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Xu X, Feng G, Liang Y, Shuai Y, Liu Q, Nie G, Yang Z, Hang L, Zhang X. Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.). BMC PLANT BIOLOGY 2020; 20:369. [PMID: 32758131 PMCID: PMC7409468 DOI: 10.1186/s12870-020-02582-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/27/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Tillering is an important agronomic trait underlying the yields and reproduction of orchardgrass (Dactylis glomerata), an important perennial forage grass. Although some genes affecting tiller initiation have been identified, the tillering regulatory network is still largely unknown, especially in perennial forage grasses. Thus, unraveling the regulatory mechanisms of tillering in orchardgrass could be helpful in developing selective strategies for high-yield perennial grasses. In this study, we generated high-throughput RNA-sequencing data from multiple tissues of tillering stage plants to identify differentially expressed genes (DEGs) between high- and low-tillering orchardgrass genotypes. Gene Ontology and pathway enrichment analyses connecting the DEGs to tillering number diversity were conducted. RESULTS In the present study, approximately 26,282 DEGs were identified between two orchardgrass genotypes, AKZ-NRGR667 (a high-tillering genotype) and D20170203 (a low-tillering genotype), which significantly differed in tiller number. Pathway enrichment analysis indicated that DEGs related to the biosynthesis of three classes of phytohormones, i.e., strigolactones (SLs), abscisic acid (ABA), and gibberellic acid (GA), as well as nitrogen metabolism dominated such differences between the high- and low-tillering genotypes. We also confirmed that under phosphorus deficiency, the expression level of the major SL biosynthesis genes encoding DWARF27 (D27), 9-cis-beta-carotene 9',10'-cleaving dioxygenase (CCD7), carlactone synthase (CCD8), and more axillary branching1 (MAX1) proteins in the high-tillering orchardgrass genotype increased more slowly relative to the low-tillering genotype. CONCLUSIONS Here, we used transcriptomic data to study the tillering mechanism of perennial forage grasses. We demonstrated that differential expression patterns of genes involved in SL, ABA, and GA biosynthesis may differentiate high- and low-tillering orchardgrass genotypes at the tillering stage. Furthermore, the core SL biosynthesis-associated genes in high-tillering orchardgrass were more insensitive than the low-tillering genotype to phosphorus deficiency which can lead to increases in SL biosynthesis, raising the possibility that there may be distinct SL biosynthesis way in tillering regulation in orchardgrass. Our research has revealed some candidate genes involved in the regulation of tillering in perennial grasses that is available for establishment of new breeding resources for high-yield perennial grasses and will serve as a new resource for future studies into molecular mechanism of tillering regulation in orchardgrass.
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Affiliation(s)
- Xiaoheng Xu
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Guangyan Feng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yueyang Liang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Shuai
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiuxu Liu
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Gang Nie
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhongfu Yang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linkai Hang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Wen X, Sun L, Chen Y, Xue P, Yang Q, Wang B, Yu N, Cao Y, Zhang Y, Gong K, Wu W, Chen D, Cao L, Cheng S, Zhang Y, Zhan X. Rice dwarf and low tillering 10 (OsDLT10) regulates tiller number by monitoring auxin homeostasis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110502. [PMID: 32563453 DOI: 10.1016/j.plantsci.2020.110502] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/30/2020] [Accepted: 04/12/2020] [Indexed: 05/18/2023]
Abstract
Tiller number is a crucial agronomic trait that directly affects the number of effective panicles and yield formation in rice. Here, we report a semi-dwarf and low tillering mutant Osdlt10 (dwarf and low tillering 10) that exhibited reduced tiller number, semi-dwarfism, increased grain width, low seed-setting rate, curled leaf tip and a series of abnormalities of agronomic traits. Phenotypic observations showed that Osdlt10 mutants had defects in tiller bud formation and grew slowly at the tillering stage. Map-based cloning revealed that LOC_Os10g41310 was the responsible gene for OsDLT10, which was subsequently demonstrated using the CRISPR/Cas9 system and a complementary experiment. Expression pattern analysis indicated that OsDLT10 was primarily expressed in the stem node, the basic part of axillary bud and leaf sheath, pulvinus. The hormone treatment investigation indicated that extremely high of exogenous auxin concentrations can inhibit the expression of OsDLT10. Endogenous auxin content decreased significantly at the base of stem node and axillary bud in Osdlt10 mutants. The results showed that OsDLT10 was related to auxin. qPCR analysis results further showed that the expression levels of auxin transport genes (PINs) and early response genes (IAAs) were significantly increased. The expression levels of WUS-like and FON1 were substantially decreased in the Osdlt10 mutants. These results revealed that OsDLT10 played a critical role in influencing tiller number, likely in association with hormone signals and the WUS-CLV pathway, to regulate axillary bud development in rice.
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Affiliation(s)
- Xiaoxia Wen
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Lianping Sun
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yuyu Chen
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Pao Xue
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Qinqin Yang
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Beifang Wang
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Ning Yu
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yongrun Cao
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yue Zhang
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Ke Gong
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Weixun Wu
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Daibo Chen
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yingxin Zhang
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
| | - Xiaodeng Zhan
- Key Laboratory for Zhejiang Super Rice Research & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China; China National Center For Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
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Walla A, Wilma van Esse G, Kirschner GK, Guo G, Brünje A, Finkemeier I, Simon R, von Korff M. An Acyl-CoA N-Acyltransferase Regulates Meristem Phase Change and Plant Architecture in Barley. PLANT PHYSIOLOGY 2020; 183:1088-1109. [PMID: 32376761 PMCID: PMC7333700 DOI: 10.1104/pp.20.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/19/2020] [Indexed: 05/04/2023]
Abstract
The modification of shoot architecture and increased investment into reproductive structures is key for crop improvement and is achieved through coordinated changes in the development and determinacy of different shoot meristems. A fundamental question is how the development of different shoot meristems is genetically coordinated to optimize the balance between vegetative and reproductive organs. Here we identify the MANY NODED DWARF1 (HvMND1) gene as a major regulator of plant architecture in barley (Hordeum vulgare). The mnd1.a mutant displayed an extended vegetative program with increased phytomer, leaf, and tiller production but a reduction in the number and size of grains. The induction of vegetative structures continued even after the transition to reproductive growth, resulting in a marked increase in longevity. Using mapping by RNA sequencing, we found that the HvMND1 gene encodes an acyl-CoA N-acyltransferase that is predominately expressed in developing axillary meristems and young inflorescences. Exploration of the expression network modulated by HvMND1 revealed differential expression of the developmental microRNAs miR156 and miR172 and several key cell cycle and developmental genes. Our data suggest that HvMND1 plays a significant role in the coordinated regulation of reproductive phase transitions, thereby promoting reproductive growth and whole plant senescence in barley.
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Affiliation(s)
- Agatha Walla
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
| | - G Wilma van Esse
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Laboratory for Molecular Biology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Gwendolyn K Kirschner
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Annika Brünje
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
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Alamin M, Sultana MH, Xu H, Mollah MNH. Robustification of Linear Regression and Its Application in Genome-Wide Association Studies. Front Genet 2020; 11:549. [PMID: 32582288 PMCID: PMC7295010 DOI: 10.3389/fgene.2020.00549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 05/07/2020] [Indexed: 11/13/2022] Open
Abstract
Regression analysis is one of the most popular statistical techniques that attempt to explore the relationships between a response (dependent) variable and one or more explanatory (independent) variables. To test the overall significance of regression, F-statistic is used if the parameters are estimated by the least-squares estimators (LSEs), while if the parameters are estimated by the maximum likelihood estimators (MLEs), the likelihood ratio test (LRT) statistic is used. However, both procedures produce misleading results and often fail to provide good fits to the reasonable space of the dataset in the presence of outlying observations. Moreover, outliers occur very frequently in any real datasets as well as in the molecular OMICS datasets. Hence, an effort is made in this study to robustify MLE based regression analysis by maximizing the β-likelihood function. The tuning parameter β is selected by cross-validation. For β = 0, the proposed method reduces to the classical MLE based regression analysis. We inspect the performance of the proposed method using both synthetic and real data analysis. The results of simulations indicate that the proposed method performs better than traditional methods in both outliers and high leverage points to estimate the parameters and mean square errors. The results of relative efficiency analysis show that the proposed estimator is relatively less affected than the popular estimators, including S, MM, and fast-S for normal error distribution in case high dimension and outliers. Also, real data analysis results demonstrated that the proposed method shows robust properties with respect to data contaminations, overcome the drawback of the traditional methods. Genome-wide association studies (GWAS) by the proposed method identify the vital gene influencing hypertension and iron level in the liver and spleen of mice. Furthermore, we have identified 15 and 21 significant SNPs for chalkiness degree and chalkiness percentage, respectively, by GWAS based on the proposed method. The variant of the SNPs might be provided the new resources for grain quality traits and could be used for further molecular and physiological analysis to enhance the better quality of rice grain. These results offer an important basis for further understanding of the robust regression analysis, which might be applied in various fields, including business, genetics, and bioinformatics.
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Affiliation(s)
- Md Alamin
- Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.,Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Most Humaira Sultana
- Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haiming Xu
- Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Md Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
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55
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Zhou W, Shi H, Wang Z, Zhao Y, Gou X, Li C, Chen G, Liu S, Deng M, Ma J, Zheng Y, Wei Y, Liu Y. Identification of lncRNAs involved in wheat tillering development in two pairs of near-isogenic lines. Funct Integr Genomics 2020; 20:669-679. [PMID: 32488459 DOI: 10.1007/s10142-020-00742-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
Emerging evidence demonstrates that lncRNAs participate in various developmental processes in plants via post-transcription regulation. However, few lncRNAs have been identified as regulators of tiller development in wheat (Triticum aestivum L.). In this study, high-throughput ribosomal depleted RNA sequencing was performed on the tillering nodes of two pairs of near-isogenic lines that differed only in the tillering trait. We identified 5399 lncRNA transcripts using bioinformational analyses. KEGG pathway analysis revealed 74 common differentially expressed lncRNAs substantially enriched in photosynthesis-related, phenylpropanoid biosynthesis, phosphatidylinositol signaling, brassinosteroid biosynthesis, zeatin biosynthesis, and carotenoid biosynthesis pathways. Detailed functional annotations of target genes were used to identify 27 tillering-associated lncRNAs. Among these, 10 were in photosynthesis-related pathways; 15 were in secondary metabolite pathways; and 8 were in plant hormone pathways, with 6 enriched in two kinds of pathways. These findings contribute to identifying tillering-associated lncRNAs in wheat and enable further investigation into the functions and roles of key candidate lncRNAs, and more experimental evidence was also needed if breeders wanted to utilize these candidate lncRNAs in wheat crop yield improvement in the future.
