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Lian X, Zhong L, Bai Y, Guang X, Tang S, Guo X, Wei T, Yang F, Zhang Y, Huang G, Zhang J, Shao L, Lei G, Li Z, Sahu SK, Zhang S, Liu H, Hu F. Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1652-1668. [PMID: 38345936 PMCID: PMC11123419 DOI: 10.1111/pbi.14294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double-haplotype genome of O. longistaminata, which displays a 48-fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding.
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Affiliation(s)
- Xiaoping Lian
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Liyuan Zhong
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Yixuan Bai
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Xuanmin Guang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Sijia Tang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Xing Guo
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Tong Wei
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Feng Yang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Yujiao Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Guangfu Huang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Jing Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Lin Shao
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Guijie Lei
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Zheng Li
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Shilai Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Huan Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Fengyi Hu
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
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Zhao B, Wang JW. Perenniality: From model plants to applications in agriculture. MOLECULAR PLANT 2024; 17:141-157. [PMID: 38115580 DOI: 10.1016/j.molp.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
To compensate for their sessile nature, plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing environments. One such prominent feature is the evolution of diverse life history strategies, particularly such that annuals reproduce once followed by seasonal death, while perennials live longer by cycling growth seasonally. This intrinsic phenology is primarily genetic and can be altered by environmental factors. Although evolutionary transitions between annual and perennial life history strategies are common, perennials account for most species in nature because they survive well under year-round stresses. This proportion, however, is reversed in agriculture. Hence, perennial crops promise to likewise protect and enhance the resilience of agricultural ecosystems in response to climate change. Despite significant endeavors that have been made to generate perennial crops, progress is slow because of barriers in studying perennials, and many developed species await further improvement. Recent findings in model species have illustrated that simply rewiring existing genetic networks can lead to lifestyle variation. This implies that engineering plant life history strategy can be achieved by manipulating only a few key genes. In this review, we summarize our current understanding of genetic basis of perenniality and discuss major questions and challenges that remain to be addressed.
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Affiliation(s)
- Bo Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; New Cornerstone Science Laboratory, Shanghai 200032, China.
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Gao J, Duan M, Hasi G, Yang J, Yan C, Kang Y, Qi Z. Comparison of two contrasting Leymus chinensis accessions reveals the roles of the cell wall and auxin in rhizome development. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154003. [PMID: 37301035 DOI: 10.1016/j.jplph.2023.154003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/01/2023] [Accepted: 05/06/2023] [Indexed: 06/12/2023]
Abstract
Leymus chinensis, a perennial native forage grass, is widely distributed in the steppes of Inner Mongolia as the dominant species. The main reproductive strategy of this grass is clonal propagation, which occurs via the proliferation of subterranean horizontal stems known as rhizomes. To elucidate the mechanism underlying rhizome development in this grass, we collected 60 accessions of L. chinensis and evaluated their rhizome development. One accession, which we named SR-74 (Strong Rhizomes), had significantly better rhizome development capacity than the accession WR-16 (Weak Rhizomes) in terms of rhizome number, total and primary rhizome length, and number of rhizome seedlings. Rhizome elongation was positively correlated with the number of internodes in the rhizome, which affected plant biomass. Compared to WR-16, SR-74 had higher rhizome tip hardness, higher abundance of transcripts participating in the biosynthesis of cell wall components, and higher levels of the metabolites L-phenylalanine, trans-cinnamic acid, 3-coumaric acid, ferulic acid, and coniferin. These metabolites in the phenylpropanoid biosynthesis pathway are precursors of lignin. In addition, SR-74 rhizomes contained higher amounts of auxin and auxin metabolites, including L-Trp, IPA, IBA, IAA and IAA-Asp, as well as upregulated expression of the auxin biosynthesis and signaling genes YUCCA6, YUCCA8, YUCCA10, YUCCA11, PIN1, PIN2, UGT1, UGT2, UGT4, UGT10, GH3, IAA7, IAA23, and IAA30. We propose a network between auxin signaling and the cell wall underlying rhizome development in L. chinensis.
