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LE Q, Huang Z, Dai R, Li S, Li M, Fang Y, Wang Y, Rao Y. [Mapping of QTL associated with rice cooking quality and candidate gene analysis]. Sheng Wu Gong Cheng Xue Bao 2024; 40:122-136. [PMID: 38258636 DOI: 10.13345/j.cjb.230207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Excavating the quantitative trait locus (QTL) associated with rice cooking quality, analyzing candidate genes, and improving cooking quality-associated traits of rice varieties by genetic breeding can effectively improve the taste of rice. In this study, we used the indica rice HZ, the japonica rice Nekken2 and 120 recombinant inbred lines (RILs) populations constructed from them as experimental materials to measure the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) of rice at the maturity stage. We combined the high-density genetic map for QTL mapping. A total of 26 QTLs associated with rice cooking quality (1 QTL associated with GT, 13 QTLs associated with GC, and 12 QTLs associated with AC) were detected, among which the highest likelihood of odd (LOD) value reached 30.24. The expression levels of candidate genes in the localization interval were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), and it was found that the expression levels of six genes were significantly different from that in parents. It was speculated that the high expression of LOC_Os04g20270 and LOC_Os11g40100 may greatly increase the GC of rice, while the high expression of LOC_Os01g04920 and LOC_Os02g17500 and the low expression of LOC_Os03g02650 and LOC_Os05g25840 may reduce the AC. The results lay a molecular foundation for the cultivation of new high-quality rice varieties, and provide important genetic resources for revealing the molecular regulation mechanism of rice cooking quality.
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Affiliation(s)
- Qiaona LE
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Ziwen Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Ruohui Dai
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Sanfeng Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Mengjia Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yuan Fang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
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2
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Luo Z, Liu CL, Yang X, Zhu JK, Huang CF. Mitigating cadmium accumulation in rice without compromising growth via modifying the regulatory region of OsNRAMP5. Stress Biol 2023; 3:34. [PMID: 37676342 PMCID: PMC10441987 DOI: 10.1007/s44154-023-00117-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Cadmium (Cd) intake poses a significant health risk to humans, and the contamination of rice grains with Cd is a major concern in regions where rice is a staple food. Although the knockout of OsNRAMP5, which encodes a key transporter responsible for Cd and manganese (Mn) uptake, can significantly reduce Cd accumulation in rice grains, recent studies have revealed that this knockout adversely affects plant growth, grain yield, and increases vulnerability to abiotic and biotic stresses due to reduced Mn accumulation. In this study, we employed CRISPR/Cas9 technology to modify the regulatory region of OsNRAMP5 with the aim of reducing Cd accumulation in rice grains. Our findings demonstrate that mutations in the regulatory region of OsNRAMP5 do not impact its expression pattern but result in a reduction in translation. The decreased translation of OsNRAMP5 effectively decreases grain Cd accumulation while leaving Mn accumulation and important agronomic traits, including yield, unaffected. Thus, our study presents a practical and viable strategy for reducing Cd accumulation in rice grains without compromising Mn accumulation or overall rice production.
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Affiliation(s)
- Zhenling Luo
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao-Lei Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaofei Yang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chao-Feng Huang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Andreo-Jimenez B, Te Beest DE, Kruijer W, Vannier N, Kadam NN, Melandri G, Jagadish SVK, van der Linden G, Ruyter-Spira C, Vandenkoornhuyse P, Bouwmeester HJ. Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance. Rice (N Y) 2023; 16:26. [PMID: 37212977 DOI: 10.1186/s12284-023-00641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.
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Affiliation(s)
- Beatriz Andreo-Jimenez
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Biointeractions and Plant Health, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Dennis E Te Beest
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Niteen N Kadam
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen, The Netherlands
| | - Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
- School of Plant Sciences, University of Arizona, Tucson, USA
| | - S V Krishna Jagadish
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Kansas State University, Manhattan, KS, 66506, USA
| | | | - Carolien Ruyter-Spira
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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4
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Santos-Medellín C, Edwards J, Nguyen B, Sundaresan V. Acquisition of a complex root microbiome reshapes the transcriptomes of rice plants. New Phytol 2022; 235:2008-2021. [PMID: 35590484 DOI: 10.1111/nph.18261] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Soil microorganisms can colonize plant roots and assemble in communities engaged in symbiotic relationships with their host. Though the compositional dynamics of root-associated microbiomes have been extensively studied, the host transcriptional response to these communities is poorly understood. Here, we developed an experimental system by which rice plants grown under axenic conditions can acquire a defined endosphere microbiome. Using this setup, we performed a cross-sectional characterization of plant transcriptomes in the presence or absence of a complex microbial community. To account for compositional variation, plants were inoculated with soil-derived microbiomes harvested from three distinct agricultural sites. Soil microbiomes triggered a major shift in the transcriptional profiles of rice plants that included the downregulation of one-third to one-fourth of the families of leucine-rich repeat receptor-like kinases and nucleotide-binding leucine-rich repeat receptors expressed in roots. Though the expression of several genes was consistent across all soil sources, a large fraction of this response was differentially impacted by soil type. These results demonstrate the role of root microbiomes in sculpting the transcriptomes of host plants and highlight the potential involvement of the two main receptor families of the plant immune system in the recruitment and maintenance of an endosphere microbiome.
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Affiliation(s)
| | - Joseph Edwards
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Bao Nguyen
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
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5
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Xu W, Zhu W, Yang L, Liang W, Li H, Yang L, Chen M, Luo Z, Huang G, Duan L, Dreni L, Zhang D. SMALL REPRODUCTIVE ORGANS, a SUPERMAN-like transcription factor, regulates stamen and pistil growth in rice. New Phytol 2022; 233:1701-1718. [PMID: 34761379 DOI: 10.1111/nph.17849] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Organ size is determined mainly by cell division and cell expansion. Several genetic factors regulating development of plant lateral organs have been characterized, but those involved in determining reproductive organ size and separation in rice (Oryza sativa) remain unknown. We have isolated the rice gene SMALL REPRODUCTIVE ORGANS (SRO) encoding a nucleus-localized Cys2His2 (C2 H2 ) zinc finger protein orthologous to Arabidopsis transcription factor (TF) SUPERMAN (SUP). Combined developmental, genetic, histological and transcriptomic analyses were used to determine the function of SRO in regulating reproductive organ size. SRO affects genes involved in cell division, cell expansion and phytohormone signalling in the rice flower. SRO is specifically expressed in the first stages of stamen filament development to regulate their correct formation and separation. In addition, SRO noncell-autonomously regulates the size and functionality of male and female reproductive organs. The B-class MADS-box gene OsMADS16/SPW1 is epistatic to SRO, whereas SRO regulates reproductive organ specification and floral meristem determinacy synergistically with C-class genes OsMADS3 and OsMADS58. These findings provide insights into how an evolutionarily conserved TF has a pivotal role in reproductive organ development in core eudicots and monocots, through partially conserved expression, function and regulatory network.
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Affiliation(s)
- Wei Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanwan Zhu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liu Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Li
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China
| | - Li Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mingjiao Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhijing Luo
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lei Duan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ludovico Dreni
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
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6
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Nishizawa-Yokoi A, Saika H, Hara N, Lee LY, Toki S, Gelvin SB. Agrobacterium T-DNA integration in somatic cells does not require the activity of DNA polymerase θ. New Phytol 2021; 229:2859-2872. [PMID: 33105034 DOI: 10.1111/nph.17032] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Integration of Agrobacterium tumefaciens transferred DNA (T-DNA) into the plant genome is the last step required for stable plant genetic transformation. The mechanism of T-DNA integration remains controversial, although scientists have proposed the participation of various nonhomologous end-joining (NHEJ) pathways. Recent evidence suggests that in Arabidopsis, DNA polymerase θ (PolQ) may be a crucial enzyme involved in T-DNA integration. We conducted quantitative transformation assays of wild-type and polQ mutant Arabidopsis and rice, analyzed T-DNA/plant DNA junction sequences, and (for Arabidopsis) measured the amount of integrated T-DNA in mutant and wild-type tissue. Unexpectedly, we were able to generate stable transformants of all tested lines, although the transformation frequency of polQ mutants was c. 20% that of wild-type plants. T-DNA/plant DNA junctions from these transformed rice and Arabidopsis polQ mutants closely resembled those from wild-type plants, indicating that loss of PolQ activity does not alter the characteristics of T-DNA integration events. polQ mutant plants show growth and developmental defects, perhaps explaining previous unsuccessful attempts at their stable transformation. We suggest that either multiple redundant pathways function in T-DNA integration, and/or that integration requires some yet unknown pathway.
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Affiliation(s)
- Ayako Nishizawa-Yokoi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, 305-8634, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Hiroaki Saika
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, 305-8634, Japan
| | - Naho Hara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, 305-8634, Japan
| | - Lan-Ying Lee
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907-1392, USA
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, 305-8634, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12, Maioka-cho, Yokohama, 244-0813, Japan
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907-1392, USA
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7
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Abstract
The cereal crops rice (Oryza sativa), maize (Zea mays ssp. mays) and wheat (Triticum aestivum) provide half of the food eaten by humankind. However, understanding their biology has proved challenging due to their large size, long lifecycle and large genomes. The model plant Arabidopsis thaliana avoids these practical problems and has provided fundamental understanding of plant biology, however not all of this knowledge is directly transferrable to cereals. Recent developments in gene editing, speed breeding and genome assembly techniques mean that the challenges associated with working with the major cereal crops can be overcome. Resources such as mutant collections and genome sequences are now available for these crops, making them attractive experimental systems with which to make discoveries that are directly applicable to increasing crop production.
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Affiliation(s)
- Philippa Borrill
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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8
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Kanda Y, Nishizawa Y, Kamakura T, Mori M. Overexpressed BSR1-Mediated Enhancement of Disease Resistance Depends on the MAMP-Recognition System. Int J Mol Sci 2020; 21:ijms21155397. [PMID: 32751339 PMCID: PMC7432911 DOI: 10.3390/ijms21155397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 11/16/2022] Open
Abstract
Plant plasma membrane-localized receptors recognize microbe-associated molecular patterns (MAMPs) and activate immune responses via various signaling pathways. Receptor-like cytoplasmic kinases (RLCKs) are considered key signaling factors in plant immunity. BROAD-SPECTRUM RESISTANCE 1 (BSR1), a rice RLCK, plays a significant role in disease resistance. Overexpression of BSR1 confers strong resistance against fungal and bacterial pathogens. Our recent study revealed that MAMP-triggered immune responses are mediated by BSR1 in wild-type rice and are hyperactivated in BSR1-overexpressing rice. It was suggested that hyperactivated immune responses were responsible for the enhancement of broad-spectrum disease resistance; however, this remained to be experimentally validated. In this study, we verified the above hypothesis by disrupting the MAMP-recognition system in BSR1-overexpressing rice. To this end, we knocked out OsCERK1, which encodes a well-characterized MAMP-receptor-like protein kinase. In the background of BSR1 overaccumulation, the knockout of OsCERK1 nearly abolished the enhancement of blast resistance. This finding indicates that overexpressed BSR1-mediated enhancement of disease resistance depends on the MAMP-triggered immune system, corroborating our previously suggested model.