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Affiliation(s)
- Wanlin Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Haoran Shi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Zhiqiang Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yueting Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xiangjian Gou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shihang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. .,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China.
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. .,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China.
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56
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Xu L, Yuan K, Yuan M, Meng X, Chen M, Wu J, Li J, Qi Y. Regulation of Rice Tillering by RNA-Directed DNA Methylation at Miniature Inverted-Repeat Transposable Elements. MOLECULAR PLANT 2020; 13:851-863. [PMID: 32087371 DOI: 10.1016/j.molp.2020.02.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 05/24/2023]
Abstract
Tillering is a major determinant of rice plant architecture and grain yield. Here, we report that depletion of rice OsNRPD1a and OsNRPD1b, two orthologs of the largest subunit of RNA polymerase IV, leads to a high-tillering phenotype, in addition to dwarfism and smaller panicles. OsNRPD1a and OsNRPD1b are required for the production of 24-nt small interfering RNAs that direct DNA methylation at transposable elements (TEs) including miniature inverted-repeat TEs (MITEs). Interestingly, many genes are regulated either positively or negatively by TE methylation. Among them, OsMIR156d and OsMIR156j, which promote rice tillering, are repressed by CHH methylation at two MITEs in the promoters. By contrast, D14, which suppresses rice tillering, is activated by CHH methylation at an MITE in its downstream. Our findings reveal regulation of rice tillering by RNA-directed DNA methylation at MITEs and provide potential targets for agronomic trait enhancement through epigenome editing.
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Affiliation(s)
- Le Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kun Yuan
- 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
| | - Meng Yuan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiangbing Meng
- 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
| | - Min Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiayang Li
- 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.
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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Cao X, Jiao Y. Control of cell fate during axillary meristem initiation. Cell Mol Life Sci 2020; 77:2343-2354. [PMID: 31807816 PMCID: PMC11105066 DOI: 10.1007/s00018-019-03407-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 01/17/2023]
Abstract
Axillary meristems (AMs) are located in the leaf axil and can establish new growth axes. Whereas their neighboring cells are differentiated, the undifferentiated cells in the AM endow the AM with the same developmental potential as the shoot apical meristem. The AM is, therefore, an excellent system to study stem cell fate maintenance in plants. In this review, we summarize the current knowledge of AM initiation. Recent findings have shown that AMs derive from a stem cell lineage that is maintained in the leaf axil. This review covers AM progenitor cell fate maintenance, reactivation, and meristem establishment. We also highlight recent work that links transcription factors, phytohormones, and epigenetic regulation to AM initiation.
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Affiliation(s)
- Xiuwei Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Lin Q, Zhang Z, Wu F, Feng M, Sun Y, Chen W, Cheng Z, Zhang X, Ren Y, Lei C, Zhu S, Wang J, Zhao Z, Guo X, Wang H, Wan J. The APC/C TE E3 Ubiquitin Ligase Complex Mediates the Antagonistic Regulation of Root Growth and Tillering by ABA and GA. THE PLANT CELL 2020; 32:1973-1987. [PMID: 32265265 PMCID: PMC7268805 DOI: 10.1105/tpc.20.00101] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 05/20/2023]
Abstract
The antagonistic regulation of seed germination by the phytohormones abscisic acid (ABA) and gibberellic acid (GA) has been well-established. However, how these phytohormones antagonistically regulate root growth and branching (tillering in rice, Oryza sativa) remains obscure. Rice TILLER ENHANCER (TE) encodes an activator of the APC/CTE E3 ubiquitin ligase complex that represses tillering but promotes seed germination. In this study, we identified a dual role of GA and APC/CTE in regulating root growth. High GA levels can activate APC/CTE to promote the degradation of rice SHORT-ROOT1 (OsSHR1, a key factor promoting root growth) in the root meristem (RM) or MONOCULM1 (MOC1, a key factor promoting tillering) in the axillary meristem (AM), leading to restricted root growth and tillering, while low GA levels can activate the role of APC/CTE in stimulating RM cell division to promote root growth. In addition, moderate enhancement of ABA signaling helps maintain the RM and AM size, sustaining root growth and tillering by antagonizing the GA-promoted degradation of OsSHR1 and MOC1 through the SnRK2-APC/CTE regulatory module. We conclude that APC/CTE plays a key role in regulating plant architecture by mediating the crosstalk between ABA and GA signaling pathways.
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Affiliation(s)
- Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhe Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fuqing Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Miao Feng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yao Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weiwei Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhichao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Wang R, Qian J, Fang Z, Tang J. Transcriptomic and physiological analyses of rice seedlings under different nitrogen supplies provide insight into the regulation involved in axillary bud outgrowth. BMC PLANT BIOLOGY 2020; 20:197. [PMID: 32380960 PMCID: PMC7206722 DOI: 10.1186/s12870-020-02409-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/28/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND N is an important macronutrient required for plant development and significantly influences axillary bud outgrowth, which affects tillering and grain yield of rice. However, how different N concentrations affect axillary bud growth at the molecular and transcriptional levels remains unclear. RESULTS In this study, morphological changes in the axillary bud growth of rice seedlings under different N concentrations ranging from low to high levels were systematically observed. To investigate the expression of N-induced genes involved in axillary bud growth, we used RNA-seq technology to generate mRNA transcriptomic data from two tissue types, basal parts and axillary buds, of plants grown under six different N concentrations. In total, 10,221 and 12,180 DEGs induced by LN or HN supplies were identified in the basal parts and axillary buds, respectively, via comparisons to expression levels under NN level. Analysis of the coexpression modules from the DEGs of the basal parts and axillary buds revealed an abundance of related biological processes underlying the axillary bud growth of plants under N treatments. Among these processes, the activity of cell division and expansion was positively correlated with the growth rate of axillary buds of plants grown under different N supplies. Additionally, TFs and phytohormones were shown to play roles in determining the axillary bud growth of plants grown under different N concentrations. We have validated the functions of OsGS1;2 and OsGS2 through the rice transgenic plants with altered tiller numbers, illustrating the important valve of our transcriptomic data. CONCLUSION These results indicate that different N concentrations affect the axillary bud growth rate, and our study show comprehensive expression profiles of genes that respond to different N concentrations, providing an important resource for future studies attempting to determine how axillary bud growth is controlled by different N supplies.
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Affiliation(s)
- Rongna Wang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Junjie Qian
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Zhongming Fang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
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Gouda G, Gupta MK, Donde R, Mohapatra T, Vadde R, Behera L. Marker-assisted selection for grain number and yield-related traits of rice ( Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:885-898. [PMID: 32377039 PMCID: PMC7196572 DOI: 10.1007/s12298-020-00773-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 05/11/2023]
Abstract
Continuous rise in the human population has resulted in an upsurge in food demand, which in turn demand grain yield enhancement of cereal crops, including rice. Rice yield is estimated via the number of tillers, grain number per panicles, and the number of spikes present per panicle. Marker-assisted selection (MAS) serve as one of the best ways to introduce QTLs/gene associated with yield in the rice plant. MAS has also been employed effectively in dissecting several other complex agricultural traits, for instance, drought, cold tolerance, salinity, etc. in rice plants. Thus, in this review, authors attempted to collect information about various genes/QTLs associated with high yield, including grain number, in rice and how different scheme of MAS can be employed to introduce them in rice (Oryza sativa L.) plant, which in turn will enhance rice yield. Information obtained to date suggest that, numerous QTLs, e.g., Gn1a, Dep1, associated with grain number and yield-related traits, have been identified either via mapping or cloning approaches. These QTLs have been successfully introduced into rice plants using various schemes of MAS for grain yield enhancement in rice. However, sometimes, MAS does not perform well in breeding, which might be due to lack of resources, skilled labors, reliable markers, and high costs associated with MAS. Thus, by overcoming these problems, we can enhance the application of MAS in plant breeding, which, in turn, may help us in increasing yield, which subsequently may help in bridging the gap between demand and supply of food for the continuously growing population.
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Affiliation(s)
- Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Manoj Kumar Gupta
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Ravindra Donde
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Trilochan Mohapatra
- Secretary (DARE) and Director General (ICAR), Government of India, New Delhi, India
| | - Ramakrishna Vadde
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
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Zheng Y, Ge J, Bao C, Chang W, Liu J, Shao J, Liu X, Su L, Pan L, Zhou DX. Histone Deacetylase HDA9 and WRKY53 Transcription Factor Are Mutual Antagonists in Regulation of Plant Stress Response. MOLECULAR PLANT 2020; 12:1090-1102. [PMID: 31048024 DOI: 10.1016/j.molp.2019.04.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 05/06/2023]
Abstract
Epigenetic regulation of gene expression is important for plant adaptation to environmental changes. Previous results showed that Arabidopsis RPD3-like histone deacetylase HDA9 is known to function in repressing plant response to stress in Arabidopsis. However, how HDA9 targets to specific chromatin loci and controls gene expression networks involved in plant response to stress remains largely unclear. Here, we show that HDA9 represses stress tolerance response by interacting with and regulating the DNA binding and transcriptional activity of WRKY53, which functions as a high-hierarchy positive regulator of stress response. We found that WRKY53 is post-translationally modified by lysine acetylation at multiple sites, some of which are removed by HDA9, resulting in inhibition of WRKY53 transcription activity. Conversely, WRKY53 negatively regulates HDA9 histone deacetylase activity. Collectively, our results indicate that HDA9 and WRK53 are reciprocal negative regulators of each other's activities, illustrating how the functional interplay between a chromatin regulator and a transcription factor regulates stress tolerance in plants.
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Affiliation(s)
- Yu Zheng
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China.
| | - Jingyu Ge
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Chun Bao
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Wenwen Chang
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Jingjing Liu
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Jingjie Shao
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Lufang Su
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Lei Pan
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Dao-Xiu Zhou
- Institute of Plant Sciences Paris-Saclay, CNRS, INRAE, Université Paris-Saclay, Orsay 91405, France.
