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Zhang X, Wu Q, Lan L, Peng D, Guan H, Luo K, Bao M, Bendahmane M, Fu X, Wu Z. Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits. MOLECULAR HORTICULTURE 2024; 4:14. [PMID: 38622744 PMCID: PMC11020927 DOI: 10.1186/s43897-024-00088-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/19/2024] [Indexed: 04/17/2024]
Abstract
Roses are consistently ranked at the forefront in cut flower production. Increasing demands of market and changing climate conditions have resulted in the need to further improve the diversity and quality of traits. However, frequent hybridization leads to highly heterozygous nature, including the allelic variants. Therefore, the absence of comprehensive genomic information leads to them making it challenging to molecular breeding. Here, two haplotype-resolved chromosome genomes for Rosa chinensis 'Chilong Hanzhu' (2n = 14) which is high heterozygous diploid old Chinese rose are generated. An amount of genetic variation (1,605,616 SNPs, 209,575 indels) is identified. 13,971 allelic genes show differential expression patterns between two haplotypes. Importantly, these differences hold valuable insights into regulatory mechanisms of traits. RcMYB114b can influence cyanidin-3-glucoside accumulation and the allelic variation in its promoter leads to differences in promoter activity, which as a factor control petal color. Moreover, gene family expansion may contribute to the abundance of terpenes in floral scents. Additionally, RcANT1, RcDA1, RcAG1 and RcSVP1 genes are involved in regulation of petal number and size under heat stress treatment. This study provides a foundation for molecular breeding to improve important characteristics of roses.
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Affiliation(s)
- Xiaoni Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China
| | - Quanshu Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lan Lan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China
| | - Huilin Guan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kaiqing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mohammed Bendahmane
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
- Laboratoire Reproduction Et Development Des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, 520074, Lyon, France.
| | - Xiaopeng Fu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China.
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2
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Li XM, Jenke H, Strauss S, Bazakos C, Mosca G, Lymbouridou R, Kierzkowski D, Neumann U, Naik P, Huijser P, Laurent S, Smith RS, Runions A, Tsiantis M. Cell-cycle-linked growth reprogramming encodes developmental time into leaf morphogenesis. Curr Biol 2024; 34:541-556.e15. [PMID: 38244542 DOI: 10.1016/j.cub.2023.12.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
How is time encoded into organ growth and morphogenesis? We address this question by investigating heteroblasty, where leaf development and form are modified with progressing plant age. By combining morphometric analyses, fate-mapping through live-imaging, computational analyses, and genetics, we identify age-dependent changes in cell-cycle-associated growth and histogenesis that underpin leaf heteroblasty. We show that in juvenile leaves, cell proliferation competence is rapidly released in a "proliferation burst" coupled with fast growth, whereas in adult leaves, proliferative growth is sustained for longer and at a slower rate. These effects are mediated by the SPL9 transcription factor in response to inputs from both shoot age and individual leaf maturation along the proximodistal axis. SPL9 acts by activating CyclinD3 family genes, which are sufficient to bypass the requirement for SPL9 in the control of leaf shape and in heteroblastic reprogramming of cellular growth. In conclusion, we have identified a mechanism that bridges across cell, tissue, and whole-organism scales by linking cell-cycle-associated growth control to age-dependent changes in organ geometry.
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Affiliation(s)
- Xin-Min Li
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Hannah Jenke
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Christos Bazakos
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Gabriella Mosca
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Rena Lymbouridou
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Daniel Kierzkowski
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Ulla Neumann
- Central Microscopy (CeMic), Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Purva Naik
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Peter Huijser
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Adam Runions
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany.
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3
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Schneider M, Van Bel M, Inzé D, Baekelandt A. Leaf growth - complex regulation of a seemingly simple process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1018-1051. [PMID: 38012838 DOI: 10.1111/tpj.16558] [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: 07/19/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023]
Abstract
Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.
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Affiliation(s)
- Michele Schneider
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Michiel Van Bel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
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Hu Q, Wu Y, Hong T, Wu D, Wang L. OsMED16, a tail subunit of Mediator complex, interacts with OsE2Fa to synergistically regulate rice leaf development and blast resistance. Int J Biol Macromol 2023; 253:126728. [PMID: 37678689 DOI: 10.1016/j.ijbiomac.2023.126728] [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: 06/28/2023] [Revised: 08/20/2023] [Accepted: 09/03/2023] [Indexed: 09/09/2023]
Abstract
Mediator, a universal eukaryotic coactivator, is a multiprotein complex to transduce information from the DNA-bound transcription factors to the RNA polymerase II transcriptional machinery. In this study, the biofunctions of a rice mediator subunit OsMED16 in leaf development and blast resistance were characterized. OsMED16 encodes a putative protein of 1170 amino acids, which is 393 bp shorted than the version in Rice Genome Annotation Project databases. Overexpression of OsMED16 plants exhibited wider leaves with larger and more numerous cells in lateral axis, and enhanced resistance to M. oryzae with hyperaccumulated salicylic acid. Further analysis revealed that OsMED16 interacts with OsE2Fa in nuclei, and the complex could directly regulate the transcriptional levels of several genes involved in cell cycle regulation and SA mediated blast resistance, such as OsCC52A1, OsCDKA1, OsCDKB2;2, OsICS1 and OsWRKY45. Altogether, this study proved that OsMED16 is a positive regulator of rice leaf development and blast resistance, and providing new insights into the crosstalk between cell cycle regulation and immunity.
