Beijing 100083, China
| | - Qingfei Wu
- College of Life Sciences, Yan'an University, Yan'an 716000, China
| | - Xinyi Jia
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Hexuan Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Wenhui Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Lihao Lin
- College of Agriculture, Ningxia Universisty, Yinchuan 750002, China
| | - Xiaomeng Hu
- College of Horticulture, China Agricultural University, Beijing 100083, China
| | - Bingqing Pan
- College of Horticulture, China Agricultural University, Beijing 100083, China
| | - Ping Li
- Qingdao Academy of Agricultural Sciences, Qingdao City 266000, China
| | - Tingting Huang
- Qingdao Academy of Agricultural Sciences, Qingdao City 266000, China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Jingfu Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Minmin Du
- College of Horticulture, China Agricultural University, Beijing 100083, China
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5
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Tang L, Zhang Z, Sun L, Gao X, Zhao X, Chen X, Zhu X, Li A, Sun L. In Vivo Detection of Abscisic Acid in Tomato Leaves Based on a Disposable Stainless Steel Electrochemical Immunosensor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17666-17674. [PMID: 39051566 DOI: 10.1021/acs.jafc.4c03594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Abscisic acid (ABA) plays an important regulatory role in plants. It is very critical to obtain the dynamic changes of ABA in situ for botanical research. Herein, coupled with paper-based analysis devices, electrochemical immunoelectrodes based on disposable stainless steels sheet were developed for ABA detection in plants in situ. The stainless steel sheets were modified with carbon cement, ferrocene-graphene oxide-multi walled carbon nanotubes nanocomposites, and ABA antibodies. The system can detect the ABA in the range of 1 nM to 100 μM, with a limit of detection of 100 pM. The ABA content in tomato leaves under high salinity was detected in situ. The trend of ABA changes was similar to the expression of SlNCED1 and SlNCED2. Overall, this study offers an approach for in situ detection of ABA in plants, which will help to study the regulation mechanism of ABA in plants and to promote the development of precision agriculture.
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Affiliation(s)
- Lingjuan Tang
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, China
- Analysis and Testing Center, Nantong University, Nantong, Jiangsu 226019, China
| | - Zhiyao Zhang
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, China
| | - Ling Sun
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, China
| | - Xu Gao
- School of Chemistry and Materials Science, East China University of Technology, Nanchang, Jiangxi 330013, China
| | - Xinyue Zhao
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, China
| | - Xinru Chen
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, China
| | - Xingyu Zhu
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, China
| | - Aixue Li
- Research Center of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lijun Sun
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, China
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6
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Wang X, Yan L, Li T, Zhang J, Zhang Y, Zhang J, Lian X, Zhang H, Zheng X, Hou N, Cheng J, Wang W, Zhang L, Ye X, Li J, Feng J, Tan B. The lncRNA1-miR6288b-3p-PpTCP4-PpD2 module regulates peach branch number by affecting brassinosteroid biosynthesis. THE NEW PHYTOLOGIST 2024; 243:1050-1064. [PMID: 38872462 DOI: 10.1111/nph.19903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 05/23/2024] [Indexed: 06/15/2024]
Abstract
Branch number is one of the most important agronomic traits of fruit trees such as peach. Little is known about how LncRNA and/or miRNA modules regulate branching through transcription factors. Here, we used molecular and genetic tools to clarify the molecular mechanisms underlying brassinosteroid (BR) altering plant branching. We found that the number of sylleptic branch and BR content in pillar peach ('Zhaoshouhong') was lower than those of standard type ('Okubo'), and exogenous BR application could significantly promote branching. PpTCP4 expressed great differentially comparing 'Zhaoshouhong' with 'Okubo'. PpTCP4 could directly bind to DWARF2 (PpD2) and inhibited its expression. PpD2 was the only one differentially expressed key gene in the path of BR biosynthesis. At the same time, PpTCP4 was identified as a target of miR6288b-3p. LncRNA1 could act as the endogenous target mimic of miR6288b-3p and repress expression of miR6288b-3p. Three deletions and five SNP sites of lncRNA1 promoter were found in 'Zhaoshouhong', which was an important cause of different mRNA level of PpTCP4 and BR content. Moreover, overexpressed PpTCP4 significantly inhibited branching. A novel mechanism in which the lncRNA1-miR6288b-3p-PpTCP4-PpD2 module regulates peach branching number was proposed.
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Affiliation(s)
- Xiaobei Wang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Lixia Yan
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Tianhao Li
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Jie Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Yajia Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Junjie Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Xiaodong Lian
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Haipeng Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Nan Hou
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Jun Cheng
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Wei Wang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Langlang Zhang
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Xia Ye
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Jidong Li
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- College of Forestry, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
| | - Bin Tan
- College of Horticulture, Henan Agricultural University, 218 Pingan Road, Zhengzhou, 450046, China
- Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China
- Henan Provincial International Joint Laboratory of Horticultural Crops, Zhengzhou, 450046, China
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7
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Gomez-Cano F, Rodriguez J, Zhou P, Chu YH, Magnusson E, Gomez-Cano L, Krishnan A, Springer NM, de Leon N, Grotewold E. Prioritizing Maize Metabolic Gene Regulators through Multi-Omic Network Integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582075. [PMID: 38464086 PMCID: PMC10925184 DOI: 10.1101/2024.02.26.582075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Elucidating gene regulatory networks is a major area of study within plant systems biology. Phenotypic traits are intricately linked to specific gene expression profiles. These expression patterns arise primarily from regulatory connections between sets of transcription factors (TFs) and their target genes. Here, we integrated 46 co-expression networks, 283 protein-DNA interaction (PDI) assays, and 16 million SNPs used to identify expression quantitative trait loci (eQTL) to construct TF-target networks. In total, we analyzed ∼4.6M interactions to generate four distinct types of TF-target networks: co-expression, PDI, trans -eQTL, and cis -eQTL combined with PDIs. To functionally annotate TFs based on their target genes, we implemented three different network integration strategies. We evaluated the effectiveness of each strategy through TF loss-of function mutant inspection and random network analyses. The multi-network integration allowed us to identify transcriptional regulators of several biological processes. Using the topological properties of the fully integrated network, we identified potential functionally redundant TF paralogs. Our findings retrieved functions previously documented for numerous TFs and revealed novel functions that are crucial for informing the design of future experiments. The approach here-described lays the foundation for the integration of multi-omic datasets in maize and other plant systems. GRAPHICAL ABSTRACT
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8
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Colleoni PE, van Es SW, Winkelmolen T, Immink RGH, van Esse GW. Flowering time genes branching out. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4195-4209. [PMID: 38470076 PMCID: PMC11263490 DOI: 10.1093/jxb/erae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/11/2024] [Indexed: 03/13/2024]
Abstract
Plants are sessile by nature, and as such they have evolved to sense changes in seasonality and their surrounding environment, and adapt to these changes. One prime example of this is the regulation of flowering time in angiosperms, which is precisely timed by the coordinated action of two proteins: FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1). Both of these regulators are members of the PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN (PEBP) family of proteins. These regulatory proteins do not interact with DNA themselves, but instead interact with transcriptional regulators, such as FLOWERING LOCUS D (FD). FT and TFL1 were initially identified as key regulators of flowering time, acting through binding with FD; however, PEBP family members are also involved in shaping plant architecture and development. In addition, PEBPs can interact with TCP transcriptional regulators, such as TEOSINTE BRANCHED 1 (TB1), a well-known regulator of plant architecture, and key domestication-related genes in many crops. Here, we review the role of PEBPs in flowering time, plant architecture, and development. As these are also key yield-related traits, we highlight examples from the model plant Arabidopsis as well as important food and feed crops such as, rice, barley, wheat, tomato, and potato.
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Affiliation(s)
- Pierangela E Colleoni
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Sam W van Es
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Ton Winkelmolen
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Richard G H Immink
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - G Wilma van Esse
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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9
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Guerrero-Méndez C, Abraham-Juárez MJ. Factors specifying sex determination in maize. PLANT REPRODUCTION 2024; 37:171-178. [PMID: 37966579 PMCID: PMC11180155 DOI: 10.1007/s00497-023-00485-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/21/2023] [Indexed: 11/16/2023]
Abstract
Plant architecture is an important feature for agronomic performance in crops. In maize, which is a monoecious plant, separation of floral organs to produce specific gametes has been studied from different perspectives including genetic, biochemical and physiological. Maize mutants affected in floral organ development have been key to identifying genes, hormones and other factors like miRNAs important for sex determination. In this review, we describe floral organ formation in maize, representative mutants and genes identified with a function in establishing sexual identity either classified as feminizing or masculinizing, and its relationship with hormones associated with sexual organ identity as jasmonic acid, brassinosteroid and gibberellin. Finally, we discuss the challenges and scopes of future research in maize sex determination.
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Affiliation(s)
- Cristina Guerrero-Méndez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 36821, Irapuato, Mexico
| | - María Jazmín Abraham-Juárez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 36821, Irapuato, Mexico.
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10
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Prakash NR, Kumar K, Muthusamy V, Zunjare RU, Hossain F. Unique genetic architecture of prolificacy in 'Sikkim Primitive' maize unraveled through whole-genome resequencing-based DNA polymorphism. PLANT CELL REPORTS 2024; 43:134. [PMID: 38702564 DOI: 10.1007/s00299-024-03176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/13/2024] [Indexed: 05/06/2024]
Abstract
KEY MESSAGE 'Sikkim Primitive' maize landrace, unique for prolificacy (7-9 ears per plant) possesses unique genomic architecture in branching and inflorescence-related gene(s), and locus Zm00001eb365210 encoding glycosyltransferases was identified as the putative candidate gene underlying QTL (qProl-SP-8.05) for prolificacy. The genotype possesses immense usage in breeding high-yielding baby-corn genotypes. 'Sikkim Primitive' is a native landrace of North Eastern Himalayas, and is characterized by having 7-9 ears per plant compared to 1-2 ears in normal maize. Though 'Sikkim Primitive' was identified in the 1960s, it has not been characterized at a whole-genome scale. Here, we sequenced the entire genome of an inbred (MGUSP101) derived from 'Sikkim Primitive' along with three non-prolific (HKI1128, UMI1200, and HKI1105) and three prolific (CM150Q, CM151Q and HKI323) inbreds. A total of 942,417 SNPs, 24,160 insertions, and 27,600 deletions were identified in 'Sikkim Primitive'. The gene-specific functional mutations in 'Sikkim Primitive' were classified as 10,847 missense (54.36%), 402 non-sense (2.015%), and 8,705 silent (43.625%) mutations. The number of transitions and transversions specific to 'Sikkim Primitive' were 666,021 and 279,950, respectively. Among all base changes, (G to A) was the most frequent (215,772), while (C to G) was the rarest (22,520). Polygalacturonate 4-α-galacturonosyltransferase enzyme involved in pectin biosynthesis, cell-wall organization, nucleotide sugar, and amino-sugar metabolism was found to have unique alleles in 'Sikkim Primitive'. The analysis further revealed the Zm00001eb365210 gene encoding glycosyltransferases as the putative candidate underlying QTL (qProl-SP-8.05) for prolificacy in 'Sikkim Primitive'. High-impact nucleotide variations were found in ramosa3 (Zm00001eb327910) and zeaxanthin epoxidase1 (Zm00001eb081460) genes having a role in branching and inflorescence development in 'Sikkim Primitive'. The information generated unraveled the genetic architecture and identified key genes/alleles unique to the 'Sikkim Primitive' genome. This is the first report of whole-genome characterization of the 'Sikkim Primitive' landrace unique for its high prolificacy.