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Affiliation(s)
- Jie Gao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China
| | - Menglu Duan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China
| | - Gaowa Hasi
- Grassland Work Station of East Ujimqin Banner of Xilin Gol League of Inner Mongolia, East Ujimqin Banner, 026300, China
| | - Jia Yang
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China
| | - Chunxia Yan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China.
| | - Yan Kang
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China.
| | - Zhi Qi
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China.
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Tong S, Ashikari M, Nagai K, Pedersen O. Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication? RICE (NEW YORK, N.Y.) 2023; 16:13. [PMID: 36928797 PMCID: PMC10020418 DOI: 10.1186/s12284-023-00630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
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Affiliation(s)
- Shuai Tong
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan.
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark.
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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Li J, Li H, Yin N, Quan X, Wang W, Shan Q, Wang S, Bermudez RS, He W. Identification of LsPIN1 gene and its potential functions in rhizome turning of Leymus secalinus. BMC Genomics 2022; 23:753. [DOI: 10.1186/s12864-022-08979-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
Abstract
Background
Continuous tilling and the lateral growth of rhizomes confer rhizomatous grasses with the unique ability to laterally expand, migrate and resist disturbances. They play key roles especially in degraded grasslands, deserts, sand dunes, and other fragile ecological system. The rhizomatous plant Leymus secalinus has both rhizome buds and tiller buds that grow horizontally and upward at the ends of rhizome differentiation and elongation, respectively. The mechanisms of rhizome formation and differentiation in L. secalinus have not yet been clarified.
Results
In this study, we found that the content of gibberellin A3 (GA3) and indole-3-acetic acid (IAA) were significantly higher in upward rhizome tips than in horizontal rhizome tips; by contrast, the content of methyl jasmonate and brassinolide were significantly higher in horizontal rhizome tips than in upward rhizome tips. GA3 and IAA could stimulate the formation and turning of rhizomes. An auxin efflux carrier gene, LsPIN1, was identified from L. secalinus based on previous transcriptome data. The conserved domains of LsPIN1 and the relationship of LsPIN1 with PIN1 genes from other plants were analyzed. Subcellular localization analysis revealed that LsPIN1 was localized to the plasma membrane. The length of the primary roots (PRs) and the number of lateral roots (LRs) were higher in Arabidopsis thaliana plants overexpressing LsPIN1 than in wild-type (Col-0) plants. Auxin transport was altered and the gravitropic response and phototropic response were stronger in 35S:LsPIN1 transgenic plants compared with Col-0 plants. It also promoted auxin accumulation in root tips.
Conclusion
Our findings indicated that LsPIN1 plays key roles in auxin transport and root development. Generally, our results provide new insights into the regulatory mechanisms underlying rhizome development in L. secalinus.
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Fan Z, Huang G, Fan Y, Yang J. Sucrose Facilitates Rhizome Development of Perennial Rice ( Oryza longistaminata). Int J Mol Sci 2022; 23:13396. [PMID: 36362182 PMCID: PMC9654561 DOI: 10.3390/ijms232113396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 09/10/2023] Open
Abstract
Compared with annual crops, perennial crops with longer growing seasons and deeper root systems can fix more sunlight energy, and have advantages in reducing soil erosion and saving water, fertilizer and pesticide inputs. Rice is one of the most important food crops in the world. Perennial rice can be of great significance for protecting the ecological environment and coping with the shortage of young farmers due to urbanization. Oryza longistaminata (OL) is a rhizomatous wild rice with an AA genome and has strong biotic and abiotic resistances. The AA genome makes OL easy to cross with cultivated rice, thus making it an ideal donor material for perennial rice breeding. Sucrose plays an important role in the development and growth of plants. In this study, OL seedlings were cultured in medium with different concentrations of sucrose, and it was found that sucrose of appropriate concentrations can promote the sprout of basal axillary buds and the subsequent development of rhizomes. In order to explore the molecular mechanism, comparative transcriptome analysis was carried out with OL cultured under two concentrations of sucrose, 20 g/L and 100 g/L, respectively. The results showed that the boost of sucrose to rhizome elongation may be due to the glucose and fructose, hydrolyzed from the absorbed sucrose by vacuolar acid invertase. In addition, the consequent increased osmotic pressure of the cells would promote water absorption, which is benefit for the cell elongation, eventually causing the rhizome elongation. These results may provide a reference for elucidating the regulatory mechanism of sucrose on the rhizome development of OL.
