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Li W, Wang D, Hong X, Shi J, Hong J, Su S, Loaiciga CR, Li J, Liang W, Shi J, Zhang D. Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome. Plant Cell Rep 2023; 42:975-988. [PMID: 37016094 DOI: 10.1007/s00299-023-03006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/17/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN) of Asian cultivated rice accessions provided a useful gene reservoir for the identification of more MADS-box candidates to overcome the limitation for the usage of only 75 MADS-box genes identified in Nipponbare for rice breeding. Here, we report the identification and validation of ten MADS-box homologous genes in RPAN. Origin and identity analysis indicated that they are originated from different wild rice accessions and structure of motif analysis revealed high variations in their amino acid sequences. Phylogenetic results with 277 MADS-box genes in 41 species showed that all these ten MADS-box homologous genes belong to type I (SRF-like, M-type). Gene expression analysis confirmed the existence of these ten MADS-box genes in IRIS_313-10,394, all of them were expressed in flower tissues, and six of them were highly expressed during seed development. Altogether, we identified and validated experimentally, for the first time, ten novel MADS-box genes in RPAN, which provides new genetic sources for rice improvement.
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Affiliation(s)
- Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Duoxiang Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaokun Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Su Su
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
| | - Cristopher Reyes Loaiciga
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, Adelaide, 5064, Australia
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Xu W, Zhu W, Yang L, Liang W, Li H, Yang L, Chen M, Luo Z, Huang G, Duan L, Dreni L, Zhang D. SMALL REPRODUCTIVE ORGANS, a SUPERMAN-like transcription factor, regulates stamen and pistil growth in rice. New Phytol 2022; 233:1701-1718. [PMID: 34761379 DOI: 10.1111/nph.17849] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Organ size is determined mainly by cell division and cell expansion. Several genetic factors regulating development of plant lateral organs have been characterized, but those involved in determining reproductive organ size and separation in rice (Oryza sativa) remain unknown. We have isolated the rice gene SMALL REPRODUCTIVE ORGANS (SRO) encoding a nucleus-localized Cys2His2 (C2 H2 ) zinc finger protein orthologous to Arabidopsis transcription factor (TF) SUPERMAN (SUP). Combined developmental, genetic, histological and transcriptomic analyses were used to determine the function of SRO in regulating reproductive organ size. SRO affects genes involved in cell division, cell expansion and phytohormone signalling in the rice flower. SRO is specifically expressed in the first stages of stamen filament development to regulate their correct formation and separation. In addition, SRO noncell-autonomously regulates the size and functionality of male and female reproductive organs. The B-class MADS-box gene OsMADS16/SPW1 is epistatic to SRO, whereas SRO regulates reproductive organ specification and floral meristem determinacy synergistically with C-class genes OsMADS3 and OsMADS58. These findings provide insights into how an evolutionarily conserved TF has a pivotal role in reproductive organ development in core eudicots and monocots, through partially conserved expression, function and regulatory network.
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Affiliation(s)
- Wei Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanwan Zhu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liu Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Li
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China
| | - Li Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mingjiao Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhijing Luo
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lei Duan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ludovico Dreni
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
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Wu T, Ali A, Wang J, Song J, Fang Y, Zhou T, Luo Y, Zhang H, Chen X, Liao Y, Liu Y, Xu P, Wu X. A homologous gene of OsREL2/ASP1, ASP-LSL regulates pleiotropic phenotype including long sterile lemma in rice. BMC Plant Biol 2021; 21:390. [PMID: 34418975 PMCID: PMC8379857 DOI: 10.1186/s12870-021-03163-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Panicle is a harvesting organ of rice, and its morphology and development are closely associated with grain yield. The current study was carried on a mutant screened through an EMS (ethyl-methane sulphonate) mutagenized population of a Japonica cultivar Kitaake (WT). RESULTS A mutant, named as asp-lsl (aberrant spikelet-long sterile lemma), showed a significant decrease in plant height, number of tillers, thousand-grains weight, seed setting rate, spikelet length, kernel length and effective number of grains per panicle as compared to WT. Asp-lsl showed a pleiotropic phenotype coupled with the obvious presence of a long sterile lemma. Cross-sections of lemma showed an increase in the cell volume rather than the number of cells. Genetic segregation analysis revealed its phenotypic trait is controlled by a single recessive nuclear gene. Primary and fine mapping indicated that candidate gene controlling the phenotype of asp-lsl was located in an interval of 212 kb on the short arm of chromosome 8 between RM22445 and RM22453. Further sequencing and indels markers analysis revealed LOC_Os08g06480 harbors a single base substitution (G→A), resulting in a change of 521st amino acid(Gly→Glu. The homology comparison and phylogenetic tree analysis revealed mutation was occurred in a highly conserved domain and had a high degree of similarity in Arabidopsis, corn, and sorghum. The CRISPR/Cas9 mutant line of ASP-LSL produced a similar phenotype as that of asp-lsl. Subcellular localization of ASP-LSL revealed that its protein is localized in the nucleus. Relative expression analysis revealed ASP-LSL was preferentially expressed in panicle, stem, and leaves. The endogenous contents of GA, CTK, and IAA were found significantly decreased in asp-lsl as compared to WT. CONCLUSIONS Current study presents the novel phenotype of asp-lsl and also validate the previously reported function of OsREL2 (ROMOSA ENHANCER LOCI2), / ASP1(ABERRANT SPIKELET AND PANICLE 1).
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Affiliation(s)
- Tingkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Asif Ali
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Jinhao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Jiahe Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yongqiong Fang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Tingting Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yi Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Hongyu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Xiaoqiong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yongxiang Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yutong Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China.
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Liu Q, Liu Z, Li W, Song X. Comparative transcriptome analysis indicates conversion of stamens into pistil-like structures in male sterile wheat (Triticum aestivum L.) with Aegilops crassa cytoplasm. BMC Genomics 2020; 21:124. [PMID: 32019527 PMCID: PMC7001380 DOI: 10.1186/s12864-020-6450-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aegilops crassa cytoplasm is an important source for investigating cytoplasmic male sterility (CMS). Moreover, the stamens of line C303A exhibit a high degree of pistillody, turning almost white. However, the molecular mechanism that underlies pistillody in C303A remains unclear. Therefore, to obtain a better understanding of pistillody in C303A, the phenotypic and cytological features of C303A were observed to identify the key stage for the homeotic transformation of stamens into pistil-like structures. Transcriptome profiles were determined for stamens using Illumina RNA sequencing. RESULTS Morphological observations of the CMS wheat line with Aegilops crassa cytoplasm C303A showed that the pistils developed normally, but the stamens were ultimately aborted and they released no pollen when mature. According to paraffin section observations, the stamens began to transform into pistils or pistil-like structures in the binucleate stage (BNS). Therefore, the stamens were collected from line C303A and its maintainer 303B in the BNS for transcriptome sequencing. In total, 20,444 wheat genes were determined as differentially expressed in C303A and 303B stamens, with 10,283 upregulated and 10,161 downregulated genes. Gene Ontology enrichment analyses showed that most of the differentially expressed genes (DEGs) were annotated with GO terms comprising metabolic process, cell, cellular process, catalytic activity, and cell part. Analysis based on the Kyoto Encyclopedia of Genes and Genomes database showed that the enriched DEGs were mainly associated with energy metabolism. We also found several essential genes that may contribute to pistillody in C303A. These findings suggest that disrupted energy metabolism and reactive oxygen metabolism induce pistillody and eventually lead to abortion in C303A. CONCLUSION We determined the complex transcriptome profiles for C303A stamens and demonstrated that disrupted energy metabolism and class B MADS-box genes are related to pistillody. These findings may facilitate future studies of the mechanistic response of the wheat stamen and pollen development in CMS.
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Affiliation(s)
- Qi Liu
- College of Agronomy, Northwest A & F University, Yangling, 712100, China
| | - Zihan Liu
- College of Agronomy, Northwest A & F University, Yangling, 712100, China
| | - Wei Li
- College of Agronomy, Northwest A & F University, Yangling, 712100, China
| | - Xiyue Song
- College of Agronomy, Northwest A & F University, Yangling, 712100, China.
