1
|
Machado R, Muchut SE, Dezar C, Reutemann AG, Alesso CA, Günthardt MM, Vegetti AC, Vogel J, Uberti Manassero NG. BdRCN4, a Brachypodium distachyon TFL1 homologue, is involved in regulation of apical meristem fate. PLANT MOLECULAR BIOLOGY 2024; 114:81. [PMID: 38940986 DOI: 10.1007/s11103-024-01467-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 05/13/2024] [Indexed: 06/29/2024]
Abstract
In higher plants, the shift from vegetative to reproductive development is governed by complex interplay of internal and external signals. TERMINALFLOWER1 (TFL1) plays a crucial role in the regulation of flowering time and inflorescence architecture in Arabidopsis thaliana. This study aimed to explore the function of BdRCN4, a homolog of TFL1 in Brachypodium distachyon, through functional analyses in mutant and transgenic plants. The results revealed that overexpression of BdRCN4 in B. distachyon leads to an extended vegetative phase and reduced production of spikelets. Similar results were found in A. thaliana, where constitutive expression of BdRCN4 promoted a delay in flowering time, followed by the development of hypervegetative shoots, with no flowers or siliques produced. Our results suggest that BdRCN4 acts as a flowering repressor analogous to TFL1, negatively regulating AP1, but no LFY expression. To further validate this hypothesis, a 35S::LFY-GR co-transformation approach on 35::BdRCN4 lines was performed. Remarkably, AP1 expression levels and flower formation were restored to normal in co-transformed plants when treated with dexamethasone. Although further molecular studies will be necessary, the evidence in B. distachyon support the idea that a balance between LFY and BdRCN4/TFL1 seems to be essential for activating AP1 expression and initiating floral organ identity gene expression. This study also demonstrates interesting conservation through the molecular pathways that regulate flowering meristem transition and identity across the evolution of monocot and dicot plants.
Collapse
Affiliation(s)
- Rodrigo Machado
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Concordia, Santa Fe, Argentina
| | - Sebastián Elias Muchut
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Santa Fe, 3080, Argentina
| | - Carlos Dezar
- ICiAgro Litoral, FCA, UNL-CONICET, Esperanza, Santa Fe, 3080, Argentina
| | | | | | - María Margarita Günthardt
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Santa Fe, 3080, Argentina
| | | | - John Vogel
- DOE Joint Genome Institute, Walnut Creek, CA, 94595, USA
| | - Nora G Uberti Manassero
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Santa Fe, 3080, Argentina.
| |
Collapse
|
2
|
John JS, Christen DR, Flammer KL, Kendall TL, Nazario EC, Richter BP, Gill V, Williams TM. Conservation energetics of beluga whales: using resting and swimming metabolism to understand threats to an endangered population. J Exp Biol 2024; 227:jeb246899. [PMID: 38483264 PMCID: PMC11070638 DOI: 10.1242/jeb.246899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/24/2024] [Indexed: 05/08/2024]
Abstract
The balance between energetic costs and acquisition in free-ranging species is essential for survival, and provides important insights regarding the physiological impact of anthropogenic disturbances on wild animals. For marine mammals such as beluga whales (Delphinapterus leucas), the first step in modeling this bioenergetic balance requires an examination of resting and active metabolic demands. Here, we used open-flow respirometry to measure oxygen consumption during surface rest and submerged swimming by trained beluga whales, and compared these measurements with those of a commonly studied odontocete, the Atlantic bottlenose dolphin (Tursiops truncatus). Both resting metabolic rate (3012±126.0 kJ h-1) and total cost of transport (1.4±0.1 J kg-1 m-1) of beluga whales were consistent with predicted values for moderately sized marine mammals in temperate to cold-water environments, including dolphins measured in the present study. By coupling the rate of oxygen consumption during submerged swimming with locomotor metrics from animal-borne accelerometer tags, we developed predictive relationships for assessing energetic costs from swim speed, stroke rate and partial dynamic acceleration. Combining these energetic data with calculated aerobic dive limits for beluga whales (8.8 min), we found that high-speed responses to disturbance markedly reduce the whale's capacity for prolonged submergence, pushing the cetaceans to costly anaerobic performances that require prolonged recovery periods. Together, these species-specific energetic measurements for beluga whales provide two important metrics, gait-related locomotor costs and aerobic capacity limits, for identifying relative levels of physiological vulnerability to anthropogenic disturbances that have become increasingly pervasive in their Arctic habitats.
Collapse
Affiliation(s)
- Jason S. John
- University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | | | | | - Traci L. Kendall
- University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Emily C. Nazario
- University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Beau P. Richter
- University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Verena Gill
- NOAA Fisheries, 222 W. 7th Ave, Anchorage, AK 99501, USA
| | - Terrie M. Williams
- University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, 130 McAllister Way, Santa Cruz, CA 95060, USA
| |
Collapse
|
3
|
Sharma M, Jabaji S. Transcriptional landscape of Brachypodium distachyon roots during interaction with Bacillus velezensis strain B26. Genomics 2023; 115:110583. [PMID: 36804269 DOI: 10.1016/j.ygeno.2023.110583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/02/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023]
Abstract
Plant growth promoting rhizobacteria (PGPR) communicate with plants through roots. The molecular mechanism by which plants and PGPR respond to each other is not very well known. In the current study, we did RNA sequence analysis of Brachypodium distachyon Bd21-3 roots inoculated with PGPR, Bacillus velezensis strain B26. From our list of differentially expressed genes, we concentrated on transcripts that have a high possibility of participating in plant-PGPR interaction. Transcripts associated to the hormone signalling pathway were differentially expressed. We identified the upregulation of various transcripts linked to ion transporters. Reduction in expression of defense signalling genes indicated that B26 suppresses the plant defense mechanisms to begin successful interaction with roots. Transcripts associated with lignin branch of the phenylpropanoid pathway were upregulated as well, leading to more accumulation of lignin in the cell wall which enhances mechanical strength of plants. Overall, this study is an excellent resource for investigating associations between plant-PGPR interactions.
Collapse
Affiliation(s)
- Meha Sharma
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, H9X 3V9 Quebec, Canada.
| | - Suha Jabaji
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, H9X 3V9 Quebec, Canada.
| |
Collapse
|
4
|
Wang Y, Bi X, Zhong J. Revisiting the origin and identity specification of the spikelet: A structural innovation in grasses (Poaceae). PLANT PHYSIOLOGY 2022; 190:60-71. [PMID: 35640983 PMCID: PMC9434286 DOI: 10.1093/plphys/kiac257] [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: 01/21/2022] [Accepted: 05/03/2022] [Indexed: 05/06/2023]
Abstract
Spikelets are highly specialized and short-lived branches and function as a constitutional unit of the complex grass inflorescences. A series of genetic, genomic, and developmental studies across different clades of the family have called for and permitted a synthesis on the regulation and evolution of spikelets, and hence inflorescence diversity. Here, we have revisited the identity specification of a spikelet, focusing on the diagnostic features of a spikelet from morphological, developmental, and molecular perspectives. Particularly, recent studies on a collection of barley (Hordeum vulgare L.), wheat (Triticum spp.), and rice (Oryza sativa L.) mutants have highlighted a set of transcription factors that are important in the control of spikelet identity and the patterning of floral parts of a spikelet. In addition, we have endeavored to clarify some puzzling issues on the (in)determinacy and modifications of spikelets over the course of evolution. Meanwhile, genomes of two sister taxa of the remaining grass species have again demonstrated the importance of genome duplication and subsequent gene losses on the evolution of spikelets. Accordingly, we argue that changes in the orthologs of spikelet-related genes could be critical for the development and evolution of the spikelet, an evolutionary innovation in the grass family. Likewise, the conceptual discussions on the regulation of a fundamental unit of compound inflorescences could be translated into other organismal groups where compound structures are similarly formed, permitting a comparative perspective on the control of biological complexity.
Collapse
|
5
|
Kitagawa M, Xu X, Jackson D. Trafficking and localization of KNOTTED1 related mRNAs in shoot meristems. Commun Integr Biol 2022; 15:158-163. [PMID: 35832536 PMCID: PMC9272838 DOI: 10.1080/19420889.2022.2095125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Multicellular organisms use transcripts and proteins as signaling molecules for cell-to-cell communication. Maize KNOTTED1 (KN1) was the first homeodomain transcription factor identified in plants, and functions in maintaining shoot stem cells. KN1 acts non-cell autonomously, and both its messenger RNA (mRNA) and protein traffic between cells through intercellular nanochannels called plasmodesmata. KN1 protein and mRNA trafficking are regulated by a chaperonin subunit and a catalytic subunit of the RNA exosome, respectively. These studies suggest that the function of KN1 in stem cell regulation requires the cell-to-cell transport of both its protein and mRNA. However, in situ hybridization experiments published 25 years ago suggested that KN1 mRNA was missing from the epidermal (L1) layer of shoot meristems, suggesting that only the KN1 protein could traffic. Here, we show evidence that KN1 mRNA is present at a low level in L1 cells of maize meristems, supporting an idea that both KN1 protein and mRNA traffic to the L1 layer. We also summarize mRNA expression patterns of KN1 homologs in diverse angiosperm species, and discuss KN1 trafficking mechanisms.
Collapse
Affiliation(s)
| | - Xiaosa Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| |
Collapse
|
6
|
Kellogg EA. Genetic control of branching patterns in grass inflorescences. THE PLANT CELL 2022; 34:2518-2533. [PMID: 35258600 PMCID: PMC9252490 DOI: 10.1093/plcell/koac080] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/02/2022] [Indexed: 05/13/2023]
Abstract
Inflorescence branching in the grasses controls the number of florets and hence the number of seeds. Recent data on the underlying genetics come primarily from rice and maize, although new data are accumulating in other systems as well. This review focuses on a window in developmental time from the production of primary branches by the inflorescence meristem through to the production of glumes, which indicate the transition to producing a spikelet. Several major developmental regulatory modules appear to be conserved among most or all grasses. Placement and development of primary branches are controlled by conserved auxin regulatory genes. Subtending bracts are repressed by a network including TASSELSHEATH4, and axillary branch meristems are regulated largely by signaling centers that are adjacent to but not within the meristems themselves. Gradients of SQUAMOSA-PROMOTER BINDING-like and APETALA2-like proteins and their microRNA regulators extend along the inflorescence axis and the branches, governing the transition from production of branches to production of spikelets. The relative speed of this transition determines the extent of secondary and higher order branching. This inflorescence regulatory network is modified within individual species, particularly as regards formation of secondary branches. Differences between species are caused both by modifications of gene expression and regulators and by presence or absence of critical genes. The unified networks described here may provide tools for investigating orphan crops and grasses other than the well-studied maize and rice.