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Affiliation(s)
| | | | - Yourong Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiangyi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
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Zhang L, Xu Y, Liu X, Qin M, Li S, Jiang T, Yang Y, Jiang CZ, Gao J, Hong B, Ma C. The chrysanthemum DEAD-box RNA helicase CmRH56 regulates rhizome outgrowth in response to drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5671-5681. [PMID: 35595538 DOI: 10.1093/jxb/erac213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Plants have evolved complex mechanisms to reprogram growth in response to drought stress. In herbaceous perennial plant species, the rhizome, which is normally an organ for propagation and food storage, can also support plant growth in stressful environments, and allows the plant to perennate and survive stress damage. However, the mechanisms that regulate rhizome growth in perennial herbs during abiotic stresses are unknown. Here, we identified a chrysanthemum (Chrysanthemum morifolium) DEAD-box RNA helicase gene, CmRH56, that is specifically expressed in the rhizome shoot apex. Knock down of CmRH56 transcript levels decreased the number of rhizomes and enhanced drought stress tolerance. We determined that CmRH56 represses the expression of a putative gibberellin (GA) catabolic gene, GA2 oxidase6 (CmGA2ox6). Exogenous GA treatment and silencing of CmGA2ox6 resulted in more rhizomes. These results demonstrate that CmRH56 suppresses rhizome outgrowth under drought stress conditions by blocking GA biosynthesis.
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Affiliation(s)
- Lili Zhang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Yanjie Xu
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Xuening Liu
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Meizhu Qin
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Shenglan Li
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Tianhua Jiang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Yingjie Yang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Cai-Zhong Jiang
- Crops Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, USA
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Junping Gao
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Bo Hong
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Chao Ma
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
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Comparative Transcriptome Analysis of Two Kalanchoë Species during Plantlet Formation. PLANTS 2022; 11:plants11131643. [PMID: 35807595 PMCID: PMC9268976 DOI: 10.3390/plants11131643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
Few species in the Kalanchoë genus form plantlets on their leaf margins as an asexual reproduction strategy. The limited molecular studies on plantlet formation show that an organogenesis ortholog, SHOOTMERISTEMLESS (STM) and embryogenesis genes, such as LEAFY COTYLEDON1 (LEC1) and FUSCA3 are recruited during plantlet formation. To understand the mechanisms of two Kalanchoë plantlet-forming species with different modes of plantlet formation, RNA-sequencing analysis was performed. Differentially expressed genes between the developmental stages were clustered in K. daigremontiana (Raym.-Hamet and H. Perrier) and K. pinnata (Lam. Pers.), respectively. Of these gene clusters, GO terms that may be involved in plantlet formation of both species, such as signaling, response to wounding, reproduction, regulation of hormone level, and response to karrikin were overrepresented. Compared with the common GO terms, there were more unique GO terms overrepresented during the plantlet formation of each species. A more in-depth investigation is required to understand how these pathways are participating in plantlet formation. Nonetheless, this transcriptome analysis is presented as a reliable basis for future studies on plantlet formation and development in two Kalanchoë plantlet-forming species.
