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Mizrahi R, Ostersetzer-Biran O. Mitochondrial RNA Helicases: Key Players in the Regulation of Plant Organellar RNA Splicing and Gene Expression. Int J Mol Sci 2024; 25:5502. [PMID: 38791540 PMCID: PMC11122041 DOI: 10.3390/ijms25105502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial genomes of land plants are large and exhibit a complex mode of gene organization and expression, particularly at the post-transcriptional level. The primary organellar transcripts in plants undergo extensive maturation steps, including endo- and/or exo-nucleolytic cleavage, RNA-base modifications (mostly C-to-U deaminations) and both 'cis'- and 'trans'-splicing events. These essential processing steps rely on the activities of a large set of nuclear-encoded factors. RNA helicases serve as key players in RNA metabolism, participating in the regulation of transcription, mRNA processing and translation. They unwind RNA secondary structures and facilitate the formation of ribonucleoprotein complexes crucial for various stages of gene expression. Furthermore, RNA helicases are involved in RNA metabolism by modulating pre-mRNA maturation, transport and degradation processes. These enzymes are, therefore, pivotal in RNA quality-control mechanisms, ensuring the fidelity and efficiency of RNA processing and turnover in plant mitochondria. This review summarizes the significant roles played by helicases in regulating the highly dynamic processes of mitochondrial transcription, RNA processing and translation in plants. We further discuss recent advancements in understanding how dysregulation of mitochondrial RNA helicases affects the splicing of organellar genes, leading to respiratory dysfunctions, and consequently, altered growth, development and physiology of land plants.
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Affiliation(s)
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus—Givat Ram, Jerusalem 9190401, Israel
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Edris R, Sultan LD, Best C, Mizrahi R, Weinstein O, Chen S, Kamennaya NA, Keren N, Zer H, Zhu H, Ostersetzer-Biran O. Root Primordium Defective 1 Encodes an Essential PORR Protein Required for the Splicing of Mitochondria-Encoded Group II Introns and for Respiratory Complex I Biogenesis. PLANT & CELL PHYSIOLOGY 2024; 65:602-617. [PMID: 37702436 DOI: 10.1093/pcp/pcad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023]
Abstract
Cellular respiration involves complex organellar metabolic activities that are pivotal for plant growth and development. Mitochondria contain their own genetic system (mitogenome, mtDNA), which encodes key elements of the respiratory machinery. Plant mtDNAs are notably larger than their counterparts in Animalia, with complex genome organization and gene expression characteristics. The maturation of the plant mitochondrial transcripts involves extensive RNA editing, trimming and splicing events. These essential processing steps rely on the activities of numerous nuclear-encoded cofactors, which may also play key regulatory roles in mitochondrial biogenesis and function and hence in plant physiology. Proteins that harbor the plant organelle RNA recognition (PORR) domain are represented in a small gene family in plants. Several PORR members, including WTF1, WTF9 and LEFKOTHEA, are known to act in the splicing of organellar group II introns in angiosperms. The AT4G33495 gene locus encodes an essential PORR protein in Arabidopsis, termed ROOT PRIMORDIUM DEFECTIVE 1 (RPD1). A null mutation of At.RPD1 causes arrest in early embryogenesis, while the missense mutant lines, rpd1.1 and rpd1.2, exhibit a strong impairment in root development and retarded growth phenotypes, especially under high-temperature conditions. Here, we further show that RPD1 functions in the splicing of introns that reside in the coding regions of various complex I (CI) subunits (i.e. nad2, nad4, nad5 and nad7), as well as in the maturation of the ribosomal rps3 pre-RNA in Arabidopsis mitochondria. The altered growth and developmental phenotypes and modified respiration activities are tightly correlated with respiratory chain CI defects in rpd1 mutants.
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Affiliation(s)
- Rana Edris
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Laure D Sultan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Corinne Best
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Ron Mizrahi
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Ofir Weinstein
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Stav Chen
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Nina A Kamennaya
- The French Associates Institute for Agriculture and Biotechnology of Drylands, Bluestein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Sede Boqer 8499000, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Hagit Zer
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Hongliang Zhu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
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Wang C, Quadrado M, Mireau H. Temperature-sensitive splicing defects in Arabidopsis mitochondria caused by mutations in the ROOT PRIMORDIUM DEFECTIVE 1 gene. Nucleic Acids Res 2024; 52:4575-4587. [PMID: 38364869 PMCID: PMC11077063 DOI: 10.1093/nar/gkae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/06/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Group II introns in plant organelles have lost splicing autonomy and require the assistance of nuclear-encoded trans-factors whose roles remain to be elucidated. These factors can be mono- or poly-specific with respect to the number of introns whose splicing they facilitate. Poly-acting splicing factors are often essential and their genetic identification may benefit from the use of conditional mutations. Temperature-sensitive (TS) mutations in the ROOT PRIMORDIUM DEFECTIVE 1 (RPD1) gene were initially selected for their inhibitory effect on root formation in Arabidopsis. Further analysis revealed that RPD1 encodes a mitochondria-targeted RNA-binding protein family member, suggesting a role in mitochondrial gene expression and making its role in root formation enigmatic. We analysed the function of RPD1 and found that it is required for the removal of 9 mitochondrial group II introns and that the identified TS mutations affect the splicing function of RPD1. These results support that the inhibition of adventitious root formation at non-permissive temperature results from a reduction in RPD1 activity and thus mitochondrial activity. We further show that RPD1 physically associates in vivo with the introns whose splicing it facilitates. Preliminary mapping indicates that RPD1 may not bind to the same regions within all of its intron targets, suggesting potential variability in its influence on splicing activation.