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Affiliation(s)
- Yasukazu Kanda
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba 305-8602, Japan; (Y.K.); (Y.N.)
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan;
| | - Yoko Nishizawa
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba 305-8602, Japan; (Y.K.); (Y.N.)
| | - Takashi Kamakura
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan;
| | - Masaki Mori
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba 305-8602, Japan; (Y.K.); (Y.N.)
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan;
- Correspondence: ; Tel.: +81-29-838-7008
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9
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Kong W, Zhang C, Qiang Y, Zhong H, Zhao G, Li Y. Integrated RNA-Seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots. Int J Mol Sci 2020; 21:ijms21134615. [PMID: 32610550 PMCID: PMC7369714 DOI: 10.3390/ijms21134615] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 12/20/2022] Open
Abstract
Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.
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10
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Lin H, Arrivault S, Coe RA, Karki S, Covshoff S, Bagunu E, Lunn JE, Stitt M, Furbank RT, Hibberd JM, Quick WP. A Partial C 4 Photosynthetic Biochemical Pathway in Rice. Front Plant Sci 2020; 11:564463. [PMID: 33178234 PMCID: PMC7593541 DOI: 10.3389/fpls.2020.564463] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/25/2020] [Indexed: 05/21/2023]
Abstract
Introduction of a C4 photosynthetic pathway into C3 rice (Oryza sativa) requires installation of a biochemical pump that concentrates CO2 at the site of carboxylation in modified bundle sheath cells. To investigate the feasibility of this, we generated a quadruple line that simultaneously accumulates four of the core C4 photosynthetic enzymes from the NADP-malic enzyme subtype, phosphoenolpyruvate carboxylase (ZmPEPC), NADP-malate dehydrogenase (ZmNADP-MDH), NADP-malic enzyme (ZmNADP-ME), and pyruvate phosphate dikinase (ZmPPDK). This led to enhanced enzyme activity and mild phenotypic perturbations but was largely neutral in its effects on photosynthetic rate. Measurements of the flux of 13CO2 through photosynthetic metabolism revealed a significant increase in the incorporation of 13C into malate, consistent with increased fixation of 13CO2 via PEP carboxylase in lines expressing the maize PEPC enzyme. However, there was no significant differences in labeling of 3-phosphoglycerate (3PGA) indicating that there was no carbon flux through NADP-ME into the Calvin-Benson cycle. There was also no significant difference in labeling of phosphoenolpyruvate (PEP) indicating that there was no carbon flux through PPDK. Crossing the quadruple line with a line with reduced glycine decarboxylase H-protein (OsGDCH) abundance led to a photosynthetic phenotype characteristic of the reduced OsGDCH line and higher labeling of malate, aspartate and citrate than in the quintuple line. There was evidence of 13C labeling of aspartate indicating 13CO2 fixation into oxaloacetate by PEPC and conversion to aspartate by the endogenous aspartate aminotransferase activity. While Kranz anatomy or other anatomical modifications have not yet been installed in these plants to enable a fully functional C4 cycle, these results demonstrate for the first-time a partial flux through the carboxylation phase of NADP-ME C4 metabolism in transgenic rice containing two of the key metabolic steps in the C4 pathway.
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Affiliation(s)
- HsiangChun Lin
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam, Germany
| | - Robert A. Coe
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Shanta Karki
- National Centre for Fruit Development, Kirtipur, Nepal
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Efren Bagunu
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - John E. Lunn
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam, Germany
| | - Robert T. Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Julian M. Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - William Paul Quick
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- *Correspondence: William Paul Quick,
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11
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Affiliation(s)
- Marta Peirats-Llobet
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, Centre for AgriBioscience, La Trobe University, Bundoora, Vic., 3086, Australia
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12
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Tanaka W, Hirano HY. Antagonistic action of TILLERS ABSENT1 and FLORAL ORGAN NUMBER2 regulates stem cell maintenance during axillary meristem development in rice. New Phytol 2020; 225:974-984. [PMID: 31486529 DOI: 10.1111/nph.16163] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Shoot branches are formed from the axillary meristem and their formation is a key process in plant development. Although our understanding of the mechanisms underlying stem cell maintenance in the shoot apical meristem (SAM) is progressing, our knowledge of these mechanisms during the process of axillary meristem development is insufficient. To elucidate the genetic mechanisms underlying axillary meristem development in rice (Oryza sativa), we undertook a molecular genetic analysis focusing on TILLERS ABSENT1 (TAB1) and FLORAL ORGAN NUMBER2 (FON2), respective orthologs of the WUSCHEL and CLAVATA3 genes involved in SAM maintenance in Arabidopsis (Arabidopsis thaliana). We revealed that stem cells were established at an early stage of axillary meristem development in the wild-type, but were not maintained in tab1. By contrast, the stem cell region and TAB1 expression domain were expanded in fon2, and FON2 overexpression inhibited axillary meristem formation. These results indicate that TAB1 is required to maintain stem cells during axillary meristem development, whereas FON2 negatively regulates stem cell fate by restricting TAB1 expression. Thus, the genetic pathway regulating SAM maintenance in Arabidopsis seems to have been recruited to play a specific role within a narrow developmental window - namely, axillary meristem establishment - in rice.
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Affiliation(s)
- Wakana Tanaka
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hiro-Yuki Hirano
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
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13
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Kanda Y, Nakagawa H, Nishizawa Y, Kamakura T, Mori M. Broad-Spectrum Disease Resistance Conferred by the Overexpression of Rice RLCK BSR1 Results from an Enhanced Immune Response to Multiple MAMPs. Int J Mol Sci 2019; 20:ijms20225523. [PMID: 31698708 PMCID: PMC6888047 DOI: 10.3390/ijms20225523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Plants activate their immune system through intracellular signaling pathways after perceiving microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases mediate the intracellular signaling downstream of pattern-recognition receptors. BROAD-SPECTRUM RESISTANCE 1 (BSR1), a rice (Oryza sativa) receptor-like cytoplasmic kinase subfamily-VII protein, contributes to chitin-triggered immune responses. It is valuable for agriculture because its overexpression confers strong disease resistance to fungal and bacterial pathogens. However, it remains unclear how overexpressed BSR1 reinforces plant immunity. Here we analyzed immune responses using rice suspension-cultured cells and sliced leaf blades overexpressing BSR1. BSR1 overexpression enhances MAMP-triggered production of hydrogen peroxide (H2O2) and transcriptional activation of the defense-related gene in cultured cells and leaf strips. Furthermore, the co-cultivation of leaves with conidia of the blast fungus revealed that BSR1 overexpression allowed host plants to produce detectable oxidative bursts against compatible pathogens. BSR1 was also involved in the immune responses triggered by peptidoglycan and lipopolysaccharide. Thus, we concluded that the hyperactivation of MAMP-triggered immune responses confers BSR1-mediated robust resistance to broad-spectrum pathogens.
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Affiliation(s)
- Yasukazu Kanda
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba 305-8602, Japan; (Y.K.); (H.N.); (Y.N.)
- Graduate School of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan;
| | - Hitoshi Nakagawa
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba 305-8602, Japan; (Y.K.); (H.N.); (Y.N.)
| | - Yoko Nishizawa
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba 305-8602, Japan; (Y.K.); (H.N.); (Y.N.)
| | - Takashi Kamakura
- Graduate School of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan;
| | - Masaki Mori
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba 305-8602, Japan; (Y.K.); (H.N.); (Y.N.)
- Graduate School of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan;
- Correspondence: ; Tel.: +81-29-838-7008
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14
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Andreo-Jimenez B, Vandenkoornhuyse P, Lê Van A, Heutinck A, Duhamel M, Kadam N, Jagadish K, Ruyter-Spira C, Bouwmeester H. Plant host and drought shape the root associated fungal microbiota in rice. PeerJ 2019; 7:e7463. [PMID: 31565550 PMCID: PMC6744933 DOI: 10.7717/peerj.7463] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/11/2019] [Indexed: 11/22/2022] Open
Abstract
Background and Aim Water is an increasingly scarce resource while some crops, such as paddy rice, require large amounts of water to maintain grain production. A better understanding of rice drought adaptation and tolerance mechanisms could help to reduce this problem. There is evidence of a possible role of root-associated fungi in drought adaptation. Here, we analyzed the endospheric fungal microbiota composition in rice and its relation to plant genotype and drought. Methods Fifteen rice genotypes (Oryza sativa ssp. indica) were grown in the field, under well-watered conditions or exposed to a drought period during flowering. The effect of genotype and treatment on the root fungal microbiota composition was analyzed by 18S ribosomal DNA high throughput sequencing. Grain yield was determined after plant maturation. Results There was a host genotype effect on the fungal community composition. Drought altered the composition of the root-associated fungal community and increased fungal biodiversity. The majority of OTUs identified belonged to the Pezizomycotina subphylum and 37 of these significantly correlated with a higher plant yield under drought, one of them being assigned to Arthrinium phaeospermum. Conclusion This study shows that both plant genotype and drought affect the root-associated fungal community in rice and that some fungi correlate with improved drought tolerance. This work opens new opportunities for basic research on the understanding of how the host affects microbiota recruitment as well as the possible use of specific fungi to improve drought tolerance in rice.