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Nutan KK, Rathore RS, Tripathi AK, Mishra M, Pareek A, Singla-Pareek SL. Integrating the dynamics of yield traits in rice in response to environmental changes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:490-506. [PMID: 31410470 DOI: 10.1093/jxb/erz364] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/29/2019] [Indexed: 05/23/2023]
Abstract
Reductions in crop yields as a consequence of global climate change threaten worldwide food security. It is therefore imperative to develop high-yielding crop plants that show sustainable production under stress conditions. In order to achieve this aim through breeding or genetic engineering, it is crucial to have a complete and comprehensive understanding of the molecular basis of plant architecture and the regulation of its sub-components that contribute to yield under stress. Rice is one of the most widely consumed crops and is adversely affected by abiotic stresses such as drought and salinity. Using it as a model system, in this review we present a summary of our current knowledge of the physiological and molecular mechanisms that determine yield traits in rice under optimal growth conditions and under conditions of environmental stress. Based on physiological functioning, we also consider the best possible combination of genes that may improve grain yield under optimal as well as environmentally stressed conditions. The principles that we present here for rice will also be useful for similar studies in other grain crops.
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Affiliation(s)
- Kamlesh Kant Nutan
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ray Singh Rathore
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Amit Kumar Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Manjari Mishra
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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Yu H, Cui H, Chen J, Li X. Regulation of Aegilops tauschii Coss Tiller Bud Growth by Plant Density: Transcriptomic, Physiological and Phytohormonal Responses. FRONTIERS IN PLANT SCIENCE 2020; 11:1166. [PMID: 32849721 PMCID: PMC7403227 DOI: 10.3389/fpls.2020.01166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/20/2020] [Indexed: 05/08/2023]
Abstract
Aegilops tauschii Coss is one of the most hazardous weeds that severely infests wheat fields in China. The tillering ability of Ae. tauschii strongly affects the occurrence and spread by influencing its seed output. In this study, Ae. tauschii was sown at low plant density (LPD) and high plant density (HPD) to investigate the effect of plant density on tiller bud outgrowth and its potential regulators using RNA-Seq. Additionally, the chlorophyll content and photosynthesis, soluble sugar and phytohormone levels were also determined at different plant densities. The results showed that an increased plant density significantly inhibited the elongation of tiller buds in the axil of the first leaf at 15 days after planting, with 7.69 mm at LPD and 1.69 mm at HPD. A total of seven putative tiller-related genes were selected and validated using quantitative real-time PCR. Furthermore, chlorophyll levels, photosynthetic efficiency, and soluble sugar contents were distinctly inhibited by HPD in Ae. tauschii, which may be responsible for the restriction of tiller bud growth. In addition, differentially expressed genes (DEGs) were markedly enriched in indole-3-acetic acid (IAA), abscisic acid (ABA), and gibberellin metabolism and signaling. Accordingly, the levels of ABA and gibberellin A3 in Ae. tauschii were strikingly higher at HPD compared with those at LPD, yet the reverse tendency was observed for IAA. Undoubtedly, such results will be highly beneficial for illuminating the underlying regulators of the Ae. tauschii tillering response to plant density and may provide new ideas for the control of this weed in the future.
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Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies. Int J Mol Sci 2019; 20:ijms20235922. [PMID: 31775351 PMCID: PMC6928681 DOI: 10.3390/ijms20235922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 12/17/2022] Open
Abstract
Reducing nitrogen (N) input is a key measure to achieve a sustainable rice production in China, especially in Jiangsu Province. Tiller is the basis for achieving panicle number that plays as a major factor in the yield determination. In actual production, excessive N is often applied in order to produce enough tillers in the early stages. Understanding how N regulates tillering in rice plants is critical to generate an integrative management to reduce N use and reaching tiller number target. Aiming at this objective, we utilized RNA sequencing and weighted gene co-expression network analysis (WGCNA) to compare the transcriptomes surrounding the shoot apical meristem of indica (Yangdao6, YD6) and japonica (Nipponbare, NPB) rice subspecies. Our results showed that N rate influenced tiller number in a different pattern between the two varieties, with NPB being more sensitive to N enrichment, and YD6 being more tolerant to high N rate. Tiller number was positively related to N content in leaf, culm and root tissue, but negatively related to the soluble carbohydrate content, regardless of variety. Transcriptomic comparisons revealed that for YD6 when N rate enrichment from low (LN) to medium (MN), it caused 115 DEGs (LN vs. MN), from MN to high level (HN) triggered 162 DEGs (MN vs. HN), but direct comparison of low with high N rate showed a 511 DEGs (LN vs. HN). These numbers of DEG in NPB were 87 (LN vs. MN), 40 (MN vs. HN), and 148 (LN vs. HN). These differences indicate that continual N enrichment led to a bumpy change at the transcription level. For the reported sixty-five genes which affect tillering, thirty-six showed decent expression in SAM at tiller starting phase, among them only nineteen being significantly influenced by N level, and two genes showed significant interaction between N rate and variety. Gene ontology analysis revealed that the majority of the common DEGs are involved in general stress responses, stimulus responses, and hormonal signaling process. WGCNA network identified twenty-two co-expressing gene modules and ten candidate hubgenes for each module. Several genes associated with tillering and N rate fall on the related modules. These indicate that there are more genes participating in tillering regulation in response to N enrichment.
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65
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Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry ( Fragaria vesca). Int J Mol Sci 2019; 20:ijms20184593. [PMID: 31533278 PMCID: PMC6770801 DOI: 10.3390/ijms20184593] [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: 08/25/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/17/2022] Open
Abstract
The cultivated strawberry (Fragaria × ananassa), an allo-octoploid with non-climacteric fleshy fruits, is a popular Rosaceae horticultural crop worldwide that is mainly propagated via stolons during cultivation. Woodland strawberry (Fragaria vesca), one of the four diploid progenitor species of cultivated strawberry, is widely used as a model plant in the study of Rosaceae fruit trees, non-climacteric fruits and stolons. One GRAS transcription factor has been shown to regulate stolon formation; the other GRAS proteins in woodland strawberry remain unknown. In this study, we identified 54 FveGRAS proteins in woodland strawberry, and divided them into 14 subfamilies. Conserved motif analysis revealed that the motif composition of FveGRAS proteins was conserved within each subfamily, but diverged widely among subfamilies. We found 56 orthologous pairs of GRAS proteins between woodland strawberry and Arabidopsis thaliana, 47 orthologous pairs between woodland strawberry and rice and 92 paralogous pairs within woodland strawberry. The expression patterns of FveGRAS genes in various organs and tissues, and changes therein under cold, heat and GA3 treatments, were characterized using transcriptomic analysis. The results showed that 34 FveGRAS genes were expressed with different degrees in at least four organs, including stolons; only a few genes displayed organ-specific expression. The expression levels of 16 genes decreased, while that of four genes increased during fruit ripening; FveGRAS54 showed the largest increase in expression. Under cold, heat and GA3 treatments, around half of the FveGRAS genes displayed increased or decreased expression to some extent, suggesting differing functions of these FveGRAS genes in the responses to cold, heat and GAs. This study provides insight into the potential functions of FveGRAS genes in woodland strawberry. A few FveGRAS genes were identified as candidate genes for further study, in terms of their functions in stolon formation, fruit ripening and abiotic stresses.
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Yin X, Liu X, Xu B, Lu P, Dong T, Yang D, Ye T, Feng YQ, Wu Y. OsMADS18, a membrane-bound MADS-box transcription factor, modulates plant architecture and the abscisic acid response in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3895-3909. [PMID: 31034557 PMCID: PMC6685668 DOI: 10.1093/jxb/erz198] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/16/2019] [Indexed: 05/18/2023]
Abstract
The APETALA1 (AP1)/FRUITFULL (FUL)-like transcription factor OsMADS18 plays diverse functions in rice development, but the underlying molecular mechanisms are far from fully understood. Here, we report that down-regulation of OsMADS18 expression in RNAi lines caused a delay in seed germination and young seedling growth, whereas the overexpression of OsMADS18 produced plants with fewer tillers. In targeted OsMADS18 genome-edited mutants (osmads18-cas9), an increased number of tillers, altered panicle size, and reduced seed setting were observed. The EYFP-OsMADS18 (full-length) protein was localized to the nucleus and plasma membrane but the EYFP-OsMADS18-N (N-terminus) protein mainly localized to the nucleus. The expression of OsMADS18 could be stimulated by abscisic acid (ABA), and ABA stimulation triggered the cleavage of HA-OsMADS18 and the translocation of OsMADS18 from the plasma membrane to the nucleus. The inhibitory effect of ABA on seedling growth was less effective in the OsMADS18-overexpressing plants. The expression of a set of ABA-responsive genes was significantly reduced in the overexpressing plants. The phenotypes of transgenic plants expressing EYFP-OsMADS18-N resembled those observed in the osmads18-cas9 mutants. Analysis of the interaction of OsMADS18 with OsMADS14, OsMADS15, and OsMADS57 strongly suggests an essential role for OsMADS18 in rice development.
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Affiliation(s)
- Xiaoming Yin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiong Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Buxian Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Piaoyin Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Tian Dong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Di Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Tiantian Ye
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, China
| | - Yan Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Correspondence:
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Li Z, Liang Y, Yuan Y, Wang L, Meng X, Xiong G, Zhou J, Cai Y, Han N, Hua L, Liu G, Li J, Wang Y. OsBRXL4 Regulates Shoot Gravitropism and Rice Tiller Angle through Affecting LAZY1 Nuclear Localization. MOLECULAR PLANT 2019; 12:1143-1156. [PMID: 31200078 DOI: 10.1016/j.molp.2019.05.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/07/2019] [Accepted: 05/31/2019] [Indexed: 05/03/2023]
Abstract
Rice tiller angle is a key agronomic trait that contributes to ideal plant architecture and grain production. LAZY1 (LA1) was previously shown to control tiller angle via affecting shoot gravitropism, but the underlying molecular mechanism remains largely unknown. In this study, we identified an LA1-interacting protein named Brevis Radix Like 4 (OsBRXL4). We showed that the interaction between OsBRXL4 and LA1 occurs at the plasma membrane and that their interaction determines nuclear localization of LA1. We found that nuclear localization of LA1 is essential for its function, which is different from AtLA1, its Arabidopsis ortholog. Overexpression of OsBRXL4 leads to a prostrate growth phenotype, whereas OsBRXLs RNAi plants, in which the expression levels of OsBRXL1, OsBRXL4, and OsBRXL5 were decreased, display a compact phenotype. Further genetic analysis also supported that OsBRXL4 controls rice tiller angle by affecting nuclear localization of LA1. Consistently, we demonstrated that OsBRXL4 regulates the shoot gravitropism through affecting polar auxin transport as did LA1. Taken together, our study not only identifies OsBRXL4 as a regulatory component of rice tiller angle but also provides new insights into genetic regulation of rice plant architecture.