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Affiliation(s)
- Qin Hu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China.
| | - Yanfei Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Youyi Avenue 368, Wuhan 430062, China
| | - Tianshu Hong
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China
| | - Deng Wu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China
| | - Lulu Wang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China
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Li S, Zhang Q, Zhang H, Wang J, Sun J, Yang X, Huang S, Zhang Z. Deletion of a cyclin-dependent protein kinase inhibitor, CsSMR1, leads to dwarf and determinate growth in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:915-927. [PMID: 34841478 PMCID: PMC8942921 DOI: 10.1007/s00122-021-04006-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/23/2021] [Indexed: 05/12/2023]
Abstract
A 7.9 kb deletion which contains a cyclin-dependent protein kinase inhibitor leads to determinate growth and dwarf phenotype in cucumber. Plant architecture is a composite character which are mainly defined by shoot branching, internode elongation and shoot determinacy. Ideal architecture tends to increase the yield of plants, just like the case of "Green Revolution" increased by the application of semi-dwarf cereal crop varieties in 1960s. Cucumber (Cucumis sativus L.) is an important vegetable cultivated worldwide, and suitable architecture varieties were selected for different production systems. In this study, we obtained a novel dwarf mutant with strikingly shortened plant height and determinate growth habit. By bulked segregant analysis and map-based cloning, we delimited the dw2 locus to a 56.4 kb region which contain five genes. Among all the variations between WT and dw2 within the 56.4 kb region, a 7.9 kb deletion which resulted in complete deletion of CsaV3_5G035790 in dw2 was co-segregated with the dwarf phenotype. Haplotype analysis and gene expression analysis suggest that CsaV3_5G035790 encoding a cyclin-dependent protein kinase inhibitor (CsSMR1) be the candidate gene responsible for the dwarf phenotype in dw2. RNA-seq analysis shows that several kinesin-like proteins, cyclins and reported organ size regulators are expressed differentially between WT and dw2, which may account for the reduced organ size in dwarf plants. Additionally, the down-regulation of CsSTM and CsWOX9 in dw2 resulted in premature termination of shoot apical meristem development, which eventually reduces the internode number and plant height. Identification and characterization of the CsSMR1 provide a new insight into cucumber architecture modification to be applied to mechanized production system.
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Affiliation(s)
- Shuai Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Qiqi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huimin Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jinjing Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Zhonghua Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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Shimotohno A, Aki SS, Takahashi N, Umeda M. Regulation of the Plant Cell Cycle in Response to Hormones and the Environment. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:273-296. [PMID: 33689401 DOI: 10.1146/annurev-arplant-080720-103739] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Developmental and environmental signals converge on cell cycle machinery to achieve proper and flexible organogenesis under changing environments. Studies on the plant cell cycle began 30 years ago, and accumulated research has revealed many links between internal and external factors and the cell cycle. In this review, we focus on how phytohormones and environmental signals regulate the cell cycle to enable plants to cope with a fluctuating environment. After introducing key cell cycle regulators, we first discuss how phytohormones and their synergy are important for regulating cell cycle progression and how environmental factors positively and negatively affect cell division. We then focus on the well-studied example of stress-induced G2 arrest and view the current model from an evolutionary perspective. Finally, we discuss the mechanisms controlling the transition from the mitotic cycle to the endocycle, which greatly contributes to cell enlargement and resultant organ growth in plants.