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5
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Chandran AKN, Moon S, Yoo YH, Gho YS, Cao P, Sharma R, Sharma MK, Ronald PC, Jung KH. A web-based tool for the prediction of rice transcription factor function. Database (Oxford) 2020; 2019:5511305. [PMID: 31169887 PMCID: PMC6553503 DOI: 10.1093/database/baz061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/15/2019] [Indexed: 11/14/2022]
Abstract
Transcription factors (TFs) are an important class of regulatory molecules. Despite their importance, only a small number of genes encoding TFs have been characterized in Oryza sativa (rice), often because gene duplication and functional redundancy complicate their analysis. To address this challenge, we developed a web-based tool called the Rice Transcription Factor Phylogenomics Database (RTFDB) and demonstrate its application for predicting TF function. The RTFDB hosts transcriptome and co-expression analyses. Sources include high-throughput data from oligonucleotide microarray (Affymetrix and Agilent) as well as RNA-Seq-based expression profiles. We used the RTFDB to identify tissue-specific and stress-related gene expression. Subsequently, 273 genes preferentially expressed in specific tissues or organs, 455 genes showing a differential expression pattern in response to 4 abiotic stresses, 179 genes responsive to infection of various pathogens and 512 genes showing differential accumulation in response to various hormone treatments were identified through the meta-expression analysis. Pairwise Pearson correlation coefficient analysis between paralogous genes in a phylogenetic tree was used to assess their expression collinearity and thereby provides a hint on their genetic redundancy. Integrating transcriptome with the gene evolutionary information reveals the possible functional redundancy or dominance played by paralog genes in a highly duplicated genome such as rice. With this method, we estimated a predominant role for 83.3% (65/78) of the TF or transcriptional regulator genes that had been characterized via loss-of-function studies. In this regard, the proposed method is applicable for functional studies of other plant species with annotated genome.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Yoon-Shil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, China
| | - Rita Sharma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manoj K Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA.,Feedstocks Division, The Joint Bioenergy Institute, Emeryville, CA, USA
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
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Kong L, Duan Y, Ye Y, Cai Z, Wang F, Qu X, Qiu R, Wu C, Wu W. Screening and analysis of proteins interacting with OsMADS16 in rice (Oryza sativa L.). PLoS One 2019; 14:e0221473. [PMID: 31437207 PMCID: PMC6705763 DOI: 10.1371/journal.pone.0221473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 08/07/2019] [Indexed: 11/18/2022] Open
Abstract
OsMADS16, a class B floral organ identity gene, plays a pivotal role in stamen formation in rice. To date, little is known about the interacting partners of OsMADS16 except for several MADS-box proteins. In this study, we constructed a high-quality cDNA library of young panicles (< 5 cm in length) and performed yeast two-hybrid (Y2H) screening using OsMADS16 as bait. Eleven candidate proteins interacting with OsMADS16 were identified by Y2H and validated by BiFC and Co-IP assays. Subcellular localization results further confirmed the possibility of the interactions of OsMADS16 with 10 of the candidate proteins in natural rice cells. Bioinformatics analysis indicated that these partners exerted various molecular, cellular and physiological functions. Some of them were known or likely to be related to reproductive events, such as stamen primordium initiation, differentiation and development (OsMADS2, OsMADS4 and OsCOP9) and pollen development (OsbHLH40 and Os6PGDH). Our results provide an important reference for further research on OsMADS16-mediated regulation mechanism on floral organ development and pollen formation.
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Affiliation(s)
- Lan Kong
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuanlin Duan
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yanfang Ye
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhengzheng Cai
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Feng Wang
- Biotechnology Research Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Xiaojie Qu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ronghua Qiu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chunyan Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weiren Wu
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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7
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Ghaemizadeh F, Dashti F, Shafeinia A. Expression pattern of ABCDE model genes in floral organs of bolting garlic clone. Gene Expr Patterns 2019; 34:119059. [PMID: 31201930 DOI: 10.1016/j.gep.2019.119059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/27/2019] [Accepted: 06/03/2019] [Indexed: 11/16/2022]
Abstract
A correct understanding of the ABCDE model genes expression, especially genes involved in the development of the reproductive floral organs, in bolting and fertile garlic clones improves the process of its fertilization and breeding programs. Therefore, Real-Time PCR was employed to evaluate the temporal and spatial expression patterns of some floral organ identity genes in the inflorescence and different floret organs in the two stages of green and purple florets of bolting garlic clone. Relative expression of the studied genes, except AsSTK, in the mature inflorescence increased significantly during the early stages of initiation and differentiation of floral organs. Relative expression of the AsAP1 in the tepal and carpel, and AsAP2 in the tepal, stamen and carpel increased significantly. The highest relative expression levels of the AsAP1 and AsAP2 were found in the tepal of green florets and in the carpel of purple florets, respectively. AsAP3 and AsPI expression increased significantly in the stamen and carpel, and the highest relative expression of these two genes were observed in the green floret tepal. Relative expression of the AsAG increased significantly only in the reproductive floral organs and decreased significantly both in the carpel and stamen at floret maturity. The AsSEP1, 3 were expressed in all floral organs, but the AsSTK was only expressed in the carpel and its relative expression increased significantly at floret maturity. Finally, since considerable expression levels of the above genes were observed in the floral organs, these genes seem to be influential in the formation of floral organs in bolting garlic.
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Affiliation(s)
| | - Farshad Dashti
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran.
| | - Alireza Shafeinia
- Department of Agronomy and Plant Breeding, Ramin Agriculture and Natural University, Khuzestan, Iran.
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8
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Wu F, Zhang D, Muvunyi BP, Yan Q, Zhang Y, Yan Z, Cao M, Wang Y, Zhang J. Analysis of microRNA reveals cleistogamous and chasmogamous floret divergence in dimorphic plant. Sci Rep 2018; 8:6287. [PMID: 29674749 DOI: 10.1038/s41598-018-24477-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/04/2018] [Indexed: 12/31/2022] Open
Abstract
Cleistogenes songorica, a grass species that exhibits two spatially different type of inflorescence, chastogamy (CH), flowers localized at the top, and cleistogamy (CL) flowers embedded in leaf sheath. This study aimed at dissecting reasons underlying these distinct floral development patterns at morphological and microRNA level. Phenotyping for CH and CL was conducted and four small RNA libraries were constructed from the CH and CL flowers for high-throughput sequencing to identify the differentiated miRNAs. As results, spikelet, stigma, anther, lemma and lodicule length of CH flowers were found larger than that of CL, and so was seed setting. Also, 17 flower-related differential expression miRNAs were identified which were associated with floral organ development and morphogenesis, and the flower development. Further results showed that miR159a.1-CL3996.Contig2 pair was related to anther development, miR156a-5p-CL1954.Contig2 was linked to response to high light intensity, miR408-3p/miR408d-Unigene429 was related to pollination and Unigene429 positively regulated flower development. To our knowledge, this is the first study on differential miRNA accumulation between CH and CL flowers and our study serves as a foundation to the future elucidation of regulatory mechanisms of miRNAs in the divergent development of CL and CH flowers in a single plant.
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Sun CH, Yu JQ, Wen LZ, Guo YH, Sun X, Hao YJ, Hu DG, Zheng CS. Chrysanthemum MADS-box transcription factor CmANR1 modulates lateral root development via homo-/heterodimerization to influence auxin accumulation in Arabidopsis. Plant Sci 2018; 266:27-36. [PMID: 29241564 DOI: 10.1016/j.plantsci.2017.09.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 05/20/2023]
Abstract
Root system architecture is an important agronomic trait by which plants both acquire water and nutrients from the soil and adapt to survive in a complex environment. The adaptation of plant root systems to environmental constraints largely depends on the growth and development of lateral roots (LRs). MADS-box transcription factors (TFs) are important known regulators of plant growth, development, and response to environmental stimuli. However, the potential mechanisms by which they regulate LRs development remain poorly understood. Here, we identified a MADS-box chrysanthemum gene CmANR1, homologous to the Arabidopsis gene AtANR1, which plays a key role in the regulation of LR development. qRT-PCR assays indicated that CmANR1 was primarily expressed in chrysanthemum roots and was rapidly induced by exposure to high nitrate concentrations. Ectopic expression of CmANR1 in Arabidopsis significantly increased the number and length of emerged LRs compared to the wild-type (col) control, but had no obvious affect on primary root (PR) development. We also found that CmANR1 positively influenced auxin accumulation in LRs at least partly by improving auxin biosynthesis and transport, thereby promoting LR development. Furthermore, we found that ANR1 formed homo- and heterodimers through interactions with itself and AGL21 at its C-terminal domain. Overall, our findings provide considerable new information about the mechanisms by which the chrysanthemum MADS-box TF CmANR1 mediates LR development by directly altering auxin accumulation.
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Affiliation(s)
- Cui-Hui Sun
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Jian-Qiang Yu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Li-Zhu Wen
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Yun-Hui Guo
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Xia Sun
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Yu-Jin Hao
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Da-Gang Hu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China.
| | - Cheng-Shu Zheng
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China.
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Ye S, Yang W, Zhai R, Lu Y, Wang J, Zhang X. Mapping and application of the twin-grain1 gene in rice. Planta 2017; 245:707-716. [PMID: 27999987 DOI: 10.1007/s00425-016-2627-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
The map-based cloning and application of a flower organ number gene twin - grain1 provide great potential for improving seed production in hybrid rice. A new germplasm for high-yield rice breeding, the twin-grain1 (tg1) mutant with more than one grain in a glume, was obtained from the Zhejing 22 rice variety via physical mutagenesis. The mapping results showed that TG1 is allelic to FLORAL ORGAN NUMBER2 (FON2)/FLORAL ORGAN NUMBER4 (FON4), a flower organ number gene located at 88.7 cM on chromosome 11. The novel tg1 gene allele was introgressed into the cytoplasmic male sterility (CMS) line Zhejing 22A, giving rise to a new CMS line Zhejing 22-tg1A. The Zhejing 22-tg1A line showed enhanced glume opening and stigma exsertion, which increased the outcrossing rate in hybrid rice. A small-scale hybrid rice seed production test demonstrated that the grain yield of the Zhejing 22-tg1A/Zhejinghui 5 line was significantly increased compared to that of the Zhejing 22A/Zhejinghui 5 line. The plot yield evaluation of the F1 hybrid lines showed a higher yield for the Zhejing 22-tg1A/Zhejinghui 5 line than that of the Zhejing 22A/Zhejinghui 5 line. The results implied great potentials for the tg1 gene in hybrid rice breeding.