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Affiliation(s)
- Chuande Wang
- School of Agriculture and Biology, Joint Center for Single cell Biology/Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Jiao Tong University, Shanghai, China
| | - Martine Quadrado
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Hakim Mireau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
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Whole-genome resequencing of Sorghum bicolor and S. bicolor × S. halepense lines provides new insights for improving plant agroecological characteristics. Sci Rep 2022; 12:5556. [PMID: 35365708 PMCID: PMC8976056 DOI: 10.1038/s41598-022-09433-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/23/2022] [Indexed: 11/09/2022] Open
Abstract
Sorghum (Sorghum bicolor L. (Moench)) is the world's fifth economically most important cereal and is a staple particularly in the semi-arid tropics of Africa and Asia. Genetic gains in this crop can benefit from wild relatives such as Sorghum halepense. Genome sequences including those from this wild species can boost the study of genome-wide and intraspecific variation for dissecting the genetic basis and improving important traits in sorghum. The whole-genome resequencing carried out in this work on a panel of 172 populations of S. bicolor and S. bicolor × S. halepense (SbxSh) advanced lines generated a total of 567,046,841 SNPs, 91,825,474 indels, 1,532,171 SVs, and 4,973,961 CNVs. Clearly, SbxSh accumulated more variants and mutations with powerful effects on genetic differentiation. A total of 5,548 genes private to SbxSh mapped to biological process GO enrichment terms; 34 of these genes mapped to root system development (GO: 0022622). Two of the root specific genes i.e., ROOT PRIMORDIUM DEFECTIVE 1 (RPD1; GeneID: 8054879) and RETARDED ROOT GROWTH (RRG, GeneID: 8072111), were found to exert direct effect on root growth and development. This is the first report on whole-genome resequencing of a sorghum panel that includes S. halepense genome. Mining the private variants and genes of this wild species can provide insights capable of boosting sorghum genetic improvement, particularly the perenniality trait that is compliant with agroecological practices, sustainable agriculture, and climate change resilience.
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Wang L, Zhang W, Liu S, Tian Y, Liu X, Yan H, Cai Y, Teng X, Dong H, Chen R, Jiang X, Wang Y, Wan J. Rice FLOURY SHRUNKEN ENDOSPERM 5 Encodes a Putative Plant Organelle RNA Recognition Protein that Is Required for cis-Splicing of Mitochondrial nad4 Intron 1. RICE (NEW YORK, N.Y.) 2021; 14:29. [PMID: 33689034 PMCID: PMC7947098 DOI: 10.1186/s12284-021-00463-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The sequences of several important mitochondrion-encoded genes involved in respiration in higher plants are interrupted by introns. Many nuclear-encoded factors are involved in splicing these introns, but the mechanisms underlying this splicing remain unknown. RESULTS We isolated and characterized a rice mutant named floury shrunken endosperm 5 (fse5). In addition to having floury shrunken endosperm, the fse5 seeds either failed to germinate or produced seedlings which grew slowly and died ultimately. Fse5 encodes a putative plant organelle RNA recognition (PORR) protein targeted to mitochondria. Mutation of Fse5 hindered the splicing of the first intron of nad4, which encodes an essential subunit of mitochondrial NADH dehydrogenase complex I. The assembly and NADH dehydrogenase activity of complex I were subsequently disrupted by this mutation, and the structure of the mitochondria was abnormal in the fse5 mutant. The FSE5 protein was shown to interact with mitochondrial intron splicing factor 68 (MISF68), which is also a splicing factor for nad4 intron 1 identified previously via yeast two-hybrid (Y2H) assays. CONCLUSION Fse5 which encodes a PORR domain-containing protein, is essential for the splicing of nad4 intron 1, and loss of Fse5 function affects seed development and seedling growth.