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Affiliation(s)
- Nitish Ranjan Prakash
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, Delhi, 110012, India
| | - Vignesh Muthusamy
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India
| | | | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India.
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Jue D, Li Z, Zhang W, Tang J, Xie T, Sang X, Guo Q. Identification and functional analysis of the LEAFY gene in longan flower induction. BMC Genomics 2024; 25:308. [PMID: 38528464 DOI: 10.1186/s12864-024-10229-x] [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: 01/19/2023] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Flowering at the right time is a very important factor affecting the stable annual yield of longan. However, a lack of knowledge of the regulatory mechanism and key genes of longan flowering restricts healthy development of the longan industry. Therefore, identifying relevant genes and analysing their regulatory mechanism are essential for scientific research and longan industry development. RESULTS DlLFY (Dimocarpus longan LEAFY) contains a 1167 bp open reading frame and encodes 388 amino acids. The amino acid sequence has a typical LFY/FLO family domain. DlLFY was expressed in all tissues tested, except for the leaf, pericarp, and pulp, with the highest expression occurring in flower buds. Expression of DlLFY was significantly upregulated at the early flower induction stage in "SX" ("Shixia"). The results of subcellular localization and transactivation analysis showed that DlLFY is a typical transcription factor acting as a transcriptional activator. Moreover, overexpression of DlLFY in Arabidopsis promoted early flowering and restrained growth, resulting in reduced plant height and rosette leaf number and area in transgenic plants. DNA affinity purification sequencing (DAP-Seq) analysis showed that 13 flower-related genes corresponding to five homologous genes of Arabidopsis may have binding sites and be putative target genes. Among these five flower-related genes, only AtTFL1 (terminal flower 1) was strongly inhibited in transgenic lines. CONCLUSION Taken together, these results indicate that DlLFY plays a pivotal role in controlling longan flowering, possibly by interacting with TFL1.
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Affiliation(s)
- Dengwei Jue
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400715, Chongqing, Beibei, China
| | - Zhexin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Wenlin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Jianmin Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Ting Xie
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Xuelian Sang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China.
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400715, Chongqing, Beibei, China.
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Xie S, Luo H, Huang W, Jin W, Dong Z. Striking a growth-defense balance: Stress regulators that function in maize development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:424-442. [PMID: 37787439 DOI: 10.1111/jipb.13570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/01/2023] [Indexed: 10/04/2023]
Abstract
Maize (Zea mays) cultivation is strongly affected by both abiotic and biotic stress, leading to reduced growth and productivity. It has recently become clear that regulators of plant stress responses, including the phytohormones abscisic acid (ABA), ethylene (ET), and jasmonic acid (JA), together with reactive oxygen species (ROS), shape plant growth and development. Beyond their well established functions in stress responses, these molecules play crucial roles in balancing growth and defense, which must be finely tuned to achieve high yields in crops while maintaining some level of defense. In this review, we provide an in-depth analysis of recent research on the developmental functions of stress regulators, focusing specifically on maize. By unraveling the contributions of these regulators to maize development, we present new avenues for enhancing maize cultivation and growth while highlighting the potential risks associated with manipulating stress regulators to enhance grain yields in the face of environmental challenges.
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Affiliation(s)
- Shiyi Xie
- Maize Engineering and Technology Research Center of Hunan Province, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Hongbing Luo
- Maize Engineering and Technology Research Center of Hunan Province, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Wei Huang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiwei Jin
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- Tianjin Key Laboratory of Intelligent Breeding of Major Crops, Fresh Corn Research Center of BTH, College of Agronomy & Resources and Environment, Tianjin Agricultural University, Tianjin, 300384, China
| | - Zhaobin Dong
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
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13
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Miret JA, Griffiths CA, Paul MJ. Sucrose homeostasis: Mechanisms and opportunity in crop yield improvement. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154188. [PMID: 38295650 DOI: 10.1016/j.jplph.2024.154188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 03/10/2024]
Abstract
Sugar homeostasis is a critical feature of biological systems. In humans, raised and dysregulated blood sugar is a serious health issue. In plants, directed changes in sucrose homeostasis and allocation represent opportunities in crop improvement. Plant tissue sucrose varies more than blood glucose and is found at higher concentrations (cytosol and phloem ca. 100 mM v 3.9-6.9 mM for blood glucose). Tissue sucrose varies with developmental stage and environment, but cytosol and phloem exhibit tight sucrose control. Sucrose homeostasis is a consequence of the integration of photosynthesis, synthesis of storage end-products such as starch, transport of sucrose to sinks and sink metabolism. Trehalose 6-phosphate (T6P)-SnRK1 and TOR play central, still emerging roles in regulating and coordinating these processes. Overall, tissue sucrose levels are more strongly related to growth than to photosynthesis. As a key sucrose signal, T6P regulates sucrose levels, transport and metabolic pathways to coordinate source and sink at a whole plant level. Emerging evidence shows that T6P interacts with meristems. With careful targeting, T6P manipulation through exploiting natural variation, chemical intervention and genetic modification is delivering benefits for crop yields. Regulation of cereal grain set, filling and retention may be the most strategically important aspect of sucrose allocation and homeostasis for food security.
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Affiliation(s)
- Javier A Miret
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Cara A Griffiths
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Matthew J Paul
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
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14
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van Es SW, Muñoz-Gasca A, Romero-Campero FJ, González-Grandío E, de Los Reyes P, Tarancón C, van Dijk ADJ, van Esse W, Pascual-García A, Angenent GC, Immink RGH, Cubas P. A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1. THE NEW PHYTOLOGIST 2024; 241:1193-1209. [PMID: 38009929 DOI: 10.1111/nph.19420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/21/2023] [Indexed: 11/29/2023]
Abstract
The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in the control of shoot branching as it integrates environmental and endogenous signals that influence axillary bud growth. Despite its remarkable activity as a growth inhibitor, the mechanisms by which BRC1 promotes bud dormancy are largely unknown. We determined the genome-wide BRC1 binding sites in vivo and combined these with transcriptomic data and gene co-expression analyses to identify bona fide BRC1 direct targets. Next, we integrated multi-omics data to infer the BRC1 gene regulatory network (GRN) and used graph theory techniques to find network motifs that control the GRN dynamics. We generated an open online tool to interrogate this network. A group of BRC1 target genes encoding transcription factors (BTFs) orchestrate this intricate transcriptional network enriched in abscisic acid-related components. Promoter::β-GLUCURONIDASE transgenic lines confirmed that BTFs are expressed in axillary buds. Transient co-expression assays and studies in planta using mutant lines validated the role of BTFs in modulating the GRN and promoting bud dormancy. This knowledge provides access to the developmental mechanisms that regulate shoot branching and helps identify candidate genes to use as tools to adapt plant architecture and crop production to ever-changing environmental conditions.
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Affiliation(s)
- Sam W van Es
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Aitor Muñoz-Gasca
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Francisco J Romero-Campero
- Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla - Consejo Superior de Investigaciones Científicas, Ave. Américo Vespucio 49, 41092, Seville, Spain
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Ave. Reina Mercedes s/n, 41012, Seville, Spain
| | - Eduardo González-Grandío
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Pedro de Los Reyes
- Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla - Consejo Superior de Investigaciones Científicas, Ave. Américo Vespucio 49, 41092, Seville, Spain
| | - Carlos Tarancón
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Aalt D J van Dijk
- Bioinformatics, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Wilma van Esse
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Alberto Pascual-García
- Department of Systems Biology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Gerco C Angenent
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Richard G H Immink
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Pilar Cubas
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
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15
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Pan Z, Lu X, Xu T, Chen J, Bao L, Li Y, Gong Y, Che Y, Zou X, Tan Z, Huang P, Ge M. Epigenetic inhibition of CTCF by HN1 promotes dedifferentiation and stemness of anaplastic thyroid cancer. Cancer Lett 2024; 580:216496. [PMID: 37993084 DOI: 10.1016/j.canlet.2023.216496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/02/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023]
Abstract
Anaplastic thyroid cancer (ATC) is one of the deadliest cancers, whose important malignant feature is dedifferentiation. Chromatin remodeling is critical for tumorigenesis and progression, while its roles and regulator in facilitating dedifferentiation of ATC had been poorly understood. In our study, an emerging function of hematological and neurological expressed 1 (HN1) in promoting dedifferentiation of ATC cells was uncovered. HN1 expression was negatively correlated with the thyroid differentiation markers both at mRNA and protein level. Knockdown of HN1 in ATC cells effectively upregulated the thyroid differentiation markers and impeded the sphere formation capacity, accompanying with the loss of cancer stemness. In contrast, overexpression of HN1 drove the gain of stemness and the loss of thyroid differentiation markers. Nude mouse and zebrafish xenograft models showed that inhibition of HN1 in ATC cells effectively hindered tumor growth due to the loss of cancer stemness. Further study showed that HN1 was negatively correlated with CTCF in an independent thyroid-cancer cohort, and inhibition of HN1 enhanced the expression of CTCF in ATC cells. Overexpression of CTCF significantly reversed the dedifferentiation phenotypes of ATC cells, whereas simultaneously inhibiting HN1 and CTCF was unable to recover the level of thyroid differentiation markers. The combination of ATAC-seq and ChIP-seq analysis confirmed that CTCF regulated genes relating with thyroid gland development through influencing their chromatin accessibility. HN1 inhibited the acetylation of H3K27 at the promoter of CTCF by recruiting HDAC2, thereby inhibiting the transcriptional activation of CTCF. These findings demonstrated an essential role of HN1 in regulating the chromatin accessibility of thyroid differentiation genes during ATC dedifferentiation.