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Affiliation(s)
- Shenghai Ye
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Weibing Yang
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Rongrong Zhai
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yanting Lu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junmei Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoming Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Ai Y, Zhang C, Sun Y, Wang W, He Y, Bao M. Characterization and Functional Analysis of Five MADS-Box B Class Genes Related to Floral Organ Identification in Tagetes erecta. PLoS One 2017; 12:e0169777. [PMID: 28081202 PMCID: PMC5231280 DOI: 10.1371/journal.pone.0169777] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/21/2016] [Indexed: 11/23/2022] Open
Abstract
According to the floral organ development ABC model, B class genes specify petal and stamen identification. In order to study the function of B class genes in flower development of Tagetes erecta, five MADS-box B class genes were identified and their expression and putative functions were studied. Sequence comparisons and phylogenetic analyses indicated that there were one PI-like gene-TePI, two euAP3-like genes-TeAP3-1 and TeAP3-2, and two TM6-like genes-TeTM6-1 and TeTM6-2 in T. erecta. Strong expression levels of these genes were detected in stamens of the disk florets, but little or no expression was detected in bracts, receptacles or vegetative organs. Yeast hybrid experiments of the B class proteins showed that TePI protein could form a homodimer and heterodimers with all the other four B class proteins TeAP3-1, TeAP3-2, TeTM6-1 and TeTM6-2. No homodimer or interaction was observed between the euAP3 and TM6 clade members. Over-expression of five B class genes of T. erecta in Nicotiana rotundifolia showed that only the transgenic plants of 35S::TePI showed altered floral morphology compared with the non-transgenic line. This study could contribute to the understanding of the function of B class genes in flower development of T. erecta, and provide a theoretical basis for further research to change floral organ structures and create new materials for plant breeding.
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Affiliation(s)
- Ye Ai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou, Fujian, China
| | - Chunling Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yalin Sun
- Institute of Vegetable Science, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Weining Wang
- Gulf Coast Research and Education Center, Department of Environmental Horticulture, University of Florida, Wimauma, Florida, United States of America
| | - Yanhong He
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
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12
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Nguyen TD, Moon S, Nguyen VNT, Gho Y, Chandran AKN, Soh MS, Song JT, An G, Oh SA, Park SK, Jung KH. Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage. Plant Mol Biol 2016; 92:71-88. [PMID: 27356912 DOI: 10.1007/s11103-016-0496-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/23/2016] [Indexed: 06/06/2023]
Abstract
Microspore production using endogenous developmental programs has not been well studied. The main limitation is the difficulty in identifying genes preferentially expressed in pollen grains at early stages. To overcome this limitation, we collected transcriptome data from anthers and microspore/pollen and performed meta-expression analysis. Subsequently, we identified 410 genes showing preferential expression patterns in early developing pollen samples of both japonica and indica cultivars. The expression patterns of these genes are distinguishable from genes showing pollen mother cell or tapetum-preferred expression patterns. Gene Ontology enrichment and MapMan analyses indicated that microspores in rice are closely linked with protein degradation, nucleotide metabolism, and DNA biosynthesis and regulation, while the pollen mother cell or tapetum are strongly associated with cell wall metabolism, lipid metabolism, secondary metabolism, and RNA biosynthesis and regulation. We also generated transgenic lines under the control of the promoters of eight microspore-preferred genes and confirmed the preferred expression patterns in plants using the GUS reporting system. Furthermore, cis-regulatory element analysis revealed that pollen specific elements such as POLLEN1LELAT52, and 5659BOXLELAT5659 were commonly identified in the promoter regions of eight rice genes with more frequency than estimation. Our study will provide new sights on early pollen development in rice, a model crop plant.
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Affiliation(s)
- Tien Dung Nguyen
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Van Ngoc Tuyet Nguyen
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Yunsil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Anil Kumar Nalini Chandran
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Moon-Soo Soh
- Department of Molecular Biology, Sejong University, Seoul, 143-747, Republic of Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Sung Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea.
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
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13
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Tian X, Yu Q, Liu H, Liao J. Temporal-Spatial Transcriptome Analyses Provide Insights into the Development of Petaloid Androecium in Canna indica. Front Plant Sci 2016; 7:1194. [PMID: 27582744 PMCID: PMC4987385 DOI: 10.3389/fpls.2016.01194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Canna indica (Zingiberales) is one of the most important ornamental species characterized with beautiful petaloid staminodes, which are considered to evolve from stamens. However, the genetic basis for the development of petaloid staminodes remains unclear largely because the genomic sequences are not available. By using RNA-Seq, we sequenced the transcripts in the flower of C. indica, and quantified the temporal gene expressions in flower primordium and differentiated flower, as well as the spatial gene expressions in petal and petaloid staminode. In total, 118,869 unigenes were assembled, among which 67,299 unigenes were annotated. Quantification analysis identified the differentially expressed genes in the temporal and spatial two comparisons, based on which, Gene Ontology enrichment analysis highlighted the representative terms in each sample, such as specification of organ number in flower primordium, growth in differentiated flower, secondary cell wall biogenesis in petal and cell division in petaloid staminode. Among the 51 analyzed MADS-box unigenes, 37 were up-regulated in differentiated flower compared with those in flower primordium. A-class unigenes were expressed higher in petal than in petaloid staminode, and C-class unigenes were expressed oppositely, whereas B-class unigenes demonstrated close expression levels in these two organs, indicating that petaloid staminode retains stamen identity to some degree. In situ hybridization provided more detailed expression patterns of these unigenes, and revealed the extended expression of B-class to the carpel at later stages when the style turned flat. These results constitute a preliminary basis for the study of flower development in C. indica and can be applied in further study of the evolution of Zingiberales.
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Affiliation(s)
- Xueyi Tian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Qianxia Yu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Huanfang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Jingping Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
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14
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WEI SHUHONG. Molecular cloning, characterization and expression of WAG-2 alternative splicing transcripts in developing spikes of Aegilops tauschii. J Genet 2016; 95:581-5. [DOI: 10.1007/s12041-016-0668-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Bartlett M, Thompson B, Brabazon H, Del Gizzi R, Zhang T, Whipple C. Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein-Protein Interactions. Mol Biol Evol 2016; 33:1486-501. [PMID: 26908583 PMCID: PMC4868119 DOI: 10.1093/molbev/msw031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Protein–protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PIL) and AP3-like (AP3L) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PIL protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PIL homodimerization is an anomaly or indicative of broader trends, we characterized PIL dimerization across the Poales and uncovered unexpected evolutionary lability. Both obligate B-class heterodimerization and PIL homodimerization have evolved multiple times in the order, by distinct molecular mechanisms. For example, obligate B-class heterodimerization in maize evolved very recently from PIL homodimerization. A single amino acid change, fixed during domestication, is sufficient to toggle one maize PIL protein between homodimerization and obligate heterodimerization. We detected a signature of positive selection acting on residues preferentially clustered in predicted sites of contact between MADS-box monomers and dimers, and in motifs that mediate MADS PPI specificity in Arabidopsis. Changing one positively selected residue can alter PIL dimerization activity. Furthermore, ectopic expression of a Joinvillea PIL homodimer in Arabidopsis can homeotically transform sepals into petals. Our results provide a window into the evolutionary remodeling of PPIs, and show that novel interactions have the potential to alter plant form in a context-dependent manner.
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Affiliation(s)
- Madelaine Bartlett
- Department of Biology, University of Massachusetts Amherst Department of Biology, Brigham Young University
| | | | | | | | - Thompson Zhang
- Department of Biology, University of Massachusetts Amherst
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Xiang C, Liang X, Chu R, Duan M, Cheng J, Ding Z, Wang J. Fine mapping of a palea defective 1 (pd1), a locus associated with palea and stamen development in rice. Plant Cell Rep 2015; 34:2151-2159. [PMID: 26441054 DOI: 10.1007/s00299-015-1858-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 07/16/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
KEY MESSAGE : pd1, a genetic factor in a 69 kb region between RM11239 and RM11245 on rice chromosome 1, controls stamen number and palea development. Spikelets are important organs that store photosynthetic products in rice. Spikelet development directly affects grain yield and rice quality. Here, we report a palea defective (pd1) mutant identified from selfing progenies of indica cv. 93-11 after (60)Co γ ray treatment. pd1 mutant flowers only had four stamens (wild-type has six), but pollen fertility was not affected. Compared with 93-11 palea, pd1 mutant palea showed smaller and flatter leaf, which caused the lemma to bend excessively inward. pd1 mutants had only 46% seed setting rate and 21.6 g 1000-grain weight, which led to two-thirds loss of grain yield. Scanning electron microscope analysis revealed that pd1 mutants had reduced epidermal cell size and reduced numbers of fibrous sclerenchyma cells in both palea and lemma. To analyze the genetic factors involved, we crossed pd1 mutants with three japonica cultivars and generated F1 and F2 populations. The F1 phenotype and F2 segregation ratio indicated that a recessive gene controlled the mutant traits. Using the F2 population, we found that pd1 mapped between the simple sequence repeat markers RM11236 and RM11280 on rice chromosome 1. From a segregating population of 2836 plants, 77 recombinants were screened by RM11236 and RM11280. High-resolution linkage analysis narrowed the pd1 locus to a 69 kb region between RM11239 and RM11245 that contained 10 open reading frames (ORFs). Sequence alignment and quantitative real-time PCR expression analysis of these ORFs between 93-11 and pd1 mutant plants found no unequivocal evidence to identify the pd1 gene.
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Affiliation(s)
- Chunyan Xiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinxing Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruizhen Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinping Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhengquan Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianfei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Abstract
CHD3 is one of the chromatin-remodeling factors that contribute to controlling the expression of genes associated with plant development. Loss-of-function mutants display morphological and growth defects. However, the molecular mechanisms underlying CHD3 regulation of plant development remain unclear. In this study, a rice CHD3 protein, CHR729, was identified. The corresponding mutant line (t483) exhibited late seed germination, low germination rate, dwarfism, low tiller number, root growth inhibition, adaxial albino leaves, and short and narrow leaves. CHR729 encoded a nuclear protein and was expressed in almost all organs. RNA-sequencing analysis showed that several plant hormone-related genes were up- or down-regulated in t483 compared to wild type. In particular, expression of the gibberellin synthetase gibberellin 20 oxidase 4 gene was elevated in the mutant. Endogenous gibberellin assays demonstrated that the content of bioactive GA3 was reduced in t483 compared to wild type. Moreover, the seedling dwarfism, late seed germination, and short root length phenotypes of t483 were partially rescued by treatment with exogenous GA3. These results suggest that the rice CHD3 protein CHR729 plays an important role in many aspects of seedling development and controls this development via the gibberellin pathway.