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Affiliation(s)
- Liang Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenwei Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haigang Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yue Cai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongbo Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaokang Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Li SW. Molecular Bases for the Regulation of Adventitious Root Generation in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:614072. [PMID: 33584771 PMCID: PMC7876083 DOI: 10.3389/fpls.2021.614072] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/08/2021] [Indexed: 05/08/2023]
Abstract
The formation of adventitious roots (ARs) is an ecologically and economically important developmental process in plants. The evolution of AR systems is an important way for plants to cope with various environmental stresses. This review focuses on identified genes that have known to regulate the induction and initiation of ARs and offers an analysis of this process at the molecular level. The critical genes involved in adventitious rooting are the auxin signaling-responsive genes, including the AUXIN RESPONSE FACTOR (ARF) and the LATERAL ORGAN BOUNDARIES-DOMAIN (LOB) gene families, and genes associated with auxin transport and homeostasis, the quiescent center (QC) maintenance, and the root apical meristem (RAM) initiation. Several genes involved in cell wall modulation are also known to be involved in the regulation of adventitious rooting. Furthermore, the molecular processes that play roles in the ethylene, cytokinin, and jasmonic acid signaling pathways and their crosstalk modulate the generation of ARs. The crosstalk and interaction among many molecular processes generates complex networks that regulate AR generation.
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Zhang H, Yang Y, Sun C, Liu X, Lv L, Hu Z, Yu D, Zhang D. Up-regulating GmETO1 improves phosphorus uptake and use efficiency by promoting root growth in soybean. PLANT, CELL & ENVIRONMENT 2020; 43:2080-2094. [PMID: 32515009 DOI: 10.1111/pce.13816] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/26/2020] [Indexed: 05/21/2023]
Abstract
Soybean is a high inorganic phosphate (Pi) demanding crop; its production is strongly suppressed when Pi is deficient in soil. However, the regulatory mechanism of Pi deficiency tolerance in soybean is still largely unclear. Here, our findings highlighted the pivotal role of the ethylene-associated pathway in soybean tolerance to Pi deficiency by comparatively studying transcriptome changes between a representative Pi-deficiency-tolerant soybean genotype NN94156 and a sensitive genotype Bogao under different Pi supplies. By further integrating high-confident linkage and association mapping, we identified that Ethylene-Overproduction Protein 1 (GmETO1), an essential ethylene-biosynthesis regulator, underlies the major quantitative trait locus (QTL) q14-2 controlling Pi uptake. GmETO1 was also the representative member of ETO1 family members that was strongly induced by Pi deficiency. Overexpressing GmETO1 significantly enhanced Pi deficiency tolerance by increasing proliferation and elongation of hairy roots, Pi uptake and use efficiency, and conversely, silencing of GmETO1 led to opposite findings. We further demonstrated that Pi-deficiency inducible genes critical for root morphological and physiological traits including GmACP1/2, Pht1;4, Expansin-A7 and Root Primordium Defective 1 functioned downstream of GmETO1. Our study provides comprehensive insight into the complex regulatory mechanism of Pi deficiency tolerance in soybean and a potential way to genetically improve soybean low-Pi tolerance.
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Affiliation(s)
- Hengyou Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Lingling Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhenbin Hu
- The Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
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Chen QJ, Deng BH, Gao J, Zhao ZY, Chen ZL, Song SR, Wang L, Zhao LP, Xu WP, Zhang CX, Ma C, Wang SP. A miRNA-Encoded Small Peptide, vvi-miPEP171d1, Regulates Adventitious Root Formation. PLANT PHYSIOLOGY 2020; 183:656-670. [PMID: 32241877 PMCID: PMC7271809 DOI: 10.1104/pp.20.00197] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/17/2020] [Indexed: 05/07/2023]
Abstract
One of the biggest challenges in clonal propagation of grapevine (Vitis vinifera) is difficulty of rooting. Adventitious root initiation and development are the critical steps in the cutting and layering process of grapevine, but the molecular mechanism of these processes remains unclear. Previous reports have found that microRNA (miRNA)-encoded peptides (miPEPs) can regulate plant root development by increasing the transcription of their corresponding primary miRNA. Here, we report the role of a miPEP in increasing adventitious root formation in grapevine. In this study, we performed a global analysis of miPEPs in grapevine and characterized the function of vvi-miPEP171d1, a functional, small peptide encoded by primary-miR171d. There were three small open reading frames in the 500-bp upstream sequence of pre-miR171d. One of them encoded a small peptide, vvi-miPEP171d1, which could increase the transcription of vvi-MIR171d Exogenous application of vvi-miPEP171d1 to grape tissue culture plantlets promoted adventitious root development by activating the expression of vvi-MIR171d Interestingly, neither exogenous application of the vvi-miPEP171d1 peptide nor overexpression of the vvi-miPEP171d1 coding sequence resulted in phenotypic changes in Arabidopsis (Arabidopsis thaliana). Similarly, application of synthetic ath-miPEP171c, the small peptide encoded by the Arabidopsis ortholog of vvi-MIR171d, inhibited the growth of primary roots and induced the early initiation of lateral and adventitious roots in Arabidopsis, while it had no effect on grape root development. Our findings reveal that miPEP171d1 regulates root development by promoting vvi-MIR171d expression in a species-specific manner, further enriching the theoretical research into miPEPs.