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Affiliation(s)
- Zongfu Pan
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, China
| | - Xixuan Lu
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China
| | - Tong Xu
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China
| | - Jinming Chen
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China
| | - Lisha Bao
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China
| | - Ying Li
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China
| | - Yingying Gong
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China
| | - Yulu Che
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China
| | - Xiaozhou Zou
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, China
| | - Zhuo Tan
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, China
| | - Ping Huang
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, China.
| | - Minghua Ge
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, China.
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16
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Lindsay P, Swentowsky KW, Jackson D. Cultivating potential: Harnessing plant stem cells for agricultural crop improvement. MOLECULAR PLANT 2024; 17:50-74. [PMID: 38130059 DOI: 10.1016/j.molp.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.
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Affiliation(s)
- Penelope Lindsay
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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17
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Duan A, Liu R, Liu C, Wu F, Su H, Zhou S, Huang M, Tian X, Jia H, Liu Y, Li M, Du H. Mutation of the gene encoding the PHD-type transcription factor SAB23 confers submergence tolerance in rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:168-179. [PMID: 37798132 DOI: 10.1093/jxb/erad388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023]
Abstract
Submergence is a major constraint on rice production in South and Southeast Asia. In this study, we determined that a gene of the Sub1A-binding protein family, SAB23, encodes a plant homeodomain (PHD)-type transcription factor that has a novel function of negatively regulating submergence tolerance in rice. The T-DNA insertion mutant sab23 displayed reduced plant height, delayed seed maturation, and lower percentage seed set. Importantly, this mutant also exhibited enhanced submergence tolerance. In addition, CRISPR/Cas9 knock out of SAB23 resulted in a significant reduction in the content of the gibberellin GA4 and a dramatic increase in the content of GA1 in the plants. SAB23 binds to the promoter of CYTOCHROME P450 714B2 (CYP714B2), which encodes a GA13-oxidase that catalyses the conversion of GA53 to GA19. Disruption of SAB23 function led to increased CYP714B2 transcription, and overexpression of CYP714B2 produced phenotypes similar to those of the SAB23-knockout plants. Taken together, our results reveal that SAB23 negatively regulates rice submergence tolerance by modulating CYP714B2 expression, which has significant potential for use in future breeding.
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Affiliation(s)
- Ao Duan
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Rui Liu
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Changchang Liu
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Fei Wu
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Hang Su
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Shuangzhen Zhou
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Min Huang
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Xiaohai Tian
- Hubei Collaborative Innovation Center for Grain Crops, Yangzte University, Jingzhou 434025, P.R. China
| | - Haitao Jia
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, P.R. China
| | - Ya Liu
- Maize Research Institute, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100097, P.R. China
| | - Manfei Li
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Hewei Du
- College of Life Science, Yangtze University, Jingzhou, Hubei 434025, P.R. China
- Hubei Collaborative Innovation Center for Grain Crops, Yangzte University, Jingzhou 434025, P.R. China
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18
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Gallagher JP, Man J, Chiaramida A, Rozza IK, Patterson EL, Powell MM, Schrager-Lavelle A, Multani DS, Meeley RB, Bartlett ME. GRASSY TILLERS1 ( GT1) and SIX-ROWED SPIKE1 ( VRS1) homologs share conserved roles in growth repression. Proc Natl Acad Sci U S A 2023; 120:e2311961120. [PMID: 38096411 PMCID: PMC10742383 DOI: 10.1073/pnas.2311961120] [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: 07/21/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Crop engineering and de novo domestication using gene editing are new frontiers in agriculture. However, outside of well-studied crops and model systems, prioritizing engineering targets remains challenging. Evolution can guide us, revealing genes with deeply conserved roles that have repeatedly been selected in the evolution of plant form. Homologs of the transcription factor genes GRASSY TILLERS1 (GT1) and SIX-ROWED SPIKE1 (VRS1) have repeatedly been targets of selection in domestication and evolution, where they repress growth in many developmental contexts. This suggests a conserved role for these genes in regulating growth repression. To test this, we determined the roles of GT1 and VRS1 homologs in maize (Zea mays) and the distantly related grass brachypodium (Brachypodium distachyon) using gene editing and mutant analysis. In maize, gt1; vrs1-like1 (vrl1) mutants have derepressed growth of floral organs. In addition, gt1; vrl1 mutants bore more ears and more branches, indicating broad roles in growth repression. In brachypodium, Bdgt1; Bdvrl1 mutants have more branches, spikelets, and flowers than wild-type plants, indicating conserved roles for GT1 and VRS1 homologs in growth suppression over ca. 59 My of grass evolution. Importantly, many of these traits influence crop productivity. Notably, maize GT1 can suppress growth in arabidopsis (Arabidopsis thaliana) floral organs, despite ca. 160 My of evolution separating the grasses and arabidopsis. Thus, GT1 and VRS1 maintain their potency as growth regulators across vast timescales and in distinct developmental contexts. This work highlights the power of evolution to inform gene editing in crop improvement.
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Affiliation(s)
- Joseph P. Gallagher
- Biology Department, University of Massachusetts, Amherst, MA01003
- Forage Seed and Cereal Research Unit, US Department of Agriculture, Agricultural Research Service, Corvallis, OR97331
| | - Jarrett Man
- Biology Department, University of Massachusetts, Amherst, MA01003
| | | | | | | | - Morgan M. Powell
- Biology Department, University of Massachusetts, Amherst, MA01003
| | | | - Dilbag S. Multani
- Corteva Agriscience, Johnston, IA50131
- Napigen, Inc., Wilmington, DE19803
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19
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Göbel M, Fichtner F. Functions of sucrose and trehalose 6-phosphate in controlling plant development. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154140. [PMID: 38007969 DOI: 10.1016/j.jplph.2023.154140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/28/2023]
Abstract
Plants exhibit enormous plasticity in regulating their architecture to be able to adapt to a constantly changing environment and carry out vital functions such as photosynthesis, anchoring, and nutrient uptake. Phytohormones play a role in regulating these responses, but sugar signalling mechanisms are also crucial. Sucrose is not only an important source of carbon and energy fuelling plant growth, but it also functions as a signalling molecule that influences various developmental processes. Trehalose 6-phosphate (Tre6P), a sucrose-specific signalling metabolite, is emerging as an important regulator in plant metabolism and development. Key players involved in sucrose and Tre6P signalling pathways, including MAX2, SnRK1, bZIP11, and TOR, have been implicated in processes such as flowering, branching, and root growth. We will summarize our current knowledge of how these pathways shape shoot and root architecture and highlight how sucrose and Tre6P signalling are integrated with known signalling networks in shaping plant growth.
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Affiliation(s)
- Moritz Göbel
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Plant Biochemistry, Germany; Cluster of Excellences on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Germany
| | - Franziska Fichtner
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Plant Biochemistry, Germany; Cluster of Excellences on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Germany.
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20
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Sen S, Woodhouse MR, Portwood JL, Andorf CM. Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications. Database (Oxford) 2023; 2023:baad078. [PMID: 37935586 PMCID: PMC10634621 DOI: 10.1093/database/baad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 09/16/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The big-data analysis of complex data associated with maize genomes accelerates genetic research and improves agronomic traits. As a result, efforts have increased to integrate diverse datasets and extract meaning from these measurements. Machine learning models are a powerful tool for gaining knowledge from large and complex datasets. However, these models must be trained on high-quality features to succeed. Currently, there are no solutions to host maize multi-omics datasets with end-to-end solutions for evaluating and linking features to target gene annotations. Our work presents the Maize Feature Store (MFS), a versatile application that combines features built on complex data to facilitate exploration, modeling and analysis. Feature stores allow researchers to rapidly deploy machine learning applications by managing and providing access to frequently used features. We populated the MFS for the maize reference genome with over 14 000 gene-based features based on published genomic, transcriptomic, epigenomic, variomic and proteomics datasets. Using the MFS, we created an accurate pan-genome classification model with an AUC-ROC score of 0.87. The MFS is publicly available through the maize genetics and genomics database. Database URL https://mfs.maizegdb.org/.
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Affiliation(s)
- Shatabdi Sen
- Department of Plant Pathology & Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg, 2213 Pammel Dr, Ames, IA 50011, USA
| | - Margaret R Woodhouse
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, IA 50011, USA
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, IA 50011, USA
- Department of Computer Science, Iowa State University, Atanasoff Hall, 2434 Osborn Dr, Ames, IA 50011, USA
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21
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Shanmugaraj N, Rajaraman J, Kale S, Kamal R, Huang Y, Thirulogachandar V, Garibay-Hernández A, Budhagatapalli N, Tandron Moya YA, Hajirezaei MR, Rutten T, Hensel G, Melzer M, Kumlehn J, von Wirén N, Mock HP, Schnurbusch T. Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence. THE PLANT CELL 2023; 35:3973-4001. [PMID: 37282730 PMCID: PMC10615218 DOI: 10.1093/plcell/koad164] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/17/2023] [Accepted: 06/04/2023] [Indexed: 06/08/2023]
Abstract
Leaf and floral tissue degeneration is a common feature in plants. In cereal crops such as barley (Hordeum vulgare L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of the inflorescence meristem dome, which is followed basipetally by the degeneration of floral primordia and the central axis. Due to its quantitative nature and environmental sensitivity, inflorescence PTD constitutes a complex, multilayered trait affecting final grain number. This trait appears to be highly predictable and heritable under standardized growth conditions, consistent with a developmentally programmed mechanism. To elucidate the molecular underpinnings of inflorescence PTD, we combined metabolomic, transcriptomic, and genetic approaches to show that barley inflorescence PTD is accompanied by sugar depletion, amino acid degradation, and abscisic acid responses involving transcriptional regulators of senescence, defense, and light signaling. Based on transcriptome analyses, we identified GRASSY TILLERS1 (HvGT1), encoding an HD-ZIP transcription factor, as an important modulator of inflorescence PTD. A gene-edited knockout mutant of HvGT1 delayed PTD and increased differentiated apical spikelets and final spikelet number, suggesting a possible strategy to increase grain number in cereals. We propose a molecular framework that leads to barley PTD, the manipulation of which may increase yield potential in barley and other related cereals.