Collapse
|
7
|
Zhong J, Kong F. The control of compound inflorescences: insights from grasses and legumes. TRENDS IN PLANT SCIENCE 2022; 27:564-576. [PMID: 34973922 DOI: 10.1016/j.tplants.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/16/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
A major challenge in biology is to understand how organisms have increased developmental complexity during evolution. Inflorescences, with remarkable variation in branching systems, are a fitting model to understand architectural complexity. Inflorescences bear flowers that may become fruits and/or seeds, impacting crop productivity and species fitness. Great advances have been achieved in understanding the regulation of complex inflorescences, particularly in economically and ecologically important grasses and legumes. Surprisingly, a synthesis is still lacking regarding the common or distinct principles underlying the regulation of inflorescence complexity. Here, we synthesize the similarities and differences in the regulation of compound inflorescences in grasses and legumes, and propose that the emergence of novel higher-order repetitive modules is key to the evolution of inflorescence complexity.
Collapse
Affiliation(s)
- Jinshun Zhong
- School of Life Sciences, South China Agricultural University, Wushan Street 483, Guangzhou 510642, China; Institute for Plant Genetics, Heinrich-Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany; Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Köln, Germany; Cluster of Excellence on Plant Sciences, 'SMART Plants for Tomorrow's Needs', Heinrich-Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany.
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
| |
Collapse
|
8
|
Chen Q, Tian F, Cheng T, Jiang J, Zhu G, Gao Z, Lin H, Hu J, Qian Q, Fang X, Chen F. Translational repression of FZP mediated by CU-rich element/OsPTB interactions modulates panicle development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1319-1331. [PMID: 35293072 DOI: 10.1111/tpj.15737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Panicle development is an important determinant of the grain number in rice. A thorough characterization of the molecular mechanism underlying panicle development will lead to improved breeding of high-yielding rice varieties. Frizzy Panicle (FZP), a critical gene for panicle development, is regulated by OsBZR1 and OsARFs at the transcriptional stage. However, the translational modulation of FZP has not been reported. We reveal that the CU-rich elements (CUREs) in the 3' UTR of the FZP mRNA are crucial for efficient FZP translation. The knockout of CUREs in the FZP 3' UTR or the over-expression of the FZP 3' UTR fragment containing CUREs resulted in an increase in FZP mRNA translation efficiency. Moreover, the number of secondary branches (NSB) and the grain number per panicle (GNP) decreased in the transformed rice plants. The CUREs in the 3' UTR of FZP mRNA were verified as the targets of the polypyrimidine tract-binding proteins OsPTB1 and OsPTB2 in rice. Both OsPTB1 and OsPTB2 were highly expressed in young panicles. The knockout of OsPTB1/2 resulted in an increase in the FZP translational efficiency and a decrease in the NSB and GNP. Furthermore, the over-expression of OsPTB1/2 decreased the translation of the reporter gene fused to FZP 3' UTR in vivo and in vitro. These results suggest that OsPTB1/2 can mediate FZP translational repression by interacting with CUREs in the 3' UTR of FZP mRNA, leading to changes in the NSB and GNP. Accordingly, in addition to transcriptional regulation, FZP expression is also fine-tuned at the translational stage during rice panicle development.
Collapse
Affiliation(s)
- Qiong Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Fa'an Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Cheng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun'e Jiang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanlin Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Haiyan Lin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaohua Fang
- Genetic Resource R&D Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chang Zhou, 213001, China
| | - Fan Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| |
Collapse
|
9
|
Raissig MT, Woods DP. The wild grass Brachypodium distachyon as a developmental model system. Curr Top Dev Biol 2022; 147:33-71. [PMID: 35337454 DOI: 10.1016/bs.ctdb.2021.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The arrival of cheap and high-throughput sequencing paired with efficient gene editing technologies allows us to use non-traditional model systems and mechanistically approach biological phenomena beyond what was conceivable just a decade ago. Venturing into different model systems enables us to explore for example clade-specific environmental responses to changing climates or the genetics and development of clade-specific organs, tissues and cell types. We-both early career researchers working with the wild grass model Brachypodium distachyon-want to use this review to (1) highlight why we think B. distachyon is a fantastic grass developmental model system, (2) summarize the tools and resources that have enabled discoveries made in B. distachyon, and (3) discuss a handful of developmental biology vignettes made possible by using B. distachyon as a model system. Finally, we want to conclude by (4) relating our personal stories with this emerging model system and (5) share what we think is important to consider before starting work with an emerging model system.
Collapse
Affiliation(s)
- Michael T Raissig
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany; Institute of Plant Sciences, University of Bern, Bern, Switzerland.
| | - Daniel P Woods
- Department of Plant Sciences, University of California, Davis, CA, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.
| |
Collapse
|
10
|
Li J, Zhang L, G. Elbaiomy R, Chen L, Wang Z, Jiao J, Zhu J, Zhou W, Chen B, Soaud SA, Abbas M, Lin N, El-Sappah AH. Evolution analysis of FRIZZY PANICLE ( FZP) orthologs explored the mutations in DNA coding sequences in the grass family (Poaceae). PeerJ 2022; 10:e12880. [PMID: 35295554 PMCID: PMC8919851 DOI: 10.7717/peerj.12880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/13/2022] [Indexed: 01/11/2023] Open
Abstract
FRIZZY PANICLE (FZP), an essential gene that controls spikelet differentiation and development in the grass family (Poaceae), prevents the formation of axillary bud meristems and is closely associated with crop yields. It is unclear whether the FZP gene or its orthologs were selected during the evolutionary process of grass species, which possess diverse spike morphologies. In the present study, we adopted bioinformatics methods for the evolutionary analysis of FZP orthologs in species of the grass family. Thirty-five orthologs with protein sequences identical to that of the FZP gene were identified from 29 grass species. Analysis of conserved domains revealed that the AP2/ERF domains were highly conserved with almost no amino acid mutations. However, species of the tribe Triticeae, genus Oryza, and C4 plants exhibited more significant amino acid mutations in the acidic C-terminus region. Results of the phylogenetic analysis showed that the 29 grass species could be classified into three groups, namely, Triticeae, Oryza, and C4 plants. Within the Triticeae group, the FZP genes originating from the same genome were classified into the same sub-group. When selection pressure analysis was performed, significant positive selection sites were detected in species of the Triticeae and Oryza groups. Our results show that the FZP gene was selected during the grass family's evolutionary process, and functional divergence may have already occurred among the various species. Therefore, researchers investigating the FZP gene's functions should take note of the possible presence of various roles in other grass species.
Collapse
Affiliation(s)
- Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Litian Zhang
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, China,State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | | | - Lilan Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Zhenrong Wang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jie Jiao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jiliang Zhu
- Agriculture and Rural Bureau of Zhongjiang County, Deyang, Sichuan, China
| | - Wanhai Zhou
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Bo Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Na Lin
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China,Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| |
Collapse
|
11
|
Koppolu R, Chen S, Schnurbusch T. Evolution of inflorescence branch modifications in cereal crops. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102168. [PMID: 35016076 DOI: 10.1016/j.pbi.2021.102168] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Grasses are ubiquitous in our daily lives, with gramineous cereal crops such as maize, rice, and wheat constituting a large proportion of our daily staple food intake. Evolutionary forces, especially over the past ∼20 million years, have shaped grass adaptability, inflorescence architecture, and reproductive success. Here, we provide basic information on grass evolution and inflorescence structures mainly related to two inflorescence types: branched panicle- and spike-type inflorescences, the latter of which has highly modified branching. We summarize and compare known genetic pathways underlying each infloresecence type and discuss how the maize RAMOSA, rice ABERRANT PANICLE ORGANIZATION, and Triticeae COMPOSITUM pathways are regulated. Our analyses might lay the foundation for understanding species-specific gene regulatory networks that could result in improved sink capacities.
Collapse
Affiliation(s)
- Ravi Koppolu
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - Shulin Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Thorsten Schnurbusch
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany.
| |
Collapse
|
12
|
Liu S, Magne K, Daniel S, Sibout R, Ratet P. Brachypodium distachyon UNICULME4 and LAXATUM-A are redundantly required for development. PLANT PHYSIOLOGY 2022; 188:363-381. [PMID: 34662405 PMCID: PMC8774750 DOI: 10.1093/plphys/kiab456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
In cultivated grasses, tillering, leaf, and inflorescence architecture, as well as abscission ability, are major agronomical traits. In barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and brachypodium (Brachypodium distachyon), NOOT-BOP-COCH-LIKE (NBCL) genes are essential regulators of vegetative and reproductive development. Grass species usually possess 2-4 NBCL copies and until now a single study in O. sativa showed that the disruption of all NBCL genes strongly altered O. sativa leaf development. To improve our understanding of the role of NBCL genes in grasses, we extended the study of the two NBCL paralogs BdUNICULME4 (CUL4) and BdLAXATUM-A (LAXA) in the nondomesticated grass B. distachyon. For this, we applied reversed genetics and generated original B. distachyon single and double nbcl mutants by clustered regularly interspaced short palindromic repeats - CRISPR associated protein 9 (CRISPR-Cas9) approaches and genetic crossing between nbcl targeting induced local lesions in genomes (TILLING) mutants. Through the study of original single laxa CRISPR-Cas9 null alleles, we validated functions previously proposed for LAXA in tillering, leaf patterning, inflorescence, and flower development and also unveiled roles for these genes in seed yield. Furthermore, the characterization of cul4laxa double mutants revealed essential functions for nbcl genes in B. distachyon development, especially in the regulation of tillering, stem cell elongation and secondary cell wall composition as well as for the transition toward the reproductive phase. Our results also highlight recurrent antagonist interactions between NBCLs occurring in multiple aspects of B. distachyon development.
Collapse
Affiliation(s)
- Shengbin Liu
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
| | - Kévin Magne
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
| | - Sylviane Daniel
- UR1268 BIA (Biopolymères Interactions Assemblages), INRAE, Nantes 44300, France
| | - Richard Sibout
- UR1268 BIA (Biopolymères Interactions Assemblages), INRAE, Nantes 44300, France
| | - Pascal Ratet
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
| |
Collapse
|
13
|
DNA Methylation-An Epigenetic Mark in Mutagen-Treated Brachypodium distachyon Cells. PLANTS 2021; 10:plants10071408. [PMID: 34371611 PMCID: PMC8309452 DOI: 10.3390/plants10071408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022]
Abstract
The chromatin structure is significantly influenced by some epigenetic modifications including DNA methylation. The nuclear organization plays an essential role in the cell response to external stresses including mutagens. We present an analysis of the correlation between epigenetic modifications and the instability of the Brachypodium distachyon genome, which are observed as micronuclei, following maleic hydrazide (MH) and nitroso-N-methylurea (MNU) treatments. We compared the level of DNA methylation in the control (untreated) and mutagen-treated B. distachyon nuclei. An immunostaining method using specific antibodies against modified DNA anti-5-methylcytosine was used for the evaluation of DNA methylation in a single nucleus and micronucleus. Interestingly, we showed an alteration of DNA methylation in cells after mutagenic treatments. The results indicate that DNA methylation might be involved in the response of the B. distachyon genome to mutagenic treatments. This demonstrates that analyses of the epigenetic modifications should be integrated into current plant genetic toxicology in order to explain the mechanisms of DNA damage and repair in plants.