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Affiliation(s)
- Akie Shimotohno
- Department of Biological Science, The University of Tokyo, Tokyo 113-0033, Japan
- Current affiliation: Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan;
| | - Shiori S Aki
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan; , ,
| | - Naoki Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan; , ,
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan; , ,
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Huang S, Liu W, Xu J, Liu Z, Li C, Feng H. The SAP function in pistil development was proved by two allelic mutations in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC PLANT BIOLOGY 2020; 20:538. [PMID: 33256588 PMCID: PMC7708145 DOI: 10.1186/s12870-020-02741-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Pistil development is a complicated process in plants, and female sterile mutants are ideal material for screening and cloning pistil development-related genes. Using the female sterile mutant (fsm1), BraA04g009730.3C was previously predicted as a candidate mutant gene encoding the STERILE APETALA (SAP) transcriptional regulator. In the current study, a parallel female sterile mutant (fsm2) was derived from EMS mutagenesis of a Chinese cabbage DH line 'FT' seeds. RESULTS Both fsm2 and fsm1 mutant phenotypes exhibited pistil abortion and smaller floral organs. Genetic analysis indicated that the phenotype of mutant fsm2 was also controlled by a single recessive nuclear gene. Allelism testing showed that the mutated fsm1 and fsm2 genes were allelic. A single-nucleotide mutation (G-to-A) in the first exon of BraA04g009730.3C caused a missense mutation from GAA (glutamic acid) to GGA (glycine) in mutant fsm2 plants. Both allelic mutations of BraA04g009730.3C in fsm1 and fsm2 conferred the similar pistil abortion phenotype, which verified the SAP function in pistil development. To probe the mechanism of SAP-induced pistil abortion, we compared the mutant fsm1 and wild-type 'FT' pistil transcriptomes. Among the 3855 differentially expressed genes obtained, 29 were related to ovule development and 16 were related to organ size. CONCLUSION Our study clarified the function of BraA04g009730.3C and revealed that it was responsible for ovule development and organ size. These results lay a foundation to elucidate the molecular mechanism of pistil development in Chinese cabbage.
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Affiliation(s)
- Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Wenjie Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Junjie Xu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Chengyu Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
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Lin Y, Laosatit K, Chen J, Yuan X, Wu R, Amkul K, Chen X, Somta P. Mapping and Functional Characterization of Stigma Exposed 1, a DUF1005 Gene Controlling Petal and Stigma Cells in Mungbean ( Vigna radiata). FRONTIERS IN PLANT SCIENCE 2020; 11:575922. [PMID: 33329637 PMCID: PMC7710877 DOI: 10.3389/fpls.2020.575922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/22/2020] [Indexed: 05/23/2023]
Abstract
Flowers with exposed stigma increase the outcrossing rate and are useful in developing improved hybrid crop cultivars. This exposure results mainly from the cellular morphology of the petal and pistil, but what affects the formation of the petal and pistil in the late developmental stages is less understood. Here, we characterized a novel floral mutant in mungbean (Vigna radiata), stigma exposed 1 (se1), which displays irregular petals and pistils. Floral organ initiation in the se1 mutant was normal, but petal and pistil growth malfunctioned during late development. A histological analysis revealed that the se1 mutant had wrinkled petals with knotted structures and elongated styles. The cellular morphology of the epidermal layers of the se1 petals was deformed, while the cell lengths in the styles increased. A genetic analysis indicated that the se1 phenotype is controlled by a single recessive gene, and it was mapped to chromosome 11. A sequence analysis suggested that a DUF1005-encoding gene, LOC106777793, is the gene controlling the se1 phenotype. The se1 mutant possessed a single-nucleotide polymorphism that resulted in an amino acid change in VrDUF1005. Overexpression of VrDUF1005 in Arabidopsis resulted in rolling leaves and reduced floral size. Consequently, we proposed that VrSE1 functions to modulate cell division in petals and cell expansion in styles during the late developmental stages in mungbean. The se1 mutant is a new genetic resource for mung bean hybrid breeding.
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Affiliation(s)
- Yun Lin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ranran Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, Thailand
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9
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Investigation of genes associated with petal variations between diploid and autotetraploid in Chinese cabbage (Brassica rapa L. ssp. pekinensis) by RNA-seq and sRNA-seq. Mol Genet Genomics 2020; 295:1459-1476. [PMID: 32683543 DOI: 10.1007/s00438-020-01713-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/11/2020] [Indexed: 11/27/2022]
Abstract
Polyploidy promotes morphological, physiological, and reproductive diversity in plants. The imminent effect of chromosome doubling in plants is the enlargement of organs such as flowers and fruits, which increases the commercial value of crops. Flowering plays a vital role in the growth and development of angiosperms. Here, we prepared an isolated microspore culture of 'FT', a doubled haploid (DH) line of Chinese cabbage (Brassica rapa L. ssp. pekinensis), and obtained diploid and autotetraploid plants with the same genetic background. Compared with diploids, the autotetraploids were characterized by large floral organs, dark petals, delayed flowering, and reduced fertility. The indole-3-acetic acid (IAA) and jasmonic acid (JA) levels in autotetraploid petals were significantly higher and the abscisic acid (ABA) level was significantly lower than those in the diploid petals. The lutein level in autotetraploid petals was nearly two times higher than that in the diploid petals. A comparative transcriptome analysis revealed 14,412 differentially expressed genes (DEGs) between the diploids and autotetraploids, and they were enriched in 117 Gene Ontology terms and 110 Kyoto Encyclopedia of Genes and Genomes pathways. We detected 231 DEGs related to phytohormone signal transduction and 29 DEGs involved in carotenoid biosynthesis. An miRNA-target mRNA analysis showed that 32 DEGs regulated by 16 DEMs were associated with flowering timing (BraA03000336, BraA09004319, and BraA09000515), petal development (BraA05002408, BraA01004006, BraA09004069, and BraA04000966), flower opening (BraA07000350), and pollen development (BraA01000720, BraA09005727, and BraA01000253). This study provides information to help elucidate the molecular mechanisms underlying phenotypic variations induced by autopolyploidy in Chinese cabbage.