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Affiliation(s)
- Beatriz Andreo-Jimenez
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.,Biointeractions & Plant Health Business Unit, Wageningen University & Research, Wageningen, Netherlands
| | | | | | - Arvid Heutinck
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Marie Duhamel
- EcoBio, Université Rennes I, Rennes, France.,IBL Plant Sciences and Natural Products, Leiden University, Leiden, Netherlands
| | - Niteen Kadam
- International Rice Research Institute, Los Baños, Philippines
| | - Krishna Jagadish
- International Rice Research Institute, Los Baños, Philippines.,Department of Agronomy, Kansas State University, Manhattan, KS, United States of America
| | | | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.,Plant Hormone Biology group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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15
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Kong W, An B, Zhang Y, Yang J, Li S, Sun T, Li Y. Sugar Transporter Proteins (STPs) in Gramineae Crops: Comparative Analysis, Phylogeny, Evolution, and Expression Profiling. Cells 2019; 8:cells8060560. [PMID: 31181814 PMCID: PMC6628381 DOI: 10.3390/cells8060560] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/07/2019] [Accepted: 06/07/2019] [Indexed: 01/07/2023] Open
Abstract
Sugar transporter proteins (STPs), such as H+/sugar symporters, play essential roles in plants’ sugar transport, growth, and development, and possess an important potential to enhance plants’ performance of multiple agronomic traits, especially crop yield and stress tolerance. However, the evolutionary dynamics of this important gene family in Gramineae crops are still not well-documented and functional differentiation of rice STP genes remain unclear. To address this gap, we conducted a comparative genomic study of STP genes in seven representative Gramineae crops, which are Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Setaria italica (Si), Sorghum bicolor (Sb), Zea mays (Zm), Oryza rufipogon (Or), and Oryza sativa ssp. japonica (Os). In this case, a total of 177 STP genes were identified and grouped into four clades. Of four clades, the Clade I, Clade III, and Clade IV showed an observable number expansion compared to Clade II. Our results of identified duplication events and divergence time of duplicate gene pairs indicated that tandem, Whole genome duplication (WGD)/segmental duplication events play crucial roles in the STP gene family expansion of some Gramineae crops (expect for Hv) during a long-term evolutionary process. However, expansion mechanisms of the STP gene family among the tested species were different. Further selective force studies revealed that the STP gene family in Gramineae crops was under purifying selective forces and different clades and orthologous groups with different selective forces. Furthermore, expression analysis showed that rice STP genes play important roles not only in flower organs development but also under various abiotic stresses (cold, high-temperature, and submergence stresses), blast infection, and wounding. The current study highlighted the expansion and evolutionary patterns of the STP gene family in Gramineae genomes and provided some important messages for the future functional analysis of Gramineae crop STP genes.
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Affiliation(s)
- Weilong Kong
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Baoguang An
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Yue Zhang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China. Yue.Zhang-@whu.edu.cn
| | - Jing Yang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Shuangmiao Li
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Tong Sun
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Yangsheng Li
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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16
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Jyoti A, Kaushik S, Srivastava VK, Datta M, Kumar S, Yugandhar P, Kothari SL, Rai V, Jain A. The potential application of genome editing by using CRISPR/Cas9, and its engineered and ortholog variants for studying the transcription factors involved in the maintenance of phosphate homeostasis in model plants. Semin Cell Dev Biol 2019; 96:77-90. [PMID: 30951893 DOI: 10.1016/j.semcdb.2019.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/26/2022]
Abstract
Phosphorus (P), an essential macronutrient, is pivotal for growth and development of plants. Availability of phosphate (Pi), the only assimilable P, is often suboptimal in rhizospheres. Pi deficiency triggers an array of spatiotemporal adaptive responses including the differential regulation of several transcription factors (TFs). Studies on MYB TF PHR1 in Arabidopsis thaliana (Arabidopsis) and its orthologs OsPHRs in Oryza sativa (rice) have provided empirical evidence of their significant roles in the maintenance of Pi homeostasis. Since the functional characterization of PHR1 in 2001, several other TFs have now been identified in these model plants. This raised a pertinent question whether there are any likely interactions across these TFs. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has provided an attractive paradigm for editing genome in plants. Here, we review the applications and challenges of this technique for genome editing of the TFs for deciphering the function and plausible interactions across them. This technology could thus provide a much-needed fillip towards engineering TFs for generating Pi use efficient plants for sustainable agriculture. Furthermore, we contemplate whether this technology could be a viable alternative to the controversial genetically modified (GM) rice or it may also eventually embroil into a limbo.
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Affiliation(s)
- Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Manali Datta
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Shailesh Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Poli Yugandhar
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Shanker L Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, 110012, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India.
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17
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Yao W, Li G, Yu Y, Ouyang Y. funRiceGenes dataset for comprehensive understanding and application of rice functional genes. Gigascience 2018; 7:1-9. [PMID: 29220485 PMCID: PMC5765555 DOI: 10.1093/gigascience/gix119] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 11/22/2017] [Indexed: 12/26/2022] Open
Abstract
Background As a main staple food, rice is also a model plant for functional genomic studies of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement. Findings We built a comprehensive and accurate dataset of ∼2800 functionally characterized rice genes and ∼5000 members of different gene families by integrating data from available databases and reviewing every publication on rice functional genomic studies. The dataset accounts for 19.2% of the 39 045 annotated protein-coding rice genes, which provides the most exhaustive archive for investigating the functions of rice genes. We also constructed 214 gene interaction networks based on 1841 connections between 1310 genes. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. Increasing degree of conservation of the flowering pathway was observed among more closely related plants, implying substantial value of rice genes for future dissection of flowering regulation in other crops. All data are deposited in the funRiceGenes database (https://funricegenes.github.io/). Functionality for advanced search and continuous updating of the database are provided by a Shiny application (http://funricegenes.ncpgr.cn/). Conclusions The funRiceGenes dataset would enable further exploring of the crosslink between gene functions and natural variations in rice, which can also facilitate breeding design to improve target agronomic traits of rice.
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Affiliation(s)
- Wen Yao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Yu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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18
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Ellsworth PV, Ellsworth PZ, Koteyeva NK, Cousins AB. Cell wall properties in Oryza sativa influence mesophyll CO 2 conductance. New Phytol 2018; 219:66-76. [PMID: 29676468 DOI: 10.1111/nph.15173] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/18/2018] [Indexed: 06/08/2023]
Abstract
Diffusion of CO2 from the leaf intercellular air space to the site of carboxylation (gm ) is a potential trait for increasing net rates of CO2 assimilation (Anet ), photosynthetic efficiency, and crop productivity. Leaf anatomy plays a key role in this process; however, there are few investigations into how cell wall properties impact gm and Anet . Online carbon isotope discrimination was used to determine gm and Anet in Oryza sativa wild-type (WT) plants and mutants with disruptions in cell wall mixed-linkage glucan (MLG) production (CslF6 knockouts) under high- and low-light growth conditions. Cell wall thickness (Tcw ), surface area of chloroplast exposed to intercellular air spaces (Sc ), leaf dry mass per area (LMA), effective porosity, and other leaf anatomical traits were also analyzed. The gm of CslF6 mutants decreased by 83% relative to the WT, with c. 28% of the reduction in gm explained by Sc . Although Anet /LMA and Anet /Chl partially explained differences in Anet between genotypes, the change in cell wall properties influenced the diffusivity and availability of CO2 . The data presented here indicate that the loss of MLG in CslF6 plants had an impact on gm and demonstrate the importance of cell wall effective porosity and liquid path length on gm .
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Affiliation(s)
- Patrícia V Ellsworth
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Patrick Z Ellsworth
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Nuria K Koteyeva
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
- Laboratory of Anatomy and Morphology, V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St Petersburg, 197376, Russia
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
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19
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Yoneyama K, Mori N, Sato T, Yoda A, Xie X, Okamoto M, Iwanaga M, Ohnishi T, Nishiwaki H, Asami T, Yokota T, Akiyama K, Yoneyama K, Nomura T. Conversion of carlactone to carlactonoic acid is a conserved function of MAX1 homologs in strigolactone biosynthesis. New Phytol 2018; 218:1522-1533. [PMID: 29479714 DOI: 10.1111/nph.15055] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/12/2018] [Indexed: 05/23/2023]
Abstract
Strigolactones (SLs) are a class of plant hormones which regulate shoot branching and function as host recognition signals for symbionts and parasites in the rhizosphere. However, steps in SL biosynthesis after carlactone (CL) formation remain elusive. This study elucidated the common and diverse functions of MAX1 homologs which catalyze CL oxidation. We have reported previously that ArabidopsisMAX1 converts CL to carlactonoic acid (CLA), whereas a rice MAX1 homolog has been shown to catalyze the conversion of CL to 4-deoxyorobanchol (4DO). To determine which reaction is conserved in the plant kingdom, we investigated the enzymatic function of MAX1 homologs in Arabidopsis, rice, maize, tomato, poplar and Selaginella moellendorffii. The conversion of CL to CLA was found to be a common reaction catalyzed by MAX1 homologs, and MAX1s can be classified into three types: A1-type, converting CL to CLA; A2-type, converting CL to 4DO via CLA; and A3-type, converting CL to CLA and 4DO to orobanchol. CLA was detected in root exudates from poplar and Selaginella, but not ubiquitously in other plants examined in this study, suggesting its role as a species-specific signal in the rhizosphere. This study provides new insights into the roles of MAX1 in endogenous and rhizosphere signaling.
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Affiliation(s)
- Kaori Yoneyama
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, 321-8505, Japan
- Graduate School of Agriculture, Ehime University, Ehime, 790-8566, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
| | - Narumi Mori
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Tomoyasu Sato
- Department of Bioproductive Science, Graduate School of Agriculture, Utsunomiya University, Utsunomiya, 321-8505, Japan
| | - Akiyoshi Yoda
- Department of Bioproductive Science, Graduate School of Agriculture, Utsunomiya University, Utsunomiya, 321-8505, Japan
| | - Xiaonan Xie
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, 321-8505, Japan
- Department of Bioproductive Science, Graduate School of Agriculture, Utsunomiya University, Utsunomiya, 321-8505, Japan
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, 321-8505, Japan
| | - Masashi Iwanaga
- Department of Bioproductive Science, Graduate School of Agriculture, Utsunomiya University, Utsunomiya, 321-8505, Japan
| | - Toshiyuki Ohnishi
- Department of Applied Biochemistry, Graduate School of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hisashi Nishiwaki
- Graduate School of Agriculture, Ehime University, Ehime, 790-8566, Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Takao Yokota
- Department of Biosciences, Teikyo University, Utsunomiya, 320-8551, Japan
| | - Kohki Akiyama
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Koichi Yoneyama
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, 321-8505, Japan
| | - Takahito Nomura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, 321-8505, Japan
- Department of Bioproductive Science, Graduate School of Agriculture, Utsunomiya University, Utsunomiya, 321-8505, Japan
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20
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Desaki Y, Kouzai Y, Ninomiya Y, Iwase R, Shimizu Y, Seko K, Molinaro A, Minami E, Shibuya N, Kaku H, Nishizawa Y. OsCERK1 plays a crucial role in the lipopolysaccharide-induced immune response of rice. New Phytol 2018; 217:1042-1049. [PMID: 29194635 DOI: 10.1111/nph.14941] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/09/2017] [Indexed: 05/20/2023]
Abstract
Plant cell surface receptor-like kinases (RLKs) mediate the signals from microbe-associated molecular patterns (MAMPs) that induce immune responses. Lipopolysaccharide (LPS), the major constituent of the outer membrane of gram-negative bacteria, is a common MAMP perceived by animals and plants; however, the plant receptors/co-receptors are unknown except for LORE, a bulb-type lectin S-domain RLK (B-lectin SD1-RLK) in Arabidopsis. OsCERK1 is a multifunctional RLK in rice that contains lysin motifs (LysMs) and is essential for the perception of chitin, a fungal MAMP, and peptidoglycan, a bacterial MAMP. Here, we analyzed the relevance of OsCERK1 to LPS perception in rice. Using OsCERK1-knockout mutants (oscerk1), we evaluated hydrogen peroxide (H2 O2 ) production and gene expression after LPS treatment. We also examined the LPS response in knockout mutants for the B-lectin SD1-RLK genes in rice and for all LysM-protein genes in Arabidopsis. Compared with wild-type rice cells, LPS responses in oscerk1 cells were mostly diminished. By contrast, rice lines mutated in either of three B-lectin SD1-RLK genes and Arabidopsis lines mutated in the LysM-protein genes responded normally to LPS. From these results, we conclude that OsCERK1 is an LPS receptor/co-receptor and that the LPS perception systems of rice and Arabidopsis are significantly different.