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Affiliation(s)
- Xiaoding Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Ma
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Honghong Zhai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Peiyong Xin
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jinfang Chu
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yongli Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longzhi Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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Xu Y, Wang Y, Long Q, Huang J, Wang Y, Zhou K, Zheng M, Sun J, Chen H, Chen S, Jiang L, Wang C, Wan J. Overexpression of OsZHD1, a zinc finger homeodomain class homeobox transcription factor, induces abaxially curled and drooping leaf in rice. Planta 2014; 239:803-16. [PMID: 24385091 DOI: 10.1007/s00425-013-2009-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/08/2013] [Indexed: 05/05/2023]
Abstract
Leaf rolling is receiving considerable attention as an important agronomic trait in rice (Oryza sativa L.). However, little has been known on the molecular mechanism of rice leaf rolling, especially the abaxial rolling. We identified a novel abaxially curled and drooping leaf-dominant mutant from a T₁ transgenic rice line. The abaxially curled leaf phenotypes, co-segregating with the inserted transferred DNA, were caused by overexpression of a zinc finger homeodomain class homeobox transcription factor (OsZHD1). OsZHD1 exhibited a constitutive expression pattern in wild-type plants and accumulated in the developing leaves and panicles. Artificial overexpression of OsZHD1 or its closest homolog OsZHD2 induced the abaxial leaf curling. Histological analysis indicated that both the increased number and the abnormal arrangement of bulliform cells in leaf were responsible for the abaxially curled leaves. We herein reported OsZHD1 with key roles in rice morphogenesis, especially in the modulating of leaf rolling, which provided a novel insight into the molecular mechanism of leaf development in rice.
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Affiliation(s)
- Yang Xu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
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Fu Q, Liu H, Almeida AMR, Kuang Y, Zou P, Liao J. Molecular basis of floral petaloidy: insights from androecia of Canna indica. AoB Plants 2014; 6:plu015. [PMID: 24876297 PMCID: PMC4011470 DOI: 10.1093/aobpla/plu015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 03/18/2014] [Indexed: 06/03/2023]
Abstract
Floral organs that take on the characteristics of petals can occur in all whorls of the monocot order Zingiberales. In Canna indica, the most ornamental or 'petaloid' parts of the flowers are of androecial origin and are considered staminodes. However, the precise nature of these petaloid organs is yet to be determined. In order to gain a better understanding of the genetic basis of androecial identity, a molecular investigation of B- and C-class genes was carried out. Two MADS-box genes GLOBOSA (GLO) and AGAMOUS (AG) were isolated from young inflorescences of C. indica by 3' rapid amplification of cDNA ends polymerase chain reaction (3'-RACE PCR). Sequence characterization and phylogenetic analyses show that CiGLO and CiAG belong to the B- and C-class MADS-box gene family, respectively. CiAG is expressed in petaloid staminodes, the labellum, the fertile stamen and carpels. CiGLO is expressed in petals, petaloid staminodes, the labellum, the fertile stamen and carpels. Expression patterns in mature tissues of CiGLO and CiAG suggest that petaloid staminodes and the labellum are of androecial identity, in agreement with their position within the flower and with described Arabidopsis thaliana expression patterns. Although B- and C-class genes are important components of androecial determination, their expression patterns are not sufficient to explain the distinct morphology observed in staminodes and the fertile stamen in C. indica.
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Affiliation(s)
- Qian Fu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Huanfang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Ana M R Almeida
- Department of Plant and Microbial Biology and the University and Jepson Herbaria, University of California, Berkeley, CA 94720, USA
| | - Yanfeng Kuang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Pu Zou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Jingping Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
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20
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Li X, Liu C, Da F, Ma N, Shen H. Expression pattern of Class B gene PAP3 in flower development of pepper. Int J Mol Sci 2013; 14:24643-55. [PMID: 24351839 PMCID: PMC3876133 DOI: 10.3390/ijms141224643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/24/2013] [Accepted: 12/03/2013] [Indexed: 11/26/2022] Open
Abstract
Class B gene APETALA3 (AP3) plays a key role in the development of petals and stamens. Here, we investigated the expression pattern of PAP3 gene (genbank accession number: HM104635) in the buds of cytoplasmic male sterility line 121A and its near-isogenic restorer line 121C at four developmental stages and analyzed the possible association between Class B genes and cytoplasmic male sterility of pepper. Semi-quantitative PCR and quantitative real-time RT-PCR (qRT-PCR) as well as RNA in situ hybridization showed increased expression of PAP3 at late phase of anther development and its higher expression in restorer line compared with sterility line indicating PAP3’s role at late developmental stage of anther and suppressed expression in sterility line. RNA in situ hybridization showed Class B gene features: high abundance in stamen and petal; lower expression in pistil; no expression in sepal. Results of transient expression in onion epidermal cells also showed PAP3 localized in the nucleus, which is consistent with the expression pattern of transcription factors of MADS-box gene family.
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Affiliation(s)
| | | | | | | | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.
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21
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Liu S, Sun Y, Du X, Xu Q, Wu F, Meng Z. Analysis of the APETALA3- and PISTILLATA-like genes in Hedyosmum orientale (Chloranthaceae) provides insight into the evolution of the floral homeotic B-function in angiosperms. Ann Bot 2013; 112:1239-51. [PMID: 23956161 PMCID: PMC3806522 DOI: 10.1093/aob/mct182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/28/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS According to the floral ABC model, B-function genes appear to play a key role in the origin and diversification of the perianth during the evolution of angiosperms. The basal angiosperm Hedyosmum orientale (Chloranthaceae) has unisexual inflorescences associated with a seemingly primitive reproductive morphology and a reduced perianth structure in female flowers. The aim of this study was to investigate the nature of the perianth and the evolutionary state of the B-function programme in this species. METHODS A series of experiments were conducted to characterize B-gene homologues isolated from H. orientale, including scanning electron microscopy to observe the development of floral organs, phylogenetic analysis to reconstruct gene evolutionary history, reverse transcription-PCR, quantitative real-time PCR and in situ hybridization to identify gene expression patterns, the yeast two-hybrid assay to explore protein dimerization affinities, and transgenic analyses in Arabidopsis thaliana to determine activities of the encoded proteins. KEY RESULTS The expression of HoAP3 genes was restricted to stamens, whereas HoPI genes were broadly expressed in all floral organs. HoAP3 was able to partially restore the stamen but not petal identity in Arabidopsis ap3-3 mutants. In contrast, HoPI could rescue aspects of both stamen and petal development in Arabidopsis pi-1 mutants. When the complete C-terminal sequence of HoPI was deleted, however, no or weak transgenic phenotypes were observed and homodimerization capability was completely abolished. CONCLUSIONS The results suggest that Hedyosmum AP3-like genes have an ancestral function in specifying male reproductive organs, and that the activity of the encoded PI-like proteins is highly conserved between Hedyosmum and Arabidopsis. Moreover, there is evidence that the C-terminal region is important for the function of HoPI. Our findings indicate that the development of the proposed perianth in Hedyosmum does not rely on the B homeotic function.
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Affiliation(s)
- Shujun Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghua Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoqiu Du
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qijiang Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Department of Botany, Northeast Forestry University, Haerbin 150040, China
| | - Feng Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zheng Meng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- For correspondence. E-mail
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Wei X, Zhang X, Shao G, He J, Jiao G, Xie L, Sheng Z, Tang S, Hu P. Fine mapping of BH1, a gene controlling lemma and palea development in rice. Plant Cell Rep 2013; 32:1455-1463. [PMID: 23689259 DOI: 10.1007/s00299-013-1457-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 05/02/2013] [Accepted: 05/03/2013] [Indexed: 06/02/2023]
Abstract
A new rice floral organ mutant bh1 , had a negative effect on grain yield. BH1 was fine mapped to 87.5 kb on chr2. A 55 kb chromosome segment was deleted in bh1. The cereal spikelet is enclosed by the lemma and palea. The lemma and palea of the floral mutant designated bh1, a selection from a T-DNA library generated from the rice cultivar Asominori, takes on an abnormal curve-shaped appearance only late in floral development, finally forming a beak-shaped hull. The mutation had a negative effect on thousand grain weight, seed set rate and germination rate. Genetic analysis indicated that the mutant phenotype was determined by a single recessive gene. Through map-based approach, BH1 gene was finally located to a ~87.5-kbp region on the long arm of chromosome 2. An analysis of the gene content of this region indicated that the mutation involves the loss of a 55-kbp stretch, harboring four open reading frames. Transcription profiling based on qRT-PCR revealed that the genes OsMADS1, OsMADS14, OsMADS15, OsMADS18, REP1, CFO1, and DL, all of which are also involved in lemma and palea development and identity specification, were down-regulated in the bh1 mutant. BH1 is therefore an important floral organ development gene.