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Affiliation(s)
- Qiu-Ju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo-Han Deng
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Gao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhong-Yang Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zi-Li Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shi-Ren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li-Ping Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wen-Ping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cai-Xi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shi-Ping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Agro-food Science and Technology/Key Laboratory of Agro-products Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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Guo W, Zhang X, Peng Q, Luo D, Jiao K, Su S. Love on wings, a Dof family protein regulates floral vasculature in Vigna radiata. BMC PLANT BIOLOGY 2019; 19:495. [PMID: 31726995 PMCID: PMC6854777 DOI: 10.1186/s12870-019-2099-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/24/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND The interaction among plants and their pollinators has been a major factor which enriched floral traits known as pollination syndromes and promoted the diversification of flowering plants. One of the bee-pollination syndromes in Faboideae with keel blossoms is the formation of a landing platform by wing and keel petals. However, the molecular mechanisms of elaborating a keel blossom remain unclear. RESULTS By performing large scale mutagenesis, we isolated and characterized a mutant in Vigna radiata, love on wings (low), which shows developmental defects in petal asymmetry and vasculature, leading to a failure in landing platform formation. We cloned the locus through map-based cloning together with RNA-sequencing (RNA-seq) analysis. We found that LOW encoded a nucleus-localized Dof-like protein and was expressed in the flower provascular and vascular tissues. A single copy of LOW was detected in legumes, in contrast with other taxa where there seems to be at least 2 copies. Thirty one Dof proteins have been identified from the V. radiata's genome, which can be further divided into four Major Cluster of Orthologous Groups (MCOGs). We also showed that ectopic expression of LOW in Arabidopsis driven by its native promoter caused changes in petal vasculature pattern. CONCLUSIONS To summarize, our study isolated a legume Dof-like factor LOW from V. radiata, which affects vasculature development in this species and this change can, in turn, impact petal development and overall morphology of keel blossom.
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Affiliation(s)
- Wuxiu Guo
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Haizhu district, Guangzhou, 510275 Guangdong China
| | - Xue Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Haizhu district, Guangzhou, 510275 Guangdong China
| | - Qincheng Peng
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Haizhu district, Guangzhou, 510275 Guangdong China
| | - Da Luo
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Haizhu district, Guangzhou, 510275 Guangdong China
| | - Keyuan Jiao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632 Guangdong China
| | - Shihao Su
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
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10
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Daras G, Rigas S, Alatzas A, Samiotaki M, Chatzopoulos D, Tsitsekian D, Papadaki V, Templalexis D, Banilas G, Athanasiadou AM, Kostourou V, Panayotou G, Hatzopoulos P. LEFKOTHEA Regulates Nuclear and Chloroplast mRNA Splicing in Plants. Dev Cell 2019; 50:767-779.e7. [PMID: 31447263 DOI: 10.1016/j.devcel.2019.07.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 04/27/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022]
Abstract
Eukaryotic organisms accomplish the removal of introns to produce mature mRNAs through splicing. Nuclear and organelle splicing mechanisms are distinctively executed by spliceosome and group II intron complex, respectively. Here, we show that LEFKOTHEA, a nuclear encoded RNA-binding protein, participates in chloroplast group II intron and nuclear pre-mRNA splicing. Transiently optimized LEFKOTHEA nuclear activity is fundamental for plant growth, whereas the loss of function abruptly arrests embryogenesis. Nucleocytoplasmic partitioning and chloroplast allocation are efficiently balanced via functional motifs in LEFKOTHEA polypeptide. In the context of nuclear-chloroplast coevolution, our results provide a strong paradigm of the convergence of RNA maturation mechanisms in the nucleus and chloroplasts to coordinately regulate gene expression and effectively control plant growth.
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Affiliation(s)
- Gerasimos Daras
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Anastasios Alatzas
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | | | - Dikran Tsitsekian
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Vassiliki Papadaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | | | - Georgios Banilas
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | | | - Vassiliki Kostourou
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | - George Panayotou
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
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11
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Soriano JM, Alvaro F. Discovering consensus genomic regions in wheat for root-related traits by QTL meta-analysis. Sci Rep 2019; 9:10537. [PMID: 31332216 PMCID: PMC6646344 DOI: 10.1038/s41598-019-47038-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 07/09/2019] [Indexed: 11/25/2022] Open
Abstract
Root system architecture is crucial for wheat adaptation to drought stress, but phenotyping for root traits in breeding programmes is difficult and time-consuming owing to the belowground characteristics of the system. Identifying quantitative trait loci (QTLs) and linked molecular markers and using marker-assisted selection is an efficient way to increase selection efficiency and boost genetic gains in breeding programmes. Hundreds of QTLs have been identified for different root traits in the last few years. In the current study, consensus QTL regions were identified through QTL meta-analysis. First, a consensus map comprising 7352 markers was constructed. For the meta-analysis, 754 QTLs were retrieved from the literature and 634 of them were projected onto the consensus map. Meta-analysis grouped 557 QTLs in 94 consensus QTL regions, or meta-QTLs (MQTLs), and 18 QTLs remained as singletons. The recently published genome sequence of wheat was used to search for gene models within the MQTL peaks. As a result, gene models for 68 of the 94 Root_MQTLs were found, 35 of them related to root architecture and/or drought stress response. This work will facilitate QTL cloning and pyramiding to develop new cultivars with specific root architecture for coping with environmental constraints.
