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Qiao L, Wu Q, Yuan L, Huang X, Yang Y, Li Q, Shahzad N, Li H, Li W. SMALL PLANT AND ORGAN 1 ( SPO1) Encoding a Cellulose Synthase-like Protein D4 (OsCSLD4) Is an Important Regulator for Plant Architecture and Organ Size in Rice. Int J Mol Sci 2023; 24:16974. [PMID: 38069299 PMCID: PMC10707047 DOI: 10.3390/ijms242316974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and characterized the small plant and organ 1 (spo1) mutant in rice (Oryza sativa), which exhibits narrow and rolled leaf, reductions in plant height, root length, and grain width, and other morphological defects. Map-based cloning revealed that SPO1 is allelic with OsCSLD4, a gene encoding the cellulose synthase-like protein D4, and is highly expressed in the roots at the seedling and tillering stages. Microscopic observation revealed the spo1 mutant had reduced number and width in leaf veins, smaller size of leaf bulliform cells, reduced cell length and cell area in the culm, and decreased width of epidermal cells in the outer glume of the grain. These results indicate the role of SPO1 in modulating cell division and cell expansion, which modulates plant architecture and organ size. It is showed that the contents of endogenous hormones including auxin, abscisic acid, gibberellin, and zeatin tested in the spo1 mutant were significantly altered, compared to the wild type. Furthermore, the transcriptome analysis revealed that the differentially expressed genes (DEGs) are significantly enriched in the pathways associated with plant hormone signal transduction, cell cycle progression, and cell wall formation. These results indicated that the loss of SPO1/OsCSLD4 function disrupted cell wall cellulose synthase and hormones homeostasis and signaling, thus leading to smaller plant and organ size in spo1. Taken together, we suggest the functional role of SPO1/OsCSLD4 in the control of rice plant and organ size by modulating cell division and expansion, likely through the effects of multiple hormonal pathways on cell wall formation.
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Affiliation(s)
- Lei Qiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Qilong Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Liuzhen Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Xudong Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Yutao Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Qinying Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Nida Shahzad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Haifeng Li
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Wenqiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
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OsARF11 Promotes Growth, Meristem, Seed, and Vein Formation during Rice Plant Development. Int J Mol Sci 2021; 22:ijms22084089. [PMID: 33920962 PMCID: PMC8071273 DOI: 10.3390/ijms22084089] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022] Open
Abstract
The plant hormone auxin acts as a mediator providing positional instructions in a range of developmental processes. Studies in Arabidopsis thaliana L. show that auxin acts in large part via activation of Auxin Response Factors (ARFs) that in turn regulate the expression of downstream genes. The rice (Oryza sativa L.) gene OsARF11 is of interest because of its expression in developing rice organs and its high sequence similarity with MONOPTEROS/ARF5, a gene with prominent roles in A. thaliana development. We have assessed the phenotype of homozygous insertion mutants in the OsARF11 gene and found that in relation to wildtype, osarf11 seedlings produced fewer and shorter roots as well as shorter and less wide leaves. Leaves developed fewer veins and larger areoles. Mature osarf11 plants had a reduced root system, fewer branches per panicle, fewer grains per panicle and fewer filled seeds. Mutants had a reduced sensitivity to auxin-mediated callus formation and inhibition of root elongation, and phenylboronic acid (PBA)-mediated inhibition of vein formation. Taken together, our results implicate OsARF11 in auxin-mediated growth of multiple organs and leaf veins. OsARF11 also appears to play a central role in the formation of lateral root, panicle branch, and grain meristems.