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Affiliation(s)
- Xiangjin Wei
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 310006, China
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Kim YS, Kim IS, Bae MJ, Choe YH, Kim YH, Park HM, Kang HG, Yoon HS. Homologous expression of cytosolic dehydroascorbate reductase increases grain yield and biomass under paddy field conditions in transgenic rice (Oryza sativa L. japonica). Planta 2013; 237:1613-25. [PMID: 23519921 DOI: 10.1007/s00425-013-1862-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/23/2013] [Indexed: 05/25/2023]
Abstract
Dehydroascorbate reductase (DHAR, EC 1.8.5.1) maintains redox pools of ascorbate (AsA) by recycling oxidized AsA to reduced AsA. To investigate whether DHAR affects rice yield under normal environmental conditions, cDNA-encoding DHAR (OsDHAR1) was isolated from rice and used to develop OsDHAR1-overexpressing transgenic rice plants, under the regulation of a maize ubiquitin promoter. Incorporation and expression of the transgene in transgenic rice plants was confirmed by genomic polymerase chain reaction (PCR), semi-quantitative reverse transcription PCR (RT-PCR), western blot, and enzyme activity. The expression levels were at least twofold higher in transgenic (TG) rice plants than in control wild-type (WT) rice plants. In addition, OsDHAR1-overexpression in seven-independent homologous transgenic plants, as compared to WT plants, increased photosynthetic capacity and antioxidant enzyme activities under paddy field conditions, which led to an improved AsA pool and redox homeostasis. Furthermore, OsDHAR1 overexpression significantly improved grain yield and biomass due to the increase of culm and root weights and to enhance panicle and spikelet numbers in the same seven independent TG rice plants during the farming season (2010 and 2011) in South Korea. The OsDHAR protein contained the redox-active site (Cys20), as well as the conserved GSH-binding region, GSH-binding motif, glutathione-S-transferase (GST) N-terminal domain, C-terminal domain interface, and GST C-terminal domain. Therefore, our results indicate that OsDHAR1 overexpression, capable of functioning in AsA recycling, and protein folding increases environmental adaptation to paddy field conditions by the improving AsA pool and redox homeostasis, which enhances rice grain yield and biomass.
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Affiliation(s)
- Young-Saeng Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 702-701, South Korea.
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Abstract
Genes of the AGAMOUS subfamily have been shown to play crucial roles in reproductive organ identity determination, fruit, and seed development. They have been deeply studied in eudicot species and especially in Arabidopsis. Recently, the AGAMOUS subfamily of rice has been studied for their role in flower development and an enormous amount of data has been generated. In this review, we provide an overview of these data and discuss the conservation of gene functions between rice and Arabidopsis.
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Affiliation(s)
- Ludovico Dreni
- Department of Biosciences, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy
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25
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Choe YH, Kim YS, Kim IS, Bae MJ, Lee EJ, Kim YH, Park HM, Yoon HS. Homologous expression of γ-glutamylcysteine synthetase increases grain yield and tolerance of transgenic rice plants to environmental stresses. J Plant Physiol 2013; 170:610-8. [PMID: 23294545 DOI: 10.1016/j.jplph.2012.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 12/03/2012] [Accepted: 12/03/2012] [Indexed: 05/17/2023]
Abstract
Various environmental stresses induce reactive oxygen species (ROS), causing deleterious effects on plant cells. Glutathione (GSH), a critical antioxidant, is used to combat ROS. GSH is produced by γ-glutamylcysteine synthetase (γ-ECS) and glutathione synthetase (GS). To evaluate the functional roles of the Oryza sativa L. Japonica cv. Ilmi ECS (OsECS) gene, we generated transgenic rice plants overexpressing OsECS under the control of an inducible promoter (Rab21). When grown under saline conditions (100mM) for 4 weeks, 2-independent transgenic (TGR1 and TGR2) rice plants remained bright green in comparison to control wild-type (WT) rice plants. TGR1 and TGR2 rice plants also showed a higher GSH/GSSG ratio than did WT rice plants in the presence of 100mM NaCl, which led to enhanced redox homeostasis. TGR1 and TGR2 rice plants also showed lower ion leakage and higher chlorophyll-fluorescence when exposed to 10μM methyl viologen (MV). Furthermore, the TGR1 and TGR2 rice seeds had approximately 1.5-fold higher germination rates in the presence of 200mM salt. Under paddy field conditions, OsECS-overexpression in transgenic rice plants increased rice grain yield (TGW) and improved biomass. Overall, our results show that OsECS overexpression in transgenic rice increases tolerance and germination rate in the presence of abiotic stress by improving redox homeostasis via an enhanced GSH pool. Our findings suggest that increases in grain yield by OsECS overexpression could improve crop yields under natural environmental conditions.
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MESH Headings
- Acclimatization
- Agrobacterium/genetics
- Cloning, Molecular
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- Epistasis, Genetic
- Gene Expression Regulation, Plant
- Glutamate-Cysteine Ligase/genetics
- Glutamate-Cysteine Ligase/metabolism
- Glutathione/genetics
- Glutathione/metabolism
- Homeostasis
- Oryza/genetics
- Oryza/growth & development
- Oryza/physiology
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/growth & development
- Plants, Genetically Modified/physiology
- Polymerase Chain Reaction
- Promoter Regions, Genetic
- Salt Tolerance
- Stress, Physiological
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Affiliation(s)
- Yong-Hoe Choe
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 702-701, South Korea.
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Liu Z, Ma L, Nan Z, Wang Y. Comparative transcriptional profiling provides insights into the evolution and development of the zygomorphic flower of Vicia sativa (Papilionoideae). PLoS One 2013; 8:e57338. [PMID: 23437373 PMCID: PMC3578871 DOI: 10.1371/journal.pone.0057338] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/21/2013] [Indexed: 01/07/2023] Open
Abstract
Background Vicia sativa (the common vetch) possesses a predominant zygomorphic flower and belongs to the subfamily Papilionoideae, which is related to Arabidopsis thaliana in the eurosid II clade of the core eudicots. Each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center. Methodology/Principal Findings We explored the floral transcriptome to examine a genome-scale genetic model of the zygomorphic flower of vetch. mRNA was obtained from an equal mixture of six floral organs, leaves and roots. De novo assembly of the vetch transcriptome using Illumina paired-end technology produced 71,553 unigenes with an average length of 511 bp. We then compared the expression changes in the 71,553 unigenes in the eight independent organs through RNA-Seq Quantification analysis. We predominantly analyzed gene expression patterns specific to each floral organ and combinations of floral organs that corresponded to the traditional ABC model domains. Comparative analyses were performed in the floral transcriptomes of vetch and Arabidopsis, and genomes of vetch and Medicago truncatula. Conclusions/Significance Our comparative analysis of vetch and Arabidopsis showed that the vetch flowers conform to a strict ABC model. We analyzed the evolution and expression of the TCP gene family in vetch at a whole-genome level, and several unigenes specific to three different vetch petals, which might offer some clues toward elucidating the molecular mechanisms underlying floral zygomorphy. Our results provide the first insights into the genome-scale molecular regulatory network that controls the evolution and development of the zygomorphic flower in Papilionoideae.
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Affiliation(s)
- Zhipeng Liu
- State Key Laboratory of Grassland Agro-ecosystems, School of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
- * E-mail: (ZL); (YW)
| | - Lichao Ma
- State Key Laboratory of Grassland Agro-ecosystems, School of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-ecosystems, School of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, School of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
- * E-mail: (ZL); (YW)
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Zhang XM, Zhao L, Larson-Rabin Z, Li DZ, Guo ZH. De novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae). PLoS One 2012; 7:e42082. [PMID: 22916120 DOI: 10.1371/journal.pone.0042082] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 07/02/2012] [Indexed: 12/13/2022] Open
Abstract
Background Transcriptome sequencing can be used to determine gene sequences and transcript abundance in non-model species, and the advent of next-generation sequencing (NGS) technologies has greatly decreased the cost and time required for this process. Transcriptome data are especially desirable in bamboo species, as certain members constitute an economically and culturally important group of mostly semelparous plants with remarkable flowering features, yet little bamboo genomic research has been performed. Here we present, for the first time, extensive sequence and transcript abundance data for the floral transcriptome of a key bamboo species, Dendrocalamus latiflorus, obtained using the Illumina GAII sequencing platform. Our further goal was to identify patterns of gene expression during bamboo flower development. Results Approximately 96 million sequencing reads were generated and assembled de novo, yielding 146,395 high quality unigenes with an average length of 461 bp. Of these, 80,418 were identified as putative homologs of annotated sequences in the public protein databases, of which 290 were associated with the floral transition and 47 were related to flower development. Digital abundance analysis identified 26,529 transcripts differentially enriched between two developmental stages, young flower buds and older developing flowers. Unigenes found at each stage were categorized according to their putative functional categories. These sequence and putative function data comprise a resource for future investigation of the floral transition and flower development in bamboo species. Conclusions Our results present the first broad survey of a bamboo floral transcriptome. Although it will be necessary to validate the functions carried out by these genes, these results represent a starting point for future functional research on D. latiflorus and related species.
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28
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Lee DY, An G. Two AP2 family genes, supernumerary bract (SNB) and Osindeterminate spikelet 1 (OsIDS1), synergistically control inflorescence architecture and floral meristem establishment in rice. Plant J 2012; 69:445-61. [PMID: 22003982 DOI: 10.1111/j.1365-313x.2011.04804.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Meristem identity is crucial in determining the inflorescence architecture of grass species. We previously reported that SUPERNUMERARY BRACT (SNB) regulates the transition of spikelet meristems into floral meristems in rice (Oryza sativa). Here we demonstrated that SNB and Oryza sativa INDETERMINATE SPIKELET 1 (OsIDS1) together play important roles in inflorescence architecture and the establishment of floral meristems. In snb osids1 double mutants, the numbers of branches and spikelets within a panicle are significantly decreased, and the transition to a floral meristem is further delayed compared with the snb single mutant. Expression analyses showed that SNB and OsIDS1 are required for spatio-temporal expression of B- and E-function floral organ identity genes in the lodicules. In addition, the AP2 family genes are important for determining the degree of ramification in branch meristems, regulating the spatio-temporal expression of spikelet meristem genes, such as FRIZZY PANICLE (FZP). Furthermore, overexpression of microRNA172 (miR172) causes reductions in SNB and OsIDS1 transcript levels, and phenotypes of the transgenic plants are more severe than for snb osids1. This indicates that additional gene(s) participate in the development of branch and floral meristems. Preferential expression of mature miR172s in the area around the spikelet meristems implies that depletion of the AP2 family genes in those meristems via miR172 is an important step in controlling inflorescence branching and the formation of floral organs.