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Affiliation(s)
- Zhen Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yundong Yuan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guosheng Xiong
- Plant Phenomics Research Center, Nanjing Agriculture University, Nanjing 210095, China
| | - Jie Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yueyue Cai
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ningpei Han
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lekai Hua
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Wang Z, Shi H, Yu S, Zhou W, Li J, Liu S, Deng M, Ma J, Wei Y, Zheng Y, Liu Y. Comprehensive transcriptomics, proteomics, and metabolomics analyses of the mechanisms regulating tiller production in low-tillering wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2181-2193. [PMID: 31020386 DOI: 10.1007/s00122-019-03345-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Tiller development in low-tillering wheat is related to several differentially expressed genes, proteins, and metabolites, as determined by an integrated omics approach combining transcriptome analysis, iTRAQ, and HPLC-MS on multiple NILs. Tillering is an important aspect of plant morphology that affects spike number, thereby contributing to the final crop yield. However, the mechanisms inhibiting tiller production in low-tillering wheat are poorly characterized. To investigate this aspect of wheat biology, two pairs of near-isogenic lines were developed, and an integrated omics approach combining transcriptome analysis, isobaric tags for relative and absolute quantification, and high-performance liquid chromatography-mass spectrometry were used to compare the free-tillering and low-tillering caused by an allele at Qltn.sicau-2D in wheat samples. Overall, 474 genes, 166 proteins, and 28 metabolites were identified as tillering-associated differentially expressed genes, proteins, and metabolites (DEGs, DEPs, and DEMs, respectively). Functional analysis indicated that the abundance of DEGs/DEPs/DEMs was related to lignin and cellulose metabolism, cell division, cell cycle processes, and glycerophospholipid metabolism; three transcription factor families, GRAS, GRF, and REV, might be related to the decrease in tillering in low-tillering wheat. These findings contribute to improve our understanding of the mechanisms responsible for the inhibition of tiller development in low-tillering wheat cultivars.
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Affiliation(s)
- Zhiqiang Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Haoran Shi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shifan Yu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Wanlin Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shihang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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SLR1 inhibits MOC1 degradation to coordinate tiller number and plant height in rice. Nat Commun 2019; 10:2738. [PMID: 31227696 PMCID: PMC6588547 DOI: 10.1038/s41467-019-10667-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 05/14/2019] [Indexed: 11/15/2022] Open
Abstract
The breeding of cereals with altered gibberellin (GA) signaling propelled the ‘Green Revolution’ by generating semidwarf plants with increased tiller number. The mechanism by which GAs promote shoot height has been studied extensively, but it is not known what causes the inverse relationship between plant height and tiller number. Here we show that rice tiller number regulator MONOCULM 1 (MOC1) is protected from degradation by binding to the DELLA protein SLENDER RICE 1 (SLR1). GAs trigger the degradation of SLR1, leading to stem elongation and also to the degradation of MOC1, and hence a decrease in tiller number. This discovery provides a molecular explanation for the coordinated control of plant height and tiller number in rice by GAs, SLR1 and MOC1. Due to reduced gibberellin sensitivity, modern rice cultivars are shorter than traditional varieties but produce more tillers and have higher yields. Here Liao et al. show that gibberellin contributes to decreased tiller number by degrading the MOC1 protein that suppresses bud outgrowth.
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Xiang X, Zhang P, Yu P, Zhang Y, Yang Z, Sun L, Wu W, Khan RM, Abbas A, Cheng S, Cao L. LSSR1 facilitates seed setting rate by promoting fertilization in rice. RICE (NEW YORK, N.Y.) 2019; 12:31. [PMID: 31073866 PMCID: PMC6509318 DOI: 10.1186/s12284-019-0280-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/25/2019] [Indexed: 05/03/2023]
Abstract
Seed setting rate is one of the major components that determine rice (Oryza sativa L.) yield. Successful fertilization is necessary for normal seed setting. However, little is known about the molecular mechanisms governing this process. In this study, we report a novel rice gene, LOW SEED SETTING RATE1 (LSSR1), which regulates the seed setting rate by facilitating rice fertilization. LSSR1 encodes a putative GH5 cellulase, which is highly conserved in plants. LSSR1 is predominantly expressed in anthers during the microsporogenesis stage, and its encoded protein contains a signal peptide at the N-terminal, which may be a secretory protein that stores in pollen grains and functions during rice fertilization. To explore the physiological function of LSSR1 in rice, loss-of-function mutants of LSSR1 were created through the CRISPR-Cas9 system, which showed a significant decrease in rice seed setting rate. However, the morphology of the vegetative and reproductive organs appears normal in lssr1 mutant lines. In addition, lssr1 pollen grains could be normally stained by I2-KI solution. Cytological results demonstrate that the blockage of fertilization mostly accounted for the low seed setting rate in lssr1 mutant lines, which was most likely caused by abnormal pollen grain germination, failed pollen tube penetration, and retarded pollen tube elongation. Together, our results suggest that LSSR1 plays an important role in rice fertilization, which in turn is vital for maintaining rice seed setting rate.
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Affiliation(s)
- Xiaojiao Xiang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Peipei Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Ping Yu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Yingxin Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zhengfu Yang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lianping Sun
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Weixun Wu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Riaz Muhammad Khan
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Adil Abbas
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
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Duan E, Wang Y, Li X, Lin Q, Zhang T, Wang Y, Zhou C, Zhang H, Jiang L, Wang J, Lei C, Zhang X, Guo X, Wang H, Wan J. OsSHI1 Regulates Plant Architecture Through Modulating the Transcriptional Activity of IPA1 in Rice. THE PLANT CELL 2019; 31:1026-1042. [PMID: 30914468 PMCID: PMC6533028 DOI: 10.1105/tpc.19.00023] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/27/2019] [Accepted: 03/24/2019] [Indexed: 05/20/2023]
Abstract
Tillering and panicle branching are important determinants of plant architecture and yield potential in rice (Oryza sativa). IDEAL PLANT ARCHITECTURE1 (IPA1) encodesSQUAMOSA PROMOTER BINDING PROTEIN-LIKE14, which acts as a key transcription factor regulating tiller outgrowth and panicle branching by directly activating the expression of O. sativa TEOSINTE BRANCHED1 (OsTB1) and O. sativa DENSE AND ERECT PANICLE1 (OsDEP1), thereby influencing grain yield in rice. Here, we report the identification of a rice mutant named shi1 that is characterized by dramatically reduced tiller number, enhanced culm strength, and increased panicle branch number. Map-based cloning revealed that O. sativa SHORT INTERNODES1 (OsSHI1) encodes a plant-specific transcription factor of the SHI family with a characteristic family-specific IGGH domain and a conserved zinc-finger DNA binding domain. Consistent with the mutant phenotype, OsSHI1 is predominantly expressed in axillary buds and young panicle, and its encoded protein is exclusively targeted to the nucleus. We show that OsSHI1 physically interacts with IPA1 both in vitro and in vivo. Moreover, OsSHI1 could bind directly to the promoter regions of both OsTB1 and OsDEP1 through a previously unrecognized cis-element (T/GCTCTAC motif). OsSHI1 repressed the transcriptional activation activity of IPA1 by affecting its DNA binding activity toward the promoters of both OsTB1 and OsDEP1, resulting in increased tiller number and diminished panicle size. Taken together, our results demonstrate that OsSHI1 regulates plant architecture through modulating the transcriptional activity of IPA1 and provide insight into the establishment of plant architecture in rice.
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Affiliation(s)
- Erchao Duan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohui Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ting Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yupeng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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72
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Shi L, Zhang XB, Shi YF, Xu X, He Y, Shao G, Huang QN, Wu JL. OsCDC48/48E complex is required for plant survival in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2019; 100:163-179. [PMID: 30937701 PMCID: PMC6513905 DOI: 10.1007/s11103-019-00851-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
We demonstrate that the C-terminus of OsCDC48 is essential for maintaining its full ATPase activity and OsCDC48/48E interaction is required to modulate cellular processes and plant survival in rice. Cell division cycle 48 (CDC48) belongs to the superfamily protein of ATPases associated with diverse cellular activities (AAA). We previously isolated a rice CDC48 mutant (psd128) displaying premature senescence and death phenotype. Here, we showed that OsCDC48 (Os03g0151800) interacted with OsCDC48E (Os10g0442600), a homologue of OsCDC48, to control plant survival in rice. OsCDC48E knockout plants exhibited similar behavior to psd128 with premature senescence and plant death. Removal of the C-terminus of OsCDC48 caused altered expression of cell cycle-related genes, changed the percentage of cells in G1 and G2/M phases, and abolished the interaction between OsCDC48 itself and between OsCDC48 and OsCDC48E, respectively. Furthermore, the truncated OsCDC48-PSD128 protein lacking the C-terminal 27 amino acid residues showed a decreased level of ATPase activity. Overexpression of OsCDC48-psd128 resulted in differential expression of AAA-ATPase associated genes leading to increased total ATPase activity, accumulation of reactive oxygen species and decreased plant tiller numbers while overexpression of OsCDC48 also resulted in differential expression of AAA-ATPase associated genes leading to increased total ATPase activity, but increased plant tiller numbers and grain yield, indicating its potential utilization for yield improvement. Our results demonstrated that the C-terminal region of OsCDC48 was essential for maintaining the full ATPase activity and OsCDC48/48E complex might function in form of heteromultimers to modulate cellular processes and plant survival in rice.
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Affiliation(s)
- Lei Shi
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiao-Bo Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Yong-Feng Shi
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Xia Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guosheng Shao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Qi-Na Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China.
| | - Jian-Li Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China.
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73
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Ustyantsev KV, Goncharov NP. Homology of Genes Controlling Architectonics of Vegetative and Generative Organs in Barley and Rice and Their Application for Wheat Biodiversity Expansion and Breeding. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419050156] [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]
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74
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Chongloi GL, Prakash S, Vijayraghavan U. Regulation of meristem maintenance and organ identity during rice reproductive development. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1719-1736. [PMID: 30753578 DOI: 10.1093/jxb/erz046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Grasses have evolved complex inflorescences, where the primary unit is the specialized short branch called a spikelet. Detailed studies of the cumulative action of the genetic regulators that direct the progressive change in axillary meristem identity and their terminal differentiation are crucial to understanding the complexities of the inflorescence and the development of a determinate floret. Grass florets also pose interesting questions concerning the morphologies and functions of organs as compared to other monocots and eudicots. In this review, we summarize our current knowledge of the regulation of the transitions that occur in grass inflorescence meristems, and of the specification of floret meristems and their determinate development. We primarily use rice as a model, with appropriate comparisons to other crop models and to the extensively studied eudicot Arabidopsis. The role of MADS-domain transcription factors in floral organ patterning is well documented in many eudicots and in grasses. However, there is evidence to suggest that some of these rice floral regulators have evolved distinctive functions and that other grass species-specific factors and regulatory pathways occur - for example the LOFSEP 'E' class genes OsMADS1 and OsMAD34, and ramosa genes. A better understanding of these systems and the epigenetic regulators and hormone signaling pathways that interact with them will provide new insights into the rice inflorescence meristem and the differentiation of its floret organs, and should indicate genetic tools that can be used to control yield-related traits in both rice and other cereal crops.