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Moin M, Bakshi A, Madhav MS, Kirti PB. Cas9/sgRNA-based genome editing and other reverse genetic approaches for functional genomic studies in rice. Brief Funct Genomics 2018; 17:339-351. [PMID: 29579147 DOI: 10.1093/bfgp/ely010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
One of the important and direct ways of investigating the function of a gene is to characterize the phenotypic consequences associated with loss or gain-of-function of the corresponding gene. These mutagenesis strategies have been successfully deployed in Arabidopsis, and subsequently extended to crop species including rice. Researchers have made vast advancements in the area of rice genomics and functional genomics, as it is a diploid plant with a relatively smaller genome size unlike other cereals. The advent of rice genome research and the annotation of high-quality genome sequencing along with the developments in databases and computer searches have enabled the functional characterization of unknown genes in rice. Further, with the improvements in the efficiency of regeneration and transformation protocols, it has now become feasible to produce sizable mutant populations in indica rice varieties also. In this review, various mutagenesis methods, the current status of the mutant resources, limitations and strengths of insertional mutagenesis approaches and also results obtained with suitable screens for stress tolerance in rice are discussed. In addition, targeted genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or Cas9/single-guide RNA system and its potential applications in generating transgene-free rice plants through genome engineering as an efficient alternative to classical transgenic technology are also discussed.
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Affiliation(s)
- Mazahar Moin
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), India
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Achala Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - M S Madhav
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Qiao L, Zhang W, Li X, Zhang L, Zhang X, Li X, Guo H, Ren Y, Zheng J, Chang Z. Characterization and Expression Patterns of Auxin Response Factors in Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1395. [PMID: 30283490 PMCID: PMC6157421 DOI: 10.3389/fpls.2018.01395] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 09/03/2018] [Indexed: 05/22/2023]
Abstract
Auxin response factors (ARFs) are important transcription factors involved in both the auxin signaling pathway and the regulatory development of various plant organs. In this study, 23 TaARF members encoded by a total of 68 homeoalleles were isolated from 18 wheat chromosomes (excluding chromosome 4). The TaARFs, including their conserved domains, exon/intron structures, related microRNAs, and alternative splicing (AS) variants, were then characterized. Phylogenetic analysis revealed that members of the TaARF family share close homology with ARFs in other grass species. qRT-PCR analyses revealed that 20 TaARF members were expressed in different organs and tissues and that the expression of some members significantly differed in the roots, stems, and leaves of wheat seedlings in response to exogenous auxin treatment. Moreover, protein network analyses and co-expression results showed that TaTIR1-TaARF15/18/19-TaIAA13 may interact at both the protein and genetic levels. The results of subsequent evolutionary analyses showed that three transcripts of TaARF15 in the A subgenome of wheat exhibited high evolutionary rate and underwent positive selection. Transgenic analyses indicated that TaARF15-A.1 promoted the growth of roots and leaves of Arabidopsis thaliana and was upregulated in the overexpression plants after auxin treatment. Our results will provide reference information for subsequent research and utilization of the TaARF gene family.
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Affiliation(s)
- Linyi Qiao
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Wenping Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyan Li
- Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital Affiliated with the Capital Medical University, Beijing, China
| | - Lei Zhang
- Department of Plant Protection, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Xiaojun Zhang
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xin Li
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Huijuan Guo
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yuan Ren
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Jun Zheng
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- *Correspondence: Jun Zheng, Zhijian Chang,
| | - Zhijian Chang
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- *Correspondence: Jun Zheng, Zhijian Chang,
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Wu L, Tian Z, Zhang J. Functional Dissection of Auxin Response Factors in Regulating Tomato Leaf Shape Development. FRONTIERS IN PLANT SCIENCE 2018; 9:957. [PMID: 30022995 PMCID: PMC6040142 DOI: 10.3389/fpls.2018.00957] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/14/2018] [Indexed: 05/08/2023]
Abstract
The phytohormone auxin is involved in many aspects of plant growth and developmental processes. The tomato Aux/IAA transcription factor SlIAA9/ENTIRE/E plays an important role in leaf morphogenesis and fruit development, and the E gene encodes a protein from the Aux/IAA family of auxin response repressors. Both SlIAA9-RNAi transgenic and entire (e) mutant plants reduce the leaf complexity in tomato, but the underlying mechanism is not yet completely resolved. Auxin signaling is known to regulate target genes expression via Aux/IAA and ARFs (auxin response factors) transcriptional regulators. ARFs mediate a wide range of developmental processes. Through an Y2H (yeast two-hybrid) assay coupled with expression profiling of the SlARF genes family, we identified a group of ARFs: SlARF6A, SlARF8A, SlARF8B, and SlARF24. Pull-down and BiFC (Bimolecular Fluorescence Complementation) results demonstrated that these SlARFs interact with SlIAA9 in vitro and in vivo, and the e mutation altered the expression patterns of multiple SlARFs. The simple leaves of the e mutant were partially converted to wild-type compound leaves by VIGS (virus-induced gene silencing) of these four SlARFs. Furthermore, IAA content in these samples was significantly increased compared to the e mutant. In addition, SlARF6A and SlARF24 bound to the SlPIN1 promoter and act as transcriptional activators to regulate genes expression involved in leaflet initiation. It may also suggest that SlARFs regulate leaf morphology through direct binding to auxin-responsive genes in the absence of SlIAA9, providing an insight for the role of SlARFs in leaf shape development.