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Affiliation(s)
- Dong-Yeon Lee
- Department of Plant Molecular Systems Biotechnology, Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
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29
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Lee S, Ryoo N, Jeon JS, Guerinot ML, An G. Activation of rice Yellow Stripe1-Like 16 (OsYSL16) enhances iron efficiency. Mol Cells 2012; 33:117-26. [PMID: 22228180 PMCID: PMC3887722 DOI: 10.1007/s10059-012-2165-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 11/16/2011] [Accepted: 11/17/2011] [Indexed: 10/14/2022] Open
Abstract
Graminaceous plants release ferric-chelating phytosiderophores that bind to iron. These ferric-phytosiderophore complexes are transported across the plasma membrane by a protein produced from Yellow Stripe 1 (YS1). Here, we report the characterization of OsYSL16, one of the YS1-like genes in rice. Real-time analysis revealed that this gene was constitutively expressed irrespective of metal status. Promoter fusions of OsYSL16 to β-glucuronidase (GUS) showed that OsYSL16 was highly expressed in the vascular tissues of the root, leaf, and spikelet, and in leaf mesophyll cells. The OsYSL16-green fluorescence protein (GFP) fusion protein was localized to the plasma membrane. From a pool of rice T-DNA insertional lines, we identified two independent activation-tagging mutants in OsYSL16. On an Fe-deficient medium, those mutants retained relatively high chlorophyll concentrations compared with the wild-type (WT) controls, indicating that they are more tolerant to a lack of iron. The Fe concentration in shoots was also higher in the OsYSL16 activation lines than in the WT. During germination, the rate of Fe-utilization from the seeds was higher in the OsYSL16 activation lines than in the WT seeds. Our results suggest that the function of OsYSL16 in Fe-homeostasis is to enable distribution of iron within a plant.
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Affiliation(s)
- Sichul Lee
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire,
USA
| | - Nayeon Ryoo
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701,
Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701,
Korea
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire,
USA
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 446-701,
Korea
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Sato H, Yoshida K, Mitsuda N, Ohme-Takagi M, Takamizo T. Male-sterile and cleistogamous phenotypes in tall fescue induced by chimeric repressors of SUPERWOMAN1 and OsMADS58. Plant Sci 2012; 183:183-189. [PMID: 22195592 DOI: 10.1016/j.plantsci.2011.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 08/19/2011] [Accepted: 08/24/2011] [Indexed: 05/31/2023]
Abstract
Since tall fescue (Festuca arundinacea Schreb.) is an anemophilous (wind-pollinated) grass species, male sterility is strongly desired for transgenic tall fescue to prevent pollen dispersal. To create male-sterile tall fescue, we applied Chimeric REpressor gene-Silencing Technology (CRES-T) based on rice APETALA3 (AP3) and AGAMOUS (AG) orthologues that specify the formation of stamens. We fused the coding regions of rice AP3 orthologue SUPERWOMAN1 (SPW1), and rice AG orthologues, Os12g0207000, Os01g0886200 and OsMADS58, respectively with the artificial sequence encoding the modified EAR-like motif repression domain (SRDX). We first introduced Os12g0207000SRDX, Os01g0886200SRDX and OsMADS58SRDX into rice for evaluation of their abilities to induce male sterility. The transgenic rice expressing OsMADS58SRDX had reiterated formation of lodicule-like organs instead of stamens and carpel, a typical phenotype of ag mutant. Thus, we found that OsMADS58SRDX was most suitable for our purpose. Next, we introduced SPW1SRDX and OsMADS58SRDX into tall fescue. Although the transgenic tall fescue did not have the stamen alterations seen in SPW1SRDX and OsMADS58SRDX rice, they either produced no pollen or produced immature pollen; thus, the anthers were not dehiscent and the plants were male-sterile. In addition to the male sterility, SPW1SRDX tall fescue showed a cleistogamous (closed) phenotype in which anthers were not observed outside the glumes, with thin, abnormally elongated lodicules. Some lines of OsMADS58SRDX tall fescue showed a cleistogamous phenotype in which the lodicules were homeotically transformed into lemma-like organs. In both cases, cleistogamous phenotype was associated with morphological changes to the lodicules. We also obtained a mild phenotype of OsMADS58SRDX tall fescue, which exhibited only the male sterility. In this study, we produced novel male-sterile phenotypes using chimeric repressors and thus suggest CRES-T as a tool for transgenic improvement of forage and turf grasses.
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Affiliation(s)
- Hiroko Sato
- Forage Crop Research Division, NARO Institute of Livestock and Grassland Science, 768 Senbonmatsu, Nasushiobara, Tochigi 329-2793, Japan.
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Landis JB, Barnett LL, Hileman LC. Evolution of petaloid sepals independent of shifts in B-class MADS box gene expression. Dev Genes Evol 2011; 222:19-28. [PMID: 22198545 DOI: 10.1007/s00427-011-0385-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 12/06/2011] [Indexed: 01/09/2023]
Abstract
Attractive petals are an integral component of animal-pollinated flowers and in many flowering plant species are restricted to the second floral whorl. Interestingly, multiple times during angiosperm evolution, petaloid characteristics have expanded to adjacent floral whorls or to extra-floral organs. Here, we investigate developmental characteristics of petaloid sepals in Rhodochiton atrosanguineum, a close relative of the model species Antirrhinum majus (snapdragon). We undertook this in two ways, first using scanning electron microscopy we investigate the micromorphology of petals and sepals, followed by expression studies of genes usually responsible for the formation of petaloid structures. From our data, we conclude that R. atrosanguineum petaloid sepals lack micromorphological characteristics of petals and that petaloid sepals did not evolve through regulatory evolution of B-class MADS box genes, which have been shown to specify second whorl petal identity in a number of model flowering plant species including snapdragon. These data, in conjunction with other studies, suggests multiple convergent pathways for the evolution of showy sepals.
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Affiliation(s)
- Jacob B Landis
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA.
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Jaligot E, Adler S, Debladis É, Beulé T, Richaud F, Ilbert P, Finnegan EJ, Rival A. Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. Ann Bot 2011; 108:1453-62. [PMID: 21224269 PMCID: PMC3219487 DOI: 10.1093/aob/mcq266] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/19/2010] [Indexed: 05/24/2023]
Abstract
BACKGROUND The large-scale clonal propagation of oil palm (Elaeis guineensis) is being stalled by the occurrence of the mantled somaclonal variation. Indeed, this abnormality which presents a homeotic-like conversion of male floral organs into carpelloid structures, hampers oil production since the supernumerary female organs are either sterile or produce fruits with poor oil yields. SCOPE In the last 15 years, the prevailing point of view on the origin of the mantled floral phenotype has evolved from a random mutation event triggered by in vitro culture to a hormone-dependent dysfunction of gene regulation processes. In this review, we retrace the history of the research on the mantled variation in the light of the parallel advances made in the understanding of plant development regulation in model systems and more specifically in the role of epigenetic mechanisms. An overview of the current state of oil palm genomic and transcriptomic resources, which are key to any comparison with model organisms, is given. We show that, while displaying original characteristics, the mantled phenotype of oil palm is morphologically, and possibly molecularly, related to MADS-box genes mutants described in model plants. We also discuss the occurrence of comparable floral phenotypes in other palm species. CONCLUSIONS Beyond its primary interest in the search for discriminating markers against an economically crippling phenotype, the study of the mantled abnormality also provides a unique opportunity to investigate the regulation of reproductive development in a perennial tropical palm. On the basis of recent results, we propose that future efforts should concentrate on the epigenetic regulation targeting MADS-box genes and transposable elements of oil palm, since both types of sequences are most likely to be involved in the mantled variant phenotype.
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Affiliation(s)
- Estelle Jaligot
- UMR DIADE (IRD, UM2), IRD/CIRAD Palm Development Group, 911 avenue Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France.
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Jin Y, Luo Q, Tong H, Wang A, Cheng Z, Tang J, Li D, Zhao X, Li X, Wan J, Jiao Y, Chu C, Zhu L. An AT-hook gene is required for palea formation and floral organ number control in rice. Dev Biol 2011; 359:277-88. [DOI: 10.1016/j.ydbio.2011.08.023] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 11/17/2022]
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Ciaffi M, Paolacci AR, Tanzarella OA, Porceddu E. Molecular aspects of flower development in grasses. ACTA ACUST UNITED AC 2011; 24:247-82. [PMID: 21877128 DOI: 10.1007/s00497-011-0175-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 08/11/2011] [Indexed: 10/17/2022]
Abstract
The grass family (Poaceae) of the monocotyledons includes about 10,000 species and represents one of the most important taxa among angiosperms. Their flower morphology is remarkably different from those of other monocotyledons and higher eudicots. The peculiar floral structure of grasses is the floret, which contains carpels and stamens, like eudicots, but lacks petals and sepals. The reproductive organs are surrounded by two lodicules, which correspond to eudicot petals, and by a palea and lemma, whose correspondence to eudicot organs remains controversial. The molecular and genetic analysis of floral morphogenesis and organ specification, primarily performed in eudicot model species, led to the ABCDE model of flower development. Several genes required for floral development in grasses correspond to class A, B, C, D, and E genes of eudicots, but others appear to have unique and diversified functions. In this paper, we outline the present knowledge on the evolution and diversification of grass genes encoding MIKC-type MADS-box transcription factors, based on information derived from studies in rice, maize, and wheat. Moreover, we review recent advances in studying the genes involved in the control of flower development and the extent of structural and functional conservation of these genes between grasses and eudicots.