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Kawai M, Tabata R, Ohashi M, Honda H, Kamiya T, Kojima M, Takebayashi Y, Oishi S, Okamoto S, Hachiya T, Sakakibara H. Regulation of ammonium acquisition and use in Oryza longistaminata ramets under nitrogen source heterogeneity. PLANT PHYSIOLOGY 2022; 188:2364-2376. [PMID: 35134987 PMCID: PMC8968255 DOI: 10.1093/plphys/kiac025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/18/2021] [Indexed: 05/31/2023]
Abstract
Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We studied the response of ramet pairs to heterogeneous nitrogen availability using a split hydroponic system that allowed each ramet root to be exposed to different conditions. Ammonium uptake was compensatively enhanced in the sufficient-side root when roots of the ramet pairs were exposed to ammonium-sufficient and ammonium-deficient conditions. Comparative transcriptome analysis revealed that a gene regulatory network for effective ammonium assimilation and amino acid biosynthesis was activated in the sufficient-side roots. Allocation of absorbed nitrogen from the nitrogen-sufficient to the nitrogen-deficient ramets was rather limited. Nitrogen was preferentially used for newly growing axillary buds on the sufficient-side ramets. Biosynthesis of trans-zeatin (tZ), a cytokinin, was upregulated in response to the nitrogen supply, but tZ appeared not to target the compensatory regulation. Our results also implied that the O. longistaminata putative ortholog of rice (Oryza sativa) C-terminally encoded peptide1 plays a role as a nitrogen-deficient signal in inter-ramet communication, providing compensatory upregulation of nitrogen assimilatory genes. These results provide insights into the molecular basis for efficient growth strategies of asexually proliferating plants growing in areas where the distribution of ammonium ions is spatially heterogeneous.
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Affiliation(s)
- Misato Kawai
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Ryo Tabata
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Miwa Ohashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Haruno Honda
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Takehiro Kamiya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya464-8602, Japan
| | - Satoru Okamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Takushi Hachiya
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Department of Molecular and Function Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue 690-8504, Japan
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Rajakani R, Sellamuthu G, Ishikawa T, Ahmed HAI, Bharathan S, Kumari K, Shabala L, Zhou M, Chen ZH, Shabala S, Venkataraman G. Reduced apoplastic barriers in tissues of shoot-proximal rhizomes of Oryza coarctata are associated with Na+ sequestration. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:998-1015. [PMID: 34606587 DOI: 10.1093/jxb/erab440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
Oryza coarctata is the only wild rice species with significant salinity tolerance. The present work examines the role of the substantial rhizomatous tissues of O. coarctata in conferring salinity tolerance. Transition to an erect phenotype (shoot emergence) from prostrate growth of rhizome tissues is characterized by marked lignification and suberization of supporting sclerenchymatous tissue, epidermis, and bundle sheath cells in aerial shoot-proximal nodes and internodes in O. coarctata. With salinity, however, aerial shoot-proximal internodal tissues show reductions in lignification and suberization, most probably related to re-direction of carbon flux towards synthesis of the osmporotectant proline. Concurrent with hypolignification and reduced suberization, the aerial rhizomatous biomass of O. coarctata appears to have evolved mechanisms to store Na+ in these specific tissues under salinity. This was confirmed by histochemical staining, quantitative real-time reverse transcription-PCR expression patterns of genes involved in lignification/suberization, Na+ and K+ contents of internodal tissues, as well as non-invasive microelectrode ion flux measurements of NaCl-induced net Na+, K+, and H+ flux profiles of aerial nodes were determined. In O. coarctata, aerial proximal internodes appear to act as 'traffic controllers', sending required amounts of Na+ and K+ into developing leaves for osmotic adjustment and turgor-driven growth, while more deeply positioned internodes assume a Na+ buffering/storage role.
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Affiliation(s)
- Raja Rajakani
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600 113, India
| | - Gothandapani Sellamuthu
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600 113, India
- Forest Molecular Entomology Laboratory, Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague-16500, Czech Republic
| | - Tetsuya Ishikawa
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
| | - Hassan Ahmed Ibraheem Ahmed
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
- Department of Botany, Faculty of Science, Port Said University, Port Said 42522, Egypt
| | - Subhashree Bharathan
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thirumalaisamudram, Thanjavur-613401, Tamil Nadu, India
| | - Kumkum Kumari
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600 113, India
| | - Lana Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600 113, India
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11
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Li Z, Lathe RS, Li J, He H, Bhalerao RP. Towards understanding the biological foundations of perenniality. TRENDS IN PLANT SCIENCE 2022; 27:56-68. [PMID: 34561180 DOI: 10.1016/j.tplants.2021.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Perennial life cycles enable plants to have remarkably long lifespans, as exemplified by trees that can live for thousands of years. For this, they require sophisticated regulatory networks that sense environmental changes and initiate adaptive responses in their growth patterns. Recent research has gradually elucidated fundamental mechanisms underlying the perennial life cycle. Intriguingly, several conserved components of the floral transition pathway in annuals such as Arabidopsis thaliana also participate in these regulatory mechanisms underpinning perenniality. Here, we provide an overview of perennials' physiological features and summarise their recently discovered molecular foundations. We also highlight the importance of deepening our understanding of perenniality in the development of perennial grain crops, which are promising elements of future sustainable agriculture.