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Affiliation(s)
- Grace L Chongloi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sandhan Prakash
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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75
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Liu J, Zhi P, Wang X, Fan Q, Chang C. Wheat WD40-repeat protein TaHOS15 functions in a histone deacetylase complex to fine-tune defense responses to Blumeria graminis f.sp. tritici. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:255-268. [PMID: 30204899 DOI: 10.1093/jxb/ery330] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 09/10/2018] [Indexed: 05/23/2023]
Abstract
Powdery mildew caused by Blumeria graminis f.sp. tritici (Bgt) seriously threatens the production of common wheat (Triticum aestivum). In eukaryotes, WD40-repeat (WDR) proteins usually participate in assembling protein complexes involved in a wide range of cellular processes, including defense responses. However, the potential function of WDR proteins in regulating crop resistance to biotrophic fungal pathogens, such as Bgt, remains unclear. In this study, we isolated TaHOS15, encoding a WDR protein, from the Bgt-susceptible wheat cultivar Jing411 and demonstrated that knockdown of TaHOS15 expression using virus- or transient-induced gene-silencing attenuated wheat susceptibility to Bgt. Biochemical and molecular-biological assays revealed that TaHOS15 interacts with TaHDA6, a wheat homolog of Arabidopsis histone deacetylase AtHDA6, to constitute a transcriptional repressor complex. We determined the role of TaHOS15, which might act as an adaptor protein recruiting TaHDA6 to the chromatin of wheat defense-related genes including TaPR1, TaPR2, TaPR5, and TaWRKY45, where they repress histone acetylation. Reduced TaHOS15 or TaHDA6 transcript levels led to decreased susceptibility to Bgt together with enhanced defense-related transcription under Bgt infection. Collectively, these results demonstrate that TaHOS15 functions in a histone deacetylase complex with TaHDA6 to fine-tune the defense response to Bgt in common wheat.
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Affiliation(s)
- Jiao Liu
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Pengfei Zhi
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Xiaoyu Wang
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Qingxin Fan
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Cheng Chang
- College of Life Sciences, Qingdao University, Qingdao, China
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76
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Li P, Chang T, Chang S, Ouyang X, Qu M, Song Q, Xiao L, Xia S, Deng Q, Zhu XG. Systems model-guided rice yield improvements based on genes controlling source, sink, and flow. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1154-1180. [PMID: 30415497 DOI: 10.1111/jipb.12738] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
A large number of genes related to source, sink, and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow; then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level, and the non-linear complex interaction between source, sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.
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Affiliation(s)
- Pan Li
- State Key Laboratory of Hybrid Rice, Key Laboratory of Phytochromes, Hunan Agriculture University, Changsha 410125, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Tiangen Chang
- National Key Laboratory for Plant Molecular Genetics, CAS Center of Excellence of Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai 200031, China
| | - Shuoqi Chang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Xiang Ouyang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Mingnan Qu
- National Key Laboratory for Plant Molecular Genetics, CAS Center of Excellence of Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai 200031, China
| | - Qingfeng Song
- National Key Laboratory for Plant Molecular Genetics, CAS Center of Excellence of Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai 200031, China
| | - Langtao Xiao
- State Key Laboratory of Hybrid Rice, Key Laboratory of Phytochromes, Hunan Agriculture University, Changsha 410125, China
| | - Shitou Xia
- State Key Laboratory of Hybrid Rice, Key Laboratory of Phytochromes, Hunan Agriculture University, Changsha 410125, China
| | - Qiyun Deng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Xin-Guang Zhu
- National Key Laboratory for Plant Molecular Genetics, CAS Center of Excellence of Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai 200031, China
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77
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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.
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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
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78
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Zhang N, Yu H, Yu H, Cai Y, Huang L, Xu C, Xiong G, Meng X, Wang J, Chen H, Liu G, Jing Y, Yuan Y, Liang Y, Li S, Smith SM, Li J, Wang Y. A Core Regulatory Pathway Controlling Rice Tiller Angle Mediated by the LAZY1-Dependent Asymmetric Distribution of Auxin. THE PLANT CELL 2018; 30:1461-1475. [PMID: 29915152 PMCID: PMC6096585 DOI: 10.1105/tpc.18.00063] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/08/2018] [Accepted: 06/15/2018] [Indexed: 05/18/2023]
Abstract
Tiller angle in cereals is a key shoot architecture trait that strongly influences grain yield. Studies in rice (Oryza sativa) have implicated shoot gravitropism in the regulation of tiller angle. However, the functional link between shoot gravitropism and tiller angle is unknown. Here, we conducted a large-scale transcriptome analysis of rice shoots in response to gravistimulation and identified two new nodes of a shoot gravitropism regulatory gene network that also controls rice tiller angle. We demonstrate that HEAT STRESS TRANSCRIPTION FACTOR 2D (HSFA2D) is an upstream positive regulator of the LAZY1-mediated asymmetric auxin distribution pathway. We also show that two functionally redundant transcription factor genes, WUSCHEL RELATED HOMEOBOX6 (WOX6) and WOX11, are expressed asymmetrically in response to auxin to connect gravitropism responses with the control of rice tiller angle. These findings define upstream and downstream genetic components that link shoot gravitropism, asymmetric auxin distribution, and rice tiller angle. The results highlight the power of the high-temporal-resolution RNA-seq data set and its use to explore further genetic components controlling tiller angle. Collectively, these approaches will identify genes to improve grain yields by facilitating the optimization of plant architecture.
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Affiliation(s)
- Ning Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yueyue Cai
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Linzhou Huang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Cao Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guosheng Xiong
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiyao Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Haofeng Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhui Jing
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yundong Yuan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shujia Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Steven M Smith
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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79
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Peng D, Tan X, Zhang L, Yuan D, Lin J, Liu X, Jiang Y, Zhou B. Increasing branch and seed yield through heterologous expression of the novel rice S-acyl transferase gene OsPAT15 in Brassica napus L. BREEDING SCIENCE 2018; 68:326-335. [PMID: 30100799 PMCID: PMC6081303 DOI: 10.1270/jsbbs.17126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/18/2018] [Indexed: 06/08/2023]
Abstract
Branching is a predominant element in the plant architecture of Brassica napus L. and represents an important determinant of seed yield. OsPAT15 (OsDHHC1), a novel DHHC-type zinc finger protein gene, was reported to regulate rice plant architecture by altering the tillering. However, whether heterologous overexpression of the OsPAT15 gene from the monocot rice into the dicot B. napus L. would have the same effect on branching or seed yield is unknown. In this study, the DHHC-type zinc finger protein gene OsPAT15 was determined to have sulfur acyl transferase activity in the akr1Δ yeast mutant in a complementation experiment. Heterologously expressing OsPAT15 transgenic B. napus L. plants were obtained using the Agrobacterium-mediated floral-dip transformation method. As anticipated, OsPAT15 transgenic plants exhibited branching and seed yield. Compared with non-transgenic plants, OsPAT15 transgenic plants had increased primary branches (1.58-1.76-fold) and siliques (1.86-1.89-fold), resulting in a significant increase in seed yield (around 2.39-2.51-fold). Therefore, overexpression of the sulfur acyl transferase gene OsPAT15 in B. napus L. could be used to increase seed yield and produce excellent varieties.
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Affiliation(s)
- Dan Peng
- Faculty of Life Science and Technology, Central South University of Forestry and Technology,
410004, Changsha,
China
- Forestry Biotechnology Hunan Key Laboratories,
410004, Changsha,
China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology,
410004, Changsha,
China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Tree, Central South University of Forestry and Technology,
410004, Changsha,
China
- Collaborative Innovation Central of Cultivation and Utilization for Non-Wood Forest Tree Central South University of Forestry and Technology,
410004, Changsha,
China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology,
410004, Changsha,
China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Tree, Central South University of Forestry and Technology,
410004, Changsha,
China
- Collaborative Innovation Central of Cultivation and Utilization for Non-Wood Forest Tree Central South University of Forestry and Technology,
410004, Changsha,
China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology,
410004, Changsha,
China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Tree, Central South University of Forestry and Technology,
410004, Changsha,
China
- Collaborative Innovation Central of Cultivation and Utilization for Non-Wood Forest Tree Central South University of Forestry and Technology,
410004, Changsha,
China
| | - Jianzhong Lin
- Key Laboratory of Plant Function Genomic for Development and Regulation, Hunan University,
410082, Changsha,
China
| | - Xuanming Liu
- Key Laboratory of Plant Function Genomic for Development and Regulation, Hunan University,
410082, Changsha,
China
| | - Yueqiao Jiang
- Faculty of Life Science and Technology, Central South University of Forestry and Technology,
410004, Changsha,
China
| | - Bo Zhou
- Faculty of Life Science and Technology, Central South University of Forestry and Technology,
410004, Changsha,
China
- Key Laboratory of Plant Function Genomic for Development and Regulation, Hunan University,
410082, Changsha,
China
- Forestry Biotechnology Hunan Key Laboratories,
410004, Changsha,
China
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80
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He R, Ni Y, Li J, Jiao Z, Zhu X, Jiang Y, Li Q, Niu J. Quantitative Changes in the Transcription of Phytohormone-Related Genes: Some Transcription Factors Are Major Causes of the Wheat Mutant dmc Not Tillering. Int J Mol Sci 2018; 19:ijms19051324. [PMID: 29710831 PMCID: PMC5983577 DOI: 10.3390/ijms19051324] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/17/2023] Open
Abstract
Tiller number is an important agronomic trait for grain yield of wheat (Triticum aestivum L.). A dwarf-monoculm wheat mutant (dmc) was obtained from cultivar Guomai 301 (wild type, WT). Here, we explored the molecular basis for the restrained tiller development of the mutant dmc. Two bulked samples of the mutant dmc (T1, T2 and T3) and WT (T4, T5 and T6) with three biological replicates were comparatively analyzed at the transcriptional level by bulked RNA sequencing (RNA-Seq). In total, 68.8 Gb data and 463 million reads were generated, 80% of which were mapped to the wheat reference genome of Chinese Spring. A total of 4904 differentially expressed genes (DEGs) were identified between the mutant dmc and WT. DEGs and their related major biological functions were characterized based on GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) categories. These results were confirmed by quantitatively analyzing the expression profiles of twelve selected DEGs via real-time qRT-PCR. The down-regulated gene expressions related to phytohormone syntheses of auxin, zeatin, cytokinin and some transcription factor (TF) families of TALE, and WOX might be the major causes of the mutant dmc, not tillering. Our work provides a foundation for subsequent tiller development research in the future.