Collapse
|
14
|
Du D, Zhang D, Yuan J, Feng M, Li Z, Wang Z, Zhang Z, Li X, Ke W, Li R, Chen Z, Chai L, Hu Z, Guo W, Xing J, Su Z, Peng H, Xin M, Yao Y, Sun Q, Liu J, Ni Z. FRIZZY PANICLE defines a regulatory hub for simultaneously controlling spikelet formation and awn elongation in bread wheat. THE NEW PHYTOLOGIST 2021; 231:814-833. [PMID: 33837555 DOI: 10.1111/nph.17388] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/01/2021] [Indexed: 05/25/2023]
Abstract
Grain yield in bread wheat (Triticum aestivum L.) is largely determined by inflorescence architecture. Zang734 is an endemic Tibetan wheat variety that exhibits a rare triple spikelet (TRS) phenotype with significantly increased spikelet/floret number per spike. However, the molecular basis underlying this specific spike morphology is completely unknown. Through map-based cloning, the causal genes for TRS trait in Zang734 were isolated. Furthermore, using CRISPR/Cas9-based gene mutation, transcriptome sequencing and protein-protein interaction, the downstream signalling networks related to spikelet formation and awn elongation were defined. Results showed that the null mutation in WFZP-A together with deletion of WFZP-D led to the TRS trait in Zang734. More interestingly, WFZP plays a dual role in simultaneously repressing spikelet formation gene TaBA1 and activating awn development genes, basically through the recruitments of chromatin remodelling elements and the Mediator complex. Our findings provide insights into the molecular bases by which WFZP suppresses spikelet formation but promotes awn elongation and, more importantly, define WFZP-D as a favourable gene for high-yield crop breeding.
Collapse
Affiliation(s)
- Dejie Du
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Dongxue Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jun Yuan
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Man Feng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaoju Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zihao Wang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaoheng Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiongtao Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Renhan Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhenqi Su
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
15
|
Wolde GM, Schreiber M, Trautewig C, Himmelbach A, Sakuma S, Mascher M, Schnurbusch T. Genome-wide identification of loci modifying spike-branching in tetraploid wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1925-1943. [PMID: 33961064 PMCID: PMC8263435 DOI: 10.1007/s00122-020-03743-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/27/2020] [Indexed: 05/03/2023]
Abstract
Genetic modification of spike architecture is essential for improving wheat yield. Newly identified loci for the 'Miracle wheat' phenotype on chromosomes 1AS and 2BS have significant effects on spike traits. The wheat (Triticum ssp.) inflorescence, also known as a spike, forms an unbranched inflorescence in which the inflorescence meristem generates axillary spikelet meristems (SMs) destined to become sessile spikelets. Previously, we identified the putatively causative mutation in the branched headt (bht) gene (TtBH-A1) of tetraploid wheat (T. turgidum convar. compositum (L.f.) Filat.) responsible for the loss of SM identity, converting the non-branching spike to a branched wheat spike. In the current study, we performed whole-genome quantitative trait loci (QTL) analysis using 146 recombinant inbred lines (RILs) derived from a cross between spike-branching wheat ('Miracle wheat') and an elite durum wheat cultivar showing broad phenotypic variation for spike architecture. Besides the previously found gene at the bht-A1 locus on the short arm of chromosome 2A, we also mapped two new modifier QTL for spike-branching on the short arm of chromosome 1A, termed bht-A2, and 2BS. Using biparental mapping population and GWAS in 302 diverse accessions, the 2BS locus was highly associated with coding sequence variation found at the homoeo-allele of TtBH-B1 (bht-B1). Thus, RILs that combined both bht-A1 and bht-B1 alleles showed additive genetic effects leading to increased penetrance and expressivity of the supernumerary spikelet and/or mini-spike formation.
Collapse
Affiliation(s)
- Gizaw M Wolde
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany.
- Department of Plant Sciences One Shields Avenue, University of California, Davis, CA, 95616, USA.
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Corinna Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Shun Sakuma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
- Faculty of Agriculture, Tottori University, 4-101 Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany.
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany.
| |
Collapse
|
16
|
Li Y, Li L, Zhao M, Guo L, Guo X, Zhao D, Batool A, Dong B, Xu H, Cui S, Zhang A, Fu X, Li J, Jing R, Liu X. Wheat FRIZZY PANICLE activates VERNALIZATION1-A and HOMEOBOX4-A to regulate spike development in wheat. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1141-1154. [PMID: 33368973 PMCID: PMC8196646 DOI: 10.1111/pbi.13535] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/27/2020] [Accepted: 12/14/2020] [Indexed: 05/22/2023]
Abstract
Kernel number per spike determined by the spike or inflorescence development is one important agricultural trait for wheat yield that is critical for global food security. While a few important genes for wheat spike development were identified, the genetic regulatory mechanism underlying supernumerary spikelets (SSs) is still unclear. Here, we cloned the wheat FRIZZY PANICLE (WFZP) gene from one local wheat cultivar. WFZP is specifically expressed at the sites where the spikelet meristem and floral meristem are initiated, which differs from the expression patterns of its homologs FZP/BD1 in rice and maize, indicative of its functional divergence during species differentiation. Moreover, WFZP directly activates VERNALIZATION1 (VRN1) and wheat HOMEOBOX4 (TaHOX4) to regulate the initiation and development of spikelet. The haplotypes analysis showed that the favourable alleles of WFZP associated with spikelet number per spike (SNS) were preferentially selected during breeding. Our findings provide insights into the molecular and genetic mechanisms underlying wheat spike development and characterize the WFZP as elite resource for wheat molecular breeding with enhanced crop yield.
Collapse
Affiliation(s)
- Yongpeng Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Meicheng Zhao
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Lin Guo
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
- Ministry of Education Key Laboratory of Molecular and Cellular BiologyHebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuangChina
| | - Xinxin Guo
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Dan Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular BiologyHebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuangChina
| | - Aamana Batool
- University of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Agricultural Water ResourcesHebei Laboratory of Agricultural Water‐SavingCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesShijiazhuangChina
| | - Baodi Dong
- Key Laboratory of Agricultural Water ResourcesHebei Laboratory of Agricultural Water‐SavingCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesShijiazhuangChina
| | - Hongxing Xu
- Key Laboratory of Agricultural Water ResourcesHebei Laboratory of Agricultural Water‐SavingCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesShijiazhuangChina
- State Key Laboratory of Crop Stress Adaptation and ImprovementState Key laboratory of Cotton BiologySchool of Life SciencesHenan UniversityKaifengChina
| | - Sujuan Cui
- Ministry of Education Key Laboratory of Molecular and Cellular BiologyHebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuangChina
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Junming Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xigang Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
- Ministry of Education Key Laboratory of Molecular and Cellular BiologyHebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuangChina
| |
Collapse
|
17
|
Ma PF, Liu YL, Jin GH, Liu JX, Wu H, He J, Guo ZH, Li DZ. The Pharus latifolius genome bridges the gap of early grass evolution. THE PLANT CELL 2021; 33:846-864. [PMID: 33630094 PMCID: PMC8226297 DOI: 10.1093/plcell/koab015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/11/2021] [Indexed: 05/07/2023]
Abstract
The grass family (Poaceae) includes all commercial cereal crops and is a major contributor to biomass in various terrestrial ecosystems. The ancestry of all grass genomes includes a shared whole-genome duplication (WGD), named rho (ρ) WGD, but the evolutionary significance of ρ-WGD remains elusive. We sequenced the genome of Pharus latifolius, a grass species (producing a true spikelet) in the subfamily Pharoideae, a sister lineage to the core Poaceae including the (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) and Bambusoideae, Oryzoideae, and Pooideae (BOP) clades. Our results indicate that the P. latifolius genome has evolved slowly relative to cereal grass genomes, as reflected by moderate rates of molecular evolution, limited chromosome rearrangements and a low rate of gene loss for duplicated genes. We show that the ρ-WGD event occurred approximately 98.2 million years ago (Ma) in a common ancestor of the Pharoideae and the PACMAD and BOP grasses. This was followed by contrasting patterns of diploidization in the Pharus and core Poaceae lineages. The presence of two FRIZZY PANICLE-like genes in P. latifolius, and duplicated MADS-box genes, support the hypothesis that the ρ-WGD may have played a role in the origin and functional diversification of the spikelet, an adaptation in grasses related directly to cereal yields. The P. latifolius genome sheds light on the origin and early evolution of grasses underpinning the biology and breeding of cereals.
Collapse
Affiliation(s)
- Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Gui-Hua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, China
| | - Jun He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, China
- Author for correspondence: (D.-Z.L)
| |
Collapse
|
18
|
Sheng H, Jiang Y, Rahmati M, Chia JC, Dokuchayeva T, Kavulych Y, Zavodna TO, Mendoza PN, Huang R, Smieshka LM, Miller J, Woll AR, Terek OI, Romanyuk ND, Piñeros M, Zhou Y, Vatamaniuk OK. YSL3-mediated copper distribution is required for fertility, seed size and protein accumulation in Brachypodium. PLANT PHYSIOLOGY 2021; 186:655-676. [PMID: 33576792 PMCID: PMC8154065 DOI: 10.1093/plphys/kiab054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 01/18/2021] [Indexed: 05/05/2023]
Abstract
Addressing the looming global food security crisis requires the development of high-yielding crops. In agricultural soils, deficiency in the micronutrient copper significantly decreases grain yield in wheat (Triticum aestivum), a globally important crop. In cereals, grain yield is determined by inflorescence architecture, flower fertility, grain size, and weight. Whether copper is involved in these processes, and how it is delivered to the reproductive organs is not well understood. We show that copper deficiency alters not only the grain set but also flower development in both wheat and its recognized model, Brachypodium distachyon. We then show that the Brachypodium yellow stripe-like 3 (YSL3) transporter localizes to the phloem, transports copper in frog (Xenopus laevis) oocytes, and facilitates copper delivery to reproductive organs and grains. Failure to deliver copper, but not iron, zinc, or manganese to these structures in the ysl3 CRISPR-Cas9 mutant results in delayed flowering, altered inflorescence architecture, reduced floret fertility, grain size, weight, and protein accumulation. These defects are rescued by copper supplementation and are complemented by YSL3 cDNA. This knowledge will help to devise sustainable approaches for improving grain yield in regions where soil quality is a major obstacle for crop production. Copper distribution by a phloem-localized transporter is essential for the transition to flowering, inflorescence architecture, floret fertility, size, weight, and protein accumulation in seeds.