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Affiliation(s)
- Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain.
| | - Fanny Alvaro
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
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12
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Wen X, Wang J, Zhang D, Wang Y. A Gene Regulatory Network Controlled by BpERF2 and BpMYB102 in Birch under Drought Conditions. Int J Mol Sci 2019; 20:ijms20123071. [PMID: 31234595 PMCID: PMC6627136 DOI: 10.3390/ijms20123071] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022] Open
Abstract
Gene expression profiles are powerful tools for investigating mechanisms of plant stress tolerance. Betula platyphylla (birch) is a widely distributed tree, but its drought-tolerance mechanism has been little studied. Using RNA-Seq, we identified 2917 birch genes involved in its response to drought stress. These drought-responsive genes include the late embryogenesis abundant (LEA) family, heat shock protein (HSP) family, water shortage-related and ROS-scavenging proteins, and many transcription factors (TFs). Among the drought-induced TFs, the ethylene responsive factor (ERF) and myeloblastosis oncogene (MYB) families were the most abundant. BpERF2 and BpMYB102, which were strongly induced by drought and had high transcription levels, were selected to study their regulatory networks. BpERF2 and BpMYB102 both played roles in enhancing drought tolerance in birch. Chromatin immunoprecipitation combined with qRT-PCR indicated that BpERF2 regulated genes such as those in the LEA and HSP families, while BpMYB102 regulated genes such as Pathogenesis-related Protein 1 (PRP1) and 4-Coumarate:Coenzyme A Ligase 10 (4CL10). Multiple genes were regulated by both BpERF2 and BpMYB102. We further characterized the function of some of these genes, and the genes that encode Root Primordium Defective 1 (RPD1), PRP1, 4CL10, LEA1, SOD5, and HSPs were found to be involved in drought tolerance. Therefore, our results suggest that BpERF2 and BpMYB102 serve as transcription factors that regulate a series of drought-tolerance genes in B. platyphylla to improve drought tolerance.
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Affiliation(s)
- Xuejing Wen
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China.
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jingxin Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.
| | - Daoyuan Zhang
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China.
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China.
| | - Yucheng Wang
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China.
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China.
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13
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Yang Y, Wang Y, Jia L, Yang G, Xu X, Zhai H, He S, Li J, Dai X, Qin N, Zhu C, Liu Q. Involvement of an ABI-like protein and a Ca2+-ATPase in drought tolerance as revealed by transcript profiling of a sweetpotato somatic hybrid and its parents Ipomoea batatas (L.) Lam. and I. triloba L. PLoS One 2018; 13:e0193193. [PMID: 29466419 PMCID: PMC5821372 DOI: 10.1371/journal.pone.0193193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/06/2018] [Indexed: 12/14/2022] Open
Abstract
Previously, we obtained the sweetpotato somatic hybrid KT1 from a cross between sweetpotato (Ipomoea batatas (L.) Lam.) cv. Kokei No. 14 and its drought-tolerant wild relative I. triloba L. KT1 not only inherited the thick storage root characteristic of Kokei No. 14 but also the drought-tolerance trait of I. triloba L. The aim of this study was to explore the molecular mechanism of the drought tolerance of KT1. Four-week-old in vitro-grown plants of KT1, Kokei No. 14, and I. triloba L. were subjected to a simulated drought stress treatment (30% PEG6000) for 0, 6, 12 and 24 h. Total RNA was extracted from samples at each time point, and then used for transcriptome sequencing. The gene transcript profiles of KT1 and its parents were compared to identify differentially expressed genes, and drought-related modules were screened by a weighted gene co-expression network analysis. The functions of ABI-like protein and Ca2+-ATPase, two proteins screened from the cyan and light yellow modules, were analyzed in terms of their potential roles in drought tolerance in KT1 and its parents. These analyses of the drought responses of KT1 and its somatic donors at the transcriptional level provide new annotations for the molecular mechanism of drought tolerance in the somatic hybrid KT1 and its parents.