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Abstract
Gene duplication plays an important role in the evolution of organisms by allowing functional innovation and the divergence of duplicate genes. Previous studies found two PI-like genes in grass species, suggesting functional divergence between the paralogous copies. Here, we reconstructed the evolutionary history of two PI genes from major lineages of grasses and other monocot species, and demonstrated that two PI genes (PI1 and PI2) arose from a whole genome duplication that occurred in a common ancestor of extant grasses. Molecular evolutionary analyses at the family and tribal levels found strong purifying selection acting on two genes in grasses, consistent with the conserved class B function of the PI genes. Importantly, we detected different patterns of selective relaxation between the duplicated PI genes although no signature of positive selection was found. Likelihood ratio tests revealed that the ω ratio for M domain is significantly higher in PI1 than in PI2 but that for K domain is significantly higher in PI2 than in PI1. These findings imply that complementary selective relaxation occurs in two PI genes after duplication, and provide additional molecular evidence for the subfunctionalization of the duplicated PI genes in grasses.
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Affiliation(s)
- Ruo-Xun Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
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36
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Abstract
Importin β1 interacts with nuclear transport factors and mediates the import of nuclear proteins. We isolated a pollen-expressed gene, rice Importin β1 (OsImpβ1), from a T-DNA insertional population that was trapped by a promoterless β-glucuronidase (GUS) gene. The GUS reporter was expressed in the anthers and ovaries from early through mature developmental stages. Its expression was also observed in all floral organs. However, these patterns changed as the spikelet developed. T-DNA was inserted into the OsImpβ1 gene at 339 bp downstream from the translation initiation site. We obtained another T-DNA insertional allele by searching the flanking sequence tag database. In both lines, the wild-type and T-DNA-carrying progeny segregated at a ratio close to 1:1. The latter genotype was heterozygous (OsImpβ1/osimpβ1). Reciprocal crosses between WT and heterozygous plants demonstrated that the mutant alleles could not be transmitted through the male gametophyte. Close examination of the heterozygous anthers revealed that the mutant pollen matured normally. However, in vitro assays showed that tube elongation was hampered in the mutant grains. These results indicate that OsImpβ1 is specifically required for pollen tube elongation.
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Affiliation(s)
- Min-Jung Han
- Crop Biotech Institute and Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea
- Present address: POSTECH Biotechnology Center, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Ki-Hong Jung
- Crop Biotech Institute and Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Gihwan Yi
- International Technical Cooperation Center, Rural Development Administration, Suwon 441-707, Korea
| | - Gynheung An
- Crop Biotech Institute and Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea
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Hu L, Liang W, Yin C, Cui X, Zong J, Wang X, Hu J, Zhang D. Rice MADS3 regulates ROS homeostasis during late anther development. Plant Cell 2011; 23:515-33. [PMID: 21297036 PMCID: PMC3077785 DOI: 10.1105/tpc.110.074369] [Citation(s) in RCA: 197] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Revised: 01/06/2011] [Accepted: 01/19/2011] [Indexed: 05/17/2023]
Abstract
The rice (Oryza sativa) floral homeotic C-class gene, MADS3, was previously shown to be required for stamen identity determination during early flower development. Here, we describe a role for MADS3 in regulating late anther development and pollen formation. Consistent with this role, MADS3 is highly expressed in the tapetum and microspores during late anther development, and a newly identified MADS3 mutant allele, mads3-4, displays defective anther walls, aborted microspores, and complete male sterility. During late anther development, mads3-4 exhibits oxidative stress-related phenotypes. Microarray analysis revealed expression level changes in many genes in mads3-4 anthers. Some of these genes encode proteins involved in reactive oxygen species (ROS) homeostasis; among them is MT-1-4b, which encodes a type 1 small Cys-rich and metal binding protein. In vivo and in vitro assays showed that MADS3 is associated with the promoter of MT-1-4b, and recombinant MT-1-4b has superoxide anion and hydroxyl radical scavenging activity. Reducing the expression of MT-1-4b causes decreased pollen fertility and an increased level of superoxide anion in transgenic plants. Our findings suggest that MADS3 is a key transcriptional regulator that functions in rice male reproductive development, at least in part, by modulating ROS levels through MT-1-4b.
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Affiliation(s)
- Lifang Hu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Bio-X Research Center, Key Laboratory of Genetics and Development and Neuropsychiatric Diseases, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wanqi Liang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Changsong Yin
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiao Cui
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Xing Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianping Hu
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Dabing Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Bio-X Research Center, Key Laboratory of Genetics and Development and Neuropsychiatric Diseases, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
- Address correspondence to
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Duan Y, Diao Z, Liu H, Cai M, Wang F, Lan T, Wu W. Molecular cloning and functional characterization of OsJAG gene based on a complete-deletion mutant in rice (Oryza sativa L.). Plant Mol Biol 2010; 74:605-615. [PMID: 20938801 DOI: 10.1007/s11103-010-9703-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 09/30/2010] [Indexed: 05/30/2023]
Abstract
In this article, we report an independent work of positional cloning and functional characterization of OsJAG gene in rice. The merit of our work is that we used a genuine null mutant, in which the wild-type allele was completely deleted. This allowed us to identify the mutant phenotypes accurately without the interference of residual function of the target gene. OsJAG is an important gene with pleiotropy, expressing almost throughout the plant and acting in both vegetative phase and reproductive phase. But its main and crucial roles are in regulating the development of all floral organs, especially in specifying the identity of stamens. Interestingly, OsJAG does not affect the number of floral organ primordial and so of floral organs in each whorl, suggesting that OsJAG does not influence the initiation of floral organ primordia, but affect the developmental fate of all floral organs after their primordia have initiated. Loss of OsJAG function results in maldevelopment of all floral organs, such as degenerated lemma and palea, elongated lodicules and deformed and sterile pistil. The stamen appears to be more sensitive to the mutation. All the six stamens in a mutant floret were thoroughly transformed into six pistil-like organs developed at the presumptive positions of the stamens in whorl 3.
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Affiliation(s)
- Yuanlin Duan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, People's Republic of China
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Yoo MJ, Chanderbali AS, Altman NS, Soltis PS, Soltis DE. Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeaceae). Plant J 2010; 64:687-98. [PMID: 21070420 DOI: 10.1111/j.1365-313x.2010.04357.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Current understanding of floral developmental genetics comes primarily from the core eudicot model Arabidopsis thaliana. Here, we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. We identify several thousand Nuphar genes with significantly upregulated floral expression, including homologs of the well-known ABCE floral regulators, deployed in broadly overlapping transcriptional programs across floral organ categories. Strong similarities in the expression profiles of different organ categories in Nuphar flowers are shared with the magnoliid Persea americana (avocado), in contrast to the largely organ-specific transcriptional cascades evident in Arabidopsis, supporting the inference that this is the ancestral condition in angiosperms. In contrast to most eudicots, floral organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived, and correlate with a shift towards morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. Our findings suggest that the genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, University of Florida, Gainesville, FL 32611, USA.
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40
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Wang N, Sang XC, Li YF, Yang ZL, Zhao FM, Ling YH, Zhang ZS, He GH. Identification and gene mapping of a novel mutant supernumerary lodicules (snl) in rice. J Integr Plant Biol 2010; 52:265-272. [PMID: 20377687 DOI: 10.1111/j.1744-7909.2010.00896.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In order to gain a better understanding of rice flower development, a rice flower mutant supernumerary lodicules (snl), which was identified from ethyl methane sulfonate (EMS)-treated Jinhui10 (Oryza sativa L. ssp. indica) was used in the present study. In the snl mutant, the palea obtained lemma identity, additional glume-like organs formed, lodicules increased and elongated, stamens decreased, and a few aberrant carpels formed. These phenotypes suggest that SNL is involved in the entire rice flower development. SNL was mapped between two simple sequence repeat markers RM3512 and RM1342 on chromosome 2, an approximate 800 kb region, and it co-segregated with SSR215. We conclude that SNL is a novel gene involved in flower development in rice. The present study will be useful for further cloning of the SNL gene, which will contribute to the elucidation of rice flower development.
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Affiliation(s)
- Nan Wang
- Rice Research Institute, Key Laboratory of Biotechnology and Crop Quality Improvement Ministry of Agriculture, Southwest University, Chongqing 400715, China
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41
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Hong L, Qian Q, Zhu K, Tang D, Huang Z, Gao L, Li M, Gu M, Cheng Z. ELE restrains empty glumes from developing into lemmas. J Genet Genomics 2010; 37:101-15. [DOI: 10.1016/s1673-8527(09)60029-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Revised: 01/18/2010] [Accepted: 01/18/2010] [Indexed: 11/25/2022]
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42
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Ferrándiz C, Fourquin C, Prunet N, Scutt CP, Sundberg E, Trehin C, Vialette-Guiraud AC. Carpel Development. Advances in Botanical Research 2010. [PMID: 0 DOI: 10.1016/b978-0-12-380868-4.00001-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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43
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Nair SK, Wang N, Turuspekov Y, Pourkheirandish M, Sinsuwongwat S, Chen G, Sameri M, Tagiri A, Honda I, Watanabe Y, Kanamori H, Wicker T, Stein N, Nagamura Y, Matsumoto T, Komatsuda T. Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage. Proc Natl Acad Sci U S A 2010; 107:490-5. [PMID: 20018663 DOI: 10.1073/pnas.0909097107] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cleistogamous flower sheds its pollen before opening, forcing plants with this habit to be almost entirely autogamous. Cleistogamy also provides a means of escape from cereal head blight infection and minimizes pollen-mediated gene flow. The lodicule in cleistogamous barley is atrophied. We have isolated cleistogamy 1 (Cly1) by positional cloning and show that it encodes a transcription factor containing two AP2 domains and a putative microRNA miR172 targeting site, which is an ortholog of Arabidopsis thaliana AP2. The expression of Cly1 was concentrated within the lodicule primordia. We established a perfect association between a synonymous nucleotide substitution at the miR172 targeting site and cleistogamy. Cleavage of mRNA directed by miR172 was detectable only in a noncleistogamous background. We conclude that the miR172-derived down-regulation of Cly1 promotes the development of the lodicules, thereby ensuring noncleistogamy, although the single nucleotide change at the miR172 targeting site results in the failure of the lodicules to develop properly, producing the cleistogamous phenotype.