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Slovak R, Setzer C, Roiuk M, Bertels J, Göschl C, Jandrasits K, Beemster GTS, Busch W. Ribosome assembly factor Adenylate Kinase 6 maintains cell proliferation and cell size homeostasis during root growth. THE NEW PHYTOLOGIST 2020; 225:2064-2076. [PMID: 31665812 PMCID: PMC7028144 DOI: 10.1111/nph.16291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/19/2019] [Indexed: 05/06/2023]
Abstract
From the cellular perspective, organ growth is determined by production and growth of cells. Uncovering how these two processes are coordinated is essential for understanding organogenesis and regulation of organ growth. We utilized phenotypic and genetic variation of 252 natural accessions of Arabidopsis thaliana to conduct genome-wide association studies (GWAS) for identifying genes underlying root growth variation; using a T-DNA line candidate approach, we identified one gene involved in root growth control and characterized its function using microscopy, root growth kinematics, G2/M phase cell count, ploidy levels and ribosome polysome profiles. We identified a factor contributing to root growth control: Arabidopsis Adenylate Kinase 6 (AAK6). AAK6 is required for normal cell production and normal cell elongation, and its natural genetic variation is involved in determining root growth differences between Arabidopsis accessions. A lack of AAK6 reduces cell production in the aak6 root apex, but this is partially compensated for by longer mature root cells. Thereby, aak6 mutants exhibit compensatory cell enlargement, a phenomenon unexpected in roots. Moreover, aak6 plants accumulate 80S ribosomes while the polysome profile remains unchanged, consistent with a phenotype of perturbed ribosome biogenesis. In conclusion, AAK6 impacts ribosome abundance, cell production and thereby root growth.
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Affiliation(s)
- Radka Slovak
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 31030ViennaAustria
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Claudia Setzer
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 31030ViennaAustria
| | - Mykola Roiuk
- Max F. Perutz Laboratories (MFPL)Vienna Biocenter (VBC)Dr Bohr‐Gasse 91030ViennaAustria
| | - Jonas Bertels
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES)Department of BiologyUniversity of AntwerpGroenenborgerlaan 1712020AntwerpenBelgium
| | - Christian Göschl
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 31030ViennaAustria
| | - Katharina Jandrasits
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 31030ViennaAustria
| | - Gerrit T. S. Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES)Department of BiologyUniversity of AntwerpGroenenborgerlaan 1712020AntwerpenBelgium
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 31030ViennaAustria
- Plant Molecular and Cellular Biology LaboratorySalk Institute For Biological Studies10010 N Torrey Pines RdLa JollaCA92037USA
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11
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Nelissen H, Gonzalez N. Understanding plant organ growth: a multidisciplinary field. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7-10. [PMID: 31725876 DOI: 10.1093/jxb/erz448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Gent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Gent, Belgium
| | - Nathalie Gonzalez
- INRA, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882, Villenave d'Ornon cedex, France
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12
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Abstract
Plant leaves are differentiated organs that arise sequentially from a population of pluripotent stem cells at the shoot apical meristem (SAM). There is substantial diversity in leaf shape, much of which depends on the size and arrangement of outgrowths at the leaf margin. These outgrowths are generated by a patterning mechanism similar to the phyllotactic processes producing organs at the SAM, which involves the transcription factors CUP-SHAPED COTYLEDON and the phytohormone auxin. In the leaf, this patterning mechanism creates sequential protrusions and indentations along the margin. The size, shape, and distribution of these protrusions also depend on the overall growth of the leaf lamina. Globally, growth is regulated by a complex genetic network controlling the distribution of cell proliferation and the timing of differentiation. Evolutionary changes in margin form arise from changes in two different classes of homeobox genes that modify the outcome of marginal patterning in diverse ways, and are under intense investigation.