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Affiliation(s)
- Zheng Li
- State Key Laboratory for Conservation and Utilisation of Bio-Resources in Yunnan, Research Centre for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, 650091 Kunming, China.
| | - Rahul S Lathe
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden
| | - Jinping Li
- State Key Laboratory for Conservation and Utilisation of Bio-Resources in Yunnan, Research Centre for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, 650091 Kunming, China
| | - Hong He
- State Key Laboratory for Conservation and Utilisation of Bio-Resources in Yunnan, Research Centre for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, 650091 Kunming, China
| | - Rishikesh P Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden.
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12
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Yang W, Liu W, Niu K, Ma X, Jia Z, Ma H, Wang Y, Liu M. Transcriptional Regulation of Different Rhizome Parts Reveal the Candidate Genes That Regulate Rhizome Development in Poa pratensis. DNA Cell Biol 2021; 41:151-168. [PMID: 34813368 DOI: 10.1089/dna.2021.0337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A strong rhizome can enhance the ability of a plant to resist drought, low temperature, and other stresses, as it can help plants rapidly obtain water and nutrients. Poa pratensis var. anceps Gaud. cv. Qinghai (QH) is a variant of P. pratensis that is widely distributed in natural grasslands above 3000 m above sea level on the Qinghai-Tibet Plateau. It forms turf easily and has strong soil-fixing ability due to its well-developed rhizomes. Understanding the molecular mechanism of rhizome development in this species is essential for cultivating new varieties of rhizome-type pasture for ecological protection. To clarify the transcriptional regulatory changes in different parts of the rhizome, we analyzed three different rhizome parts (rhizome buds, rhizome nodes, and rhizome internodes) of QH and weak-rhizome wild P. pratensis material (SN) using RNA sequencing. A total of 3806 genes were specifically expressed in Q_B, 1104 genes were specifically expressed in Q_N, and 1181 genes were specifically expressed in Q_I. Analysis showed that MYB, B3, NAC, BBR-BPC, AP2 MIKC_MADS, BSE1, and C2H2 may be key transcription factors regulating rhizome development. These genes interacted with multiple functional genes related to carbohydrate, secondary metabolism, and signal transduction, thus ensuring the normal development of the rhizomes. In particular, SUS (sucrose synthase) [EC:2.4.1.13] is specifically expressed in Q_I, which may be an inducing factor for the production of new plants from Q_B and Q_N. Additionally, PYL, PP2C, and SNRK2, which are involved in the abscisic acid signaling pathway, were differentially expressed in Q_N. In addition, genes related to protein modification and degradation, such as CIPKs, MAPKs, E2, and E3 ubiquitin ligases, were also involved in rhizome development. This study laid a foundation for further functional genomics studies on rhizome development in P. pratensis.