Collapse
Affiliation(s)
- Huajin Sheng
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Yulin Jiang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Maryam Rahmati
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Ju-Chen Chia
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Tatyana Dokuchayeva
- Cornell Nutrient Analysis Laboratory, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Yana Kavulych
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Department of Biology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Tetiana-Olena Zavodna
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Patrick N Mendoza
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Rong Huang
- Cornell University, Cornell High Energy Synchrotron Source (CHESS), Ithaca, NY 14853, USA
| | - Louisa M Smieshka
- Cornell University, Cornell High Energy Synchrotron Source (CHESS), Ithaca, NY 14853, USA
| | - Julia Miller
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853, USA
| | - Arthur R Woll
- Cornell University, Cornell High Energy Synchrotron Source (CHESS), Ithaca, NY 14853, USA
| | - Olga I Terek
- Department of Biology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Nataliya D Romanyuk
- Department of Biology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Miguel Piñeros
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853, USA
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Olena K Vatamaniuk
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Author for communication:
| |
Collapse
|
19
|
Shang Y, Yuan L, Di Z, Jia Y, Zhang Z, Li S, Xing L, Qi Z, Wang X, Zhu J, Hua W, Wu X, Zhu M, Li G, Li C. A CYC/TB1-type TCP transcription factor controls spikelet meristem identity in barley. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7118-7131. [PMID: 32915968 DOI: 10.1093/jxb/eraa416] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/09/2020] [Indexed: 05/08/2023]
Abstract
Barley possesses a branchless, spike-shaped inflorescence where determinate spikelets attach directly to the main axis, but the developmental mechanism of spikelet identity remains largely unknown. Here we report the functional analysis of the barley gene BRANCHED AND INDETERMINATE SPIKELET 1 (BDI1), which encodes a TCP transcription factor and plays a crucial role in determining barley inflorescence architecture and spikelet development. The bdi1 mutant exhibited indeterminate spikelet meristems that continued to grow and differentiate after producing a floret meristem; some spikelet meristems at the base of the spike formed two fully developed seeds or converted to branched spikelets, producing a branched inflorescence. Map-based cloning analysis showed that this mutant has a deletion of ~600 kb on chromosome 5H containing three putative genes. Expression analysis and virus-induced gene silencing confirmed that the causative gene, BDI1, encodes a CYC/TB1-type TCP transcription factor and is highly conserved in both wild and cultivated barley. Transcriptome and regulatory network analysis demonstrated that BDI1 may integrate regulation of gene transcription cell wall modification and known trehalose-6-phosphate homeostasis to control spikelet development. Together, our findings reveal that BDI1 represents a key regulator of inflorescence architecture and meristem determinacy in cereal crop plants.
Collapse
Affiliation(s)
- Yi Shang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Lu Yuan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Zhaocan Di
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Yong Jia
- Western Barley Genetics Alliance, Murdoch University, Murdoch WA, Australia
| | - Zhenlan Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Sujuan Li
- Central Laboratory of Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Zengjun Qi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Xiaoyun Wang
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Jinghuan Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Wei Hua
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Xiaojian Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Minqiu Zhu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Gang Li
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- School of Agriculture, Food, and Wine, University of Adelaide, Waite campus, Urrbrae, South Australia, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China
| |
Collapse
|
20
|
Dobrovolskaya OB. Supernumerary Spikelet Wheat Forms as Models for Studying Genetic Regulation of Inflorescence Development. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420110034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
21
|
Sharma M, Saleh D, Charron JB, Jabaji S. A Crosstalk Between Brachypodium Root Exudates, Organic Acids, and Bacillus velezensis B26, a Growth Promoting Bacterium. Front Microbiol 2020; 11:575578. [PMID: 33123106 PMCID: PMC7573104 DOI: 10.3389/fmicb.2020.575578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are associated with plant roots and use organic compounds that are secreted from root exudates as food and energy source. Root exudates can chemoattract and help bacteria to colonize the surface of plant roots by inducing chemotactic responses of rhizospheric bacteria. In this study, we show that root colonization of Brachypodium distachyon by Bacillus velezensis strain B26 depends on several factors. These include root exudates, organic acids, and their biosynthetic genes, chemotaxis, biofilm formation and the induction of biofilm encoding genes. Analysis of root exudates by GC-MS identified five intermediates of the TCA cycle; malic, fumaric, citric, succinic, oxaloacetic acids, and were subsequently evaluated. The strongest chemotactic responses were induced by malic, succinic, citric, and fumaric acids. In comparison, the biofilm formation was induced by all organic acids with maximal induction by citric acid. Relative to the control, the individual organic acids, succinic and citric acids activated the epsD gene related to EPS biofilm, and also the genes encoding membrane protein (yqXM) and hydrophobin component (bslA) of the biofilm of strain B26. Whereas epsA and epsB genes were highly induced genes by succinic acid. Similarly, concentrated exudates released from inoculated roots after 48 h post-inoculation also induced all biofilm-associated genes. The addition of strain B26 to wild type and to icdh mutant line led to a slight induction but not biologically significant relative to their respective controls. Thus, B26 has no effect on the expression of the ICDH gene, both in the wild type and the mutant backgrounds. Our results indicate that root exudates and individual organic acids play an important role in selective recruitment and colonization of PGPR and inducing biofilm. The current study increases the understanding of molecular mechanisms behind biofilm induction by organic acids.
Collapse
Affiliation(s)
- Meha Sharma
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Dina Saleh
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Jean-Benoit Charron
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Suha Jabaji
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| |
Collapse
|
22
|
Molecular and genetic pathways for optimizing spikelet development and grain yield. ABIOTECH 2020; 1:276-292. [PMID: 36304128 PMCID: PMC9590455 DOI: 10.1007/s42994-020-00026-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/11/2020] [Indexed: 01/25/2023]
Abstract
The spikelet is a unique structure of inflorescence in grasses that generates one to many flowers depending on its determinate or indeterminate meristem activity. The growth patterns and number of spikelets, furthermore, define inflorescence architecture and yield. Therefore, understanding the molecular mechanisms underlying spikelet development and evolution are attractive to both biologists and breeders. Based on the progress in rice and maize, along with increasing numbers of genetic mutants and genome sequences from other grass families, the regulatory networks underpinning spikelet development are becoming clearer. This is particularly evident for domesticated traits in agriculture. This review focuses on recent progress on spikelet initiation, and spikelet and floret fertility, by comparing results from Arabidopsis with that of rice, sorghum, maize, barley, wheat, Brachypodium distachyon, and Setaria viridis. This progress may benefit genetic engineering and molecular breeding to enhance grain yield.
Collapse
|
23
|
Guo T, Lu ZQ, Shan JX, Ye WW, Dong NQ, Lin HX. ERECTA1 Acts Upstream of the OsMKKK10-OsMKK4-OsMPK6 Cascade to Control Spikelet Number by Regulating Cytokinin Metabolism in Rice. THE PLANT CELL 2020; 32:2763-2779. [PMID: 32616661 PMCID: PMC7474279 DOI: 10.1105/tpc.20.00351] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 05/20/2023]
Abstract
Grain number is a flexible trait that strongly contributes to grain yield. In rice (Oryza sativa), the OsMKKK10-OsMKK4-OsMPK6 cascade, which is negatively regulated by the dual-specificity phosphatase GSN1, coordinates the trade-off between grain number and grain size. However, the specific components upstream and downstream of the GSN1-MAPK module that regulate spikelet number per panicle remain obscure. Here, we report that ERECTA1 (OsER1), a negative regulator of spikelet number per panicle, acts upstream of the OsMKKK10-OsMKK4-OsMPK6 cascade and that the OsER1-OsMKKK10-OsMKK4-OsMPK6 pathway is required to maintain cytokinin homeostasis. OsMPK6 directly interacts with and phosphorylates the zinc finger transcription factor DST to enhance its transcriptional activation of CYTOKININ OXIDASE2 (OsCKX2), indicating that the OsER1-OsMKKK10-OsMKK4-OsMPK6 pathway shapes panicle morphology by regulating cytokinin metabolism. Furthermore, overexpression of either DST or OsCKX2 rescued the spikelet number phenotype of the oser1, osmkkk10, osmkk4, and osmpk6 mutants, suggesting that the DST-OsCKX2 module genetically functions downstream of the OsER1-OsMKKK10-OsMKK4-OsMPK6 pathway. These findings reveal specific crosstalk between a MAPK signaling pathway and cytokinin metabolism, shedding light on how developmental signals modulate phytohormone homeostasis to shape the inflorescence.
Collapse
Affiliation(s)
- Tao Guo
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
24
|
Magne K, Liu S, Massot S, Dalmais M, Morin H, Sibout R, Bendahmane A, Ratet P. Roles of BdUNICULME4 and BdLAXATUM-A in the non-domesticated grass Brachypodium distachyon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:645-659. [PMID: 32343459 DOI: 10.1111/tpj.14758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/11/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
In cultivated grasses, tillering, spike architecture and seed shattering represent major agronomical traits. In barley, maize and rice, the NOOT-BOP-COCH-LIKE (NBCL) genes play important roles in development, especially in ligule development, tillering and flower identity. However, compared with dicots, the role of grass NBCL genes is underinvestigated. To better understand the role of grass NBCLs and to overcome any effects of domestication that might conceal their original functions, we studied TILLING nbcl mutants in the non-domesticated grass Brachypodium distachyon. In B. distachyon, the NBCL genes BdUNICULME4 (CUL4) and BdLAXATUM-A (LAXA) are orthologous, respectively, to the barley HvUniculme4 and HvLaxatum-a, to the maize Zmtassels replace upper ears1 and Zmtassels replace upper ears2 and to the rice OsBLADE-ON-PETIOLE1 and OsBLADE-ON-PETIOLE2/3. In B. distachyon, our reverse genetics study shows that CUL4 is not essential for the establishment of the blade-sheath boundary but is necessary for the development of the ligule and auricles. We report that CUL4 also exerts a positive role in tillering and a negative role in spikelet meristem activity. On the other hand, we demonstrate that LAXA plays a negative role in tillering, positively participates in spikelet development and contributes to the control of floral organ number and identity. In this work, we functionally characterized two new NBCL genes in a context of non-domesticated grass and highlighted original roles for grass NBCL genes that are related to important agronomical traits.