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Affiliation(s)
- Yoshitake Desaki
- Department of Life Sciences, School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Yusuke Kouzai
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yusuke Ninomiya
- Department of Life Sciences, School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Ryosuke Iwase
- Department of Life Sciences, School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Yumi Shimizu
- Department of Life Sciences, School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Keito Seko
- Department of Life Sciences, School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Naples, Italy
| | - Eiichi Minami
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Yoko Nishizawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
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21
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Formentin E, Sudiro C, Perin G, Riccadonna S, Barizza E, Baldoni E, Lavezzo E, Stevanato P, Sacchi GA, Fontana P, Toppo S, Morosinotto T, Zottini M, Lo Schiavo F. Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses. Front Plant Sci 2018; 9:204. [PMID: 29556243 PMCID: PMC5844958 DOI: 10.3389/fpls.2018.00204] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/02/2018] [Indexed: 05/20/2023]
Abstract
Salinity tolerance has been extensively investigated in recent years due to its agricultural importance. Several features, such as the regulation of ionic transporters and metabolic adjustments, have been identified as salt tolerance hallmarks. Nevertheless, due to the complexity of the trait, the results achieved to date have met with limited success in improving the salt tolerance of rice plants when tested in the field, thus suggesting that a better understanding of the tolerance mechanisms is still required. In this work, differences between two varieties of rice with contrasting salt sensitivities were revealed by the imaging of photosynthetic parameters, ion content analysis and a transcriptomic approach. The transcriptomic analysis conducted on tolerant plants supported the setting up of an adaptive program consisting of sodium distribution preferentially limited to the roots and older leaves, and in the activation of regulatory mechanisms of photosynthesis in the new leaves. As a result, plants resumed grow even under prolonged saline stress. In contrast, in the sensitive variety, RNA-seq analysis revealed a misleading response, ending in senescence and cell death. The physiological response at the cellular level was investigated by measuring the intracellular profile of H2O2 in the roots, using a fluorescent probe. In the roots of tolerant plants, a quick response was observed with an increase in H2O2 production within 5 min after salt treatment. The expression analysis of some of the genes involved in perception, signal transduction and salt stress response confirmed their early induction in the roots of tolerant plants compared to sensitive ones. By inhibiting the synthesis of apoplastic H2O2, a reduction in the expression of these genes was detected. Our results indicate that quick H2O2 signaling in the roots is part of a coordinated response that leads to adaptation instead of senescence in salt-treated rice plants.
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Affiliation(s)
- Elide Formentin
- Department of Biology, University of Padova, Padova, Italy
- *Correspondence: Elide Formentin,
| | | | - Giorgio Perin
- Department of Biology, University of Padova, Padova, Italy
| | - Samantha Riccadonna
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, Italy
| | | | - Elena Baldoni
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padova, Padova, Italy
| | - Gian Attilio Sacchi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Paolo Fontana
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padova, Italy
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22
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Scafaro AP, Atwell BJ, Muylaert S, Reusel BV, Ruiz GA, Rie JV, Gallé A. A Thermotolerant Variant of Rubisco Activase From a Wild Relative Improves Growth and Seed Yield in Rice Under Heat Stress. Front Plant Sci 2018; 9:1663. [PMID: 30524456 PMCID: PMC6256286 DOI: 10.3389/fpls.2018.01663] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 10/26/2018] [Indexed: 05/03/2023]
Abstract
Genes encoding thermostable variants of the photosynthesis heat-labile protein Rubisco activase (Rca) from a wild relative Oryza australiensis were overexpressed in domesticated rice (Oryza sativa). Proteomics was used to quantify the abundance of O. australiensis Rca (Rca-Oa) in the resulting plants. Plants were grown to maturity in growth rooms and from early tillering until immediately prior to anthesis, they were exposed to daytime maximum temperatures of 28, 40, and 45°C and constant night temperatures of 22°C. Non-destructive measurements of leaf elongation and photosynthesis were used to compare the null segregant with a transfected line in which 19% of its total Rca content was the recombinant O. australiensis Rca (T-Oa-19). Height, fresh mass, panicle number, seed set, and seed number were measured at final harvest. Traits at maturity after heat stress at 45°C correlated strongly with recombinant protein abundance. Seed number was far the most responsive trait to an increase in Rca-Oa abundance, improving by up to 150%. Leaf elongation rates (LER) and tiller number were significantly greater in the transformed plants in the first two weeks of exposure to 45°C but tiller numbers later became equal in the two genotypes. Gas exchange measurements showed that T-Oa-19 had faster light induction of photosynthesis but not significantly higher CO2 assimilation rates, indicating that the carbon gain that resulted in large yield improvement after growth at 45°C was not strongly correlated with an instantaneous measurement of steady-state photosynthesis. When plants were grown at 40°C daytime maximum, there was no improvement in the final biomass, panicle or seed number when compared with 28°C, indicating that the threshold for heat damage and beneficial effects of the thermostable Rca recombinant protein was between 40 and 45°C, which corresponded to leaf temperatures in the range 38-42°C. The results suggest that the thermotolerant form of Rca from O. australiensis was sufficient to enhance carbohydrate accumulation and storage by rice over the life of the plant, dramatically improving yields after exposure to heat throughout the vegetative phase.
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Affiliation(s)
- Andrew P. Scafaro
- Bayer CropScience SA-NV, Innovation Center Ghent, Ghent, Belgium
- *Correspondence: Andrew P. Scafaro,
| | - Brian J. Atwell
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Steven Muylaert
- Bayer CropScience SA-NV, Innovation Center Ghent, Ghent, Belgium
| | | | | | - Jeroen Van Rie
- Bayer CropScience SA-NV, Innovation Center Ghent, Ghent, Belgium
| | - Alexander Gallé
- Bayer CropScience SA-NV, Innovation Center Ghent, Ghent, Belgium
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23
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Li G, Li X, Wang Y, Mi J, Xing F, Zhang D, Dong Q, Li X, Xiao J, Zhang Q, Ouyang Y. Three representative inter and intra-subspecific crosses reveal the genetic architecture of reproductive isolation in rice. Plant J 2017; 92:349-362. [PMID: 28805257 DOI: 10.1111/tpj.13661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/25/2017] [Accepted: 08/07/2017] [Indexed: 05/28/2023]
Abstract
Systematic characterization of genetic and molecular mechanisms in the formation of hybrid sterility is of fundamental importance in understanding reproductive isolation and speciation. Using ultra-high-density genetic maps, 43 single-locus quantitative trait loci (QTLs) and 223 digenic interactions for embryo-sac, pollen, and spikelet fertility are depicted from three crosses between representative varieties of japonica and two varietal groups of indica, which provide an extensive archive for investigating the genetic basis of reproductive isolation in rice. Ten newly detected single-locus QTLs for inter- and intra-subspecific fertility are identified. Three loci for embryo-sac fertility are detected in both Nip × ZS97 and Nip × MH63 crosses, whereas QTLs for pollen fertility are not in common between the two crosses thus leading to fertility variation. Five loci responsible for fertility and segregation distortion are observed in the ZS97 × MH63 cross. The importance of two-locus interactions on fertility are quantified in the whole genome, which identify that three types of interaction contribute to fertility reduction in the hybrid. These results construct the genetic architecture with respect to various forms of reproductive barriers in rice, which have significant implications in utilization of inter-subspecific heterosis along with improvement in the fertility of indica-indica hybrids at single- and multi-locus level.
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Affiliation(s)
- Guangwei Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoting Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiaming Mi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Xing
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Dahan Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiyan Dong
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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24
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Wang P, Hendron RW, Kelly S. Transcriptional control of photosynthetic capacity: conservation and divergence from Arabidopsis to rice. New Phytol 2017; 216:32-45. [PMID: 28727145 DOI: 10.1111/nph.14682] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 05/16/2017] [Indexed: 05/12/2023]
Abstract
Contents 32 I. 32 II. 33 III. 36 IV. 41 43 References 43 SUMMARY: Photosynthesis is one of the most important biological processes on Earth. It provides the consumable energy upon which almost all organisms are dependent, and modulates the composition of the planet's atmosphere. To carry out photosynthesis, plants require a large cohort of genes. These genes encode proteins that capture light energy, store energy in sugars and build the subcellular structures required to facilitate this energy capture. Although the function of many of these genes is known, little is understood about the transcriptional networks that coordinate their expression. This review places our understanding of the transcriptional regulation of photosynthesis in Arabidopsis thaliana in an evolutionary context, to provide new insight into transcriptional regulatory networks that control photosynthesis gene expression in grasses. The similarities and differences between the rice and Arabidopsis networks are highlighted, revealing substantial disparity between the two systems. In addition, avenues are identified that may be exploited for photosynthesis engineering projects in the future.