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Affiliation(s)
- Nandhakumar Shanmugaraj
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Sandip Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Venkatasubbu Thirulogachandar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Adriana Garibay-Hernández
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Nagaveni Budhagatapalli
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Yudelsy Antonia Tandron Moya
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Mohammed R Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
- Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Halle 06120,Germany
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22
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Chen S, Song X, Zheng Q, Liu Y, Yu J, Zhou Y, Xia X. The transcription factor SPL13 mediates strigolactone suppression of shoot branching by inhibiting cytokinin synthesis in Solanum lycopersicum. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5722-5735. [PMID: 37504507 PMCID: PMC10540736 DOI: 10.1093/jxb/erad303] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
Plant architecture imposes a large impact on crop yield. IDEAL PLANT ARCHITECTURE 1 (IPA1), which encodes a SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor, is a target of molecular design for improving grain yield. However, the roles of SPL transcription factors in regulating tomato (Solanum lycopersicum) plant architecture are unclear. Here, we show that the expression of SPL13 is down-regulated in the lateral buds of strigolactone (SL)-deficient ccd mutants and is induced by GR24 (a synthetic analog of SL). Knockout of SPL13 by CRISPR/Cas9 resulted in higher levels of cytokinins (CKs) and transcripts of the CK synthesis gene ISOPENTENYL TRANSFERASES 1 (IPT1) in the stem nodes, and more growth of lateral buds. GR24 suppresses CK synthesis and lateral bud growth in ccd mutants, but is not effective in spl13 mutants. On the other hand, silencing of the IPT1 gene inhibited bud growth of spl13 mutants. Interestingly, SL levels in root extracts and exudates are significantly increased in spl13 mutants. Molecular studies indicated that SPL13 directly represses the transcription of IPT1 and the SL synthesis genes CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7) and MORE AXILLARY GROWTH 1 (MAX1). The results demonstrate that SPL13 acts downstream of SL to suppress lateral bud growth by inhibiting CK synthesis in tomato. Tuning the expression of SPL13 is a potential approach for decreasing the number of lateral shoots in tomato.
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Affiliation(s)
- Shangyu Chen
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Xuewei Song
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Qixiang Zheng
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Yuqi Liu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Jingquan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
- Hainan Institute, Zhejiang University, Sanya 572025, PR China
- Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310058, PR China
| | - Yanhong Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
- Hainan Institute, Zhejiang University, Sanya 572025, PR China
| | - Xiaojian Xia
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
- Hainan Institute, Zhejiang University, Sanya 572025, PR China
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23
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Dun EA, Brewer PB, Gillam EMJ, Beveridge CA. Strigolactones and Shoot Branching: What Is the Real Hormone and How Does It Work? PLANT & CELL PHYSIOLOGY 2023; 64:967-983. [PMID: 37526426 PMCID: PMC10504579 DOI: 10.1093/pcp/pcad088] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/02/2023]
Abstract
There have been substantial advances in our understanding of many aspects of strigolactone regulation of branching since the discovery of strigolactones as phytohormones. These include further insights into the network of phytohormones and other signals that regulate branching, as well as deep insights into strigolactone biosynthesis, metabolism, transport, perception and downstream signaling. In this review, we provide an update on recent advances in our understanding of how the strigolactone pathway co-ordinately and dynamically regulates bud outgrowth and pose some important outstanding questions that are yet to be resolved.
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Affiliation(s)
- Elizabeth A Dun
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD 4072, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Philip B Brewer
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD 4072, Australia
- Waite Research Institute, School of Agriculture Food & Wine, The University of Adelaide, Adelaide, SA 5064, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Christine A Beveridge
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD 4072, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
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24
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Ma F, Zhang S, Yao Y, Chen M, Zhang N, Deng M, Chen W, Ma C, Zhang X, Guo C, Huang X, Zhang Z, Li Y, Li T, Zhou J, Sun Q, Sun J. Jujube witches' broom phytoplasmas inhibit ZjBRC1-mediated abscisic acid metabolism to induce shoot proliferation. HORTICULTURE RESEARCH 2023; 10:uhad148. [PMID: 37691966 PMCID: PMC10483173 DOI: 10.1093/hr/uhad148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/13/2023] [Indexed: 09/12/2023]
Abstract
Jujube witches' broom (JWB) phytoplasmas parasitize the sieve tubes of diseased phloem and cause an excessive proliferation of axillary shoots from dormant lateral buds to favour their transmission. In previous research, two JWB effectors, SJP1 and SJP2, were identified to induce lateral bud outgrowth by disrupting ZjBRC1-mediated auxin flux. However, the pathogenesis of JWB disease remains largely unknown. Here, tissue-specific transcriptional reprogramming was examined to gain insight into the genetic mechanisms acting inside jujube lateral buds under JWB phytoplasma infection. JWB phytoplasmas modulated a series of plant signalling networks involved in lateral bud development and defence, including auxin, abscisic acid (ABA), ethylene, jasmonic acid, and salicylic acid. JWB-induced bud outgrowth was accompanied by downregulation of ABA synthesis within lateral buds. ABA application rescued the bushy appearances of transgenic Arabidopsis overexpressing SJP1 and SJP2 in Col-0 and ZjBRC1 in the brc1-2 mutant. Furthermore, the expression of ZjBRC1 and ABA-related genes ZjHB40 and ZjNCED3 was negatively correlated with lateral main bud outgrowth in decapitated healthy jujube. Molecular evidence showed that ZjBRC1 interacted with ZjBRC2 via its N-terminus to activate ZjHB40 and ZjNCED3 expression and ABA accumulation in transgenic jujube calli. In addition, ZjBRC1 widely regulated differentially expressed genes related to ABA homeostasis and ABA signalling, especially by binding to and suppressing ABA receptors. Therefore, these results suggest that JWB phytoplasmas hijack the ZjBRC1-mediated ABA pathways to stimulate lateral bud outgrowth and expansion, providing a strategy to engineer plants resistant to JWB phytoplasma disease and regulate woody plant architecture to promote crop yield and quality.
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Affiliation(s)
- Fuli Ma
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Shanqi Zhang
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Yu Yao
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Mengting Chen
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Ning Zhang
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Mingsheng Deng
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Wei Chen
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Chi Ma
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Xinyue Zhang
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Chenglong Guo
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Xiang Huang
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Zhenyuan Zhang
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Yamei Li
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Tingyi Li
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
| | - Junyong Zhou
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
- Horticulture Research Institute, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei City 230031, Anhui Province, China
| | - Qibao Sun
- Horticulture Research Institute, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei City 230031, Anhui Province, China
| | - Jun Sun
- College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City 230036, Anhui Province, China
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25
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Li Z, Li C, Zhang R, Duan M, Tian H, Yi H, Xu L, Wang F, Shi Z, Wang X, Wang J, Su A, Wang S, Sun X, Zhao Y, Wang S, Zhang Y, Wang Y, Song W, Zhao J. Genomic analysis of a new heterotic maize group reveals key loci for pedigree breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1213675. [PMID: 37636101 PMCID: PMC10451083 DOI: 10.3389/fpls.2023.1213675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023]
Abstract
Genome-wide analyses of maize populations have clarified the genetic basis of crop domestication and improvement. However, limited information is available on how breeding improvement reshaped the genome in the process of the formation of heterotic groups. In this study, we identified a new heterotic group (X group) based on an examination of 512 Chinese maize inbred lines. The X group was clearly distinct from the other non-H&L groups, implying that X × HIL is a new heterotic pattern. We selected the core inbred lines for an analysis of yield-related traits. Almost all yield-related traits were better in the X lines than those in the parental lines, indicating that the primary genetic improvement in the X group during breeding was yield-related traits. We generated whole-genome sequences of these lines with an average coverage of 17.35× to explore genome changes further. We analyzed the identity-by-descent (IBD) segments transferred from the two parents to the X lines and identified 29 and 28 IBD conserved regions (ICRs) from the parents PH4CV and PH6WC, respectively, accounting for 28.8% and 12.8% of the genome. We also identified 103, 89, and 131 selective sweeps (SSWs) using methods that involved the π, Tajima's D, and CLR values, respectively. Notably, 96.13% of the ICRs co-localized with SSWs, indicating that SSW signals concentrated in ICRs. We identified 171 annotated genes associated with yield-related traits in maize both in ICRs and SSWs. To identify the genetic factors associated with yield improvement, we conducted QTL mapping for 240 lines from a DH population (PH4CV × PH6WC, which are the parents of X1132X) for ten key yield-related traits and identified a total of 55 QTLs. Furthermore, we detected three QTL clusters both in ICRs and SSWs. Based on the genetic evidence, we finally identified three key genes contributing to yield improvement in breeding the X group. These findings reveal key loci and genes targeted during pedigree breeding and provide new insights for future genomic breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yuandong Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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26
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Balarynová J, Klčová B, Tarkowská D, Turečková V, Trněný O, Špundová M, Ochatt S, Smýkal P. Domestication has altered the ABA and gibberellin profiles in developing pea seeds. PLANTA 2023; 258:25. [PMID: 37351659 PMCID: PMC10290032 DOI: 10.1007/s00425-023-04184-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
MAIN CONCLUSION We showed that wild pea seeds contained a more diverse combination of bioactive GAs and had higher ABA content than domesticated peas. Although the role of abscisic acid (ABA) and gibberellins (GAs) interplay has been extensively studied in Arabidopsis and cereals models, comparatively little is known about the effect of domestication on the level of phytohormones in legume seeds. In legumes, as in other crops, seed dormancy has been largely or entirely removed during domestication. In this study, we have measured the endogenous levels of ABA and GAs comparatively between wild and domesticated pea seeds during their development. We have shown that wild seeds contained more ABA than domesticated ones, which could be important for preparing the seeds for the period of dormancy. ABA was catabolised particularly by an 8´-hydroxylation pathway, and dihydrophaseic acid was the main catabolite in seed coats as well as embryos. Besides, the seed coats of wild and pigmented cultivated genotypes were characterised by a broader spectrum of bioactive GAs compared to non-pigmented domesticated seeds. GAs in both seed coat and embryo were synthesized mainly by a 13-hydroxylation pathway, with GA29 being the most abundant in the seed coat and GA20 in the embryos. Measuring seed water content and water loss indicated domesticated pea seeds´ desiccation was slower than that of wild pea seeds. Altogether, we showed that pea domestication led to a change in bioactive GA composition and a lower ABA content during seed development.