Collapse
Affiliation(s)
- Kévin Magne
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| | - Shengbin Liu
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| | - Sophie Massot
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| | - Marion Dalmais
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| | - Halima Morin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| | - Richard Sibout
- Institut Jean-Pierre Bourgin, UMR 1318, INRAE, AgroParisTech, CNRS, Université Paris-Saclay, Versailles Cedex, France
- INRAE, UR BIA, F-44316, Nantes, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| | - Pascal Ratet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| |
Collapse
|
25
|
Zhu Y, Wagner D. Plant Inflorescence Architecture: The Formation, Activity, and Fate of Axillary Meristems. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a034652. [PMID: 31308142 DOI: 10.1101/cshperspect.a034652] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The above-ground plant body in different plant species can have very distinct forms or architectures that arise by recurrent redeployment of a finite set of building blocks-leaves with axillary meristems, stems or branches, and flowers. The unique architectures of plant inflorescences in different plant families and species, on which this review focuses, determine the reproductive success and yield of wild and cultivated plants. Major contributors to the inflorescence architecture are the activity and developmental trajectories adopted by axillary meristems, which determine the degree of branching and the number of flowers formed. Recent advances in genetic and molecular analyses in diverse flowering plants have uncovered both common regulatory principles and unique players and/or regulatory interactions that underlie inflorescence architecture. Modulating activity of these regulators has already led to yield increases in the field. Additional insight into the underlying regulatory interactions and principles will not only uncover how their rewiring resulted in altered plant form, but will also enhance efforts at optimizing plant architecture in desirable ways in crop species.
Collapse
Affiliation(s)
- Yang Zhu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
26
|
Li J, Jiao Z, He R, Sun Y, Xu Q, Zhang J, Jiang Y, Li Q, Niu J. Gene Expression Profiles and microRNA Regulation Networks in Tiller Primordia, Stem Tips, and Young Spikes of Wheat Guomai 301. Genes (Basel) 2019; 10:genes10090686. [PMID: 31500166 PMCID: PMC6770858 DOI: 10.3390/genes10090686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/07/2019] [Accepted: 08/22/2019] [Indexed: 01/26/2023] Open
Abstract
Tillering and spike differentiation are two key events for wheat (Triticum aestivum L.). A study on the transcriptomes and microRNA group profiles of wheat at the two key developmental stages will bring insight into the molecular regulation mechanisms. Guomai 301 is a representative excellent new high yield wheat cultivar in the Henan province in China. The transcriptomes and microRNA (miRNA) groups of tiller primordia (TPs), stem tips (STs), and young spikes (YSs) in Guomai 301 were compared to each other. A total of 1741 tillering specifically expressed and 281 early spikes differentiating specifically expressed differentially expressed genes (DEGs) were identified. Six major expression profile clusters of tissue-specific DEGs for the three tissues were classified by gene co-expression analysis using K-means cluster. The ribosome (ko03010), photosynthesis-antenna proteins (ko00196), and plant hormone signal transduction (ko04075) were the main metabolic pathways in TPs, STs, and YSs, respectively. Similarly, 67 TP specifically expressed and 19 YS specifically expressed differentially expressed miRNAs were identified, 65 of them were novel. The roles of 3 well known miRNAs, tae-miR156, tae-miR164, and tae-miR167a, in post-transcriptional regulation were similar to that of other researches. There were 651 significant negative miRNA-mRNA interaction pairs in TPs and YSs, involving 63 differentially expressed miRNAs (fold change > 4) and 416 differentially expressed mRNAs. Among them 12 key known miRNAs and 16 novel miRNAs were further analyzed, and miRNA-mRNA regulatory networks during tillering and early spike differentiating were established.
Collapse
Affiliation(s)
- Junchang Li
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhixin Jiao
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruishi He
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Yulong Sun
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiaoqiao Xu
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Jing Zhang
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Yumei Jiang
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiaoyun Li
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| |
Collapse
|
27
|
Wu Q, Bai X, Zhao W, Shi X, Xiang D, Wan Y, Wu X, Sun Y, Zhao J, Peng L, Zhao G. Investigation into the underlying regulatory mechanisms shaping inflorescence architecture in Chenopodium quinoa. BMC Genomics 2019; 20:658. [PMID: 31419932 PMCID: PMC6698048 DOI: 10.1186/s12864-019-6027-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 08/12/2019] [Indexed: 11/10/2022] Open
Abstract
Background Inflorescence architecture is denoted by the spatial arrangement of various lateral branches and florets formed on them, which is shaped by a complex of regulators. Unveiling of the regulatory mechanisms underlying inflorescence architecture is pivotal for improving crop yield potential. Quinoa (Chenopodium quinoa Willd), a pseudo cereal originated from Andean region of South America, has been widely recognized as a functional super food due to its excellent nutritional elements. Increasing worldwide consumption of this crop urgently calls for its yield improvement. However, dissection of the regulatory networks underlying quinoa inflorescence patterning is lacking. Results In this study, we performed RNA-seq analysis on quinoa inflorescence samples collected from six developmental stages, yielding a total of 138.8 GB data. We screened 21,610 differentially expressed genes (DEGs) among all the stages through comparative analysis. Weighted Gene Co-Expression Network Analysis (WGCNA) was performed to categorize the DEGs into ten different modules. Subsequently, we placed emphasis on investigating the modules associated with none branched and branched inflorescence samples. We manually refined the coexpression networks with stringent edge weight cutoffs, and generated core networks using transcription factors and key inflorescence architecture related genes as seed nodes. The core networks were visualized and analyzed by Cytoscape to obtain hub genes in each network. Our finding indicates that the specific occurrence of B3, TALE, WOX, LSH, LFY, GRAS, bHLH, EIL, DOF, G2-like and YABBY family members in early reproductive stage modules, and of TFL, ERF, bZIP, HD-ZIP, C2H2, LBD, NAC, C3H, Nin-like and FAR1 family members in late reproductive stage modules, as well as the several different MADS subfamily members identified in both stages may account for shaping quinoa inflorescence architecture. Conclusion In this study we carried out comparative transcriptome analysis of six different stages quinoa inflorescences, and using WGCNA we obtained the most highly potential central hubs for shaping inflorescence. The data obtained from this study will enhance our understanding of the gene network regulating quinoa inflorescence architecture, as well will supply with valuable genetic resources for high-yield elite breeding in the future. Electronic supplementary material The online version of this article (10.1186/s12864-019-6027-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Qi Wu
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China. .,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Xue Bai
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Wei Zhao
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Xiaodong Shi
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Xiaoyong Wu
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Yanxia Sun
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jianglin Zhao
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.,National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| |
Collapse
|
28
|
Ali Z, Raza Q, Atif RM, Aslam U, Ajmal M, Chung G. Genetic and Molecular Control of Floral Organ Identity in Cereals. Int J Mol Sci 2019; 20:E2743. [PMID: 31167420 PMCID: PMC6600504 DOI: 10.3390/ijms20112743] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for yield improvement purposes in cereals, however, the exact genetic mechanism of floral organogenesis remains elusive due to their complex inflorescence architecture. Extensive molecular analyses of Arabidopsis and other plant genera and species have established the ABCDE floral organ identity model. According to this model, hierarchical combinatorial activities of A, B, C, D, and E classes of homeotic genes regulate the identity of different floral organs with partial conservation and partial diversification between eudicots and cereals. Here, we review the developmental role of A, B, C, D, and E gene classes and explore the recent advances in understanding the floral development and subsequent organ specification in major cereals with reference to model plants. Furthermore, we discuss the evolutionary relationships among known floral organ identity genes. This comparative overview of floral developmental genes and associated regulatory factors, within and between species, will provide a thorough understanding of underlying complex genetic and molecular control of flower development and floral organ identity, which can be helpful to devise innovative strategies for grain yield improvement in cereals.
Collapse
Affiliation(s)
- Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan 66000, Pakistan.
| | - Qasim Raza
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku 39020, Pakistan.
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Usman Aslam
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Ajmal
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea.
| |
Collapse
|
29
|
Koppolu R, Schnurbusch T. Developmental pathways for shaping spike inflorescence architecture in barley and wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:278-295. [PMID: 30609316 DOI: 10.1111/jipb.12771] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/18/2018] [Indexed: 05/19/2023]
Abstract
Grass species display a wide array of inflorescences ranging from highly branched compound/panicle inflorescences to unbranched spike inflorescences. The unbranched spike is a characteristic feature of the species of tribe Triticeae, including economically important crops, such as wheat and barley. In this review, we describe two important developmental genetic mechanisms regulating spike inflorescence architecture in barley and wheat. These include genetic regulation of (i) row-type pathway specific to Hordeum species and (ii) unbranched spike development in barley and wheat. For a comparative understanding, we describe the branched inflorescence phenotypes of rice and maize along with unbranched Triticeae inflorescences. In the end, we propose a simplified model describing a probable mechanism leading to unbranched spike formation in Triticeae species.
Collapse
Affiliation(s)
- Ravi Koppolu
- Independant HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - Thorsten Schnurbusch
- Independant HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, 06120 Halle, Germany
| |
Collapse
|
30
|
Dobrovolskaya OB, Dresvyannikova AE. Cereal inflorescence: features of morphology, development and genetic regulation of morphogenesis. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cereals (Poaceae Barnh.) are the largest family of monocotyledonous flowering plants growing on all continents and constituting a significant part of Earth's many ecological communities. The Poaceae includes many important crops, such as rice, maize, wheat, barley, and rye. The qualitative and quantitative characteristics of cereal inflorescences are directly related to yield and are determined by the features of inflorescence development. This review considers modern concepts of the morphology, development and genetic mechanisms regulating the cereal inflorescence development. A common feature of cereal inflorescences is a spikelet, a reduced branch that bears florets with a similar structure and common scheme of development in all cereals. The length and the structure of the main axis, the presence and type of lateral branches cause a great variety of cereal inflorescences. Complex cereal inflorescences are formed from meristems of several types. The transition from the activity of one meristem to another is a multi-step process. The genes involved in the control of the cereal inflorescence development have been identified using mutants (mainly maize and rice) with altered inflorescence and floret morphology; most of these genes regulate the initiation and fate of meristems. The presence of some genetic mechanisms in cereals confirms the models previously discovered in dicotyledonous plants; on the other hand, there are cereal-specific developmental processes that are controlled by new modules of genetic regulation, in particular, associated with the formation of a branched inflorescence. An important aspect is the presence of quantitative variability of traits under the control of developmental genes, which is a prerequisite for the use of weak alleles contributing to the variability of plant growth and yield in breeding programs (for example, genes of the CLAVATA signaling pathway).