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Affiliation(s)
- Peng Wang
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ross-William Hendron
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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25
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Datta M, Kaushik S, Jyoti A, Mathur N, Kothari SL, Jain A. SIZ1-mediated SUMOylation during phosphate homeostasis in plants: Looking beyond the tip of the iceberg. Semin Cell Dev Biol 2017; 74:123-132. [PMID: 28903074 DOI: 10.1016/j.semcdb.2017.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 11/27/2022]
Abstract
Availability of phosphate (Pi) is often limited in rhizospheres in different agroclimatic zones and adversely affects growth and development of plants. To circumvent this impasse, there is an urgent need and global consensus to develop Pi use efficient crops. To achieve this goal, it is essential to identify the molecular entities that exert regulatory influences on the sensing and signaling cascade governing Pi homeostasis. SIZ1 encodes a small ubiquitin-like modifier (SUMO E3) ligase, and plays a pivotal role in the post-translational SUMOylation of proteins. In this review, we discuss the reverse genetics approach conventionally used for providing circumstantial evidence towards the regulatory influences of SIZ1 on several morphophysiological and molecular traits that govern Pi homeostasis in taxonomically diverse Arabidopsis thaliana (Arabidopsis) and Oryza sativa (rice) model species. However, the efforts have been rather modest in identifying SUMO protein targets that play key roles in the maintenance of Pi homeostasis in these model plants contrary to the plethora of them now known in lower organisms and animals. Therefore, to predict the SIZ1-mediated SUMOylome involved in Pi homeostasis, the state-of-the-art high-throughput technologies often used for animals thus provide an attractive paradigm towards achieving the long-term goal of developing Pi use efficient crops.
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Affiliation(s)
- Manali Datta
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Anupam Jyoti
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Nidhi Mathur
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Shanker L Kothari
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Ajay Jain
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India.
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26
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Watanabe KA, Homayouni A, Gu L, Huang KY, Ho THD, Shen QJ. Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element. Plant Cell Environ 2017. [PMID: 28626890 DOI: 10.1111/pce.13006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (ABA). The ABA responsive element (ABRE) is a key cis-regulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABA-induced genes in rice aleurone cells, suggesting other ABREs may exist. To identify novel ABREs, RNA sequencing was performed on aleurone cells of rice seeds treated with 20 μM ABA. Gibbs sampling was used to identify enriched elements, and particle bombardment-mediated transient expression studies were performed to verify the function. Gene ontology analysis was performed to predict the roles of genes containing the novel ABREs. This study revealed 2443 ABA-inducible genes and a novel ABRE, designated as ABREN, which was experimentally verified to mediate ABA signalling in rice aleurone cells. Many of the ABREN-containing genes are predicted to be involved in stress responses and transcription. Analysis of other species suggests that the ABREN may be monocot specific. This study also revealed interesting expression patterns of genes involved in ABA metabolism and signalling. Collectively, this study advanced our understanding of diverse cis-regulatory sequences and the transcriptomes underlying ABA responses in rice aleurone cells.
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Affiliation(s)
- Kenneth A Watanabe
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Arielle Homayouni
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Lingkun Gu
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Kuan-Ying Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
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27
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Lou Q, Chen L, Mei H, Xu K, Wei H, Feng F, Li T, Pang X, Shi C, Luo L, Zhong Y. Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice ( Oryza sativa L.). Front Plant Sci 2017; 8:1314. [PMID: 28798764 PMCID: PMC5526896 DOI: 10.3389/fpls.2017.01314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/12/2017] [Indexed: 05/19/2023]
Abstract
Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs. S) were significantly enriched in metabolic pathways especially energy metabolism. Ten quantitative trait transcripts (QTTs) were identified and some were involved in energy metabolism. Forty-nine candidate DEGs were confirmed by qRT-PCR and microarray. Through weighted gene co-expression network analysis (WGCNA), we found 18 hub genes. Surprisingly, all these hub genes expressed higher in deep roots than in shallow roots, furthermore half of them functioned in energy metabolism. We also estimated that the ATP production in the deep roots was faster than shallow roots. Our results provided a lot of reliable candidate genes to improve deep rooting, and firstly highlight the importance of energy metabolism to the development of deep roots.
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Affiliation(s)
- Qiaojun Lou
- Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan UniversityShanghai, China
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Liang Chen
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Hanwei Mei
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Kai Xu
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Haibin Wei
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Fangjun Feng
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Tiemei Li
- Shanghai Agrobiological Gene CenterShanghai, China
| | | | - Caiping Shi
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd.Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Yang Zhong
- Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan UniversityShanghai, China
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28
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Tanaka W, Toriba T, Hirano HY. Three TOB1-related YABBY genes are required to maintain proper function of the spikelet and branch meristems in rice. New Phytol 2017; 215:825-839. [PMID: 28556940 DOI: 10.1111/nph.14617] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/19/2017] [Indexed: 05/06/2023]
Abstract
YABBY genes play important roles in the development of lateral organs such as leaves and floral organs in Angiosperms. However, the function of YABBY genes is poorly understood in monocots. We focused on three rice (Oryza sativa) YABBY genes, TONGARI-BOUSHI (TOB1, TOB2, TOB3), which are closely related to Arabidopsis (Arabidopsis thaliana) FILAMENTOUS FLOWER (FIL). To elucidate the function of these YABBY genes, we employed a reverse genetic approach. TOB genes were expressed in bract and lateral organ primordia, but not in meristems. RNAi knockdown of TOB2 or TOB3 in the tob1 mutant caused abnormal spikelet development. Furthermore, simultaneous knockdown of both TOB2 and TOB3 in tob1 affected not only spikelet, but also inflorescence development. In severe cases, the inflorescences comprised naked branches without spikelets. Analysis of inflorescence development at an early stage showed that the observed phenotypic defects were closely associated with a failure to initiate and maintain reproductive meristems. These results indicate that the TOB genes regulate the maintenance and fate of all reproductive meristems. It is likely that the function of FIL/TOB clade YABBY genes has been conserved between Arabidopsis and rice to maintain the proper function of meristems, even though these genes are expressed in lateral organ primordia.
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Affiliation(s)
- Wakana Tanaka
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Taiyo Toriba
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hiro-Yuki Hirano
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
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29
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He Y, Zhang H, Sun Z, Li J, Hong G, Zhu Q, Zhou X, MacFarlane S, Yan F, Chen J. Jasmonic acid-mediated defense suppresses brassinosteroid-mediated susceptibility to Rice black streaked dwarf virus infection in rice. New Phytol 2017; 214:388-399. [PMID: 27976810 DOI: 10.1111/nph.14376] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 11/06/2016] [Indexed: 05/22/2023]
Abstract
Plant hormones play a vital role in plant immune responses. However, in contrast to the relative wealth of information on hormone-mediated immunity in dicot plants, little information is available on monocot-virus defense systems. We used a high-throughput-sequencing approach to compare the global gene expression of Rice black-streaked dwarf virus (RBSDV)-infected rice plants with that of healthy plants. Exogenous hormone applications and transgenic rice were used to test RBSDV infectivity and pathogenicity. Our results revealed that the jasmonic acid (JA) pathway was induced while the brassinosteroid (BR) pathway was suppressed in infected plants. Foliar application of methyl jasmonate (MeJA) or brassinazole (BRZ) resulted in a significant reduction in RBSDV incidence, while epibrassinolide (BL) treatment increased RBSDV infection. Infection studies using coi1-13 and Go mutants demonstrated JA-mediated resistance and BR-mediated susceptibility to RBSDV infection. A mixture of MeJA and BL treatment resulted in a significant reduction in RBSDV infection compared with a single BL treatment. MeJA application efficiently suppressed the expression of BR pathway genes, and this inhibition depended on the JA coreceptor OsCOI1. Collectively, our results reveal that JA-mediated defense can suppress the BR-mediated susceptibility to RBSDV infection.
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Affiliation(s)
- Yuqing He
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hehong Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zongtao Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junmin Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Gaojie Hong
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qisong Zhu
- Shandong Rice Research Institute, Jinan, 250100, China
| | - Xuebiao Zhou
- Shandong Rice Research Institute, Jinan, 250100, China
| | - Stuart MacFarlane
- The James Hutton Institute, Cell and Molecular Sciences Group, Invergowrie, Dundee, DD2 5DA, UK
| | - Fei Yan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jianping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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30
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Uematsu S, Vandenhove H, Sweeck L, Hees MV, Wannijn J, Smolders E. Foliar uptake of radiocaesium from irrigation water by paddy rice (Oryza sativa): an overlooked pathway in contaminated environments. New Phytol 2017; 214:820-829. [PMID: 28102551 DOI: 10.1111/nph.14416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
Flooded (paddy) rice (Oryza sativa) can take up ions from the irrigation water by foliar uptake via the exposed stem base. We hypothesised that the stem base uptake of radiocaesium (RCs) is a pathway for rice grown in RCs-contaminated environments. We developed a bi-compartmental device which discriminates the stem base from root RCs uptake from solutions, thereby using RCs isotopes (137 Cs and 134 Cs) with < 2% solution leak between the compartments. Radiocaesium uptake was linear over time (0-24 h). Radiocaesium uptake to the entire plant, expressed per dry weight of the exposed parts, was sixfold higher for the roots than for the exposed stem base. At equal RCs concentrations in both compartments, the exposed stem base and root uptake contributed almost equally to the total shoot RCs concentrations. Reducing potassium supply to the roots not only increased the root RCs uptake but also increased RCs uptake by the stem base. This study was the first to experimentally demonstrate active and internally regulated RCs uptake by the stem base of rice. Scenario calculations for the Fukushima-affected area predict that RCs in irrigation water could be an important source of RCs in rice as indirectly suggested from field data.
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Affiliation(s)
- Shinichiro Uematsu
- Biosphere Impact Studies, SCK CEN, Belgian Nuclear Research Centre, Boeretang 200, B-2400, Mol, Belgium
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
| | - Hildegarde Vandenhove
- Biosphere Impact Studies, SCK CEN, Belgian Nuclear Research Centre, Boeretang 200, B-2400, Mol, Belgium
| | - Lieve Sweeck
- Biosphere Impact Studies, SCK CEN, Belgian Nuclear Research Centre, Boeretang 200, B-2400, Mol, Belgium
| | - May Van Hees
- Biosphere Impact Studies, SCK CEN, Belgian Nuclear Research Centre, Boeretang 200, B-2400, Mol, Belgium
| | - Jean Wannijn
- Biosphere Impact Studies, SCK CEN, Belgian Nuclear Research Centre, Boeretang 200, B-2400, Mol, Belgium
| | - Erik Smolders
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
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Kudo T, Terashima S, Takaki Y, Tomita K, Saito M, Kanno M, Yokoyama K, Yano K. PlantExpress: A Database Integrating OryzaExpress and ArthaExpress for Single-species and Cross-species Gene Expression Network Analyses with Microarray-Based Transcriptome Data. Plant Cell Physiol 2017; 58:e1. [PMID: 28158643 DOI: 10.1093/pcp/pcw208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/19/2016] [Indexed: 06/06/2023]
Abstract
Publicly available microarray-based transcriptome data on plants are remarkably valuable in terms of abundance and variation of samples, particularly for Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Here, we introduce the web database PlantExpress (http://plantomics.mind.meiji.ac.jp/PlantExpress/) as a platform for gene expression network (GEN) analysis with the public microarray data of rice and Arabidopsis. PlantExpress has two functional modes. The single-species mode is specialized for GEN analysis within one of the species, while the cross-species mode is optimized for comparative GEN analysis between the species. The single-species mode for rice is the new version of OryzaExpress, which we have maintained since 2006. The single-species mode for Arabidopsis, named ArthaExpress, was newly developed. PlantExpress stores data obtained from three microarrays, the Affymetrix Rice Genome Array, the Agilent Rice Gene Expression 4x44K Microarray, and the Affymetrix Arabidopsis ATH1 Genome Array, with respective totals of 2,678, 1,206, and 10,940 samples. This database employs a ‘MyList’ function with which users may save lists of arbitrary genes and samples (experimental conditions) to use in analyses. In cross-species mode, the MyList function allows performing comparative GEN analysis between rice and Arabidopsis. In addition, the gene lists saved in MyList can be directly exported to the PODC database, which provides information and a platform for comparative GEN analysis based on RNA-seq data and knowledge-based functional annotation of plant genes. PlantExpress will facilitate understanding the biological functions of plant genes.