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Affiliation(s)
| | - Adam Runions
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mainak Das Gupta
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Miltos Tsiantis
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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13
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Kuluev B, Avalbaev A, Nikonorov Y, Ermoshin A, Yuldashev R, Akhiarova G, Shakirova F, Chemeris A. Effect of constitutive expression of Arabidopsis CLAVATA3 on cell growth and possible role of cytokinins in leaf size control in transgenic tobacco plants. JOURNAL OF PLANT PHYSIOLOGY 2018; 231:244-250. [PMID: 30317073 DOI: 10.1016/j.jplph.2018.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
We generated transgenic tobacco plants (Nicotiana tabacum L.) with overexpression of the Arabidopsis thaliana CLAVATA3 (CLV3) gene which is known to be a negative regulator of cell division. Surprisingly, most of the 35S::CLV3 transgenic plants showed no phenotypic differences with the wild type plants. However, there were considerable changes in the morphological parameters between 35S::CLV3 overexpressors and wild type plants. As expected, the number of meristematic cells in the shoot apical meristem was reduced in 35S::CLV3 plants as compared to the wild type plants. Moreover, overexpression of CLV3 exerted morphological changes not only to shoot apical meristem but also to leaves and flowers. Thus, transgenic plants were characterized by reduced number of epidermal and mesophyll cells as well as stomatal pores in mature leaves. However, there was a compensatory increase in leaf cell size of 35S::CLV3 plants that contributed to maintenance of organ size within the normal range. We observed that expression of cell expansion-promoted genes, expansin NtEXPA4 and endo-xyloglucan transferase NtEXGT, were elevated in mature leaves. In contrast, there was a decrease in the transcript level of the cell division-related AINTEGUMENTA-like (NtANTL) gene in 35S::CLV3 transgenic plants. In addition, we detected an increase in cytokinin level without any changes in the contents of IAA and ABA in 35S::CLV3 overexpressors. Interestingly, cytokinin treatment was shown to stimulate the expression of NtEXPA4 and NtEXGT genes in 35S::CLV3 transgenic plants. We propose that observed compensatory cell expansion in leaves of 35S::CLV3 transgenic plants may be due, at least in part, to a possible link between cytokinin signalling and cell expansion-related genes.
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Affiliation(s)
- Bulat Kuluev
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia.
| | - Azamat Avalbaev
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia.
| | - Yuri Nikonorov
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
| | - Alexander Ermoshin
- Institute of Natural Sciences, Ural Federal University, 620002, Yekaterinburg, Russia
| | - Ruslan Yuldashev
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
| | - Guzel Akhiarova
- Ufa Institute of Biology - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054, Ufa, Russia
| | - Farida Shakirova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
| | - Aleksey Chemeris
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
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14
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Spatiotemporal coordination of cell division and growth during organ morphogenesis. PLoS Biol 2018; 16:e2005952. [PMID: 30383040 PMCID: PMC6211367 DOI: 10.1371/journal.pbio.2005952] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 09/20/2018] [Indexed: 11/30/2022] Open
Abstract
A developing plant organ exhibits complex spatiotemporal patterns of growth, cell division, cell size, cell shape, and organ shape. Explaining these patterns presents a challenge because of their dynamics and cross-correlations, which can make it difficult to disentangle causes from effects. To address these problems, we used live imaging to determine the spatiotemporal patterns of leaf growth and division in different genetic and tissue contexts. In the simplifying background of the speechless (spch) mutant, which lacks stomatal lineages, the epidermal cell layer exhibits defined patterns of division, cell size, cell shape, and growth along the proximodistal and mediolateral axes. The patterns and correlations are distinctive from those observed in the connected subepidermal layer and also different from the epidermal layer of wild type. Through computational modelling we show that the results can be accounted for by a dual control model in which spatiotemporal control operates on both growth and cell division, with cross-connections between them. The interactions between resulting growth and division patterns lead to a dynamic distributions of cell sizes and shapes within a deforming leaf. By modulating parameters of the model, we illustrate how phenotypes with correlated changes in cell size, cell number, and organ size may be generated. The model thus provides an integrated view of growth and division that can act as a framework for further experimental study. Organ morphogenesis involves two coordinated processes: growth of tissue and increase in cell number through cell division. Both processes have been analysed individually in many systems and shown to exhibit complex patterns in space and time. However, it is unclear how these patterns of growth and cell division are coordinated in a growing leaf that is undergoing shape changes. We have addressed this problem using live imaging to track growth and cell division in the developing leaf of the mustard plant Arabidopsis thaliana. Using subsequent computational modelling, we propose an integrated model of leaf growth and cell division, which generates dynamic distributions of cell size and shape in different tissue layers, closely matching those observed experimentally. A key aspect of the model is dual control of spatiotemporal patterns of growth and cell division parameters. By modulating parameters in the model, we illustrate how phenotypes may correlate with changes in cell size, cell number, and organ size.