Collapse
Affiliation(s)
- O. B. Dobrovolskaya
- Institute of Cytology and Genetics, SB RAS; All-Russian Plant Quarantine Centre
| | | |
Collapse
|
31
|
Huang Y, Zhao S, Fu Y, Sun H, Ma X, Tan L, Liu F, Sun X, Sun H, Gu P, Xie D, Sun C, Zhu Z. Variation in the regulatory region of FZP causes increases in secondary inflorescence branching and grain yield in rice domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:716-733. [PMID: 30101570 DOI: 10.1111/tpj.14062] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/09/2018] [Accepted: 08/06/2018] [Indexed: 05/08/2023]
Abstract
Inflorescence branching is a key agronomic trait determining rice yield. The primary branch of the ancestral wild rice (Oryza rufipogon Griff.) bears few grains, due to minimal secondary branching. By contrast, Oryza sativa cultivars have been selected to produce large panicles with more secondary branches. Here we showed that the CONTROL OF SECONDARY BRANCH 1 (COS1) gene, which is identical to FRIZZY PANICLE (FZP), plays an important role in the key transition from few secondary branches in wild rice to more secondary branches in domesticated rice cultivars. A 4-bp tandem repeat deletion approximately 2.7 kb upstream of FZP may affect the binding activities of auxin response factors to the FZP promoter, decrease the expression level of FZP and significantly enhance the number of secondary branches and grain yield in cultivated rice. Functional analyses showed that NARROW LEAF 1 (NAL1), a trypsin-like serine and cysteine protease, interacted with FZP and promoted its degradation. Consistently, downregulating FZP expression or upregulating NAL1 expression in the commercial cultivar Zhonghua 17 increased the number of secondary branches per panicle, grain number per panicle and grain yield per plant. Our findings not only provide insights into the molecular mechanism of increasing grain number and yield during rice domestication, but also offer favorable genes for improving the grain yield of rice.
Collapse
Affiliation(s)
- Yongyu Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Shuangshuang Zhao
- MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yongcai Fu
- MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Hengdi Sun
- State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xin Ma
- MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Lubin Tan
- MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Fengxia Liu
- State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xianyou Sun
- State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Hongying Sun
- State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Ping Gu
- State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Daoxin Xie
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zuofeng Zhu
- MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
32
|
O'Connor DL. Live Confocal Imaging of Brachypodium Spikelet Meristems. Bio Protoc 2018; 8:e3026. [PMID: 34395812 DOI: 10.21769/bioprotoc.3026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 11/02/2022] Open
Abstract
Live confocal imaging of fluorescent reporters and stains in plant meristems provides valuable measurements of gene expression, protein dynamics, cell polarity, cell division, and growth. The spikelet meristem in the grass Brachypodium distachyon (Brachypodium) is well suited to live imaging because of the ease of dissection, small meristem size, simple arrangement of organs, and because each plant provides abundant spikelet meristems. Brachypodium is also far easier to genetically transform than other grass species. Presented here is a protocol for the growth, staging, dissection, mounting, and imaging of Brachypodium spikelet meristems for live confocal imaging.
Collapse
Affiliation(s)
- Devin Lee O'Connor
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
33
|
Zhu C, Yang J, Box MS, Kellogg EA, Eveland AL. A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative Genomics. FRONTIERS IN PLANT SCIENCE 2018; 9:1309. [PMID: 30258452 PMCID: PMC6143762 DOI: 10.3389/fpls.2018.01309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/20/2018] [Indexed: 05/29/2023]
Abstract
The morphological and functional diversity of plant form is governed by dynamic gene regulatory networks. In cereal crops, grain and/or pollen-bearing inflorescences exhibit vast architectural diversity and developmental complexity, yet the underlying genetic framework is only partly known. Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report a detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.
Collapse
|
34
|
Zhang C, Simpson RJ, Kim CM, Warthmann N, Delhaize E, Dolan L, Byrne ME, Wu Y, Ryan PR. Do longer root hairs improve phosphorus uptake? Testing the hypothesis with transgenic Brachypodium distachyon lines overexpressing endogenous RSL genes. THE NEW PHYTOLOGIST 2018; 217:1654-1666. [PMID: 29341123 DOI: 10.1111/nph.14980] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/04/2017] [Indexed: 05/14/2023]
Abstract
Mutants without root hairs show reduced inorganic orthophosphate (Pi) uptake and compromised growth on soils when Pi availability is restricted. What is less clear is whether root hairs that are longer than wild-type provide an additional benefit to phosphorus (P) nutrition. This was tested using transgenic Brachypodium lines with longer root hairs. The lines were transformed with the endogenous BdRSL2 and BdRSL3 genes using either a constitutive promoter or a root hair-specific promoter. Plants were grown for 32 d in soil amended with various Pi concentrations. Plant biomass and P uptake were measured and genotypes were compared on the basis of critical Pi values and P uptake per unit root length. Ectopic expression of RSL2 and RSL3 increased root hair length three-fold but decreased plant biomass. Constitutive expression of BdRSL2, but not expression of BdRSL3, consistently improved P nutrition as measured by lowering the critical Pi values and increasing Pi uptake per unit root length. Increasing root hair length through breeding or biotechnology can improve P uptake efficiency if the pleotropic effects on plant biomass are avoided. Long root hairs, alone, appear to be insufficient to improve Pi uptake and need to be combined with other traits to benefit P nutrition.
Collapse
Affiliation(s)
- Chunyan Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Richard J Simpson
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Chul Min Kim
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Norman Warthmann
- College of Medicine, Biology and Environment, Australian National University, Canberra, ACT, 2601, Australia
| | - Emmanuel Delhaize
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Mary E Byrne
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Peter R Ryan
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| |
Collapse
|
35
|
Chandler JW. Class VIIIb APETALA2 Ethylene Response Factors in Plant Development. TRENDS IN PLANT SCIENCE 2018; 23:151-162. [PMID: 29074232 DOI: 10.1016/j.tplants.2017.09.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 05/21/2023]
Abstract
The APETALA2 (AP2) transcription factor superfamily in many plant species is extremely large. In addition to well-documented roles in stress responses, some AP2 members in arabidopsis, such as those of subgroup VIIIb, which includes DORNRÖSCHEN, DORNRÖSCHEN-LIKE, PUCHI, and LEAFY PETIOLE, are also important developmental regulators throughout the plant life cycle. Information is accumulating from orthologs of these proteins in important crop species that they influence key agronomic traits, such as the release of bud-burst in woody perennials and floral meristem identity and branching in cereals, and thereby represent potential for agronomic improvement. Given the increasing recognition of their developmental significance, this review highlights the function of these proteins and addresses their phylogenetic and evolutionary relationships.
Collapse
Affiliation(s)
- John W Chandler
- Institute for Developmental Biology, Cologne Biocenter, University of Cologne, Zuelpicher Strasse 47b, D-50674 Cologne, Germany.
| |
Collapse
|
36
|
|
37
|
Yang J, Thames S, Best NB, Jiang H, Huang P, Dilkes BP, Eveland AL. Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology in Setaria viridis. THE PLANT CELL 2018; 30:48-66. [PMID: 29263085 PMCID: PMC5810575 DOI: 10.1105/tpc.17.00816] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/20/2017] [Accepted: 12/13/2017] [Indexed: 05/08/2023]
Abstract
Inflorescence architecture is a key determinant of yield potential in many crops and is patterned by the organization and developmental fate of axillary meristems. In cereals, flowers and grain are borne from spikelets, which differentiate in the final iteration of axillary meristem branching. In Setaria spp, inflorescence branches terminate in either a spikelet or a sterile bristle, and these structures appear to be paired. In this work, we leverage Setaria viridis to investigate a role for the phytohormones brassinosteroids (BRs) in specifying bristle identity and maintaining spikelet meristem determinacy. We report the molecular identification and characterization of the Bristleless1 (Bsl1) locus in S. viridis, which encodes a rate-limiting enzyme in BR biosynthesis. Loss-of-function bsl1 mutants fail to initiate a bristle identity program, resulting in homeotic conversion of bristles to spikelets. In addition, spikelet meristem determinacy is altered in the mutants, which produce two florets per spikelet instead of one. Both of these phenotypes provide avenues for enhanced grain production in cereal crops. Our results indicate that the spatiotemporal restriction of BR biosynthesis at boundary domains influences meristem fate decisions during inflorescence development. The bsl1 mutants provide insight into the molecular basis underlying morphological variation in inflorescence architecture.
Collapse
Affiliation(s)
- Jiani Yang
- Donald Danforth Plant Science Center, Saint Louis, Missouri 63132
| | - Shuiyi Thames
- Donald Danforth Plant Science Center, Saint Louis, Missouri 63132
| | - Norman B Best
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
| | - Hui Jiang
- Donald Danforth Plant Science Center, Saint Louis, Missouri 63132
| | - Pu Huang
- Donald Danforth Plant Science Center, Saint Louis, Missouri 63132
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Andrea L Eveland
- Donald Danforth Plant Science Center, Saint Louis, Missouri 63132
| |
Collapse
|
38
|
Dobrovolskaya OB, Amagai Y, Popova KI, Dresvyannikova AE, Martinek P, Krasnikov AA, Watanabe N. Genes WHEAT FRIZZY PANICLE and SHAM RAMIFICATION 2 independently regulate differentiation of floral meristems in wheat. BMC PLANT BIOLOGY 2017; 17:252. [PMID: 29297328 PMCID: PMC5751757 DOI: 10.1186/s12870-017-1191-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
BACKGROUND Inflorescences of wheat species, spikes, are characteristically unbranched and bear one sessile spikelet at a spike rachis node. Development of supernumerary spikelets (SSs) at rachis nodes or on the extended rachillas is abnormal. Various wheat morphotypes with altered spike morphology, associated with the development of SSs, present an important genetic resource for studies on genetic regulation of wheat inflorescence development. RESULTS Here we characterized diploid and tetraploid wheat lines of various non-standard spike morphotypes, which allowed for identification of a new mutant allele of the WHEAT FRIZZY PANICLE (WFZP) gene that determines spike branching in diploid wheat Ttiticum monococcum L. Moreover, we found that the development of SSs and spike branching in wheat T. durum Desf. was a result of a wfzp-A/TtBH-A1 mutation that originated from spontaneous hybridization with T. turgidum convar. сompositum (L.f.) Filat. Detailed characterization of the false-true ramification phenotype controlled by the recessive sham ramification 2 (shr2) gene in tetraploid wheat T. turgidum L. allowed us to suggest putative functions of the SHR2 gene that may be involved in the regulation of spikelet meristem fate and in specification of floret meristems. The results of a gene interaction test suggested that genes WFZP and SHR2 function independently in different processes during spikelet development, whereas another spike ramification gene(s) interact(s) with SHR2 and share(s) common functions. CONCLUSIONS SS mutants represent an important genetic tool for research on the development of the wheat spikelet and for identification of genes that control meristem activities. Further studies on different non-standard SS morphotypes and wheat lines with altered spike morphology will allow researchers to identify new genes that control meristem identity and determinacy, to elucidate the interaction between the genes, and to understand how these genes, acting in concert, regulate the development of the wheat spike.