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Affiliation(s)
- Wei Yang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Wenhui Liu
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, China.,Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, People's Republic of China.,Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, China
| | - Kuiju Niu
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Xiang Ma
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, China.,Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, People's Republic of China.,Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, China
| | - Zhifeng Jia
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, China.,Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, People's Republic of China.,Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, China
| | - Huiling Ma
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Yong Wang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Minjie Liu
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, China.,Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, People's Republic of China.,Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, China
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13
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Shibasaki K, Takebayashi A, Makita N, Kojima M, Takebayashi Y, Kawai M, Hachiya T, Sakakibara H. Nitrogen Nutrition Promotes Rhizome Bud Outgrowth via Regulation of Cytokinin Biosynthesis Genes and an Oryza longistaminata Ortholog of FINE CULM 1. FRONTIERS IN PLANT SCIENCE 2021; 12:670101. [PMID: 33995465 PMCID: PMC8120282 DOI: 10.3389/fpls.2021.670101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/08/2021] [Indexed: 06/01/2023]
Abstract
Oryza longistaminata, a wild rice, can propagate vegetatively via rhizome formation and, thereby, expand its territory through horizontal growth of branched rhizomes. The structural features of rhizomes are similar to those of aerial stems; however, the physiological roles of the two organs are different. Nitrogen nutrition is presumed to be linked to the vegetative propagation activity of rhizomes, but the regulation of rhizome growth in response to nitrogen nutrition and the underlying biological processes have not been well characterized. In this study, we analyzed rhizome axillary bud growth in response to nitrogen nutrition and examined the involvement of cytokinin-mediated regulation in the promotion of bud outgrowth in O. longistaminata. Our results showed that nitrogen nutrition sufficiency promoted rhizome bud outgrowth to form secondary rhizomes. In early stages of the response to nitrogen application, glutamine accumulated rapidly, two cytokinin biosynthesis genes, isopentenyltransferase, and CYP735A, were up-regulated with accompanying cytokinin accumulation, and expression of an ortholog of FINE CULM1, a negative regulator of axillary bud outgrowth, was severely repressed in rhizomes. These results suggest that, despite differences in physiological roles of these organs, the nitrogen-dependent outgrowth of rhizome axillary buds in O. longistaminata is regulated by a mechanism similar to that of shoot axillary buds in O. sativa. Our findings provide a clue for understanding how branched rhizome growth is regulated to enhance nutrient acquisition strategies.
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Affiliation(s)
| | | | - Nobue Makita
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Misato Kawai
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takushi Hachiya
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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14
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Guo L, Plunkert M, Luo X, Liu Z. Developmental regulation of stolon and rhizome. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101970. [PMID: 33296747 DOI: 10.1016/j.pbi.2020.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/30/2020] [Accepted: 10/02/2020] [Indexed: 05/20/2023]
Abstract
Stolons and rhizomes are modified stems for vegetative reproduction. While stolons grow above the ground, rhizomes grow beneath the ground. Stolons and rhizomes maintain the genotypes of hybrids and hence are invaluable for agricultural propagation. Diploid strawberry is a model for studying stolon development. At the axillary meristems, gibberellins and MADS box gene SOC1 promote stolon formation, while the DELLA repressor inhibits stolon development. Photoperiod regulates stolon formation through regulating GA biosynthesis or balancing asexual with sexual mode of reproduction in the axillary meristems. In rhizomatous wild rice, the BLADE-ON-PETIOLE gene promotes sheath-to-blade ratio to confer rhizome tip stiffness and support underground growth. Together, this review aims to encourage further investigations into stolon and rhizome to benefit agriculture and environment.
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Affiliation(s)
- Lei Guo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Madison Plunkert
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Xi Luo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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15
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Ma X, Yu J, Zhuang L, Shi Y, Meyer W, Huang B. Differential regulatory pathways associated with drought-inhibition and post-drought recuperation of rhizome development in perennial grass. ANNALS OF BOTANY 2020; 126:481-497. [PMID: 32445476 PMCID: PMC7424744 DOI: 10.1093/aob/mcaa099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/06/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND AND AIMS Rhizomes are key organs for the establishment of perennial grass stands and adaptation to environmental stress. However, mechanisms regulating rhizome initiation and elongation under drought stress and during post-drought recovery remain unclear. The objective of this study is to investigate molecular factors and metabolic processes involved in drought effects and post-drought recovery in rhizome growth in perennial grass species by comparative transcriptomic and proteomic profiling. METHODS Tall fescue (Festuca arundinacea) (B-type rhizome genotype, 'BR') plants were exposed to drought stress and re-watering in growth chambers. The number and length of rhizomes were measured following drought stress and re-watering. Hormone and sugar contents were analysed, and transcriptomic and proteomic analyses were performed to identify metabolic factors, genes and proteins associated with rhizome development. KEY RESULTS Rhizome initiation and elongation were inhibited by drought stress, and were associated with increases in the contents of abscisic acid (ABA) and soluble sugars, but declines in the contents of indoleacetic acid (IAA), zeatin riboside (ZR) and gibberellin (GA4). Genes involved in multiple metabolic processes and stress defence systems related to rhizome initiation exhibited different responses to drought stress, including ABA signalling, energy metabolism and stress protection. Drought-inhibition of rhizome elongation could be mainly associated with the alteration of GA4 and antioxidants contents, energy metabolism and stress response proteins. Upon re-watering, new rhizomes were regenerated from rhizome nodes previously exposed to drought stress, which was accompanied by the decline in ABA content and increases in IAA, ZR and GA4, as well as genes and proteins for auxin, lipids, lignin and nitrogen metabolism. CONCLUSIONS Drought-inhibition of rhizome initiation and elongation in tall fescue was mainly associated with adjustments in hormone metabolism, carbohydrate metabolism and stress-defence systems. Rhizome regeneration in response to re-watering involved reactivation of hormone and lipid metabolism, secondary cell-wall development, and nitrogen remobilization and cycling.