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15
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Abstract
The angiosperm flower develops through a modular programme which, although ancient and conserved, provides the flexibility that has allowed an almost infinite variety of floral forms to emerge. In this review, we explore the evolution of floral diversity, focusing on our recent understanding of the mechanistic basis of evolutionary change. We discuss the various ways in which flower size and floral organ size can be modified, the means by which flower shape and symmetry can change, and the ways in which floral organ position can be varied. We conclude that many challenges remain before we fully understand the ecological and molecular processes that facilitate the diversification of flower structure.
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16
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Dunn JC, Stockdale JE, Moorhouse-Gann RJ, McCubbin A, Hipperson H, Morris AJ, Grice PV, Symondson WOC. The decline of the Turtle Dove: Dietary associations with body condition and competition with other columbids analysed using high-throughput sequencing. Mol Ecol 2018; 27:3386-3407. [PMID: 29927007 DOI: 10.1111/mec.14766] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/20/2017] [Indexed: 12/16/2022]
Abstract
Dietary changes linked to the availability of anthropogenic food resources can have complex implications for species and ecosystems, especially when species are in decline. Here, we use recently developed primers targeting the ITS2 region of plants to characterize diet from faecal samples of four UK columbids, with particular focus on the European turtle dove (Streptopelia turtur), a rapidly declining obligate granivore. We examine dietary overlap between species (potential competition), associations with body condition in turtle doves and spatiotemporal variation in diet. We identified 143 taxonomic units, of which we classified 55% to species, another 34% to genus and the remaining 11% to family. We found significant dietary overlap between all columbid species, with the highest between turtle doves and stock doves (Columba oenas), then between turtle doves and woodpigeons (Columba palumbus). The lowest overlap was between woodpigeons and collared doves (Streptopelia decaocto). We show considerable change in columbid diets compared to previous studies, probably reflecting opportunistic foraging behaviour by columbids within a highly anthropogenically modified landscape, although our data for nonturtle doves should be considered preliminary. Nestling turtle doves in better condition had a higher dietary proportion of taxonomic units from natural arable plant species and a lower proportion of taxonomic units from anthropogenic food resources such as garden bird seed mixes and brassicas. This suggests that breeding ground conservation strategies for turtle doves should include provision of anthropogenic seeds for adults early in the breeding season, coupled with habitat rich in accessible seeds from arable plants once chicks have hatched.
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Affiliation(s)
- Jenny C Dunn
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, Bedfordshire, UK
- Cardiff School of Biosciences, Cardiff, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Joseph Banks Laboratories, School of Life Sciences, University of Lincoln, Lincoln, UK
| | | | | | | | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Antony J Morris
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, Bedfordshire, UK
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17
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Moorhouse-Gann RJ, Dunn JC, de Vere N, Goder M, Cole N, Hipperson H, Symondson WOC. New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones. Sci Rep 2018; 8:8542. [PMID: 29867115 PMCID: PMC5986805 DOI: 10.1038/s41598-018-26648-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/15/2018] [Indexed: 11/20/2022] Open
Abstract
DNA metabarcoding is a rapidly growing technique for obtaining detailed dietary information. Current metabarcoding methods for herbivory, using a single locus, can lack taxonomic resolution for some applications. We present novel primers for the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) designed for dietary studies in Mauritius and the UK, which have the potential to give unrivalled taxonomic coverage and resolution from a short-amplicon barcode. In silico testing used three databases of plant ITS2 sequences from UK and Mauritian floras (native and introduced) totalling 6561 sequences from 1790 species across 174 families. Our primers were well-matched in silico to 88% of species, providing taxonomic resolution of 86.1%, 99.4% and 99.9% at the species, genus and family levels, respectively. In vitro, the primers amplified 99% of Mauritian (n = 169) and 100% of UK (n = 33) species, and co-amplified multiple plant species from degraded faecal DNA from reptiles and birds in two case studies. For the ITS2 region, we advocate taxonomic assignment based on best sequence match instead of a clustering approach. With short amplicons of 187-387 bp, these primers are suitable for metabarcoding plant DNA from faecal samples, across a broad geographic range, whilst delivering unparalleled taxonomic resolution.
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Affiliation(s)
- Rosemary J Moorhouse-Gann
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - Jenny C Dunn
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, The Lodge, Potton Road, Sandy, Bedfordshire, SG19 2DL, UK.
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, LN6 7TS, UK.