Collapse
Affiliation(s)
- Oxana B. Dobrovolskaya
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, Pirogova, 2, Novosibirsk, 630090 Russia
| | - Yumiko Amagai
- College of Agriculture, Ibaraki University, Ibaraki, Japan
| | - Karina I. Popova
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
| | - Alina E. Dresvyannikova
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, Pirogova, 2, Novosibirsk, 630090 Russia
| | | | | | | |
Collapse
|
39
|
O'Connor DL, Elton S, Ticchiarelli F, Hsia MM, Vogel JP, Leyser O. Cross-species functional diversity within the PIN auxin efflux protein family. eLife 2017; 6. [PMID: 29064367 PMCID: PMC5655145 DOI: 10.7554/elife.31804] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/12/2017] [Indexed: 01/21/2023] Open
Abstract
In Arabidopsis, development during flowering is coordinated by transport of the hormone auxin mediated by polar-localized PIN-FORMED1 (AtPIN1). However Arabidopsis has lost a PIN clade sister to AtPIN1, Sister-of-PIN1 (SoPIN1), which is conserved in flowering plants. We previously proposed that the AtPIN1 organ initiation and vein patterning functions are split between the SoPIN1 and PIN1 clades in grasses. Here we show that in the grass Brachypodium sopin1 mutants have organ initiation defects similar to Arabidopsis atpin1, while loss of PIN1 function in Brachypodium has little effect on organ initiation but alters stem growth. Heterologous expression of Brachypodium SoPIN1 and PIN1b in Arabidopsis provides further evidence of functional specificity. SoPIN1 but not PIN1b can mediate flower formation in null atpin1 mutants, although both can complement a missense allele. The behavior of SoPIN1 and PIN1b in Arabidopsis illustrates how membrane and tissue-level accumulation, transport activity, and interaction contribute to PIN functional specificity.
Collapse
Affiliation(s)
- Devin Lee O'Connor
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Samuel Elton
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | | | - Mon Mandy Hsia
- Western Regional Research Center, USDA-ARS, Albany, United States
| | - John P Vogel
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Ottoline Leyser
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
40
|
O'Connor DL, Elton S, Ticchiarelli F, Hsia MM, Vogel JP, Leyser O. Cross-species functional diversity within the PIN auxin efflux protein family. eLife 2017; 6:e31804. [PMID: 29064367 DOI: 10.7554/elife.31804.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/12/2017] [Indexed: 05/27/2023] Open
Abstract
In Arabidopsis, development during flowering is coordinated by transport of the hormone auxin mediated by polar-localized PIN-FORMED1 (AtPIN1). However Arabidopsis has lost a PIN clade sister to AtPIN1, Sister-of-PIN1 (SoPIN1), which is conserved in flowering plants. We previously proposed that the AtPIN1 organ initiation and vein patterning functions are split between the SoPIN1 and PIN1 clades in grasses. Here we show that in the grass Brachypodium sopin1 mutants have organ initiation defects similar to Arabidopsis atpin1, while loss of PIN1 function in Brachypodium has little effect on organ initiation but alters stem growth. Heterologous expression of Brachypodium SoPIN1 and PIN1b in Arabidopsis provides further evidence of functional specificity. SoPIN1 but not PIN1b can mediate flower formation in null atpin1 mutants, although both can complement a missense allele. The behavior of SoPIN1 and PIN1b in Arabidopsis illustrates how membrane and tissue-level accumulation, transport activity, and interaction contribute to PIN functional specificity.
Collapse
Affiliation(s)
- Devin Lee O'Connor
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Samuel Elton
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | | | - Mon Mandy Hsia
- Western Regional Research Center, USDA-ARS, Albany, United States
| | - John P Vogel
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Ottoline Leyser
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
41
|
Grass inflorescence architecture and meristem determinacy. Semin Cell Dev Biol 2017; 79:37-47. [PMID: 29020602 DOI: 10.1016/j.semcdb.2017.10.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 11/22/2022]
Abstract
The grass inflorescence is striking not only for its beauty and diversity, but also for its developmental complexity. While models of inflorescence architecture have been proposed in both eudicots and grasses, these are inadequate to fully explain the complex branching events that occur during the development of the grass inflorescence. Key to understanding grass inflorescence architecture is the meristem determinacy/indeterminacy decision, which regulates the number of branching events that occur. Here we review what has been learned about meristem determinacy from grass mutants with defects in inflorescence development. A picture is emerging of a complex network of signaling molecules and meristem identity factors that interact to regulate inflorescence meristem activity, many of which have been modified during crop domestication directly affecting yield traits.
Collapse
|
42
|
Wang Y, Yu H, Tian C, Sajjad M, Gao C, Tong Y, Wang X, Jiao Y. Transcriptome Association Identifies Regulators of Wheat Spike Architecture. PLANT PHYSIOLOGY 2017; 175:746-757. [PMID: 28807930 PMCID: PMC5619896 DOI: 10.1104/pp.17.00694] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/11/2017] [Indexed: 05/20/2023]
Abstract
The architecture of wheat (Triticum aestivum) inflorescence and its complexity is among the most important agronomic traits that influence yield. For example, wheat spikes vary considerably in the number of spikelets, which are specialized reproductive branches, and the number of florets, which are spikelet branches that produce seeds. The large and repetitive nature of the three homologous and highly similar subgenomes of wheat has impeded attempts at using genetic approaches to uncover beneficial alleles that can be utilized for yield improvement. Using a population-associative transcriptomic approach, we analyzed the transcriptomes of developing spikes in 90 wheat lines comprising 74 landrace and 16 elite varieties and correlated expression with variations in spike complexity traits. In combination with coexpression network analysis, we inferred the identities of genes related to spike complexity. Importantly, further experimental studies identified regulatory genes whose expression is associated with and influences spike complexity. The associative transcriptomic approach utilized in this study allows rapid identification of the genetic basis of important agronomic traits in crops with complex genomes.
Collapse
Affiliation(s)
- Yuange Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haopeng Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caihuan Tian
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Muhammad Sajjad
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangfeng Wang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
43
|
Whipple CJ. Grass inflorescence architecture and evolution: the origin of novel signaling centers. THE NEW PHYTOLOGIST 2017; 216:367-372. [PMID: 28375574 DOI: 10.1111/nph.14538] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/10/2017] [Indexed: 05/18/2023]
Abstract
Contents 367 I. 367 II. 368 III. 370 IV. 371 371 References 371 SUMMARY: A central goal of evo-devo is to understand how morphological diversity arises from existing developmental mechanisms, requiring a clear, predictive explanatory framework of the underlying developmental mechanisms. Despite an ever-increasing literature on genes regulating grass inflorescence development, an effective model of inflorescence patterning is lacking. I argue that the existing framework for grass inflorescence development, which invokes homeotic shifts in multiple distinct meristem identities, obscures a recurring theme emerging from developmental genetic studies in grass models, that is that inflorescence branching is regulated by novel localized signaling centers. Understanding the origin and function of these novel signaling centers will be key to future evo-devo work on the grass inflorescence.
Collapse
Affiliation(s)
- Clinton J Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT, 84602, USA
| |
Collapse
|
44
|
Liu J, Cheng X, Liu P, Sun J. miR156-Targeted SBP-Box Transcription Factors Interact with DWARF53 to Regulate TEOSINTE BRANCHED1 and BARREN STALK1 Expression in Bread Wheat. PLANT PHYSIOLOGY 2017; 174:1931-1948. [PMID: 28526703 PMCID: PMC5490914 DOI: 10.1104/pp.17.00445] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/16/2017] [Indexed: 05/18/2023]
Abstract
Genetic and environmental factors affect bread wheat (Triticum aestivum) plant architecture, which determines grain yield. In this study, we demonstrate that miR156 controls bread wheat plant architecture. We show that overexpression of tae-miR156 in bread wheat cultivar Kenong199 leads to increased tiller number and severe defects in spikelet formation, probably due to the tae-miR156-mediated repression of a group of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes. Furthermore, we found that the expression of two genes TEOSINTE BRANCHED1 (TaTB1) and BARREN STALK1 (TaBA1), whose orthologous genes in diverse plant species play conserved roles in regulating plant architecture, is markedly reduced in the tae-miR156-OE bread wheat plants. Significantly, we demonstrate that the strigolactone (SL) signaling repressor DWARF53 (TaD53), which physically associates with the transcriptional corepressor TOPLESS, can directly interact with the N-terminal domains of miR156-controlled TaSPL3/17. Most importantly, TaSPL3/17-mediated transcriptional activation of TaBA1 and TaTB1 can be largely repressed by TaD53 in the transient expression system. Our results reveal potential association between miR156-TaSPLs and SL signaling pathways during bread wheat tillering and spikelet development.
Collapse
Affiliation(s)
- Jie Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiliu Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pan Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
45
|
Chandler JW, Werr W. DORNRÖSCHEN, DORNRÖSCHEN-LIKE, and PUCHI redundantly control floral meristem identity and organ initiation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3457-3472. [PMID: 28859377 DOI: 10.1093/jxb/erx208] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/26/2017] [Indexed: 05/02/2023]
Abstract
The biphasic floral transition in Arabidopsis thaliana involves many redundant intersecting regulatory networks. The related AP2 transcription factors DORNRÖSCHEN (DRN), DORNRÖSCHEN-LIKE (DRNL), and PUCHI individually execute well-characterized functions in diverse developmental contexts, including floral development. Here, we show that their combined loss of function leads to synergistic floral phenotypes, including reduced floral merosity in all whorls, which reflects redundant functions of all three genes in organ initiation rather than outgrowth. Additional loss of BLADE-ON-PETIOLE1 (BOP1) and BOP2 functions results in the complete conversion of floral meristems into secondary inflorescence shoots, demonstrating that all five genes define an essential regulatory network for establishing floral meristem identity, and we show that their functions converge to regulate LEAFY expression. Thus, despite their largely discrete spatiotemporal expression domains in the inflorescence meristem and early floral meristem, PUCHI, DRN, and DRNL interdependently contribute to cellular fate decisions. Auxin might represent one potential non-cell-autonomous mediator of their gene functions, because PUCHI, DRN, and DRNL all interact with auxin transport and biosynthesis pathways.