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Affiliation(s)
- Jana Balarynová
- Department of Botany, Faculty of Science, Palacky University, 783 71, Olomouc, Czech Republic
| | - Barbora Klčová
- Department of Botany, Faculty of Science, Palacky University, 783 71, Olomouc, Czech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Palacky University and Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc, Czech Republic
| | - Veronika Turečková
- Laboratory of Growth Regulators, Palacky University and Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc, Czech Republic
| | - Oldřich Trněný
- Agriculture Research Ltd., 664 41, Troubsko, Czech Republic
| | - Martina Špundová
- Department of Biophysics, Faculty of Science, Palacky University, 783 71, Olomouc, Czech Republic
| | - Sergio Ochatt
- Agroécologie, InstitutAgro Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacky University, 783 71, Olomouc, Czech Republic.
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27
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Tao XY, Guan XY, Hong GJ, He YQ, Li SJ, Feng SL, Wang J, Chen G, Xu F, Wang JW, Xu SC. Biotinylated Tn5 transposase-mediated CUT&Tag efficiently profiles transcription factor-DNA interactions in plants. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1191-1205. [PMID: 36786225 DOI: 10.1111/pbi.14029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 05/27/2023]
Abstract
In contrast to CUT&Tag approaches for profiling bulk histone modifications, current CUT&Tag methods for analysing specific transcription factor (TF)-DNA interactions remain technically challenging due to TFs having relatively low abundance. Moreover, an efficient CUT&Tag strategy for plant TFs is not yet available. Here, we first applied biotinylated Tn5 transposase-mediated CUT&Tag (B-CUT&Tag) to produce high-quality libraries for interrogating TF-DNA interactions. B-CUT&Tag combines streptavidin-biotin-based DNA purification with routine CUT&Tag, optimizing the removal of large amounts of intact chromatin not targeted by specific TFs. The biotinylated chromatin fragments are then purified for construction of deep sequencing libraries or qPCR analysis. We applied B-CUT&Tag to probe genome-wide DNA targets of Squamosa promoter-binding-like protein 9 (SPL9), a well-established TF in Arabidopsis; the resulting profiles were efficient and consistent in demonstrating its well-established target genes in juvenile-adult transition/flowering, trichome development, flavonoid biosynthesis, wax synthesis and branching. Interestingly, our results indicate functions of AtSPL9 in modulating growth-defence trade-offs. In addition, we established a method for applying qPCR after CUT&Tag (B-CUT&Tag-qPCR) and successfully validated the binding of SPL9 in Arabidopsis and PHR2 in rice. Our study thus provides a convenient and highly efficient CUT&Tag strategy for profiling TF-chromatin interactions that is widely applicable to the annotation of cis-regulatory elements for crop improvement.
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Affiliation(s)
- Xiao-Yuan Tao
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xue-Ying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Gao-Jie Hong
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yu-Qing He
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Su-Juan Li
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shou-Li Feng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jian Wang
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fei Xu
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Sheng-Chun Xu
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Xianghu Laboratory, Hangzhou, China
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Cao D, Chabikwa T, Barbier F, Dun EA, Fichtner F, Dong L, Kerr SC, Beveridge CA. Auxin-independent effects of apical dominance induce changes in phytohormones correlated with bud outgrowth. PLANT PHYSIOLOGY 2023; 192:1420-1434. [PMID: 36690819 PMCID: PMC10231355 DOI: 10.1093/plphys/kiad034] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 06/01/2023]
Abstract
The inhibition of shoot branching by the growing shoot tip of plants, termed apical dominance, was originally thought to be mediated by auxin. Recently, the importance of the shoot tip sink strength during apical dominance has re-emerged with recent studies highlighting roles for sugars in promoting branching. This raises many unanswered questions on the relative roles of auxin and sugars in apical dominance. Here we show that auxin depletion after decapitation is not always the initial trigger of rapid cytokinin (CK) increases in buds that are instead correlated with enhanced sugars. Auxin may also act through strigolactones (SLs) which have been shown to suppress branching after decapitation, but here we show that SLs do not have a significant effect on initial bud outgrowth after decapitation. We report here that when sucrose or CK is abundant, SLs are less inhibitory during the bud release stage compared to during later stages and that SL treatment rapidly inhibits CK accumulation in pea (Pisum sativum) axillary buds of intact plants. After initial bud release, we find an important role of gibberellin (GA) in promoting sustained bud growth downstream of auxin. We are, therefore, able to suggest a model of apical dominance that integrates auxin, sucrose, SLs, CKs, and GAs and describes differences in signalling across stages of bud release to sustained growth.
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Affiliation(s)
- Da Cao
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tinashe Chabikwa
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Francois Barbier
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Elizabeth A Dun
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Franziska Fichtner
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lili Dong
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Stephanie C Kerr
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christine A Beveridge
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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29
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Ishizaki T, Ueda Y, Takai T, Maruyama K, Tsujimoto Y. In-frame mutation in rice TEOSINTE BRANCHED1 (OsTB1) improves productivity under phosphorus deficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111627. [PMID: 36737003 DOI: 10.1016/j.plantsci.2023.111627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/04/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Tillering is an important trait in rice productivity. We introduced mutations into the coding region of rice TEOSINTE BRANCHED1 (OsTB1), which is a negative regulator of tillering, using CRISPR/Cas9. The frameshift mutants exhibited substantially enhanced tillering and produced 3.5 times more panicles than the non-mutated plants at maturity. This enhanced tillering resulted in increased spikelet number; however, grain yields did not increase due to substantially reduced filled grain rate and 1,000-grain weight. In contrast, in-frame mutations in OsTB1 had the effect of slightly increasing tiller numbers, and the in-frame mutants had 40% more panicles than non-mutated plants. The grain yield of in-frame mutants also did not increase on nutrient-rich soil; however, under phosphorus-deficient conditions, where tillering is constrained, the in-frame mutants gave a significantly higher grain yield than non-mutated plants due to higher spikelet number and maintained filled grain rate. Rice grassy tiller1 (OsGT1)/OsHox12, which is directly regulated by OsTB1 to suppress tillering, was moderately down-regulated in in-frame mutants, suggesting that OsTB1 with the in-frame mutation shows partial function of intact OsTB1 in regulating OsGT1/OsHox12. We propose that mildly enhanced tillering by in-frame mutation of OsTB1 can improve grain yield under low phosphorus conditions.
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Affiliation(s)
- Takuma Ishizaki
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS), Ishigaki, Okinawa 907-0002, Japan.
| | - Yoshiaki Ueda
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
| | - Toshiyuki Takai
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
| | - Kyonoshin Maruyama
- Biological Resources and Post-harvest Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
| | - Yasuhiro Tsujimoto
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
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30
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Siqueira JA, Batista-Silva W, Zsögön A, Fernie AR, Araújo WL, Nunes-Nesi A. Plant domestication: setting biological clocks. TRENDS IN PLANT SCIENCE 2023; 28:597-608. [PMID: 36822959 DOI: 10.1016/j.tplants.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 05/22/2023]
Abstract
Through domestication of wild species, humans have induced large changes in the developmental and circadian clocks of plants. As a result of these changes, modern crops are more productive and adaptive to contrasting environments from the center of origin of their wild ancestors, albeit with low genetic variability and abiotic stress tolerance. Likewise, a complete restructuring of plant metabolic timekeeping probably occurred during crop domestication. Here, we highlight that contrasting timings among organs in wild relatives of crops allowed them to recognize environmental adversities faster. We further propose that connections among biological clocks, which were established during plant domestication, may represent a fundamental source of genetic variation to improve crop resilience and yield.
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Affiliation(s)
- João Antonio Siqueira
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Willian Batista-Silva
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Agustin Zsögön
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.
| | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.
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31
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Li Q, Liu N, Wu C. Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization. PLANTA 2023; 257:94. [PMID: 37031436 DOI: 10.1007/s00425-023-04126-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.
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Affiliation(s)
- Qinglin Li
- Crop Genesis and Novel Agronomy Center, Yangling, 712100, Shaanxi, China.
| | - Ning Liu
- Shandong ZhongnongTiantai Seed Co., Ltd, Pingyi, 273300, Shandong, China
| | - Chenglai Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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32
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Hong J, Rosental L, Xu Y, Xu D, Orf I, Wang W, Hu Z, Su S, Bai S, Ashraf M, Hu C, Zhang C, Li Z, Xu J, Liu Q, Zhang H, Zhang F, Luo Z, Chen M, Chen X, Betts N, Fernie A, Liang W, Chen G, Brotman Y, Zhang D, Shi J. Genetic architecture of seed glycerolipids in Asian cultivated rice. PLANT, CELL & ENVIRONMENT 2023; 46:1278-1294. [PMID: 35698268 DOI: 10.1111/pce.14378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/30/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Glycerolipids are essential for rice development and grain quality but its genetic regulation remains unknown. Here we report its genetic base using metabolite-based genome-wide association study and metabolite-based quantitative traits locus (QTL) analyses based on lipidomic profiles of seeds from 587 Asian cultivated rice accessions and 103 chromosomal segment substitution lines, respectively. We found that two genes encoding phosphatidylcholine (PC):diacylglycerol cholinephosphotransferase (OsLP1) and granule-bound starch synthase I (Waxy) contribute to variations in saturated triacylglycerol (TAG) and lyso-PC contents, respectively. We demonstrated that allelic variation in OsLP1 sequence between indica and japonica results in different enzymatic preference for substrate PC-16:0/16:0 and different saturated TAG levels. Further evidence demonstrated that OsLP1 also affects heading date, and that co-selection of OsLP1 and a flooding-tolerant QTL in Aus results in the abundance of saturated TAGs associated with flooding tolerance. Moreover, we revealed that the sequence polymorphisms in Waxy has pleiotropic effects on lyso-PC and amylose content. We proposed that rice seed glycerolipids have been unintentionally shaped during natural and artificial selection for adaptive or import seed quality traits. Collectively, our findings provide valuable genetic resources for rice improvement and evolutionary insights into seed glycerolipid variations in rice.