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, Carmarthenshire, SA32 8HG, UK
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3DA, UK
| | - Martine Goder
- Mauritian Wildlife Foundation, Grannum Road, Vacoas, Mauritius
| | - Nik Cole
- Mauritian Wildlife Foundation, Grannum Road, Vacoas, Mauritius
- Durrell Wildlife Conservation Trust, Les Augrès Manor, La Profonde Rue, Trinity, JE3 5BP Jersey, Channel Islands, UK
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - William O C Symondson
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
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18
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Scheres B, Krizek BA. Coordination of growth in root and shoot apices by AIL/PLT transcription factors. CURRENT OPINION IN PLANT BIOLOGY 2018; 41:95-101. [PMID: 29121612 DOI: 10.1016/j.pbi.2017.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/11/2017] [Accepted: 10/17/2017] [Indexed: 05/27/2023]
Abstract
Growth at the root tip and organ generation at the shoot tip depend on the proper functioning of apical meristems and the transitioning of meristematic cell descendants from a proliferating state to cell elongation and differentiation. Members of the AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) transcription factor family, a clade of two-AP2 domain proteins, specify both stem cell fate and control cellular progression of stem cell daughter cells toward differentiation. Here we highlight the importance of an AIL/PLT protein gradient in controlling distinct cellular behaviors in the root through the regulation of distinct targets in different parts of the root tip. Within the shoot, AIL/PLT proteins also promote organ growth and inhibit differentiation pointing to conserved roles in meristem function. However, they exhibit unequal genetic redundancy in these functions and do not always act in a purely additive manner. Differences in AIL/PLT regulation and perhaps transcriptional targets in roots and shoots suggest that these growth regulators have adapted to mediate growth control in distinct ways in these organ systems.
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Affiliation(s)
- Ben Scheres
- Department of Plant Biology, Wageningen University Research, The Netherlands.
| | - Beth A Krizek
- Department of Biological Sciences, University of South Carolina, USA
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19
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Li H, Liu Q, Zhang Q, Qin E, Jin C, Wang Y, Wu M, Shen G, Chen C, Song W, Wang C. Curd development associated gene (CDAG1) in cauliflower (Brassica oleracea L. var. botrytis) could result in enlarged organ size and increased biomass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 254:82-94. [PMID: 27964787 DOI: 10.1016/j.plantsci.2016.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 05/19/2023]
Abstract
The curd is a specialized organ and the most important product organ of cauliflower (Brassica oleracea L. var. botrytis). However, the mechanism underlying the regulation of curd formation and development remains largely unknown. In the present study, a novel homologous gene containing the Organ Size Related (OSR) domain, namely, CDAG1 (Curd Development Associated Gene 1) was identified in cauliflower. Quantitative analysis indicated that CDAG1 showed significantly higher transcript levels in young tissues. Functional analysis demonstrated that the ectopic overexpression of CDAG1 in Arabidopsis and cauliflower could significantly promote organ growth and result in larger organ size and increased biomass. Organ enlargement was predominantly due to increased cell number. In addition, 228 genes involved in the CDAG1-mediated regulatory network were discovered by transcriptome analysis. Among these genes, CDAG1 was confirmed to inhibit the transcriptional expression of the endogenous OSR genes, ARGOS and ARL, while a series of ethylene-responsive transcription factors (ERFs) were found to increased expression in 35S:CDAG1 transgenic Arabidopsis plants. This implies that CDAG1 may function in the ethylene-mediated signal pathway. These findings provide new insight into the function of OSR genes, and suggest potential applications of CDAG1 in breeding high-yielding crops.
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Affiliation(s)
- Hui Li
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Qian Liu
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Qingli Zhang
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Erjun Qin
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Chuan Jin
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yu Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Mei Wu
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Guangshuang Shen
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Chengbin Chen
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Wenqin Song
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Chunguo Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
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20
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Krizek BA, Bequette CJ, Xu K, Blakley IC, Fu ZQ, Stratmann JW, Loraine AE. RNA-Seq Links the Transcription Factors AINTEGUMENTA and AINTEGUMENTA-LIKE6 to Cell Wall Remodeling and Plant Defense Pathways. PLANT PHYSIOLOGY 2016; 171:2069-84. [PMID: 27208279 PMCID: PMC4936541 DOI: 10.1104/pp.15.01625] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/18/2016] [Indexed: 05/18/2023]
Abstract
AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6 (AIL6) are two related transcription factors in Arabidopsis (Arabidopsis thaliana) that have partially overlapping roles in several aspects of flower development, including floral organ initiation, identity specification, growth, and patterning. To better understand the biological processes regulated by these two transcription factors, we performed RNA sequencing (RNA-Seq) on ant ail6 double mutants. We identified thousands of genes that are differentially expressed in the double mutant compared with the wild type. Analyses of these genes suggest that ANT and AIL6 regulate floral organ initiation and growth through modifications to the cell wall polysaccharide pectin. We found reduced levels of demethylesterified homogalacturonan and altered patterns of auxin accumulation in early stages of ant ail6 flower development. The RNA-Seq experiment also revealed cross-regulation of AIL gene expression at the transcriptional level. The presence of a number of overrepresented Gene Ontology terms related to plant defense in the set of genes differentially expressed in ant ail6 suggest that ANT and AIL6 also regulate plant defense pathways. Furthermore, we found that ant ail6 plants have elevated levels of two defense hormones: salicylic acid and jasmonic acid, and show increased resistance to the bacterial pathogen Pseudomonas syringae These results suggest that ANT and AIL6 regulate biological pathways that are critical for both development and defense.