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Affiliation(s)
- Xiqing Ma
- College of Grassland Science and Technology, China Agricultural University, Beijing, PR China
- Department of Plant Biology and Pathology Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Jingjin Yu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, PR China
| | - Lili Zhuang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, PR China
| | - Yi Shi
- College of Grassland Science, Gansu Agricultural University, Lanzhou, PR China
- Department of Plant Biology and Pathology Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - William Meyer
- Department of Plant Biology and Pathology Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Bingru Huang
- Department of Plant Biology and Pathology Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
- For correspondence. E-mail
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16
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Toriba T, Tokunaga H, Nagasawa K, Nie F, Yoshida A, Kyozuka J. Suppression of Leaf Blade Development by BLADE-ON-PETIOLE Orthologs Is a Common Strategy for Underground Rhizome Growth. Curr Biol 2020; 30:509-516.e3. [PMID: 31956025 DOI: 10.1016/j.cub.2019.11.055] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 01/17/2023]
Abstract
Rhizomes are modified stems that grow horizontally underground in various perennial species, a growth habit that is advantageous for vigorous asexual proliferation. In Oryza longistaminata, a rhizomatous wild relative of cultivated rice (Oryza sativa), leaves in the aerial shoots consist of a distal leaf blade and a proximal leaf sheath [1]. Leaf blade formation is, however, suppressed in rhizome leaves. In O. sativa, BLADE-ON-PETIOLE (BOP) genes are the main regulators of proximal-distal leaf patterning [2]. During the juvenile phase of O. sativa, BOP expression is maintained at high levels by the small regulatory RNA microRNA156 (miR156), leading to formation of leaves consisting predominantly of the sheath. Here, we show that in O. longistaminata, high expression of BOPs caused by miR156 was responsible for suppression of the blade in rhizomes and that bop loss-of-function mutants produced leaves consisting of the leaf blade only. Rhizome growth in soil was also hampered in the mutants due to a severe reduction in rhizome tip stiffness. Leaf blade formation is also suppressed in the stolons of Zoysia matrella, a monocot species, and in the rhizomes of Houttuynia cordata, a dicot species, indicating that leaf blade suppression is widely conserved. We also show that strong expression of BOP homologs in both rhizome and stolon leaves rather than in aerial leaves is another conserved feature. We propose that suppression of the leaf blade by BOP is an evolutionary strategy that has been commonly recruited by both rhizomatous and stoloniferous species to establish their unique growth habit.
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Affiliation(s)
- Taiyo Toriba
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Hiroki Tokunaga
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Kazuma Nagasawa
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Fanyu Nie
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Akiko Yoshida
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan.