Collapse
Affiliation(s)
- J W Chandler
- Institute of Developmental Biology, Cologne Biocenter, University of Cologne, Germany
| | - W Werr
- Institute of Developmental Biology, Cologne Biocenter, University of Cologne, Germany
| |
Collapse
|
46
|
Kus A, Kwasniewska J, Hasterok R. Brachypodium distachyon - A Useful Model in the Qualification of Mutagen-Induced Micronuclei Using Multicolor FISH. PLoS One 2017; 12:e0170618. [PMID: 28118403 PMCID: PMC5261735 DOI: 10.1371/journal.pone.0170618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/15/2016] [Indexed: 12/21/2022] Open
Abstract
Brachypodium distachyon (Brachypodium) is now intensively utilized as a model grass species in various biological studies. Its favorable cytological features create a unique foundation for a convenient system in mutagenesis, thereby potentially enabling the 'hot spots' and 'cold spots' of DNA damage in its genome to be analyzed. The aim of this study was to analyze the involvement of 5S rDNA, 25S rDNA, the Arabidopsis-type (TTTAGGG)n telomeric sequence and the Brachypodium-originated centromeric BAC clone CB33J12 in the micronuclei formation in Brachypodium root tip cells that were subjected to the chemical clastogenic agent maleic hydrazide (MH). To the best of our knowledge, this is the first use of a multicolor fluorescence in situ hybridization (mFISH) with four different DNA probes being used simultaneously to study plant mutagenesis. A quantitative analysis allowed ten types of micronuclei, which were characterized by the presence or absence of specific FISH signal(s), to be distinguished, thus enabling some specific rules governing the composition of the MH-induced micronuclei with the majority of them originating from the terminal regions of chromosomes, to be identified. The application of rDNA sequences as probes showed that 5S rDNA-bearing chromosomes are involved in micronuclei formation more frequently than the 25S rDNA-bearing chromosomes. These findings demonstrate the promising potential of Brachypodium to be a useful model organism to analyze the effects of various genotoxic agents on the plant nuclear genome stability, especially when the complex FISH-based and chromosome-specific approaches such as chromosome barcoding and chromosome painting will be applied in future studies.
Collapse
Affiliation(s)
- Arita Kus
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Jolanta Kwasniewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
- * E-mail:
| |
Collapse
|
47
|
Hu Y, Liang W, Yin C, Yang X, Ping B, Li A, Jia R, Chen M, Luo Z, Cai Q, Zhao X, Zhang D, Yuan Z. Interactions of OsMADS1 with Floral Homeotic Genes in Rice Flower Development. MOLECULAR PLANT 2015; 8:1366-84. [PMID: 25917758 DOI: 10.1016/j.molp.2015.04.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 04/05/2015] [Accepted: 04/16/2015] [Indexed: 05/23/2023]
Abstract
During reproductive development, rice plants develop unique flower organs which determine the final grain yield. OsMADS1, one of SEPALLATA-like MADS-box genes, has been unraveled to play critical roles in rice floral organ identity specification and floral meristem determinacy. However, the molecular mechanisms underlying interactions of OsMADS1 with other floral homeotic genes in regulating flower development remains largely elusive. In this work, we studied the genetic interactions of OsMADS1 with B-, C-, and D-class genes along with physical interactions among their proteins. We show that the physical and genetic interactions between OsMADS1 and OsMADS3 are essential for floral meristem activity maintenance and organ identity specification; while OsMADS1 physically and genetically interacts with OsMADS58 in regulating floral meristem determinacy and suppressing spikelet meristem reversion. We provided important genetic evidence to support the neofunctionalization of two rice C-class genes (OsMADS3 and OsMADS58) during flower development. Gene expression profiling and quantitative RT-PCR analyses further revealed that OsMADS1 affects the expression of many genes involved in floral identity and hormone signaling, and chromatin immunoprecipitation (ChIP)-PCR assay further demonstrated that OsMADS17 is a direct target gene of OsMADS1. Taken together, these results reveal that OsMADS1 has diversified regulatory functions in specifying rice floral organ and meristem identity, probably through its genetic and physical interactions with different floral homeotic regulators.
Collapse
Affiliation(s)
- Yun Hu
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Wanqi Liang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Changsong Yin
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Xuelian Yang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Baozhe Ping
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Anxue Li
- Shanghai Ocean University, Shanghai 201306, China
| | - Ru Jia
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Mingjiao Chen
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Zhijing Luo
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Xiangxiang Zhao
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian 223300, China
| | - Dabing Zhang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China; School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Zheng Yuan
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China.
| |
Collapse
|
48
|
Poursarebani N, Seidensticker T, Koppolu R, Trautewig C, Gawroński P, Bini F, Govind G, Rutten T, Sakuma S, Tagiri A, Wolde GM, Youssef HM, Battal A, Ciannamea S, Fusca T, Nussbaumer T, Pozzi C, Börner A, Lundqvist U, Komatsuda T, Salvi S, Tuberosa R, Uauy C, Sreenivasulu N, Rossini L, Schnurbusch T. The Genetic Basis of Composite Spike Form in Barley and 'Miracle-Wheat'. Genetics 2015; 201:155-65. [PMID: 26156223 PMCID: PMC4566260 DOI: 10.1534/genetics.115.176628] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 06/27/2015] [Indexed: 12/21/2022] Open
Abstract
Inflorescences of the tribe Triticeae, which includes wheat (Triticum sp. L.) and barley (Hordeum vulgare L.) are characterized by sessile spikelets directly borne on the main axis, thus forming a branchless spike. 'Compositum-Barley' and tetraploid 'Miracle-Wheat' (T. turgidum convar. compositum (L.f.) Filat.) display noncanonical spike-branching in which spikelets are replaced by lateral branch-like structures resembling small-sized secondary spikes. As a result of this branch formation 'Miracle-Wheat' produces significantly more grains per spike, leading to higher spike yield. In this study, we first isolated the gene underlying spike-branching in 'Compositum-Barley,' i.e., compositum 2 (com2). Moreover, we found that COM2 is orthologous to the branched head(t) (bh(t)) locus regulating spike branching in tetraploid 'Miracle-Wheat.' Both genes possess orthologs with similar functions in maize BRANCHED SILKLESS 1 (BD1) and rice FRIZZY PANICLE/BRANCHED FLORETLESS 1 (FZP/BFL1) encoding AP2/ERF transcription factors. Sequence analysis of the bh(t) locus in a collection of mutant and wild-type tetraploid wheat accessions revealed that a single amino acid substitution in the DNA-binding domain gave rise to the domestication of 'Miracle-Wheat.' mRNA in situ hybridization, microarray experiments, and independent qRT-PCR validation analyses revealed that the branch repression pathway in barley is governed through the spike architecture gene Six-rowed spike 4 regulating COM2 expression, while HvIDS1 (barley ortholog of maize INDETERMINATE SPIKELET 1) is a putative downstream target of COM2. These findings presented here provide new insights into the genetic basis of spike architecture in Triticeae, and have disclosed new targets for genetic manipulations aiming at boosting wheat's yield potential.
Collapse
Affiliation(s)
- Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Tina Seidensticker
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Corinna Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Piotr Gawroński
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Federica Bini
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Geetha Govind
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Shun Sakuma
- National Institute of Agrobiological Sciences, Plant Genome Research Unit, Tsukuba 305 8602, Japan
| | - Akemi Tagiri
- National Institute of Agrobiological Sciences, Plant Genome Research Unit, Tsukuba 305 8602, Japan
| | - Gizaw M Wolde
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Helmy M Youssef
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Abdulhamit Battal
- John Innes Centre, Department of Crop Genetics, Colney, Norwich, NR4 7UH, United Kingdom Biological Sciences, Middle East Technical University, Cankaya, 06800, Ankara, Turkey
| | | | | | - Thomas Nussbaumer
- Plant Genome and Systems Biology, Helmholtz Center Munich, D-85764, Neuherberg, Germany
| | | | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Udda Lundqvist
- Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Plant Genome Research Unit, Tsukuba 305 8602, Japan
| | - Silvio Salvi
- Dipartimento di Scienze Agrarie, University of Bologna, 40127 Bologna, Italy
| | - Roberto Tuberosa
- Dipartimento di Scienze Agrarie, University of Bologna, 40127 Bologna, Italy
| | - Cristobal Uauy
- John Innes Centre, Department of Crop Genetics, Colney, Norwich, NR4 7UH, United Kingdom
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Laura Rossini
- Parco Tecnologico Padano, 26900 Lodi, Italy Università degli Studi di Milano, DiSAA, I-20133 Milan, Italy
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, D-06466 Stadt Seeland, Germany
| |
Collapse
|
49
|
Abstract
Axillary meristems play an important role in determining final plant architecture and floral structures. Tomato Ls, Arabidopsis LAS and rice MOC1 are orthologous genes regulating axillary meristem initiation and outgrowth. Their functions are generally conserved but the functional specificities are divergent among species. Obvious differences between rice panicles and wheat spikes suggest the divergent functions of MOC1 and its wheat ortholog. We show that TaMOC1 might be involved in wheat spikelet development. TaMOC1 is a typical nucleus localized protein with transcriptional activation abilities. The variable N-termini of TaMOC1 protein is necessary for transcriptional activation. TaMOC1 is highly expressed in ears with length of 2, 3 and 6 cm. Significant associations between the TaMOC1-7A haplotype and spikelet number per spike were observed in ten environments over 3 years and 2 sites. TaMOC1-7A HapH, a favored haplotype acquired during wheat polyploidization, may make a positive contribution to spikelet number per spike. Based on evolutionary analysis, geographic distribution and frequency changes, TaMOC1-7A HapH might be associated with wheat domestication and Chinese wheat breeding history. The pyramiding favorable alleles of TaMOC1-7A HapH and TaSnRK2.10 (C, associated with higher TGW) can improve both spikelet number per spike and TGW simultaneously.
Collapse
|
50
|
Chemical and Radiation Mutagenesis: Induction and Detection by Whole Genome Sequencing. GENETICS AND GENOMICS OF BRACHYPODIUM 2015. [DOI: 10.1007/7397_2015_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|