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Affiliation(s)
- 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, Henan, China.
| | - Yongjing Ni
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu 476000, Henan, China.
| | - 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, Henan, 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, Henan, China.
| | - Xinxin Zhu
- 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, Henan, 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, Henan, 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, Henan, 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, Henan, China.
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Abstract
Shoot architecture is determined by the organization and activities of apical, axillary, intercalary, secondary, and inflorescence meristems and by the subsequent development of stems, leaves, shoot branches, and inflorescences. In this review, we discuss the unifying principles of hormonal and genetic control of shoot architecture including advances in our understanding of lateral branch outgrowth; control of stem elongation, thickness, and angle; and regulation of inflorescence development. We focus on recent progress made mainly in Arabidopsis thaliana, rice, pea, maize, and tomato, including the identification of new genes and mechanisms controlling shoot architecture. Key advances include elucidation of mechanisms by which strigolactones, auxins, and genes such as IDEAL PLANT ARCHITECTURE1 and TEOSINTE BRANCHED1 control shoot architecture. Knowledge now available provides a foundation for rational approaches to crop breeding and the generation of ideotypes with defined architectural features to improve performance and productivity.
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Affiliation(s)
- Bing 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;
| | - Steven M Smith
- 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;
- School of Natural Sciences, University of Tasmania, Hobart 7001, Australia;
| | - Jiayang Li
- 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
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82
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Li Y, Xiao J, Chen L, Huang X, Cheng Z, Han B, Zhang Q, Wu C. Rice Functional Genomics Research: Past Decade and Future. MOLECULAR PLANT 2018; 11:359-380. [PMID: 29409893 DOI: 10.1016/j.molp.2018.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/15/2018] [Accepted: 01/23/2018] [Indexed: 05/22/2023]
Abstract
Rice (Oryza sativa) is a major staple food crop for more than 3.5 billion people worldwide. Understanding the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledons. Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially characterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.
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Affiliation(s)
- Yan Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lingling Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xuehui Huang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhukuan Cheng
- National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Han
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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83
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Wang J, Lu K, Nie H, Zeng Q, Wu B, Qian J, Fang Z. Rice nitrate transporter OsNPF7.2 positively regulates tiller number and grain yield. RICE (NEW YORK, N.Y.) 2018; 11:12. [PMID: 29484500 PMCID: PMC5826914 DOI: 10.1186/s12284-018-0205-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/21/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Rice tiller number is one of the most important factors that determine grain yield, while nitrogen is essential for the crop growth and development, especially for tiller formation. Genes involved in nitrogen use efficiency processes have been identified in the previous studies, however, only a small number of these genes have been found to improve grain yield by promoting tillering. RESULTS We constructed over-expression (OX) lines and RNA-interference (Ri) lines, and selected a mutant of OsNPF7.2, a low-affinity nitrate transporter. Our analyses showed that rice tiller number and grain yield were significantly increased in OX lines, whereas Ri lines and mutant osnpf7.2 had fewer tiller number and lower grain yield. Under different nitrate concentrations, tiller buds grew faster in OX lines than in WT, but they grew slower in Ri lines and mutant osnpf7.2. These results indicated that altered expression of OsNPF7.2 plays a significant role in the control of tiller bud growth and regulation of tillering. Elevated expression of OsNPF7.2 also improved root length, root number, fresh weight, and dry weight. However, reduced expression of OsNPF7.2 had the opposite result on these characters. OsNPF7.2 OX lines showed more significantly enhanced influx of nitrate and had a higher nitrate concentration than WT. The levels of gene transcripts related to cytokinin pathway and cell cycle in tiller bud, and cytokinins concentration in tiller basal portion were higher in OX lines than that in WT, suggesting that altered expression of OsNPF7.2 controlled tiller bud growth and root development by regulating cytokinins content and cell cycle in plant cells. Altered expression of OsNPF7.2 also was responsible for the change in expression of the genes involved in strigolactone pathway, such as D27, D17, D10, Os900, Os1400, D14, D3, and OsFC1. CONCLUSION Our results suggested that OsNPF7.2 is a positive regulator of nitrate influx and concentration, and that it also regulates cell division in tiller bud and alters expression of genes involved in cytokinin and strigolactone pathways, resulting in the control over rice tiller number. Since elevated expression of OsNPF7.2 is capable of improving rice grain yield, this gene might be applied to high-yield rice breeding.
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Affiliation(s)
- Jie Wang
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
| | - Kai Lu
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
| | - Haipeng Nie
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qisen Zeng
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bowen Wu
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
| | - Junjie Qian
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
| | - Zhongming Fang
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China.
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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84
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Zhao Y, Zhang Y, Su P, Yang J, Huang L, Gao W. Genetic Transformation System for Woody Plant Tripterygium wilfordii and Its Application to Product Natural Celastrol. FRONTIERS IN PLANT SCIENCE 2018; 8:2221. [PMID: 29375599 PMCID: PMC5767223 DOI: 10.3389/fpls.2017.02221] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/18/2017] [Indexed: 05/22/2023]
Abstract
Tripterygium wilfordii is a perennial woody liana medicinal plant with several crucial biological activities. Although studies on tissue culture have previously been conducted, research on genetic transformation is much more challenging and therefore results in slower progress. In the present study, a highly efficient transformation system involving the particle bombardment of T. wilfordii with the reporter egfp gene using the PDS-1000/He system was established. A total of seven parameters affecting the genetic transformation were investigated using an L18 (6 × 36)-type orthogonal array. The result indicated that DNA delivery conditions of 3-cm target distance, 1100 psi helium pressure, 28 mmHg chamber vacuum pressure, three times number of bombardment, CaCl2 as precipitation agent, 2 μg plasmid DNA concentration and 48 h post-bombardment incubation time were optimal for T. wilfordii cell suspensions transformation. The average transformation efficiency was 19.17%. Based on this transformation system, the overexpression of two T. wilfordii farnesyl pyrophosphate synthase genes (TwFPSs) was performed in cell suspensions. Integration of the TwFPSs in the genome was verified by PCR analysis and also by Southern blotting using hygromycin gene as a probe. Real-time quantitative PCR analysis showed that the expression of TwFPS1&2 was highly up regulated in transgenic cell suspensions compared with control cells. The detection of metabolites showed that TwFPS1&2 could highly increase the celastrol content (973.60 μg/g) in transgenic cells. These results indicated that this transformation system is an effective protocol for characterizing the function of genes in the terpenoid biosynthetic pathway.
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Affiliation(s)
- Yujun Zhao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yifeng Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Ping Su
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jian Yang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
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85
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Kong L, Chang C. Suppression of wheat TaCDK8/TaWIN1 interaction negatively affects germination of Blumeria graminis f.sp. tritici by interfering with very-long-chain aldehyde biosynthesis. PLANT MOLECULAR BIOLOGY 2018; 96:165-178. [PMID: 29197938 DOI: 10.1007/s11103-017-0687-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/27/2017] [Indexed: 05/29/2023]
Abstract
Wheat TaCDK8 interacts with TaWIN1 to regulate very-long-chain aldehyde biosynthesis required for efficient germination of Blumeria graminis f.sp. tritici. Powdery mildew caused by Blumeria graminis f.sp. tritici (Bgt) is a devastating disease of common wheat (Triticum aestivum L.). Bgt infection initiates with its conidia germination on the aerial surface of wheat. In this study, we isolated the cyclin-dependent kinase 8 (TaCDK8) from wheat cultivar Jing411 and found that silencing of TaCDK8 impeded Bgt germination. The biochemical and molecular-biological assays revealed that TaCDK8 interacts with and phosphorylates the wheat transcription factor wax inducer 1 (TaWIN1) to stimulate the TaWIN1-dependent transcription. Bgt conidia on the leaves of TaWIN1-silenced plants also showed reduced germination. Gas chromatographic analysis revealed that knockdown of TaCDK8 or TaWIN1 resulted in decreases of wax components and cutin monomers in wheat leaves. Moreover, Bgt germination on leaves of TaCDK8 or TaWIN1 silenced plants could be fully restored by application of wild-type cuticular wax. In vitro studies demonstrated that very-long-chain aldehydes absent from the cuticular wax of the TaCDK8 or TaWIN1 silenced plants were capable of chemically stimulating Bgt germination. These results implicated that the suppression of TaCDK8/TaWIN1 interaction negatively affects Bgt germination by interfering with very-long-chain aldehyde biosynthesis required for efficient fungal germination.
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Affiliation(s)
- Lingyao Kong
- College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Cheng Chang
- College of Life Sciences, Qingdao University, Qingdao, 266071, China.
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86
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You Q, Zhai K, Yang D, Yang W, Wu J, Liu J, Pan W, Wang J, Zhu X, Jian Y, Liu J, Zhang Y, Deng Y, Li Q, Lou Y, Xie Q, He Z. An E3 Ubiquitin Ligase-BAG Protein Module Controls Plant Innate Immunity and Broad-Spectrum Disease Resistance. Cell Host Microbe 2017; 20:758-769. [PMID: 27978435 DOI: 10.1016/j.chom.2016.10.023] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 09/29/2016] [Accepted: 10/31/2016] [Indexed: 10/20/2022]
Abstract
Programmed cell death (PCD) and immunity in plants are tightly controlled to promote antimicrobial defense while preventing autoimmunity. However, the mechanisms contributing to this immune homeostasis are poorly understood. Here, we isolated a rice mutant ebr1 (enhanced blight and blast resistance 1) that shows enhanced broad-spectrum bacterial and fungal disease resistance, but displays spontaneous PCD, autoimmunity, and stunted growth. EBR1 encodes an E3 ubiquitin ligase that interacts with OsBAG4, which belongs to the BAG (Bcl-2-associated athanogene) family that functions in cell death, growth arrest, and immune responses in mammals. EBR1 directly targets OsBAG4 for ubiquitination-mediated degradation. Elevated levels of OsBAG4 in rice are necessary and sufficient to trigger PCD and enhanced disease resistance to pathogenic infection, most likely by activating pathogen-associated molecular patterns-triggered immunity (PTI). Together, our study suggests that an E3-BAG module orchestrates innate immune homeostasis and coordinates the trade-off between defense and growth in plants.