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Affiliation(s)
- Jun Hong
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Leah Rosental
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Dawei Xu
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Isabel Orf
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Wengsheng Wang
- Department of Rice Molecular Design Technology and Application, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqiang Hu
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Su Su
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoxing Bai
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mohammed Ashraf
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chaoyang Hu
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changquan Zhang
- Department of Agronomy, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Zhikang Li
- Department of Rice Molecular Design Technology and Application, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlong Xu
- Department of Rice Molecular Design Technology and Application, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiaoquan Liu
- Department of Agronomy, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Hui Zhang
- Department of Plant Science, School of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Fengli Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijing Luo
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingjiao Chen
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofei Chen
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Natalie Betts
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Alisdair Fernie
- Department of Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Wanqi Liang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Dabing Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Jianxin Shi
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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33
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Si C, Zhan D, Wang L, Sun X, Zhong Q, Yang S. Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum). Cells 2023; 12:cells12071015. [PMID: 37048089 PMCID: PMC10093338 DOI: 10.3390/cells12071015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/09/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Plant-specific transcription factors such as the TCP family play crucial roles in light responses and lateral branching. The commercial development of S. muricatum has been influenced by the ease with which its lateral branches can be germinated, especially under greenhouse cultivation during the winter with supplemented LED light. The present study examined the TCP family genes in S. muricatum using bioinformatics analysis (whole-genome sequencing and RNA-seq) to explore the response of this family to different light treatments. Forty-one TCP genes were identified through a genome-wide search; phylogenetic analysis revealed that the CYC/TB1, CIN and Class I subclusters contained 16 SmTCP, 11 SmTCP and 14 SmTCP proteins, respectively. Structural and conserved sequence analysis of SmTCPs indicated that the motifs in the same subcluster were highly similar in structure and the gene structure of SmTCPs was simpler than that in Arabidopsis thaliana; 40 of the 41 SmTCPs were localized to 12 chromosomes. In S. muricatum, 17 tandem repeat sequences and 17 pairs of SmTCP genes were found. We identified eight TCPs that were significantly differentially expressed (DETCPs) under blue light (B) and red light (R), using RNA-seq. The regulatory network of eight DETCPs was preliminarily constructed. All three subclusters responded to red and blue light treatment. To explore the implications of regulatory TCPs in different light treatments for each species, the TCP regulatory gene networks and GO annotations for A. thaliana and S. muricatum were compared. The regulatory mechanisms suggest that the signaling pathways downstream of the TCPs may be partially conserved between the two species. In addition to the response to light, functional regulation was mostly enriched with auxin response, hypocotyl elongation, and lateral branch genesis. In summary, our findings provide a basis for further analysis of the TCP gene family in other crops and broaden the functional insights into TCP genes regarding light responses.
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Affiliation(s)
- Cheng Si
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Deli Zhan
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Lihui Wang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
| | - Xuemei Sun
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
| | - Qiwen Zhong
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- Correspondence: (Q.Z.); (S.Y.)
| | - Shipeng Yang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Correspondence: (Q.Z.); (S.Y.)
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34
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Jin HL, Duan S, Zhang P, Yang Z, Zeng Y, Chen Z, Hong L, Li M, Luo L, Chang Z, Hu J, Wang HB. Dual roles for CND1 in maintenance of nuclear and chloroplast genome stability in plants. Cell Rep 2023; 42:112268. [PMID: 36933214 DOI: 10.1016/j.celrep.2023.112268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 12/19/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
The coordination of chloroplast and nuclear genome status is critical for plant cell function. Here, we report that Arabidopsis CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in the chloroplast and the nucleus. CND1 localizes to both compartments, and complete loss of CND1 results in embryo lethality. Partial loss of CND1 disturbs nuclear cell-cycle progression and photosynthetic activity. CND1 binds to nuclear pre-replication complexes and DNA replication origins and regulates nuclear genome stability. In chloroplasts, CND1 interacts with and facilitates binding of the regulator of chloroplast genome stability WHY1 to chloroplast DNA. The defects in nuclear cell-cycle progression and photosynthesis of cnd1 mutants are respectively rescued by compartment-restricted CND1 localization. Light promotes the association of CND1 with HSP90 and its import into chloroplasts. This study provides a paradigm of the convergence of genome status across organelles to coordinately regulate cell cycle to control plant growth and development.
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Affiliation(s)
- Hong-Lei Jin
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 263, Longxi Avenue, Guangzhou, China.
| | - Sujuan Duan
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Pengxiang Zhang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziyue Yang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Yunping Zeng
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziqi Chen
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Liu Hong
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Mengshu Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Lujun Luo
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Zhenyi Chang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Jiliang Hu
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Hong-Bin Wang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
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35
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Guan JC, Li C, Flint-Garcia S, Suzuki M, Wu S, Saunders JW, Dong L, Bouwmeester HJ, McCarty DR, Koch KE. Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture. THE PLANT CELL 2023; 35:1013-1037. [PMID: 36573016 PMCID: PMC10015167 DOI: 10.1093/plcell/koac370] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
The maize (Zea mays) ear represents one of the most striking domestication phenotypes in any crop species, with the cob conferring an exceptional yield advantage over the ancestral form of teosinte. Remodeling of the grain-bearing surface required profound developmental changes. However, the underlying mechanisms remain unclear and can only be partly attributed to the known domestication gene Teosinte glume architecture 1 (Tga1). Here we show that a more complete conversion involves strigolactones (SLs), and that these are prominent players not only in the Tga1 phenotype but also other domestication features of the ear and kernel. Genetic combinations of a teosinte tga1 allele with three SL-related mutants progressively enhanced ancestral morphologies. The SL mutants, in addition to modulating the tga1 phenotype, also reshaped kernel-bearing pedicels and cupules in a teosinte-like manner. Genetic and molecular evidence are consistent with SL regulation of TGA1, including direct interaction of TGA1 with components of the SL-signaling system shown here to mediate TGA1 availability by sequestration. Roles of the SL network extend to enhancing maize seed size and, importantly, coordinating increased kernel growth with remodeling of protective maternal tissues. Collectively, our data show that SLs have central roles in releasing kernels from restrictive maternal encasement and coordinating other factors that increase kernel size, physical support, and their exposure on the grain-bearing surface.
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Affiliation(s)
- Jiahn-Chou Guan
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32610, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32610, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Changsheng Li
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 100 BE, The Netherlands
| | - Sherry Flint-Garcia
- United States Department of Agriculture – Agricultural Research Service, Columbia, Missouri 65211, USA
| | - Masaharu Suzuki
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32610, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32610, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Shan Wu
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32610, USA
| | - Jonathan W Saunders
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32610, USA
| | - Lemeng Dong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 100 BE, The Netherlands
| | - Harro J Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 100 BE, The Netherlands
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32610, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32610, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Karen E Koch
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32610, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32610, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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36
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Mansilla N, Fonouni-Farde C, Ariel F, Lucero L. Differential chromatin binding preference is the result of the neo-functionalization of the TB1 clade of TCP transcription factors in grasses. THE NEW PHYTOLOGIST 2023; 237:2088-2103. [PMID: 36484138 DOI: 10.1111/nph.18664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The understanding of neo-functionalization of plant transcription factors (TFs) after gene duplication has been extensively focused on changes in protein-protein interactions, the expression pattern of TFs, or the variation of cis-elements bound by TFs. Yet, the main molecular role of a TF, that is, its specific chromatin binding for the direct regulation of target gene expression, continues to be mostly overlooked. Here, we studied the TB1 clade of the TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) TF family within the grasses (Poaceae). We identified an Asp/Gly amino acid replacement within the TCP domain, originated within a paralog TIG1 clade exclusive for grasses. The heterologous expression of Zea mays TB1 and its two paralogs BAD1 and TIG1 in Arabidopsis mutant plants lacking the TB1 ortholog BRC1 revealed distinct functions in plant development. Notably, the Gly acquired in the TIG1 clade does not impair TF homodimerization and heterodimerization, while it modulates chromatin binding preferences. We found that in vivo TF recognition of target promoters depends on this Asp/Gly mutation and directly impacts downstream gene expression and subsequent plant development. These results provided new insights into how natural selection fine-tunes gene expression regulation after duplication of TFs to define plant architecture.
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Affiliation(s)
- Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB/FHUC, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Camille Fonouni-Farde
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB/FHUC, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB/FHUC, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB/FHUC, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
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Hjertaas AC, Preston JC, Kainulainen K, Humphreys AM, Fjellheim S. Convergent evolution of the annual life history syndrome from perennial ancestors. FRONTIERS IN PLANT SCIENCE 2023; 13:1048656. [PMID: 36684797 PMCID: PMC9846227 DOI: 10.3389/fpls.2022.1048656] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how 'annual traits' evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.
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Affiliation(s)
- Ane C. Hjertaas
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jill C. Preston
- Department of Plant Biology, The University of Vermont, Burlington, VT, United States
| | - Kent Kainulainen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Aelys M. Humphreys
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Siri Fjellheim
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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38
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Li L, Xia T, Yang H. Seasonal patterns of rhizosphere microorganisms suggest carbohydrate-degrading and nitrogen-fixing microbes contribute to the attribute of full-year shooting in woody bamboo Cephalostachyum pingbianense. Front Microbiol 2022; 13:1033293. [PMID: 36523824 PMCID: PMC9745117 DOI: 10.3389/fmicb.2022.1033293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/11/2022] [Indexed: 10/15/2023] Open
Abstract
Compared with the ordinary single-season shooting among woody bamboos in Poaceae, the attribute of full-year shooting in Cephalostachyum pingbianense represents a unique shooting type or mechanism. Nevertheless, except for the overall physiological mechanism, the effect of ecological factors, especially soil microorganisms, on this full-year shooting characteristic remains unclear. In this study, 16S rRNA and ITS rRNA genes were sequenced using the Illumina platform. Our aims were to detect the seasonal changes in rhizospheric microbial communities of C. pingbianense and to discover the correlations of soil microbes with soil properties and bamboo shoot productivity. The results showed that seasonal change had no significant effect on bacterial alpha diversity, but significantly affected bacterial and fungal community structures as well as fungal richness. Among all soil properties examined, soil temperature, soil moisture and organic matter were the predominant factors affecting bacterial community diversity and structure. Soil temperature and soil moisture also significantly influenced fungal community structure, while available phosphorus had the greatest effect on fungal diversity. In each season, bacterial genera Acidothermus, Roseiarcus, and Bradyrhizobium, along with fungal genera Saitozyma, Mortierella, Trichoderma, etc., were dominant in bacterial and fungal communities, respectively. Bacterial community functions in four seasons were dominated by chemoheterotrophy, cellulolysis, and nitrogen fixation. Saprotrophic fungi occupied a high proportion in soil samples of all seasons. In addition, correlation analysis revealed that the bamboo shoot productivity was positively correlated with multiple microbial taxa involved in carbon and nitrogen cycles. It is proposed that highly abundant microbes involved in carbohydrate degradation and nitrogen fixation in the rhizosphere soil may contribute to the attribute of producing bamboo shoots all year round in C. pingbianense. This study is among the few cases revealing the connection between bamboo shooting characteristics and soil microorganisms, and provides new physiological and ecological insights into the forest management of woody bamboos.