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Chandler JW. Auxin response factors. PLANT, CELL & ENVIRONMENT 2016; 39:1014-28. [PMID: 26487015 DOI: 10.1111/pce.12662] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/22/2015] [Accepted: 10/05/2015] [Indexed: 05/03/2023]
Abstract
Auxin signalling involves the activation or repression of gene expression by a class of auxin response factor (ARF) proteins that bind to auxin response elements in auxin-responsive gene promoters. The release of ARF repression in the presence of auxin by the degradation of their cognate auxin/indole-3-acetic acid repressors forms a paradigm of transcriptional response to auxin. However, this mechanism only applies to activating ARFs, and further layers of complexity of ARF function and regulation are being revealed, which partly reflect their highly modular domain structure. This review summarizes our knowledge concerning ARF binding site specificity, homodimer and heterodimer multimeric ARF association and cooperative function and how activator ARFs activate target genes via chromatin remodelling and evolutionary information derived from phylogenetic comparisons from ARFs from diverse species. ARFs are regulated in diverse ways, and their importance in non-auxin-regulated pathways is becoming evident. They are also embedded within higher-order transcription factor complexes that integrate signalling pathways from other hormones and in response to the environment. The ways in which new information concerning ARFs on many levels is causing a revision of existing paradigms of auxin response are discussed.
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Affiliation(s)
- John William Chandler
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, Cologne, D-50674, Germany
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Dixit S, Kumar Biswal A, Min A, Henry A, Oane RH, Raorane ML, Longkumer T, Pabuayon IM, Mutte SK, Vardarajan AR, Miro B, Govindan G, Albano-Enriquez B, Pueffeld M, Sreenivasulu N, Slamet-Loedin I, Sundarvelpandian K, Tsai YC, Raghuvanshi S, Hsing YIC, Kumar A, Kohli A. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL. Sci Rep 2015; 5:15183. [PMID: 26507552 PMCID: PMC4623671 DOI: 10.1038/srep15183] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/21/2015] [Indexed: 02/06/2023] Open
Abstract
Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor 'no apical meristem' (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security.
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Affiliation(s)
- Shalabh Dixit
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Akshaya Kumar Biswal
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Aye Min
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Amelia Henry
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Rowena H. Oane
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Manish L. Raorane
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Toshisangba Longkumer
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Isaiah M. Pabuayon
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Sumanth K. Mutte
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Adithi R. Vardarajan
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Berta Miro
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Ganesan Govindan
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Blesilda Albano-Enriquez
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Mandy Pueffeld
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 03, 06466 Gatersleben, Germany
| | - Nese Sreenivasulu
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 03, 06466 Gatersleben, Germany
| | - Inez Slamet-Loedin
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | | | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Yue-Ie C. Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Arvind Kumar
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Ajay Kohli
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
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