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Affiliation(s)
- Quanyuan You
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Keran Zhai
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Donglei Yang
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingni Wu
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junzhong Liu
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbo Pan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianjun Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xudong Zhu
- China National Rice Research Institute, Hangzhou 310006, China
| | - Yikun Jian
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yingying Zhang
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yonggen Lou
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - Qi Xie
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Collaborative Innovation Center of Genetics and Development, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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87
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Meng X, Yu H, Zhang Y, Zhuang F, Song X, Gao S, Gao C, Li J. Construction of a Genome-Wide Mutant Library in Rice Using CRISPR/Cas9. MOLECULAR PLANT 2017. [PMID: 28645639 DOI: 10.1016/j.molp.2017.06.006] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Xiangbing Meng
- 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
| | - Hong 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
| | - Yi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | | | - Xiaoguang Song
- 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
| | - Songsong Gao
- Beijing ViewSolid Biotechnology, Beijing 102206, 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.
| | - Jiayang Li
- 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 the Chinese Academy of Sciences, Beijing 100049, China.
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88
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Mathan J, Bhattacharya J, Ranjan A. Enhancing crop yield by optimizing plant developmental features. Development 2017; 143:3283-94. [PMID: 27624833 DOI: 10.1242/dev.134072] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A number of plant features and traits, such as overall plant architecture, leaf structure and morphological features, vascular architecture and flowering time are important determinants of photosynthetic efficiency and hence the overall performance of crop plants. The optimization of such developmental traits thus has great potential to increase biomass and crop yield. Here, we provide a comprehensive review of these developmental traits in crop plants, summarizing their genetic regulation and highlighting the potential of manipulating these traits for crop improvement. We also briefly review the effects of domestication on the developmental features of crop plants. Finally, we discuss the potential of functional genomics-based approaches to optimize plant developmental traits to increase yield.
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Affiliation(s)
- Jyotirmaya Mathan
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Juhi Bhattacharya
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Aashish Ranjan
- National Institute of Plant Genome Research, New Delhi 110067, India
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89
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Shu K, Yang W. E3 Ubiquitin Ligases: Ubiquitous Actors in Plant Development and Abiotic Stress Responses. PLANT & CELL PHYSIOLOGY 2017; 58:1461-1476. [PMID: 28541504 PMCID: PMC5914405 DOI: 10.1093/pcp/pcx071] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/05/2017] [Indexed: 05/05/2023]
Abstract
Understanding the precise regulatory mechanisms of plant development and stress responses at the post-translational level is currently a topic of intensive research. Protein ubiquitination, including the sequential performances of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin ligase (E3) enzymes, is a refined post-translational modification ubiquitous in all eukaryotes. Plants are an integral part of our ecosystem and, as sessile organisms, the ability to perceive internal and external signals and to adapt well to various environmental challenges is crucial for their survival. Over recent decades, extensive studies have demonstrated that protein ubiquitination plays key roles in multiple plant developmental stages (e.g. seed dormancy and germination, root growth, flowering time control, self-incompatibility and chloroplast development) and several abiotic stress responses (e.g. drought and high salinity), by regulating the abundance, activities or subcellular localizations of a variety of regulatory polypeptides and enzymes. Importantly, diverse E3 ligases are involved in these regulatory pathways by mediating phytohormone and light signaling or other pathways. In this updated review, we mainly summarize recent advances in our understanding of the regulatory roles of protein ubiquitination in plant development and plant-environment interactions, and primarily focus on different types of E3 ligases because they play critical roles in determining substrate specificity.
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Affiliation(s)
- Kai Shu
- Department of Plant Physiology and Biochemistry, Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
- Corresponding authors: Kai Shu, E-mail, ; Wenyu Yang, E-mail,
| | - Wenyu Yang
- Department of Plant Physiology and Biochemistry, Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
- Corresponding authors: Kai Shu, E-mail, ; Wenyu Yang, E-mail,
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90
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Xu C, Park SJ, Van Eck J, Lippman ZB. Control of inflorescence architecture in tomato by BTB/POZ transcriptional regulators. Genes Dev 2017; 30:2048-2061. [PMID: 27798848 PMCID: PMC5066612 DOI: 10.1101/gad.288415.116] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/14/2016] [Indexed: 11/25/2022]
Abstract
In tomatoes, formation of multiflowered inflorescences depends on a precisely timed process of meristem maturation mediated by the transcription factor gene TERMINATING FLOWER (TMF). Xu et al. show that TMF protein acts together with homologs of the Arabidopsis BLADE-ON-PETIOLE (BOP) transcriptional cofactors, defined by the conserved BTB/POZ domain. Plant productivity depends on inflorescences, flower-bearing shoots that originate from the stem cell populations of shoot meristems. Inflorescence architecture determines flower production, which can vary dramatically both between and within species. In tomato plants, formation of multiflowered inflorescences depends on a precisely timed process of meristem maturation mediated by the transcription factor gene TERMINATING FLOWER (TMF), but the underlying mechanism is unknown. We show that TMF protein acts together with homologs of the Arabidopsis BLADE-ON-PETIOLE (BOP) transcriptional cofactors, defined by the conserved BTB (Broad complex, Tramtrack, and Bric-a-brac)/POZ (POX virus and zinc finger) domain. TMF and three tomato BOPs (SlBOPs) interact with themselves and each other, and TMF recruits SlBOPs to the nucleus, suggesting formation of a transcriptional complex. Like TMF, SlBOP gene expression is highest during vegetative and transitional stages of meristem maturation, and CRISPR/Cas9 elimination of SlBOP function causes pleiotropic defects, most notably simplification of inflorescences into single flowers, resembling tmf mutants. Flowering defects are enhanced in higher-order slbop tmf mutants, suggesting that SlBOPs function with additional factors. In support of this, SlBOPs interact with TMF homologs, mutations in which cause phenotypes like slbop mutants. Our findings reveal a new flowering module defined by SlBOP–TMF family interactions that ensures a progressive meristem maturation to promote inflorescence complexity.
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Affiliation(s)
- Cao Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Soon Ju Park
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan, Jeonbuk 54538, Republic of Korea
| | - Joyce Van Eck
- The Boyce Thompson Institute, Ithaca, New York 14853, USA
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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91
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Yu H, Zhang Y, Zhang D, Lu Y, He H, Zheng F, Wang M. Identification of a Ribose-Phosphate Pyrophosphokinase that Can Interact In Vivo with the Anaphase Promoting Complex/Cyclosome. Int J Mol Sci 2017; 18:ijms18040617. [PMID: 28358323 PMCID: PMC5412264 DOI: 10.3390/ijms18040617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 02/26/2017] [Accepted: 03/06/2017] [Indexed: 11/25/2022] Open
Abstract
5-Phospho-d-ribosyl-1-diphosphate (PRPP) synthase (PRS) catalyzes the biosynthesis of PRPP, which is an important compound of metabolism in most organisms. However, no PRS genes have been cloned, let alone studied for their biological function in rubber tree. In this study, we identify a novel protein (PRS4) that interacts in vivo with rubber tree anaphase promoting complex/cyclosome (APC/C) subunit 10 (HbAPC10) by yeast two-hybrid assays. PRS4 has been cloned from rubber tree and named as HbPRS4. Blastp search in the genome of Arabidopsis thaliana showed that HbPRS4 shared the highest similarity with AtPRS4, with 80.71% identity. qRT-PCR was used to determine the expression of HbPRS4 in different tissues and under various treatments. HbPRS4 was preferentially expressed in the bark. Moreover, the expression level of HbPRS4 was significantly induced by the proteasome inhibitor MG132 treatment, suggesting it might be regulated by the ubiquitin/26S proteasome pathway. The amount of HbPRS4 transcript was obviously decreased after mechanical wounding and abscisic acid (ABA) treatments, while a slight increase was observed at 24 h after ABA treatment. HbPRS4 transcript in the latex was significantly upregulated by ethephon (ET) and methyl jasmonate (MeJA) treatments. These results suggested that HbPRS4 may be a specific substrate of HbAPC10 indirectly regulating natural rubber biosynthesis in rubber tree.
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Affiliation(s)
- Haiyang Yu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Yu Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Dong Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Yanxi Lu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Haixia He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Fucong Zheng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Meng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
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92
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Zhou B, Lin JZ, Peng D, Yang YZ, Guo M, Tang DY, Tan X, Liu XM. Plant architecture and grain yield are regulated by the novel DHHC-type zinc finger protein genes in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 254:12-21. [PMID: 27964781 DOI: 10.1016/j.plantsci.2016.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/08/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
In many plants, architecture and grain yield are affected by both the environment and genetics. In rice, the tiller is a vital factor impacting plant architecture and regulated by many genes. In this study, we cloned a novel DHHC-type zinc finger protein gene Os02g0819100 and its alternative splice variant OsDHHC1 from the cDNA of rice (Oryza sativa L.), which regulate plant architecture by altering the tiller in rice. The tillers increased by about 40% when this type of DHHC-type zinc finger protein gene was over-expressed in Zhong Hua 11 (ZH11) rice plants. Moreover, the grain yield of transgenic rice increased approximately by 10% compared with wild-type ZH11. These findings provide an important genetic engineering approach for increasing rice yields.
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Affiliation(s)
- Bo Zhou
- College of Bioscience and Biotechnology of Central South University of Forestry and Technology, Changsha 410018, Hunan, China; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018 Changsha, China
| | - Jian Zhong Lin
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China
| | - Dan Peng
- College of Bioscience and Biotechnology of Central South University of Forestry and Technology, Changsha 410018, Hunan, China; Academy of Seed Industry of Hunan Yahua, Changsha 410013, Hunan, China; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018 Changsha, China
| | - Yuan Zhu Yang
- Academy of Seed Industry of Hunan Yahua, Changsha 410013, Hunan, China
| | - Ming Guo
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China
| | - Dong Ying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018 Changsha, China
| | - Xuan Ming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China.