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Affiliation(s)
- Toru Kudo
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Shin Terashima
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Yuno Takaki
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Ken Tomita
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Misa Saito
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Maasa Kanno
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Koji Yokoyama
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
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Lu L, Qiu W, Gao W, Tyerman SD, Shou H, Wang C. OsPAP10c, a novel secreted acid phosphatase in rice, plays an important role in the utilization of external organic phosphorus. Plant Cell Environ 2016; 39:2247-59. [PMID: 27411391 DOI: 10.1111/pce.12794] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 07/04/2016] [Accepted: 07/05/2016] [Indexed: 05/24/2023]
Abstract
Under phosphate (Pi ) starvation, plants increase the secretion of purple acid phosphatases (PAPs) into the rhizosphere to scavenge organic phosphorus (P) for plant use. To date, only a few members of the PAP family have been characterized in crops. In this study, we identified a novel secreted PAP in rice, OsPAP10c, and investigated its role in the utilization of external organic P. OsPAP10c belongs to a monocotyledon-specific subclass of Ia group PAPs and is specifically expressed in the epidermis/exodermis cell layers of roots. Both the transcript and protein levels of OsPAP10c are strongly induced by Pi starvation. OsPAP10c overexpression increased acid phosphatase (APase) activity by more than 10-fold in the culture media and almost fivefold in both roots and leaves under Pi -sufficient and Pi -deficient conditions. This increase in APase activity further improved the plant utilization efficiency of external organic P. Moreover, several APase isoforms corresponding to OsPAP10c were identified using in-gel activity assays. Under field conditions with three different Pi supply levels, OsPAP10c-overexpressing plants had significantly higher tiller numbers and shorter plant heights. This study indicates that OsPAP10c encodes a novel secreted APase that plays an important role in the utilization of external organic P in rice.
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Affiliation(s)
- Linghong Lu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenmin Qiu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenwen Gao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Stephen D Tyerman
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB1, Glen Osmond, South Australia, 5064, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chuang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
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Yan J, Wang P, Wang P, Yang M, Lian X, Tang Z, Huang CF, Salt DE, Zhao FJ. A loss-of-function allele of OsHMA3 associated with high cadmium accumulation in shoots and grain of Japonica rice cultivars. Plant Cell Environ 2016; 39:1941-54. [PMID: 27038090 DOI: 10.1111/pce.12747] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/20/2016] [Accepted: 03/24/2016] [Indexed: 05/21/2023]
Abstract
Excessive cadmium (Cd) accumulation in rice poses a risk to food safety. OsHMA3 plays an important role in restricting Cd translocation from roots to shoots. A non-functional allele of OsHMA3 has been reported in some Indica rice cultivars with high Cd accumulation, but it is not known if OsHMA3 allelic variation is associated with Cd accumulation in Japonica cultivars. In this study, we identified a Japonica cultivar with consistently high Cd accumulation in shoots and grain in both field and greenhouse experiments. The cultivar possesses an OsHMA3 allele with a predicted amino acid mutation at the 380(th) position from Ser to Arg. The haplotype had no Cd transport activity when the gene was expressed in yeast, and the allele did not complement a known nonfunctional allele of OsHMA3 in F1 test. The allele is present only in temperate Japonica cultivars among diversity panels of 1483 rice cultivars. Different cultivars possessing this allele showed greatly increased root-to-shoot Cd translocation and a shift in root Cd speciation from Cd-S to Cd-O bonding determined by synchrotron X-ray absorption spectroscopy. Our study has identified a new loss-of-function allele of OsHMA3 in Japonica rice cultivars leading to high Cd accumulation in shoots and grain.
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Affiliation(s)
- Jiali Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peitong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Meng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao-Feng Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, UK
| | - Fang Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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Cosme M, Lu J, Erb M, Stout MJ, Franken P, Wurst S. A fungal endophyte helps plants to tolerate root herbivory through changes in gibberellin and jasmonate signaling. New Phytol 2016; 211:1065-76. [PMID: 27061745 PMCID: PMC5071772 DOI: 10.1111/nph.13957] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 02/25/2016] [Indexed: 05/02/2023]
Abstract
Plant-microbe mutualisms can improve plant defense, but the impact of root endophytes on below-ground herbivore interactions remains unknown. We investigated the effects of the root endophyte Piriformospora indica on interactions between rice (Oryza sativa) plants and its root herbivore rice water weevil (RWW; Lissorhoptrus oryzophilus), and how plant jasmonic acid (JA) and GA regulate this tripartite interaction. Glasshouse experiments with wild-type rice and coi1-18 and Eui1-OX mutants combined with nutrient, jasmonate and gene expression analyses were used to test: whether RWW adult herbivory above ground influences subsequent damage caused by larval herbivory below ground; whether P. indica protects plants against RWW; and whether GA and JA signaling mediate these interactions. The endophyte induced plant tolerance to root herbivory. RWW adults and larvae acted synergistically via JA signaling to reduce root growth, while endophyte-elicited GA biosynthesis suppressed the herbivore-induced JA in roots and recovered plant growth. Our study shows for the first time the impact of a root endophyte on plant defense against below-ground herbivores, adds to growing evidence that induced tolerance may be an important root defense, and implicates GA as a signal component of inducible plant tolerance against biotic stress.
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Affiliation(s)
- Marco Cosme
- Functional BiodiversityDahlem Center of Plant SciencesInstitute of BiologyFreie Universität BerlinKönigin‐Luise‐Straße 1–314195BerlinGermany
- Department of Plant PropagationLeibniz‐Institute of Vegetable and Ornamental CropsKühnhäuser Straße 10199090Erfurt‐KühnhausenGermany
- Plant–Microbe InteractionsDepartment of BiologyFaculty of ScienceUtrecht UniversityPO Box 800.563508 TBUtrechtthe Netherlands
| | - Jing Lu
- Department of BiochemistryMax Planck Institute for Chemical EcologyHans‐Knoell‐Str. 807745JenaGermany
- Institute of Insect ScienceZijingang CampusZhejiang UniversityYuhangtang Road 866Hangzhou310058China
| | - Matthias Erb
- Department of BiochemistryMax Planck Institute for Chemical EcologyHans‐Knoell‐Str. 807745JenaGermany
- Institute of Plant SciencesUniversity of BernAltenbergrain 213013BernSwitzerland
| | - Michael Joseph Stout
- Department of EntomologyLouisiana State University Agricultural Center404 Life Sciences BuildingBaton RougeLA70803USA
| | - Philipp Franken
- Department of Plant PropagationLeibniz‐Institute of Vegetable and Ornamental CropsKühnhäuser Straße 10199090Erfurt‐KühnhausenGermany
- Department of Plant PhysiologyHumboldt Universität zu BerlinPhilippstrasse 1310115BerlinGermany
| | - Susanne Wurst
- Functional BiodiversityDahlem Center of Plant SciencesInstitute of BiologyFreie Universität BerlinKönigin‐Luise‐Straße 1–314195BerlinGermany
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Dedecker M, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Dumoulin L, Wojsznis N, Gevaert K, Vandenabeele S, De Jaeger G. Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues. Plant Mol Biol 2016; 91:341-354. [PMID: 27003905 DOI: 10.1007/s11103-016-0471-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Proteins are the cell's functional entities. Rather than operating independently, they interact with other proteins. Capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. Affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. For Oryza sativa, the technique has been initiated in callus and shoots, but has not been optimized ever since. We translated an optimized tandem affinity purification (TAP) approach from Arabidopsis thaliana toward Oryza sativa, and demonstrate its applicability in a variety of rice tissues. A list of non-specific and false positive interactors is presented, based on re-occurrence over more than 170 independent experiments, to filter bona fide interactors. We demonstrate the sensitivity of our approach by isolating the complexes for the rice ANAPHASE PROMOTING COMPLEX SUBUNIT 10 (APC10) and CYCLIN-DEPENDENT KINASE D (CDKD) proteins from the proliferation zone of the emerging fourth leaf. Next to APC10 and CDKD, we tested several additional baits in the different rice tissues and reproducibly retrieved at least one interactor for 81.4 % of the baits screened for in callus tissue and T1 seedlings. By transferring an optimized TAP tag combined with state-of-the-art mass spectrometry, our TAP protocol enables the discovery of interactors for low abundance proteins in rice and opens the possibility to capture complex dynamics by comparing tissues at different stages of a developing rice organ.
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Affiliation(s)
- Maarten Dedecker
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium.