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Affiliation(s)
- Yufeng Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Yannan Wang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Licong Jia
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Guohong Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xinzhi Xu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hong Zhai
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Shaozhen He
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Junxia Li
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaodong Dai
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Na Qin
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Cancan Zhu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qingchang Liu
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
- * E-mail:
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14
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Mangin B, Casadebaig P, Cadic E, Blanchet N, Boniface MC, Carrère S, Gouzy J, Legrand L, Mayjonade B, Pouilly N, André T, Coque M, Piquemal J, Laporte M, Vincourt P, Muños S, Langlade NB. Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modelling and genome-wide association. PLANT, CELL & ENVIRONMENT 2017; 40:2276-2291. [PMID: 28418069 DOI: 10.1111/pce.12961] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/06/2016] [Indexed: 05/08/2023]
Abstract
Understanding the genetic basis of phenotypic plasticity is crucial for predicting and managing climate change effects on wild plants and crops. Here, we combined crop modelling and quantitative genetics to study the genetic control of oil yield plasticity for multiple abiotic stresses in sunflower. First, we developed stress indicators to characterize 14 environments for three abiotic stresses (cold, drought and nitrogen) using the SUNFLO crop model and phenotypic variations of three commercial varieties. The computed plant stress indicators better explain yield variation than descriptors at the climatic or crop levels. In those environments, we observed oil yield of 317 sunflower hybrids and regressed it with three selected stress indicators. The slopes of cold stress norm reaction were used as plasticity phenotypes in the following genome-wide association study. Among the 65 534 tested Single Nucleotide Polymorphisms (SNPs), we identified nine quantitative trait loci controlling oil yield plasticity to cold stress. Associated single nucleotide polymorphisms are localized in genes previously shown to be involved in cold stress responses: oligopeptide transporters, lipid transfer protein, cystatin, alternative oxidase or root development. This novel approach opens new perspectives to identify genomic regions involved in genotype-by-environment interaction of a complex traits to multiple stresses in realistic natural or agronomical conditions.
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Affiliation(s)
- Brigitte Mangin
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Pierre Casadebaig
- AGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN, Castanet-Tolosan, F-31326, France
| | - Eléna Cadic
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Nicolas Blanchet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | | | - Sébastien Carrère
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Ludovic Legrand
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Baptiste Mayjonade
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Nicolas Pouilly
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Thierry André
- SOLTIS, Domaine de Sandreau, Mondonville, F-31700, Blagnac, France
| | - Marie Coque
- BIOGEMMA, Domaine de Sandreau, Mondonville, F-31700, Blagnac, France
| | - Joël Piquemal
- SYNGENTA SEEDS, 12 chemin Hobit, F-31790, Saint Sauveur, France
| | | | - Patrick Vincourt
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
| | - Nicolas B Langlade
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, F-31326, France
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15
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Ohbayashi I, Lin CY, Shinohara N, Matsumura Y, Machida Y, Horiguchi G, Tsukaya H, Sugiyama M. Evidence for a Role of ANAC082 as a Ribosomal Stress Response Mediator Leading to Growth Defects and Developmental Alterations in Arabidopsis. THE PLANT CELL 2017; 29:2644-2660. [PMID: 28899981 PMCID: PMC5774571 DOI: 10.1105/tpc.17.00255] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/24/2017] [Accepted: 09/11/2017] [Indexed: 05/20/2023]
Abstract
Ribosome-related mutants in Arabidopsis thaliana share several notable characteristics regarding growth and development, which implies the existence of a common pathway that responds to disorders in ribosome biogenesis. As a first step to explore this pathway genetically, we screened a mutagenized population of root initiation defective2 (rid2), a temperature-sensitive mutant that is impaired in pre-rRNA processing, and isolated suppressor of root initiation defective two1 (sriw1), a suppressor mutant in which the defects of cell proliferation observed in rid2 at the restrictive temperature was markedly rescued. sriw1 was identified as a missense mutation of the NAC transcription factor gene ANAC082 The sriw1 mutation greatly alleviated the developmental abnormalities of rid2 and four other tested ribosome-related mutants, including rid3 However, the impaired pre-rRNA processing in rid2 and rid3 was not relieved by sriw1 Expression of ANAC082 was localized to regions where phenotypic effects of ribosome-related mutations are readily evident and was elevated in rid2 and rid3 compared with the wild type. These findings suggest that ANAC082 acts downstream of perturbation of biogenesis of the ribosome and may mediate a set of stress responses leading to developmental alterations and cell proliferation defects.