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93
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MULTI-TILLERING DWARF1, a new allele of BRITTLE CULM 12, affects plant height and tiller in rice. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-015-0981-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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94
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Critical roles of soluble starch synthase SSIIIa and granule-bound starch synthase Waxy in synthesizing resistant starch in rice. Proc Natl Acad Sci U S A 2016; 113:12844-12849. [PMID: 27791174 DOI: 10.1073/pnas.1615104113] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Changes in human lifestyle and food consumption have resulted in a large increase in the incidence of type-2 diabetes, obesity, and colon disease, especially in Asia. These conditions are a growing threat to human health, but consumption of foods high in resistant starch (RS) can potentially reduce their incidence. Strategies to increase RS in rice are limited by a lack of knowledge of its molecular basis. Through map-based cloning of a RS locus in indica rice, we have identified a defective soluble starch synthase gene (SSIIIa) responsible for RS production and further showed that RS production is dependent on the high expression of the Waxya (Wxa ) allele, which is prevalent in indica varieties. The resulting RS has modified granule structure; high amylose, lipid, and amylose-lipid complex; and altered physicochemical properties. This discovery provides an opportunity to increase RS content of cooked rice, especially in the indica varieties, which predominates in southern Asia.
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95
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A Nucleus-Encoded Chloroplast Protein YL1 Is Involved in Chloroplast Development and Efficient Biogenesis of Chloroplast ATP Synthase in Rice. Sci Rep 2016; 6:32295. [PMID: 27585744 PMCID: PMC5009372 DOI: 10.1038/srep32295] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/04/2016] [Indexed: 11/16/2022] Open
Abstract
Chloroplast ATP synthase (cpATPase) is an importance thylakoid membrane-associated photosynthetic complex involved in the light-dependent reactions of photosynthesis. In this study, we isolated and characterized a rice (Oryza sativa) mutant yellow leaf 1 (yl1), which exhibits chlorotic leaves throughout developmental stages. The YL1 mutation showed reduced chlorophyll contents, abnormal chloroplast morphology, and decreased photochemical efficiency. Moreover, YL1 deficiency disrupts the expression of genes associated with chloroplast development and photosynthesis. Molecular and genetic analyses revealed that YL1 is a nucleus-encoded protein with a predicted transmembrane domain in its carboxyl-terminus that is conserved in the higher plant kingdom. YL1 localizes to chloroplasts and is preferentially expressed in green tissues containing chloroplasts. Immunoblot analyses showed that inactivation of YL1 leads to drastically reduced accumulation of AtpA (α) and AtpB (β), two core subunits of CF1αβ subcomplex of cpATPase, meanwhile, a severe decrease (ca. 41.7%) in cpATPase activity was observed in the yl1-1 mutant compared with the wild type. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation assays revealed a specific interaction between YL1 and AtpB subunit of cpATPase. Taken together, our results suggest that YL1 is a plant lineage-specific auxiliary factor involved in the biogenesis of the cpATPase complex, possibly via interacting with the β-subunit.
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96
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MicroRNA393 is involved in nitrogen-promoted rice tillering through regulation of auxin signal transduction in axillary buds. Sci Rep 2016; 6:32158. [PMID: 27574184 PMCID: PMC5004122 DOI: 10.1038/srep32158] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/03/2016] [Indexed: 02/08/2023] Open
Abstract
Rice tillering has an important influence on grain yield, and is promoted by nitrogen (N) fertilizer. Several genes controlling rice tillering, which are regulated by poor N supply, have been identified. However, the molecular mechanism associated with the regulation of tillering based on N supply is poorly understood. Here, we report that rice microRNA393 (OsmiR393) is involved in N-mediated tillering by decreasing auxin signal sensitivity in axillary buds. Expression analysis showed that N fertilizer causes up-regulation of OsmiR393, but down-regulation of two target genes (OsAFB2 and OsTB1). In situ expression analysis showed that OsmiR393 is highly expressed in the lateral axillary meristem. OsmiR393 overexpression mimicked N-mediated tillering in wild type Zhonghua 11 (ZH11). Mutation of OsMIR393 in ZH11 repressed N-promoted tillering, which simulated the effects of limited N, and this could not be restored by supplying N fertilizer. Western blot analysis showed that OsIAA6 was accumulated in both OsmiR393-overexpressing lines and N-treated wild type rice, but was reduced in the OsMIR393 mutant. Therefore, we deduced that N-induced OsmiR393 accumulation reduces the expression of OsTIR1 and OsAFB2, which alleviates sensitivity to auxin in the axillary buds and stabilizes OsIAA6, thereby promoting rice tillering.
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97
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An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci. Sci Rep 2016; 6:30143. [PMID: 27440503 PMCID: PMC4954952 DOI: 10.1038/srep30143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/29/2016] [Indexed: 11/26/2022] Open
Abstract
Studying the genetic basis of variation in plant metabolism has been greatly facilitated by genomic and metabolic profiling advances. In this study, we use metabolomics and growth measurements to map QTL in rice, a major staple crop. Previous rice metabolism studies have largely focused on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we show that in contrast to other rice studies, the heritability of primary metabolism is similar to Arabidopsis. The vast majority of metabolic QTLs had small to moderate effects with significant polygenic epistasis. Two metabolomics QTL hotspots had opposing effects on carbon and nitrogen rich metabolites suggesting that they may influence carbon and nitrogen partitioning, with one locus co-localizing with SUSIBA2 (WRKY78). Comparing QTLs for metabolomic and a variety of growth related traits identified few overlaps. Interestingly, the rice population displayed fewer loci controlling stochastic variation for metabolism than was found in Arabidopsis. Thus, it is possible that domestication has differentially impacted stochastic metabolite variation more than average metabolite variation.
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98
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Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing. Sci Rep 2016; 6:27425. [PMID: 27251022 PMCID: PMC4890301 DOI: 10.1038/srep27425] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/19/2016] [Indexed: 11/09/2022] Open
Abstract
Oryza nivara, an annual wild AA-genome species of rice, is an important gene pool for broadening the genetic diversity of cultivated rice (O. sativa L.). Towards identifying and utilizing favourable alleles from O. nivara, we developed a set of introgression lines (ILs) by introducing O. nivara segments into the elite indica rice variety 93-11 background through advanced backcrossing and repeated selfing. Using whole-genome resequencing, a high-density genetic map containing 1,070 bin-markers was constructed for the 131 ILs, with an average length of 349 kb per bin. The 131 ILs cover 95% of O. nivara genome, providing a relatively complete genomic library for introgressing O. nivara alleles for trait improvement. Using this high-density bin-map, QTL mapping for 13 yield-related traits was performed and a total of 65 QTLs were detected across two environments. At ~36.9% of detected QTLs, the alleles from O. nivara conferred improving effects on yield-associated traits. Six cloned genes, Sh4/SHA1, Bh4, Sd1, TE/TAD1, GS3 and FZP, colocalised in the peak intervals of 9 QTLs. In conclusion, we developed new genetic materials for exploration and use of beneficial alleles from wild rice and provided a basis for future fine mapping and cloning of the favourable O. nivara-derived QTLs.
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99
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Dedecker M, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Dumoulin L, Wojsznis N, Gevaert K, Vandenabeele S, De Jaeger G. Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues. PLANT MOLECULAR BIOLOGY 2016; 91:341-354. [PMID: 27003905 DOI: 10.1007/s11103-016-0471-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Proteins are the cell's functional entities. Rather than operating independently, they interact with other proteins. Capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. Affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. For Oryza sativa, the technique has been initiated in callus and shoots, but has not been optimized ever since. We translated an optimized tandem affinity purification (TAP) approach from Arabidopsis thaliana toward Oryza sativa, and demonstrate its applicability in a variety of rice tissues. A list of non-specific and false positive interactors is presented, based on re-occurrence over more than 170 independent experiments, to filter bona fide interactors. We demonstrate the sensitivity of our approach by isolating the complexes for the rice ANAPHASE PROMOTING COMPLEX SUBUNIT 10 (APC10) and CYCLIN-DEPENDENT KINASE D (CDKD) proteins from the proliferation zone of the emerging fourth leaf. Next to APC10 and CDKD, we tested several additional baits in the different rice tissues and reproducibly retrieved at least one interactor for 81.4 % of the baits screened for in callus tissue and T1 seedlings. By transferring an optimized TAP tag combined with state-of-the-art mass spectrometry, our TAP protocol enables the discovery of interactors for low abundance proteins in rice and opens the possibility to capture complex dynamics by comparing tissues at different stages of a developing rice organ.
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Affiliation(s)
- Maarten Dedecker
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium.
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Bernard Cannoot
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Leen Vercruysse
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Lies Dumoulin
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | | | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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100
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Liu Q, Shen G, Peng K, Huang Z, Tong J, Kabir MH, Wang J, Zhang J, Qin G, Xiao L. The alteration in the architecture of a T-DNA insertion rice mutant osmtd1 is caused by up-regulation of MicroRNA156f. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:819-29. [PMID: 25677853 PMCID: PMC6681133 DOI: 10.1111/jipb.12340] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/09/2015] [Indexed: 05/18/2023]
Abstract
Plant architecture is an important factor for crop production. Some members of microRNA156 (miR156) and their target genes SQUAMOSA Promoter-Binding Protein-Like (SPL) were identified to play essential roles in the establishment of plant architecture. However, the roles and regulation of miR156 is not well understood yet. Here, we identified a T-DNA insertion mutant Osmtd1 (Oryza sativa multi-tillering and dwarf mutant). Osmtd1 produced more tillers and displayed short stature phenotype. We determined that the dramatic morphological changes were caused by a single T-DNA insertion in Osmtd1. Further analysis revealed that the T-DNA insertion was located in the gene Os08g34258 encoding a putative inhibitor I family protein. Os08g34258 was knocked out and OsmiR156f was significantly upregulated in Osmtd1. Overexpression of Os08g34258 in Osmtd1 complemented the defects of the mutant architecture, while overexpression of OsmiR156f in wild-type rice phenocopied Osmtd1. We showed that the expression of OsSPL3, OsSPL12, and OsSPL14 were significantly downregulated in Osmtd1 or OsmiR156f overexpressed lines, indicating that OsSPL3, OsSPL12, and OsSPL14 were possibly direct target genes of OsmiR156f. Our results suggested that OsmiR156f controlled plant architecture by mediating plant stature and tiller outgrowth and may be regulated by an unknown protease inhibitor I family protein.
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Affiliation(s)
- Qing Liu
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Gezhi Shen
- Crop Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Keqin Peng
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Zhigang Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Mohammed Humayun Kabir
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Jianhui Wang
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jingzhe Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
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