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Bernard Cannoot
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Leen Vercruysse
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Lies Dumoulin
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | | | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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36
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Lin H, Karki S, Coe RA, Bagha S, Khoshravesh R, Balahadia CP, Ver Sagun J, Tapia R, Israel WK, Montecillo F, de Luna A, Danila FR, Lazaro A, Realubit CM, Acoba MG, Sage TL, von Caemmerer S, Furbank RT, Cousins AB, Hibberd JM, Quick WP, Covshoff S. Targeted Knockdown of GDCH in Rice Leads to a Photorespiratory-Deficient Phenotype Useful as a Building Block for C4 Rice. Plant Cell Physiol 2016; 57:919-32. [PMID: 26903527 DOI: 10.1093/pcp/pcw033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/10/2016] [Indexed: 05/07/2023]
Abstract
The glycine decarboxylase complex (GDC) plays a critical role in the photorespiratory C2 cycle of C3 species by recovering carbon following the oxygenation reaction of ribulose-1,5-bisphosphate carboxylase/oxygenase. Loss of GDC from mesophyll cells (MCs) is considered a key early step in the evolution of C4 photosynthesis. To assess the impact of preferentially reducing GDC in rice MCs, we decreased the abundance of OsGDCH (Os10g37180) using an artificial microRNA (amiRNA) driven by a promoter that preferentially drives expression in MCs. GDC H- and P-proteins were undetectable in leaves of gdch lines. Plants exhibited a photorespiratory-deficient phenotype with stunted growth, accelerated leaf senescence, reduced chlorophyll, soluble protein and sugars, and increased glycine accumulation in leaves. Gas exchange measurements indicated an impaired ability to regenerate ribulose 1,5-bisphosphate in photorespiratory conditions. In addition, MCs of gdch lines exhibited a significant reduction in chloroplast area and coverage of the cell wall when grown in air, traits that occur during the later stages of C4 evolution. The presence of these two traits important for C4 photosynthesis and the non-lethal, down-regulation of the photorespiratory C2 cycle positively contribute to efforts to produce a C4 rice prototype.
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Affiliation(s)
- HsiangChun Lin
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines These authors contributed equally to this work
| | - Shanta Karki
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines These authors contributed equally to this work
| | - Robert A Coe
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines These authors contributed equally to this work
| | - Shaheen Bagha
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada
| | - Roxana Khoshravesh
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada
| | - C Paolo Balahadia
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines
| | - Julius Ver Sagun
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines
| | - Ronald Tapia
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines
| | - W Krystler Israel
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines
| | | | - Albert de Luna
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines
| | - Florence R Danila
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines
| | - Andrea Lazaro
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines
| | - Czarina M Realubit
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines
| | - Michelle G Acoba
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines
| | - Tammy L Sage
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada
| | - Susanne von Caemmerer
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Acton, 2601, Australia
| | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Acton, 2601, Australia
| | - Asaph B Cousins
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - W Paul Quick
- C4 Rice Center, International Rice Research Institute, Los Baños, Philippines Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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Cheng Q, Zhou Y, Liu Z, Zhang L, Song G, Guo Z, Wang W, Qu X, Zhu Y, Yang D. An alternatively spliced heat shock transcription factor, OsHSFA2dI, functions in the heat stress-induced unfolded protein response in rice. Plant Biol (Stuttg) 2015; 17:419-29. [PMID: 25255693 DOI: 10.1111/plb.12267] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 09/09/2014] [Indexed: 05/25/2023]
Abstract
As sessile organisms, plants have evolved a wide range of defence pathways to cope with environmental stress such as heat shock. However, the molecular mechanism of these defence pathways remains unclear in rice. In this study, we found that OsHSFA2d, a heat shock transcriptional factor, encodes two main splice variant proteins, OsHSFA2dI and OsHSFA2dII in rice. Under normal conditions, OsHSFA2dII is the dominant but transcriptionally inactive spliced form. However, when the plant suffers heat stress, OsHSFA2d is alternatively spliced into a transcriptionally active form, OsHSFA2dI, which participates in the heat stress response (HSR). Further study found that this alternative splicing was induced by heat shock rather than photoperiod. We found that OsHSFA2dI is localised to the nucleus, whereas OsHSFA2dII is localised to the nucleus and cytoplasm. Moreover, expression of the unfolded protein response (UNFOLDED PROTEIN RESPONSE) sensors, OsIRE1, OsbZIP39/OsbZIP60 and the UNFOLDED PROTEIN RESPONSE marker OsBiP1, was up-regulated. Interestingly, OsbZIP50 was also alternatively spliced under heat stress, indicating that UNFOLDED PROTEIN RESPONSE signalling pathways were activated by heat stress to re-establish cellular protein homeostasis. We further demonstrated that OsHSFA2dI participated in the unfolded protein response by regulating expression of OsBiP1.
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Affiliation(s)
- Q Cheng
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization, Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
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Wu J, Zhu C, Pang J, Zhang X, Yang C, Xia G, Tian Y, He C. OsLOL1, a C2C2-type zinc finger protein, interacts with OsbZIP58 to promote seed germination through the modulation of gibberellin biosynthesis in Oryza sativa. Plant J 2014; 80:1118-30. [PMID: 25353370 DOI: 10.1111/tpj.12714] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 08/25/2014] [Accepted: 10/20/2014] [Indexed: 05/05/2023]
Abstract
Seed germination is a key developmental process in the plant life cycle that is influenced by various environmental cues and phytohormones through gene expression and a series of metabolism pathways. In the present study, we investigated a C2C2-type finger protein, OsLOL1, which promotes gibberellin (GA) biosynthesis and affects seed germination in Oryza sativa (rice). We used OsLOL1 antisense and sense transgenic lines to explore OsLOL1 functions. Seed germination timing in antisense plants was restored to wild type when exogenous GA3 was applied. The reduced expression of the GA biosynthesis gene OsKO2 and the accumulation of ent-kaurene were observed during germination in antisense plants. Based on yeast two-hybrid and firefly luciferase complementation analyses, OsLOL1 interacted with the basic leucine zipper protein OsbZIP58. The results from electrophoretic mobility shift and dual-luciferase reporter assays showed that OsbZIP58 binds the G-box cis-element of the OsKO2 promoter and activates LUC reporter gene expression, and that interaction between OsLOL1 and OsbZIP58 activates OsKO2 gene expression. In addition, OsLOL1 decreased SOD1 gene expression and accelerated programmed cell death (PCD) in the aleurone layer of rice grains. These findings demonstrate that the interaction between OsLOL1 and OsbZIP58 influences GA biosynthesis through the activation of OsKO2 via OsbZIP58, thereby stimulating aleurone PCD and seed germination.
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Affiliation(s)
- Jiahe Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Meng W, Hsiao AS, Gao C, Jiang L, Chye ML. Subcellular localization of rice acyl-CoA-binding proteins (ACBPs) indicates that OsACBP6::GFP is targeted to the peroxisomes. New Phytol 2014; 203:469-482. [PMID: 24738983 DOI: 10.1111/nph.12809] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/12/2014] [Indexed: 05/08/2023]
Abstract
Acyl-CoA-binding proteins (ACBPs) show conservation at the acyl-CoA-binding (ACB) domain which facilitates binding to acyl-CoA esters. In Arabidopsis thaliana, six ACBPs participate in development and stress responses. Rice (Oryza sativa) also contains six genes encoding ACBPs. We investigated differences in subcellular localization between monocot rice and eudicot A. thaliana ACBPs. The subcellular localization of the six OsACBPs was achieved via transient expression of green fluorescence protein (GFP) fusions in tobacco (Nicotiana tabacum) epidermal cells, and stable transformation of A. thaliana. As plant ACBPs had not been reported in the peroxisomes, OsACBP6::GFP localization was confirmed by transient expression in rice sheath cells. The function of OsACBP6 was investigated by overexpressing 35S::OsACBP6 in the peroxisomal abc transporter1 (pxa1) mutant defective in peroxisomal fatty acid β-oxidation. As predicted, OsACBP1::GFP and OsACBP2::GFP were localized to the cytosol, and OsACBP4::GFP and OsACBP5::GFP to the endoplasmic reticulum (ER). However, OsACBP3::GFP displayed subcellular multi-localization while OsACBP6::GFP was localized to the peroxisomes. 35S::OsACBP6-OE/pxa1 lines showed recovery in indole-3-butyric acid (IBA) peroxisomal β-oxidation, wound-induced VEGETATIVE STORAGE PROTEIN1 (VSP1) expression and jasmonic acid (JA) accumulation. These findings indicate a role for OsACBP6 in peroxisomal β-oxidation, and suggest that rice ACBPs are involved in lipid degradation in addition to lipid biosynthesis.
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Affiliation(s)
- Wei Meng
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - An-Shan Hsiao
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Caiji Gao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
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40
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Tamiru M, Abe A, Utsushi H, Yoshida K, Takagi H, Fujisaki K, Undan JR, Rakshit S, Takaichi S, Jikumaru Y, Yokota T, Terry MJ, Terauchi R. The tillering phenotype of the rice plastid terminal oxidase (PTOX) loss-of-function mutant is associated with strigolactone deficiency. New Phytol 2014; 202:116-131. [PMID: 24350905 DOI: 10.1111/nph.12630] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/07/2013] [Indexed: 06/03/2023]
Abstract
The significance of plastid terminal oxidase (PTOX) in phytoene desaturation and chloroplast function has been demonstrated using PTOX-deficient mutants, particularly in Arabidopsis. However, studies on its role in monocots are lacking. Here, we report cloning and characterization of the rice (Oryza sativa) PTOX1 gene. Using Ecotype Targeting Induced Local Lesions IN Genomes (EcoTILLING) and TILLING as forward genetic tools, we identified the causative mutation of an EMS mutant characterized by excessive tillering, semi-dwarfism and leaf variegation that corresponded to the PTOX1 gene. The tillering and semi-dwarf phenotypes of the ptox1 mutant are similar to phenotypes of known strigolactone (SL)-related rice mutants, and both phenotypic traits could be rescued by application of the synthetic SL GR24. The ptox1 mutant accumulated phytoene in white leaf sectors with a corresponding deficiency in β-carotene, consistent with the expected function of PTOX1 in promoting phytoene desaturase activity. There was also no accumulation of the carotenoid-derived SL ent-2'-epi-5-deoxystrigol in root exudates. Elevated concentrations of auxin were detected in the mutant, supporting previous observations that SL interaction with auxin is important in shoot branching control. Our results demonstrate that PTOX1 is required for both carotenoid and SL synthesis resulting in SL-deficient phenotypes in rice.