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Affiliation(s)
| | | | - Hanqi Yang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, Yunnan, China
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Wu L, Luo Z, Shi Y, Jiang Y, Li R, Miao X, Yang F, Li Q, Zhao H, Xue J, Xu S, Zhang T, Li L. A cost-effective tsCUT&Tag method for profiling transcription factor binding landscape. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2033-2038. [PMID: 36047457 DOI: 10.1111/jipb.13354] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Knowledge of the transcription factor binding landscape (TFBL) is necessary to analyze gene regulatory networks for important agronomic traits. However, a low-cost and high-throughput in vivo chromatin profiling method is still lacking in plants. Here, we developed a transient and simplified cleavage under targets and tagmentation (tsCUT&Tag) that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus extraction. Our tsCUT&Tag method provided higher data quality and signal resolution with lower sequencing depth compared with traditional ChIP-seq. Furthermore, we developed a strategy combining tsCUT&Tag with machine learning, which has great potential for profiling the TFBL across plant development.
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Affiliation(s)
- Leiming Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanni Shi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yizhe Jiang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruonan Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinxin Miao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Han Zhao
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jiquan Xue
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Shutu Xu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Tifu Zhang
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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40
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Kebrom TH, Doust AN. Activation of apoplastic sugar at the transition stage may be essential for axillary bud outgrowth in the grasses. FRONTIERS IN PLANT SCIENCE 2022; 13:1023581. [PMID: 36388483 PMCID: PMC9643854 DOI: 10.3389/fpls.2022.1023581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Shoot branches develop from buds in leaf axils. Once formed from axillary meristems, the buds enter a transition stage before growing into branches. The buds may transition into dormancy if internal and environmental factors limit sucrose supply to the buds. A fundamental question is why sucrose can be limiting at the transition stage for bud outgrowth, whereas new buds continue to be formed. Sucrose is transported to sink tissues through symplastic or apoplastic pathways and a shift from symplastic to apoplastic pathway is common during seed and fruit development. In addition, symplastic connected tissues are stronger sinks than symplastically isolated tissues that rely on sugars effluxed to the apoplast. Recent studies in sorghum, sugarcane, and maize indicate activation of apoplastic sugar in buds that transition to outgrowth but not to dormancy, although the mode of sugar transport during bud formation is still unclear. Since the apoplastic pathway in sorghum buds was specifically activated during bud outgrowth, we posit that sugar for axillary bud formation is most likely supplied through the symplastic pathway. This suggests a key developmental change at the transition stage, which alters the sugar transport pathway of newly-formed buds from symplastic to apoplastic, making the buds a less strong sink for sugars. We suggest therefore that bud outgrowth that relies on overflow of excess sucrose to the apoplast will be more sensitive to internal and environmental factors that enhance the growth of sink tissues and sucrose demand in the parent shoot; whereas bud formation that relies on symplastic sucrose will be less affected by these factors.
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Affiliation(s)
- Tesfamichael H. Kebrom
- Cooperative Agricultural Research Center, College of Agriculture and Human Sciences, Prairie View A&M University, Prairie View, TX, United States
- Center for Computational Systems Biology, College of Engineering, Prairie View A&M University, Prairie View, TX, United States
| | - Andrew N. Doust
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, United States
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41
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Han T, Yu J, Zhuang J, Wang Z, Sun X, Zhang Y. The Characterization of Columnar Apple Gene MdCoL Promoter and Its Response to Abscisic Acid, Brassinosteroid and Gibberellic Acid. Int J Mol Sci 2022; 23:ijms231810781. [PMID: 36142696 PMCID: PMC9505010 DOI: 10.3390/ijms231810781] [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: 07/30/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Columnar apple was an important germplasm resource to develop compact cultivars for labor-saving cultivation and to study fruit tree architecture. MdCoL is a strong candidate gene for controlling the columnar phenotype in apple. In this study, a 2000 bp upstream region of MdCoL was cloned as a full-length promoter, named MdCoLp1. To gain a better understanding of the characterization of the MdCoL promoter, cis-acting elements and the binding sites of transcription factors were predicted and analyzed, and four binary expression vectors consisting of the GUS reporter gene under the control of the MdCoL promoter was transformed into Arabidopsis thaliana to analyze the response to abscisic acid (ABA), brassinosteroid (BR) and gibberellic acid (GA3) of MdCoL promoters. Multiple transcription factors involving TCP, BEL1 and BES1/BZR1 and other transcription factor (TF) binding sites were predicted on the promoter of MdCoL. Histochemical staining showed that both full-length and 5′ truncated promoters could initiate GUS expression. The GUS activity was the most in leaf and stem, and mainly concentrated in the fibrovascular tissue, followed by root, and the least activity was observed in silique and flower. In addition, MdCoL expression was mainly localized in the quiescent center (QC) and lateral root growing point of root tip and the vascular tissue of stem and leaf by in situ hybridization. The results of exogenous hormones treatment showed that ABA and BR could activate the activity of the MdCoL promoter, while GA3 had opposite effects. In columnar apple seedlings, ABA treatment could upregulate the expression of MdCoL, but GA3 and BR restrained the transcription level of MdCoL. These results provide the foundation for deciphering the regulatory network of hormones affecting MdCoL transcription.
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Affiliation(s)
- Tingting Han
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Jiahui Yu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Jie Zhuang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Ziyu Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xin Sun
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yugang Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao 266109, China
- Correspondence:
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42
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Grau J, Franco‐Zorrilla JM. TDTHub, a web server tool for the analysis of transcription factor binding sites in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1203-1215. [PMID: 35713985 PMCID: PMC9541588 DOI: 10.1111/tpj.15873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/09/2022] [Accepted: 06/12/2022] [Indexed: 05/31/2023]
Abstract
Transcriptional regulation underlies most developmental programs and physiological responses to environmental changes in plants. Transcription factors (TFs) play a key role in the regulation of gene expression by binding specifically to short DNA sequences in the regulatory regions of genes: the TF binding sites (TFBSs). In recent years, several bioinformatic tools have been developed to detect TFBSs in candidate genes, either by de novo prediction or by directly mapping experimentally known TFBSs. However, most of these tools contain information for only a few species or require multi-step procedures, and are not always intuitive for non-experienced researchers. Here we present TFBS-Discovery Tool Hub (TDTHub), a web server for quick and intuitive studies of transcriptional regulation in plants. TDTHub uses pre-computed TFBSs in 40 plant species and allows the choice of two mapping algorithms, providing a higher versatility. Besides the main TFBS enrichment tool, TDTHub includes additional tools to assist in the analysis and visualization of data. In order to demonstrate the effectiveness of TDTHub, we analyzed the transcriptional regulation of the anthocyanin biosynthesis pathway. We also analyzed the transcriptional cascades in response to jasmonate and wounding in Arabidopsis and tomato (Solanum lycopersicum), respectively. In these studies, TDTHub helped to verify the most relevant TF nodes and to propose new ones with a prominent role in these pathways. TDTHub is available at http://acrab.cnb.csic.es/TDTHub/, and it will be periodically upgraded and expanded for new species and gene annotations.
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Affiliation(s)
- Joaquín Grau
- Department of Plant Molecular GeneticsCentro Nacional de BiotecnologíaCNB‐CSIC, C/Darwin 328049MadridSpain
| | - José M. Franco‐Zorrilla
- Department of Plant Molecular GeneticsCentro Nacional de BiotecnologíaCNB‐CSIC, C/Darwin 328049MadridSpain
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43
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Ajayo BS, Li Y, Wang Y, Dai C, Gao L, Liu H, Yu G, Zhang J, Huang Y, Hu Y. The novel ZmTCP7 transcription factor targets AGPase-encoding gene ZmBt2 to regulate storage starch accumulation in maize. FRONTIERS IN PLANT SCIENCE 2022; 13:943050. [PMID: 35909761 PMCID: PMC9335043 DOI: 10.3389/fpls.2022.943050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/28/2022] [Indexed: 05/27/2023]
Abstract
The process of starch biosynthesis is a major developmental event that affects the final grain yield and quality in maize (Zea mays L.), and transcriptional regulation plays a key role in modulating the expression of the main players in the pathway. ZmBt2, which encodes the small subunits of AGPase, is a rate-controlling gene of the pathway; however, much remains unknown about its transcriptional regulation. Our earlier study identifies a short functional fragment of ZmBt2 promoter (394-bp), and further shows it contains multiple putative cis-acting regulatory elements, demonstrating that several transcription factors may govern ZmBt2 expression. Here, we identified a novel TCP transcription factor (TF), ZmTCP7, that interacted with the functional fragment of the ZmBt2 promoter in a yeast one hybrid screening system. We further showed that ZmTCP7 is a non-autonomous TF targeted to the nucleus and predominantly expressed in maize endosperm. Using promoter deletion analyzes by transient expression in maize endosperm protoplasts combined with electrophoretic mobility shift assays, we found that ZmTCP7 bound to GAACCCCAC elements on the ZmBt2 promoter to suppress its expression. Transgenic overexpression of ZmTCP7 in maize caused a significant repression of ZmBt2 transcription by ~77.58%, resulting in a 21.51% decrease in AGPase activity and a 9.58% reduction in the endosperm starch content of transgenic maize. Moreover, the expressions of ZmBt1, ZmSSI, ZmSSIIa, and ZmSSIIIa were increased, while those of ZmSh2 and ZmSSIV reduced significantly in the endosperm of the transgenic maize. Overall, this study shows that ZmTCP7 functions as a transcriptional repressor of ZmBt2 and a negative regulator of endosperm starch accumulation, providing new insights into the regulatory networks that govern ZmBt2 expression and starch biosynthesis pathway in maize.
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Affiliation(s)
- Babatope Samuel Ajayo
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yangping Li
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yayun Wang
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Chengdong Dai
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Lei Gao
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Hanmei Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Guowu Yu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Junjie Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Yubi Huang
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yufeng Hu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
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44
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Richardson AE, Hake S. The power of classic maize mutants: Driving forward our fundamental understanding of plants. THE PLANT CELL 2022; 34:2505-2517. [PMID: 35274692 PMCID: PMC9252469 DOI: 10.1093/plcell/koac081] [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: 12/03/2021] [Accepted: 02/08/2022] [Indexed: 05/12/2023]
Abstract
Since Mendel, maize has been a powerhouse of fundamental genetics research. From testing the Mendelian laws of inheritance, to the first genetic and cytogenetic maps, to the use of whole-genome sequencing data for crop improvement, maize is at the forefront of genetics advances. Underpinning much of this revolutionary work are the classic morphological mutants; the "freaks" that stood out in the field to even the untrained eye. Here we review some of these classic developmental mutants and their importance in the history of genetics, as well as their key role in our fundamental understanding of plant development.