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Affiliation(s)
- Iwai Ohbayashi
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo 112-0001, Japan
| | - Chung-Yi Lin
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo 112-0001, Japan
| | - Naoki Shinohara
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo 112-0001, Japan
| | - Yoko Matsumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
- Okazaki Institute for Integrative Bioscience, Okazaki 444-8787, Japan
| | - Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo 112-0001, Japan
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16
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Zhao Y, Wang H, Chen W, Zhao P, Gong H, Sang X, Cui Y. Regional association analysis-based fine mapping of three clustered QTL for verticillium wilt resistance in cotton (G. hirsutum. L). BMC Genomics 2017; 18:661. [PMID: 28841857 PMCID: PMC6389109 DOI: 10.1186/s12864-017-4074-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/16/2017] [Indexed: 11/21/2022] Open
Abstract
Background Verticillium wilt is one of the most destructive diseases affecting global cotton production. The most effective way to control wilt disease has been the development of new cotton varieties that are resistant to VW. VW-resistant Upland cotton cultivars have been created in both the USA and China by Gossypium barbadense introgression. More than 100 VW resistance quantitative trait loci have been detected. Results Three clustered VW resistance-related QTL were detected in a 120-line association population and assigned to a genome region of 14,653,469–55,190,112 bp in Dt_chr9. A regional association analysis-based fine-mapping strategy was developed to narrow down the confidence intervals of the above QTL. The estimated LD decay of the genome region of interest was much faster than those of the Dt_chr9 chromosome and the whole genome, suggesting the existence of a recombination hotspot. Thirty-seven haplotype blocks were detected. The confidence intervals of the three clustered QTL were narrowed down to a region of 937,906 bp involving QTL-i23734Gh and a region of 1,389,417 bp involving QTL- i10740Gh, respectively. Each region contained the strongest association signal. Comparative analysis redefined the confidence intervals of the other three QTLs, qDL52T2-c19, QTL-BNL4069, and QTL-JESPR0001. The broad-spectrum VW resistance QTL qVW-D9–1 was demonstrated to be closely linked with the three redefined QTL, QTL-i23734Gh, QTL- i10740Gh and QTL-JESPR0001. Twelve functional genes were detected to be located within the redefined confidence intervals of VW resistance QTL. The mRNA CotAD_60243, encoding E3 ubiquitin-protein ligase UPL2-like, responsible for plant innate immunity and broad-spectrum disease resistance, was found to be overlapped with the strongest association signal i10740Gh. Six mRNAs encoding putative disease-resistance proteins were within the redefined confidence interval of QTL-JESPR0001, suggesting a tandem arrangement of R genes. Conclusions Our results proved that the VW resistance effect related to three clustered VW resistance-related QTL was actually controled by two redefined major QTL and severlal minor loci. The broad-spectrum VW resistance QTL qVW-D9–1 may be closely linked with the two redefined major QTLs. The tandem arrangement of R genes were detected in the redefined confidence interval of QTL-JESPR0001. The candidate genes obtained should be helpful in identifying and characterizing defense genes related to VW resistance QTL. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4074-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunlei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, Henan, 455000, China
| | - Hongmei Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, Henan, 455000, China.
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, Henan, 455000, China
| | - Pei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, Henan, 455000, China
| | - Haiyan Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, Henan, 455000, China
| | - Xiaohui Sang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, Henan, 455000, China
| | - Yanli Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, Henan, 455000, China
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17
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Liu J, Ming Y, Cheng Y, Zhang Y, Xing J, Sun Y. Comparative Transcriptome Analysis Reveal Candidate Genes Potentially Involved in Regulation of Primocane Apex Rooting in Raspberry ( Rubus spp.). FRONTIERS IN PLANT SCIENCE 2017; 8:1036. [PMID: 28659963 PMCID: PMC5469044 DOI: 10.3389/fpls.2017.01036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/30/2017] [Indexed: 05/11/2023]
Abstract
Raspberries (Rubus spp.) exhibit a unique rooting process that is initiated from the stem apex of primocane, conferring an unusual asexual mode of reproduction to this plant. However, the full complement of genes involved in this process has not been identified. To this end, the present study analyzed the transcriptomes of the Rubus primocane and floricane stem apex at three developmental stages by Digital Gene Expression profiling to identify genes that regulate rooting. Sequencing and de novo assembly yielded 26.82 Gb of nucleotides and 59,173 unigenes; 498, 7,346, 4,110, 7,900, 9,397, and 4,776 differently expressed genes were identified in paired comparisons of SAF1 (floricane at developmental stage 1) vs. SAP1 (primocane at developmental stage 1), SAF2 vs. SAP2, SAF3 vs. SAP3, SAP1 vs. SAP2, SAP1 vs. SAP3, and SAP2 vs. SAP3, respectively. SAP1 maintains an extension growth pattern; SAP2 then exhibits growth arrest and vertical (downward) gravitropic deflection; and finally, short roots begin to form on the apex of SAP3. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis of SAP1 vs. SAP2 revealed 12 pathways that were activated in response to shoot growth arrest and root differentiation, including circadian rhythm-plant (ko04712) and plant hormone signal transduction (ko04075). Our results indicate that genes related to circadian rhythm, ethylene and auxin signaling, shoot growth, and root development are potentially involved in the regulation of primocane apex rooting in Rubus. These findings provide a basis for elucidating the molecular mechanisms of primocane apex rooting in this economically valuable crop.