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17
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Bessho-Uehara K, Nugroho JE, Kondo H, Angeles-Shim RB, Ashikari M. Sucrose affects the developmental transition of rhizomes in Oryza longistaminata. JOURNAL OF PLANT RESEARCH 2018; 131:693-707. [PMID: 29740707 PMCID: PMC6488557 DOI: 10.1007/s10265-018-1033-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/08/2018] [Indexed: 05/29/2023]
Abstract
Oryza longistaminata, the African wild rice, can propagate vegetatively through rhizomes. Rhizomes elongate horizontally underground as sink organs, however, they undergo a developmental transition that shifts their growth to the surface of the ground to become aerial stems. This particular stage is essential for the establishment of new ramets. While several determinants such as abiotic stimuli and plant hormones have been reported as key factors effecting developmental transition in aerial stem, the cause of this phenomenon in rhizome remains elusive. This study shows that depletion of nutrients, particularly sucrose, is the key stimulus that induces the developmental transition in rhizomes, as indicated by the gradient of sugars from the base to the tip of the rhizome. Sugar treatments revealed that sucrose specifically represses the developmental transition from rhizome to aerial stem by inhibiting the expression of sugar metabolism and hormone synthesis genes at the bending point. Sucrose depletion affected several factors contributing to the developmental transition of rhizome including signal transduction, transcriptional regulation and plant hormone balance.
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Affiliation(s)
- Kanako Bessho-Uehara
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Jovano Erris Nugroho
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Hirono Kondo
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Rosalyn B Angeles-Shim
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8601, Japan
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8601, Japan.
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18
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Kyozuka J. Letter to the Editor: Author Response - Analysis of Rhizome Development in Oryza longistaminata, a Wild Rice Species. PLANT & CELL PHYSIOLOGY 2017; 58:1283. [PMID: 28505342 DOI: 10.1093/pcp/pcx064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Junko Kyozuka
- Tohoku University, Graduate School of Life Science, Sendai, Japan
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19
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Hu R, Yu C, Wang X, Jia C, Pei S, He K, He G, Kong Y, Zhou G. De novo Transcriptome Analysis of Miscanthus lutarioriparius Identifies Candidate Genes in Rhizome Development. FRONTIERS IN PLANT SCIENCE 2017; 8:492. [PMID: 28446913 PMCID: PMC5388781 DOI: 10.3389/fpls.2017.00492] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/21/2017] [Indexed: 05/26/2023]
Abstract
HIGHLIGHTDe novo transcriptome profiling of five tissues reveals candidate genes putatively involved in rhizome development in M. lutarioriparius. Miscanthus lutarioriparius is a promising lignocellulosic feedstock for second-generation bioethanol production. However, the genomic resource for this species is relatively limited thus hampers our understanding of the molecular mechanisms underlying many important biological processes. In this study, we performed the first de novo transcriptome analysis of five tissues (leaf, stem, root, lateral bud and rhizome bud) of M. lutarioriparius with an emphasis to identify putative genes involved in rhizome development. Approximately 66 gigabase (GB) paired-end clean reads were obtained and assembled into 169,064 unigenes with an average length of 759 bp. Among these unigenes, 103,899 (61.5%) were annotated in seven public protein databases. Differential gene expression profiling analysis revealed that 4,609, 3,188, 1,679, 1,218, and 1,077 genes were predominantly expressed in root, leaf, stem, lateral bud, and rhizome bud, respectively. Their expression patterns were further classified into 12 distinct clusters. Pathway enrichment analysis revealed that genes predominantly expressed in rhizome bud were mainly involved in primary metabolism and hormone signaling and transduction pathways. Noteworthy, 19 transcription factors (TFs) and 16 hormone signaling pathway-related genes were identified to be predominantly expressed in rhizome bud compared with the other tissues, suggesting putative roles in rhizome formation and development. In addition, a predictive regulatory network was constructed between four TFs and six auxin and abscisic acid (ABA) -related genes. Furthermore, the expression of 24 rhizome-specific genes was further validated by quantitative real-time RT-PCR (qRT-PCR) analysis. Taken together, this study provide a global portrait of gene expression across five different tissues and reveal preliminary insights into rhizome growth and development. The data presented will contribute to our understanding of the molecular mechanisms underlying rhizome development in M. lutarioriparius and remarkably enrich the genomic resources of Miscanthus.
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Affiliation(s)
- Ruibo Hu
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Changjiang Yu
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Xiaoyu Wang
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Chunlin Jia
- Shandong Institute of Agricultural Sustainable DevelopmentJinan, China
| | - Shengqiang Pei
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Kang He
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Guo He
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Yingzhen Kong
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao, China
| | - Gongke Zhou
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
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