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Affiliation(s)
- Beth A Krizek
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina (B.A.K., C.J.B., K.X., Z.Q.F., J.W.S.); andDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina (I.C.B., A.E.L.)
| | - Carlton J Bequette
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina (B.A.K., C.J.B., K.X., Z.Q.F., J.W.S.); andDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina (I.C.B., A.E.L.)
| | - Kaimei Xu
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina (B.A.K., C.J.B., K.X., Z.Q.F., J.W.S.); andDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina (I.C.B., A.E.L.)
| | - Ivory C Blakley
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina (B.A.K., C.J.B., K.X., Z.Q.F., J.W.S.); andDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina (I.C.B., A.E.L.)
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina (B.A.K., C.J.B., K.X., Z.Q.F., J.W.S.); andDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina (I.C.B., A.E.L.)
| | - Johannes W Stratmann
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina (B.A.K., C.J.B., K.X., Z.Q.F., J.W.S.); andDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina (I.C.B., A.E.L.)
| | - Ann E Loraine
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina (B.A.K., C.J.B., K.X., Z.Q.F., J.W.S.); andDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina (I.C.B., A.E.L.)
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21
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Huang T, Irish VF. Gene networks controlling petal organogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:61-8. [PMID: 26428062 DOI: 10.1093/jxb/erv444] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
One of the biggest unanswered questions in developmental biology is how growth is controlled. Petals are an excellent organ system for investigating growth control in plants: petals are dispensable, have a simple structure, and are largely refractory to environmental perturbations that can alter their size and shape. In recent studies, a number of genes controlling petal growth have been identified. The overall picture of how such genes function in petal organogenesis is beginning to be elucidated. This review will focus on studies using petals as a model system to explore the underlying gene networks that control organ initiation, growth, and final organ morphology.
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Affiliation(s)
- Tengbo Huang
- College of Life Sciences, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, PR China Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Ave., New Haven, CT 06520-8104. USA
| | - Vivian F Irish
- Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Ave., New Haven, CT 06520-8104. USA Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520-8106. USA
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22
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Randall RS, Miyashima S, Blomster T, Zhang J, Elo A, Karlberg A, Immanen J, Nieminen K, Lee JY, Kakimoto T, Blajecka K, Melnyk CW, Alcasabas A, Forzani C, Matsumoto-Kitano M, Mähönen AP, Bhalerao R, Dewitte W, Helariutta Y, Murray JAH. AINTEGUMENTA and the D-type cyclin CYCD3;1 regulate root secondary growth and respond to cytokinins. Biol Open 2015; 4:1229-36. [PMID: 26340943 PMCID: PMC4610221 DOI: 10.1242/bio.013128] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Higher plant vasculature is characterized by two distinct developmental phases. Initially, a well-defined radial primary pattern is established. In eudicots, this is followed by secondary growth, which involves development of the cambium and is required for efficient water and nutrient transport and wood formation. Regulation of secondary growth involves several phytohormones, and cytokinins have been implicated as key players, particularly in the activation of cell proliferation, but the molecular mechanisms mediating this hormonal control remain unknown. Here we show that the genes encoding the transcription factor AINTEGUMENTA (ANT) and the D-type cyclin CYCD3;1 are expressed in the vascular cambium of Arabidopsis roots, respond to cytokinins and are both required for proper root secondary thickening. Cytokinin regulation of ANT and CYCD3 also occurs during secondary thickening of poplar stems, suggesting this represents a conserved regulatory mechanism.
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Affiliation(s)
- Ricardo S Randall
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Shunsuke Miyashima
- Department of Biological Sciences, Osaka University, Graduate School of Science, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Tiina Blomster
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Jing Zhang
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Annakaisa Elo
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Anna Karlberg
- Department of Plant Physiology, Umeå University, Umeå SE-901 87, Sweden
| | - Juha Immanen
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Kaisa Nieminen
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Tatsuo Kakimoto
- Department of Biological Sciences, Osaka University, Graduate School of Science, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Karolina Blajecka
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Charles W Melnyk
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Annette Alcasabas
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Celine Forzani
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Miho Matsumoto-Kitano
- Department of Biological Sciences, Osaka University, Graduate School of Science, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Ari Pekka Mähönen
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | | | - Walter Dewitte
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Ykä Helariutta
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - James A H Murray
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
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