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18
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Álvarez C, Valledor L, Sáez P, Sánchez-Olate M, Ríos D. Proteomic Analysis through Adventitious Rooting of <i>Pinus radiata</i> Stem Cuttings with Different Rooting Capabilities. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/ajps.2016.714174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Chettoor AM, Yi G, Gomez E, Hueros G, Meeley RB, Becraft PW. A putative plant organelle RNA recognition protein gene is essential for maize kernel development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:236-46. [PMID: 24985738 DOI: 10.1111/jipb.12234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/29/2014] [Indexed: 05/29/2023]
Abstract
Basal endosperm transfer layer (BETL) cells are responsible for transferring apoplastic solutes from the maternal pedicel into the endosperm, supplying the grain with compounds required for embryo development and storage reserve accumulation. Here, we analyze the maize (Zea mays L.) empty pericarp6 (emp6) mutant, which causes early arrest in grain development. The Emp6+gene function is required independently in both the embryo and endosperm. The emp6 mutant causes a notable effect on the differentiation of BETL cells; the extensive cell wall ingrowths that distinguish BETL cells are diminished and BETL marker gene expression is compromised in mutant kernels. Transposon tagging identified the emp6 locus as encoding a putative plant organelle RNA recognition (PORR) protein, 1 of 15 PORR family members in maize. The emp6 transcript is widely detected in plant tissues with highest levels in embryos and developing kernels. EMP6-green fluorescent protein (GFP) fusion proteins transiently expressed in Nicotiana benthamiana leaves were targeted specifically to mitochondria. These results suggest that BETL cell differentiation might be particularly energy intensive, or alternatively, that mitochondria might confer a developmental function.
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Affiliation(s)
- Antony M Chettoor
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
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20
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A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing. Proc Natl Acad Sci U S A 2009; 106:4537-42. [PMID: 19251672 DOI: 10.1073/pnas.0812503106] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative genomics has provided evidence for numerous conserved protein domains whose functions remain unknown. We identified a protein harboring "domain of unknown function 860" (DUF860) as a component of group II intron ribonucleoprotein particles in maize chloroplasts. This protein, assigned the name WTF1 ("what's this factor?"), coimmunoprecipitates from chloroplast extract with group II intron RNAs, is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Both WTF1 and its resident DUF860 bind RNA in vitro, demonstrating that DUF860 is a previously unrecognized RNA-binding domain. DUF860 is found only in plants, where it is represented in a protein family comprising 14 orthologous groups in angiosperms. Most members of the DUF860 family are predicted to localize to chloroplasts or mitochondria, suggesting that proteins with this domain have multiple roles in RNA metabolism in both organelles. These findings add to emerging evidence that the coevolution of nuclear and organellar genomes spurred the evolution of diverse noncanonical RNA-binding motifs that perform organelle-specific functions.
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21
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Meinke D, Muralla R, Sweeney C, Dickerman A. Identifying essential genes in Arabidopsis thaliana. TRENDS IN PLANT SCIENCE 2008; 13:483-91. [PMID: 18684657 DOI: 10.1016/j.tplants.2008.06.003] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 06/06/2008] [Accepted: 06/10/2008] [Indexed: 05/20/2023]
Abstract
Eight years after publication of the Arabidopsis genome sequence and two years before completing the first phase of an international effort to characterize the function of every Arabidopsis gene, plant biologists remain unable to provide a definitive answer to the following basic question: what is the minimal gene set required for normal growth and development? The purpose of this review is to summarize different strategies employed to identify essential genes in Arabidopsis, an important component of the minimal gene set in plants, to present an overview of the datasets and specific genes identified to date, and to discuss the prospects for future saturation of this important class of genes. The long-term goal of this collaborative effort is to facilitate basic research in plant biology and complement ongoing research with other model organisms.
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Affiliation(s)
- David Meinke
- Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA.
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22
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Konishi M, Yanagisawa S. Sequential activation of two Dof transcription factor gene promoters during vascular development in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2007; 45:623-9. [PMID: 17583520 DOI: 10.1016/j.plaphy.2007.05.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 05/04/2007] [Indexed: 05/15/2023]
Abstract
Plant-specific Dof transcription factors play various roles in plants. We show the strictly regulated activity of two Dof gene promoters during procambium formation, an early process for vascular development, in Arabidopsis thaliana (L.) Heynh. The AtDof2.4 promoter was active in procambial cells of leaf primordia, roots and embryos, whereas the AtDof5.8 promoter activity was specifically detectable in the cells of prospective veins in leaf primordia of seedlings and cotyledons of developing embryos, and the vascular tissue of developing flower buds. The AtDof5.8 promoter but not the AtDof2.4 promoter showed strong activity in advance of perceptible procambium formation. AtDof2.4 and AtDof5.8 might function in the early but different processes for vascular development.
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Affiliation(s)
- Mineko Konishi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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