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Affiliation(s)
- Muluneh Tamiru
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
- Iwate Agricultural Research Center, Narita 20-1, Kitakami, Iwate, 024-0003, Japan
| | - Hiroe Utsushi
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Kakoto Yoshida
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Hiroki Takagi
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Koki Fujisaki
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Jerwin R Undan
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Sujay Rakshit
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Shinichi Takaichi
- Department of Biology, Nippon Medical School, Kawasaki, Kanagawa, 211-0063, Japan
| | - Yusuke Jikumaru
- Department of Biosciences, Faculty of Science and Technology, Teikyo University, Utsunomiya, Tochigi, 320-8851, Japan
| | - Takao Yokota
- Department of Biosciences, Faculty of Science and Technology, Teikyo University, Utsunomiya, Tochigi, 320-8851, Japan
| | - Matthew J Terry
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
- Centre for Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
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Ogo Y, Kakei Y, Itai RN, Kobayashi T, Nakanishi H, Takahashi H, Nakazono M, Nishizawa NK. Spatial transcriptomes of iron-deficient and cadmium-stressed rice. New Phytol 2014; 201:781-794. [PMID: 24188410 DOI: 10.1111/nph.12577] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/26/2013] [Indexed: 05/04/2023]
Abstract
Although the genes involved in metal homeostasis have been investigated over the past few decades, many genes related to metal homeostasis remain uncharacterized, and a comprehensive analysis of the expression of these genes is required. In the present study, we investigated the spatial gene expression profile of iron (Fe)-deficient and cadmium (Cd)-stressed Oryza sativa (rice) using laser microdissection and microarray analysis. Roots of Fe-deficient and Cd-stressed rice were separated into the vascular bundle, cortex, and epidermis plus exodermis. In addition, vascular bundles from new and old leaves at the lowest node, which are important for metal distribution, were analyzed separately. The spatial expression patterns were distinct in each tissue type. Fe deficiency and Cd stress also had significant effects on the transcriptomes, although these were less pronounced than the spatial effects. Genes encoding transporters involved in metal homeostasis, proteins associated with heavy metal detoxification, and phytohormone-related proteins were comprehensively investigated. Additionally, cis motifs involved in the regulation of these diverse expression changes in various tissue types were predicted. The spatial transcriptomes presented here provide novel insight into the molecular mechanisms of metal homeostasis.
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Affiliation(s)
- Yuko Ogo
- Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yusuke Kakei
- Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Reiko Nakanishi Itai
- Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takanori Kobayashi
- Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-machi, Ishikawa, 921-8836, Japan
| | - Hiromi Nakanishi
- Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hirokazu Takahashi
- Laboratory of Plant Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
| | - Mikio Nakazono
- Laboratory of Plant Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
| | - Naoko K Nishizawa
- Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-machi, Ishikawa, 921-8836, Japan
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Wang S, Zhang S, Sun C, Xu Y, Chen Y, Yu C, Qian Q, Jiang DA, Qi Y. Auxin response factor (OsARF12), a novel regulator for phosphate homeostasis in rice (Oryza sativa). New Phytol 2014; 201:91-103. [PMID: 24111723 DOI: 10.1111/nph.12499] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 08/08/2013] [Indexed: 05/21/2023]
Abstract
Phosphorus (P) is crucial nutrient element for crop growth and development. However, the network pathway regulating homeostasis of phosphate (Pi) in crops has many molecular breeding unknowns. Here, we report that an auxin response factor, OsARF12, functions in Pi homeostasis. Measurement of element content, quantitative reverse transcription polymerase chain reaction analysis and acid phosphatases (APases) activity assay showed that the osarf12 mutant and osarf12/25 double mutant with P-intoxicated phenotypes had higher P concentrations, up-regulation of the Pi transporter encoding genes and increased APase activity under Pi-sufficient/-deficient (+Pi/-Pi, 0.32/0 mM NaH2 PO4) conditions. Transcript analysis revealed that Pi-responsive genes--Phosphate starvation (OsIPS)1 and OsIPS2, SYG1/Pho81/XPR1(OsSPX1), Sulfoquinovosyldiacylglycerol 2 (OsSQD2), R2R3 MYB transcription factor (OsMYB2P-1) and Transport Inhibitor Response1 (OsTIR1)--were more abundant in the osarf12 and osarf12/25 mutants under +Pi/-Pi conditions. Knockout of OsARF12 also influenced the transcript abundances of the OsPHR2 gene and its downstream components, such as OsMiR399j, OsPHO2, OsMiR827, OsSPX-MFS1 and OsSPX-MFS2. Results from -Pi/1-naphthylphthalamic acid (NPA) treatments, and auxin reporter DR5::GUS staining suggest that root system alteration and Pi-induced auxin response were at least partially controlled by OsARF12. These findings enrich our understanding of the biological functions of OsARF12, which also acts in regulating Pi homeostasis.
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Affiliation(s)
- SuiKang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - SaiNa Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - ChenDong Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - YanXia Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yue Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - ChenLiang Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - De-An Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - YanHua Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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Dadacz-Narloch B, Kimura S, Kurusu T, Farmer EE, Becker D, Kuchitsu K, Hedrich R. On the cellular site of two-pore channel TPC1 action in the Poaceae. New Phytol 2013; 200:663-674. [PMID: 23845012 DOI: 10.1111/nph.12402] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/02/2013] [Indexed: 06/02/2023]
Abstract
The slow vacuolar (SV) channel has been characterized in different dicots by patch-clamp recordings. This channel represents the major cation conductance of the largest organelle in most plant cells. Studies with the tpc1-2 mutant of the model dicot plant Arabidopsis thaliana identified the SV channel as the product of the TPC1 gene. By contrast, research on rice and wheat TPC1 suggested that the monocot gene encodes a plasma membrane calcium-permeable channel. To explore the site of action of grass TPC1 channels, we expressed OsTPC1 from rice (Oryza sativa) and TaTPC1 from wheat (Triticum aestivum) in the background of the Arabidopsis tpc1-2 mutant. Cross-species tpc1 complementation and patch-clamping of vacuoles using Arabidopsis and rice tpc1 null mutants documented that both monocot TPC1 genes were capable of rescuing the SV channel deficit. Vacuoles from wild-type rice but not the tpc1 loss-of-function mutant harbor SV channels exhibiting the hallmark properties of dicot TPC1/SV channels. When expressed in human embryonic kidney (HEK293) cells OsTPC1 was targeted to Lysotracker-Red-positive organelles. The finding that the rice TPC1, just like those from the model plant Arabidopsis and even animal cells, is localized and active in lyso-vacuolar membranes associates this cation channel species with endomembrane function.
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Affiliation(s)
- Beata Dadacz-Narloch
- Institute for Molecular Plant Physiology and Biophysics, University of Wuerzburg, D-97082, Wuerzburg, Germany
| | - Sachie Kimura
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
| | - Takamitsu Kurusu
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
- School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo, 192-0982, Japan
| | - Edward E Farmer
- Department of Plant Molecular Biology, University of Lausanne, Biophore, 1015, Lausanne, Switzerland
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Wuerzburg, D-97082, Wuerzburg, Germany
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Wuerzburg, D-97082, Wuerzburg, Germany
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Abstract
• The characteristics of Oryza sativa roots required for internal aeration may conflict with those for efficient nutrient acquisition, particularly the surface area available for absorbing nutrients and the extent of oxygenation of the rhizosphere. • A model was developed for calculating the steady-state diffusion of O2 through a primary root and its laterals and the simultaneous consumption of O2 in respiration and loss to the soil. Results for a realistic set of parameter values were compared with available experimental data, and a sensitivity analysis given. • It was seen that a system of coarse, aerenchmymatous, primary roots with gas-impermeable walls conducting O2 to short, fine, gas-permeable laterals (i.e. the basic architecture of current rice genotypes) provided the greatest absorbing surface per unit aerated root mass. • With this architecture and typical rates of root respiration, rates of O2 loss to the soil can be sufficient to, for example, nitrify sufficient NH4 + to NO3 - to allow a plant to absorb half its N as NO3 - , as well as to oxidize toxins such as Fe2+ .
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Affiliation(s)
- Guy J D Kirk
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- National Soil Resources Institute, Cranfield University, Silsoe MK45 4DT, UK
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45
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Abstract
• Rice (Oryza sativa) is a typical Si-accumulating plant and it has been suggested that it has a specific uptake system for silicic acid in the roots. • Here, we characterized this specific system in rice roots. The ability of rice roots to take up Si was much higher than that of other gramineous species. • A kinetic study indicated that Si uptake was mediated by a type of proteinaceous transporter; the Km value was estimated to be 0.32 mm, suggesting that the transporter had a low affinity for silicic acid. Si uptake increased linearly with time, but pretreatment with Si did not affect the uptake of Si, suggesting that the system for Si uptake was not inducible. Mercuric chloride and phloretin, significantly inhibited Si uptake, but 4,4'-diisothiocyanato-stilbene-2,2'-disulfonic acid (DIDS) did not. Mercuric chloride and phloretin also inhibited water uptake, but to a lesser extent. Si uptake was unaffected by the presence of boric acid. • Taken together, the data indicate that the uptake of Si by rice roots is a transporter-mediated process and this transporter contains Cys residues but not Lys residues.
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Affiliation(s)
- Kazunori Tamai
- Faculty of Agriculture, Kagawa University, Ikenobe 2393, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Jian Feng Ma
- Faculty of Agriculture, Kagawa University, Ikenobe 2393, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
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Abstract
• Cereal grains differ greatly in their reponses to anaerobiosis. Here, the in vivo conversion of carbohydrates to ethanol and CO2 under anoxia is reported for three cereal grains. • The conversion of glucose, fructose or sucrose to ethanol under anaerobic conditions was investigated in rice (Oryza sativa), barley (Hordeum vulgare) and wheat (Triticum aestivum) grains; alcohol dehydrogenase (EC 1.1.1.1) and pyruvate decarboxylase (EC 4.1.1.1) activities were also analysed under aerobic and anaerobic incubation. • Our data suggest that rice grains are able to produce ethanol under anoxia for the whole period of anoxic treatment, whereas barley and wheat grains can produce this terminal product of fermentation only during the first days of anaerobiosis. The level of enzymes involved in the fermentation pathway increases strongly under anoxic conditions in all three cereals. • Conversion of hexose to CO2 is nearly unaffected by anoxia in wheat, barley and rice, whereas only rice grains are able to degrade and utilize sucrose efficiently under anoxia. By contrast, wheat and barley do not utilize sucrose efficiently under anaerobic conditions.
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Affiliation(s)
- Lorenzo Guglielminetti
- Dipartimento di Biologia delle Piante Agrarie, Sezione Fisiologia Vegetale, Via Mariscoglio 34, I-56124 Pisa, Italy
| | - Héctor Abel Busilacchi
- Dipartimento di Biologia delle Piante Agrarie, Sezione Fisiologia Vegetale, Via Mariscoglio 34, I-56124 Pisa, Italy
- Present address: Facultad de Ciencias Agrarias, University of Rosario, CC 14 CP (2123) Zavalla, Pcia de Santa Fe, Argentina
| | - Pierdomenico Perata
- Dipartimento di Scienze Agrarie, Università di Modena & Reggio Emilia, Via Kennedy 17, Reggio Emilia, Italy
| | - Amedeo Alpi
- Dipartimento di Biologia delle Piante Agrarie, Sezione Fisiologia Vegetale, Via Mariscoglio 34, I-56124 Pisa, Italy
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