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44
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Litt A, Kramer EM. The ABC model and the diversification of floral organ identity. Semin Cell Dev Biol 2009; 21:129-37. [PMID: 19948236 DOI: 10.1016/j.semcdb.2009.11.019] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 11/16/2009] [Accepted: 11/23/2009] [Indexed: 01/22/2023]
Abstract
Broad studies of the ABC program across angiosperms have found that interactions between gene duplication, biochemical evolution, shifts in gene expression and modification of existing identity programs have been critical to the evolution of floral morphology. Several themes can be recognized in this context. First, the original concept of "A" function applies only very narrowly to Arabidopsis and its close relatives. Second, while many types of petaloid organs are associated with the expression of AP3/PI homologs, there is growing evidence that there are other genetic mechanisms for producing petaloidy, especially in first whorl organs. Third, pre-existing organ identity programs can be modified to yield novel organ types, often in association with gene duplications. Lastly, there are many aspects of ABC gene function outside the major model systems that remain a mystery, perhaps none more so than the C-terminal amino acid motifs that distinguish specific ABC gene lineages.
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Affiliation(s)
- Amy Litt
- The New York Botanical Garden, Bronx, NY 10458, USA.
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45
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Kim SR, Yang JI, Moon S, Ryu CH, An K, Kim KM, Yim J, An G. Rice OGR1 encodes a pentatricopeptide repeat-DYW protein and is essential for RNA editing in mitochondria. Plant J 2009; 59:738-49. [PMID: 19453459 DOI: 10.1111/j.1365-313x.2009.03909.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
RNA editing is the alteration of RNA sequences via insertion, deletion and conversion of nucleotides. In flowering plants, specific cytidine residues of RNA transcribed from organellar genomes are converted into uridines. Approximately 35 editing sites are present in the chloroplasts of higher plants; six pentatricopeptide repeat genes involved in RNA editing have been identified in Arabidopsis. However, although approximately 500 editing sites are found in mitochondrial RNAs of flowering plants, only one gene in Arabidopsis has been reported to be involved in such editing. Here, we identified rice mutants that are defective in seven specific RNA editing sites on five mitochondrial transcripts. Their various phenotypes include delayed seed germination, retarded growth, dwarfism and sterility. Mutant seeds from heterozygous plants are opaque. This mutation, named opaque and growth retardation 1 (ogr1), was generated by T-DNA insertion into a gene that encodes a pentatricopeptide repeat protein containing the DYW motif. The OGR1-sGFP fusion protein is localized to mitochondria. Ectopic expression of OGR1 in the mutant complements the altered phenotypes. We conclude that OGR1 is essential for RNA editing in rice mitochondria and is required for normal growth and development.
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Affiliation(s)
- Sung-Ryul Kim
- Department of Integrative Bioscience and Biotechnology, National Research Laboratory of Plant Functional Genomics and Functional Genomic Center, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
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Yamada K, Saraike T, Shitsukawa N, Hirabayashi C, Takumi S, Murai K. Class D and B(sister) MADS-box genes are associated with ectopic ovule formation in the pistil-like stamens of alloplasmic wheat (Triticum aestivum L.). Plant Mol Biol 2009; 71:1-14. [PMID: 19488678 DOI: 10.1007/s11103-009-9504-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Accepted: 05/19/2009] [Indexed: 05/10/2023]
Abstract
Homeotic transformation of stamens into pistil-like structures (pistillody) has been reported in cytoplasmic substitution (alloplasmic) lines of bread wheat (Triticum aestivum L.) that have the cytoplasm of a related wild species, Aegilops crassa. An ectopic ovule differentiates in the pistil-like stamen in the alloplasmic wheat. The SEEDSTICK (STK)-like class D MADS-box gene, wheat STK (WSTK), was expressed in the primordia of ectopic ovules in the pistil-like stamens as well as in the true pistil, suggesting that ectopic ovule formation results from WSTK expression in the pistil-like stamens of alloplasmic wheat. The ectopic ovule is abnormal as it fails to form complete integuments. Based on the expression pattern of WSTK and B(sister) MADS-box gene, WBsis (wheat B ( sister )), we conclude that WSTK plays a role in determination of ovule identity in the pistil-like stamen, but complete ovule development fails due to aberrant expression of WBsis.
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Affiliation(s)
- Kaori Yamada
- Department of Bioscience, Fukui Prefectural University, Eiheiji-cho, Fukui, Japan
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Xiao H, Tang J, Li Y, Wang W, Li X, Jin L, Xie R, Luo H, Zhao X, Meng Z, He G, Zhu L. STAMENLESS 1, encoding a single C2H2 zinc finger protein, regulates floral organ identity in rice. Plant J 2009; 59:789-801. [PMID: 19453444 DOI: 10.1111/j.1365-313x.2009.03913.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Floral organ identity is defined by organ homoetic genes whose coordinated expression is crucial with respect to the time and place of floral organ formation. Here, we report molecular cloning and characterization of the rice STAMENLESS 1 (SL1) gene that is involved in floral development. The sl1 mutant largely resembles the rice B-class gene mutant spw1; both exhibit homeotic conversions of lodicules and stamens to palea/lemma-like organs and carpels. Additionally, sl1 produces flowers with varied numbers of inner floral organs, and amorphous tissues without floral organ identity were frequently formed in whorls 3 and 4. We also show that SL1 specifies lodicule and stamen identities through positive transcriptional regulation of SPW1/OsMADS16 expression. SL1 encodes a member of the C2H2 family of zinc finger proteins, closely related to JAG of Arabidopsis. The functional divergence between SL1 and JAG implies that SL1 was co-opted for its distinctive roles in specification of floral organ identity in rice after the lineage split from Arabidopsis.
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Affiliation(s)
- Han Xiao
- State Key Laboratory of Plant Genomics & National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China
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Viaene T, Vekemans D, Irish VF, Geeraerts A, Huysmans S, Janssens S, Smets E, Geuten K. Pistillata--duplications as a mode for floral diversification in (Basal) asterids. Mol Biol Evol 2009; 26:2627-45. [PMID: 19679752 DOI: 10.1093/molbev/msp181] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Basal asterid families, and to a lesser extent the asterids as a whole, are characterized by a high variation in petal and stamen morphology. Moreover, the stamen number, the adnation of stamens to petals, and the degree of sympetaly vary considerably among basal asterid taxa. The B group genes, members of the APETALA3 (AP3) and PISTILLATA (PI) gene lineages, have been shown to specify petal and stamen identities in several core eudicot species. Duplicate genes in these lineages have been shown in some cases to have diversified in their function; for instance in Petunia, a PI paralog is required for the fusion of stamens to the corolla tube, illustrating that such genes belonging to this lineage are not just involved in specifying the identity of the stamens and petals but can also specify novel floral morphologies. This motivated us to study the duplication history of class B genes throughout asterid lineages, which comprise approximately one-third of all flowering plants. The evolutionary history of the PI gene subfamily indicates that the two genes in Petunia result from an ancient duplication event, coinciding with the origin of core asterids. A second duplication event occurred before the speciation of basal asterid Ericales families. These and other duplications in the PI lineage are not correlated with duplications in the AP3 lineage. To understand the molecular evolution of the Ericales PI genes after duplication, we have described their expression patterns using reverse transcription polymerase chain reaction and in situ hybridization, reconstructed how selection shaped their protein sequences and tested their protein interaction specificity with other class B proteins. We find that after duplication, PI paralogs have acquired multiple different expression patterns and negative selective pressure on their codons is relaxed, whereas substitutions in sites putatively involved in protein-protein interactions show positive selection, allowing for a change in the interaction behavior of the PI paralogs after duplication. Together, these observations suggest that the asterids have preferentially recruited PI duplicate genes to diverse and potentially novel roles in asterid flower development.
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Affiliation(s)
- Tom Viaene
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, P.O. Box 2437, Leuven, Belgium.
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Li Y, Xu P, Zhang H, Peng H, Zhang Q, Wang X, Wu X. Characterization and identification of a novel mutant fon(t) on floral organ number and floral organ identity in rice. J Genet Genomics 2009; 34:730-7. [PMID: 17707217 DOI: 10.1016/s1673-8527(07)60082-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 12/07/2006] [Indexed: 11/17/2022]
Abstract
The floral-organ-number mutant fon(t) was firstly discovered in the progeny of a cross between a diploid (Chunjiang 683) and a haploid (SARIV-620-A) rice cultivar. The fon(t) mutant showed normal vegetative development and produced normal inflorescence structures. Difference between the mutant and the wild type was observed when the stamen primordia began to form. The mature flowers of fon(t) mutant showed open-hull phenotypes, which resulted in the exposure of stamens and stigmas. Normally, a single fon(t) floret consisted of six to nine stamens and one or two pistils. In addition, stamen/pistil-like structures and bulged tissues near ovaries were also observed in a few fon(t) florets. But homeotic transformation of lodicules into palea/lemma-like organs was observed almost in all the open-hull florets. The phenotypes of fon(t) flowers also suggested that fon(t) gene might affect flower organ identity in the inner whorls. Genetic analysis showed that the fon(t) mutant was controlled by a single recessive gene.
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Affiliation(s)
- Yun Li
- Rice Research Institute of Sichuan Agricultural University, Wenjiang 611130, China
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