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Affiliation(s)
- Annis E Richardson
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Sarah Hake
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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45
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Xiao Y, Guo J, Dong Z, Richardson A, Patterson E, Mangrum S, Bybee S, Bertolini E, Bartlett M, Chuck G, Eveland AL, Scanlon MJ, Whipple C. Boundary domain genes were recruited to suppress bract growth and promote branching in maize. SCIENCE ADVANCES 2022; 8:eabm6835. [PMID: 35704576 PMCID: PMC9200273 DOI: 10.1126/sciadv.abm6835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling and genetic and phylogenetic analyses to investigate tasselsheath1 (tsh1) and tsh4, two maize genes that simultaneously suppress inflorescence leaf growth and promote branching. We identify a regulatory network of inflorescence leaf suppression that involves the phase change gene tsh4 upstream of tsh1 and the ligule identity gene liguleless2 (lg2). We also find that a series of duplications in the tsh1 gene lineage facilitated its shift from boundary domain in nongrasses to suppressed inflorescence leaves of grasses. Collectively, these results suggest that the boundary domain genes tsh1 and lg2 were recruited to inflorescence leaves where they suppress growth and regulate a nonautonomous signaling center that promotes inflorescence branching, an important component of yield in cereal grasses.
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Affiliation(s)
- Yuguo Xiao
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jinyan Guo
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Zhaobin Dong
- Plant Gene Expression Center, Albany, CA 94710, USA
| | - Annis Richardson
- Plant Gene Expression Center, Albany, CA 94710, USA
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, Scotland, UK
| | - Erin Patterson
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sidney Mangrum
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Seth Bybee
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | | | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - George Chuck
- Plant Gene Expression Center, Albany, CA 94710, USA
| | | | - Michael J. Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Clinton Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
- Corresponding author.
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46
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Dixon LE, Pasquariello M, Badgami R, Levin KA, Poschet G, Ng PQ, Orford S, Chayut N, Adamski NM, Brinton J, Simmonds J, Steuernagel B, Searle IR, Uauy C, Boden SA. MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat. SCIENCE ADVANCES 2022; 8:eabn5907. [PMID: 35544571 PMCID: PMC9094671 DOI: 10.1126/sciadv.abn5907] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/25/2022] [Indexed: 05/26/2023]
Abstract
Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 (HB-2), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants; higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain.
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Affiliation(s)
- Laura E. Dixon
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Marianna Pasquariello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Roshani Badgami
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Kara A. Levin
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Gernot Poschet
- Centre of Organismal Studies (COS), University of Heidelberg, Heidelberg 69120, Germany
| | - Pei Qin Ng
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Simon Orford
- Germplasm Resources Unit, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Noam Chayut
- Germplasm Resources Unit, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nikolai M. Adamski
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jemima Brinton
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - James Simmonds
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Burkhard Steuernagel
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Iain R. Searle
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Scott A. Boden
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
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47
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Wang M, Ogé L, Pérez Garcia MD, Launay-Avon A, Clément G, Le Gourrierec J, Hamama L, Sakr S. Antagonistic Effect of Sucrose Availability and Auxin on Rosa Axillary Bud Metabolism and Signaling, Based on the Transcriptomics and Metabolomics Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:830840. [PMID: 35392520 PMCID: PMC8982072 DOI: 10.3389/fpls.2022.830840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Shoot branching is crucial for successful plant development and plant response to environmental factors. Extensive investigations have revealed the involvement of an intricate regulatory network including hormones and sugars. Recent studies have demonstrated that two major systemic regulators-auxin and sugar-antagonistically regulate plant branching. However, little is known regarding the molecular mechanisms involved in this crosstalk. We carried out two complementary untargeted approaches-RNA-seq and metabolomics-on explant stem buds fed with different concentrations of auxin and sucrose resulting in dormant and non-dormant buds. Buds responded to the combined effect of auxin and sugar by massive reprogramming of the transcriptome and metabolome. The antagonistic effect of sucrose and auxin targeted several important physiological processes, including sink strength, the amino acid metabolism, the sulfate metabolism, ribosome biogenesis, the nucleic acid metabolism, and phytohormone signaling. Further experiments revealed a role of the TOR-kinase signaling pathway in bud outgrowth through at least downregulation of Rosa hybrida BRANCHED1 (RhBRC1). These new findings represent a cornerstone to further investigate the diverse molecular mechanisms that drive the integration of endogenous factors during shoot branching.
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Affiliation(s)
- Ming Wang
- Dryland-Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
| | - Laurent Ogé
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Alexandra Launay-Avon
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Jose Le Gourrierec
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
| | - Latifa Hamama
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
| | - Soulaiman Sakr
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
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48
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Nicolas M, Torres-Pérez R, Wahl V, Cruz-Oró E, Rodríguez-Buey ML, Zamarreño AM, Martín-Jouve B, García-Mina JM, Oliveros JC, Prat S, Cubas P. Spatial control of potato tuberization by the TCP transcription factor BRANCHED1b. NATURE PLANTS 2022; 8:281-294. [PMID: 35318445 DOI: 10.1038/s41477-022-01112-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
The control of carbon allocation, storage and usage is critical for plant growth and development and is exploited for both crop food production and CO2 capture. Potato tubers are natural carbon reserves in the form of starch that have evolved to allow propagation and survival over winter. They form from stolons, below ground, where they are protected from adverse environmental conditions and animal foraging. We show that BRANCHED1b (BRC1b) acts as a tuberization repressor in aerial axillary buds, which prevents buds from competing in sink strength with stolons. BRC1b loss of function leads to ectopic production of aerial tubers and reduced underground tuberization. In aerial axillary buds, BRC1b promotes dormancy, abscisic acid responses and a reduced number of plasmodesmata. This limits sucrose accumulation and access of the tuberigen protein SP6A. BRC1b also directly interacts with SP6A and blocks its tuber-inducing activity in aerial nodes. Altogether, these actions help promote tuberization underground.
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Affiliation(s)
- Michael Nicolas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain.
| | - Rafael Torres-Pérez
- Bioinformatics for Genomics and Proteomics Unit, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Vanessa Wahl
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Eduard Cruz-Oró
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - María Luisa Rodríguez-Buey
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Angel María Zamarreño
- Department of Environmental Biology, Faculty of Sciences-BIOMA Institute, University of Navarra, Pamplona, Spain
| | - Beatriz Martín-Jouve
- Electron Microscopy Unit, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - José María García-Mina
- Department of Environmental Biology, Faculty of Sciences-BIOMA Institute, University of Navarra, Pamplona, Spain
| | - Juan Carlos Oliveros
- Bioinformatics for Genomics and Proteomics Unit, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Salomé Prat
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
- Department of Plant Development and Signal Transduction, Centre for Research in Agricultural Genomics (CRAG-CSIC), Barcelona, Spain
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain.
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49
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Pendergast TH, Qi P, Odeny DA, Dida MM, Devos KM. A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits. THE PLANT GENOME 2022; 15:e20175. [PMID: 34904374 DOI: 10.1002/tpg2.20175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/08/2021] [Indexed: 06/14/2023]
Abstract
Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F2:3 population in a Kenyan field trial. The F2:3 population was genotyped via genotyping-by-sequencing (GBS) and the UGbS-Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18-linkage-group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE-RICH REPEAT-CONTAINING PROTEIN genes, with homology to nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high-marker-density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance.
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Affiliation(s)
- Thomas H Pendergast
- Dep. of Plant Biology, Univ. of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602, USA
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Peng Qi
- Dep. of Plant Biology, Univ. of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602, USA
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Damaris Achieng Odeny
- The International Crops Research Institute for the Semi-Arid Tropics-Eastern and Southern Africa, Nairobi, Kenya
| | - Mathews M Dida
- Dep. of Applied Sciences, Maseno Univ., Private Bag-40105, Maseno, Kenya
| | - Katrien M Devos
- Dep. of Plant Biology, Univ. of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602, USA
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
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50
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Wingler A, Henriques R. Sugars and the speed of life-Metabolic signals that determine plant growth, development and death. PHYSIOLOGIA PLANTARUM 2022; 174:e13656. [PMID: 35243645 PMCID: PMC9314607 DOI: 10.1111/ppl.13656] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 05/27/2023]
Abstract
Plant growth and development depend on the availability of carbohydrates synthesised in photosynthesis (source activity) and utilisation of these carbohydrates for growth (sink activity). External conditions, such as temperature, nutrient availability and stress, can affect source as well as sink activity. Optimal utilisation of resources is under circadian clock control. This molecular timekeeper ensures that growth responses are adjusted to different photoperiod and temperature settings by modulating starch accumulation and degradation accordingly. For example, during the night, starch degradation is required to provide sugars for growth. Under favourable growth conditions, high sugar availability stimulates growth and development, resulting in an overall accelerated life cycle of annual plants. Key signalling components include trehalose-6-phosphate (Tre6P), which reflects sucrose availability and stimulates growth and branching when the conditions are favourable. Under sink limitation, Tre6P does, however, inhibit night-time starch degradation. Tre6P interacts with Sucrose-non-fermenting1-Related Kinase1 (SnRK1), a protein kinase that inhibits growth under starvation and stress conditions and delays development (including flowering and senescence). Tre6P inhibits SnRK1 activity, but SnRK1 increases the Tre6P to sucrose ratio under favourable conditions. Alongside Tre6P, Target of Rapamycin (TOR) stimulates processes such as protein synthesis and growth when sugar availability is high. In annual plants, an accelerated life cycle results in early leaf and plant senescence, thus shortening the lifespan. While the availability of carbohydrates in the form of sucrose and other sugars also plays an important role in seasonal life cycle events (phenology) of perennial plants, the sugar signalling pathways in perennials are less well understood.
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Affiliation(s)
- Astrid Wingler
- School of Biological, Earth & Environmental Sciences and Environmental Research InstituteUniversity College Cork, Distillery FieldsCork
| | - Rossana Henriques
- School of Biological, Earth & Environmental Sciences and Environmental Research InstituteUniversity College Cork, Distillery FieldsCork
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