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Yao D, Zhou J, Zhang A, Wang J, Liu Y, Wang L, Pi W, Li Z, Yue W, Cai J, Liu H, Hao W, Qu X. Advances in CRISPR/Cas9-based research related to soybean [ Glycine max (Linn.) Merr] molecular breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1247707. [PMID: 37711287 PMCID: PMC10499359 DOI: 10.3389/fpls.2023.1247707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023]
Abstract
Soybean [Glycine max (Linn.) Merr] is a source of plant-based proteins and an essential oilseed crop and industrial raw material. The increase in the demand for soybeans due to societal changes has coincided with the increase in the breeding of soybean varieties with enhanced traits. Earlier gene editing technologies involved zinc finger nucleases and transcription activator-like effector nucleases, but the third-generation gene editing technology uses clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). The rapid development of CRISPR/Cas9 technology has made it one of the most effective, straightforward, affordable, and user-friendly technologies for targeted gene editing. This review summarizes the application of CRISPR/Cas9 technology in soybean molecular breeding. More specifically, it provides an overview of the genes that have been targeted, the type of editing that occurs, the mechanism of action, and the efficiency of gene editing. Furthermore, suggestions for enhancing and accelerating the molecular breeding of novel soybean varieties with ideal traits (e.g., high yield, high quality, and durable disease resistance) are included.
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Affiliation(s)
- Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Institute of Crop Resources, Jilin Provincial Academy of Agricultural Sciences, Gongzhuling, Jilin, China
| | - Junming Zhou
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Aijing Zhang
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jiaxin Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yixuan Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Lixue Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenxuan Pi
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Zihao Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenjun Yue
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jinliang Cai
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Huijing Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenyuan Hao
- Jilin Provincial Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Xiangchun Qu
- Institute of Crop Resources, Jilin Provincial Academy of Agricultural Sciences, Gongzhuling, Jilin, China
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Nisa ZU, Wang Y, Ali N, Chen C, Zhang X, Jin X, Yu L, Jing L, Chen C, Elansary HO. Strigolactone signaling gene from soybean GmMAX2a enhances the drought and salt-alkaline resistance in Arabidopsis via regulating transcriptional profiles of stress-related genes. Funct Integr Genomics 2023; 23:216. [PMID: 37391642 DOI: 10.1007/s10142-023-01151-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Strigolactone (SL) is a new plant hormone, which not only plays an important role in stimulating seed germination, plant branching, and regulating root development, but also plays an important role in the response of plants to abiotic stresses. In this study, the full-length cDNA of a soybean SL signal transduction gene (GmMAX2a) was isolated, cloned and revealed an important role in abiotic stress responses. Tissue-specific expression analysis by qRT-PCR indicated that GmMAX2a was expressed in all tissues of soybean, but highest expression was detected in seedling stems. Moreover, upregulation of GmMAX2a transcript expression under salt, alkali, and drought conditions were noted at different time points in soybean leaves compared to roots. Additionally, histochemical GUS staining studies revealed the deep staining in PGmMAX2a: GUS transgenic lines compared to WT indicating active involvement of GmMAX2a promoter region to stress responses. To further investigate the function of GmMAX2a gene in transgenic Arabidopsis, Petri-plate experiments were performed and GmMAX2a OX lines appeared with longer roots and improved fresh biomass compared to WT plants to NaCl, NaHCO3, and mannitol supplementation. Furthermore, the expression of several stress-related genes such as RD29B, SOS1, NXH1, AtRD22, KIN1, COR15A, RD29A, COR47, H+-APase, NADP-ME, NCED3, and P5CS were significantly high in GmMAX2a OX plants after stress treatment compared to WT plants. In conclusion, GmMAX2a improves soybean tolerance towards abiotic stresses (salt, alkali, and drought). Hence, GmMAX2a can be considered a candidate gene for transgenic breeding against various abiotic stresses in plants.
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Affiliation(s)
- Zaib-Un Nisa
- Institute of Molecular Biology and Biotechnology IMBB, The University of Lahore, Lahore, Pakistan.
| | - Yudan Wang
- Department of Chemistry and Molecular biology, School of Life Science and Technology, Harbin Normal University, Harbin, 150025, People's Republic of China
| | - Naila Ali
- Institute of Molecular Biology and Biotechnology IMBB, The University of Lahore, Lahore, Pakistan
| | - Chen Chen
- Department of Chemistry and Molecular biology, School of Life Science and Technology, Harbin Normal University, Harbin, 150025, People's Republic of China
| | - Xu Zhang
- Department of Chemistry and Molecular biology, School of Life Science and Technology, Harbin Normal University, Harbin, 150025, People's Republic of China
| | - Xiaoxia Jin
- Department of Chemistry and Molecular biology, School of Life Science and Technology, Harbin Normal University, Harbin, 150025, People's Republic of China
| | - Lijie Yu
- Department of Chemistry and Molecular biology, School of Life Science and Technology, Harbin Normal University, Harbin, 150025, People's Republic of China
| | - Legang Jing
- Department of Chemistry and Molecular biology, School of Life Science and Technology, Harbin Normal University, Harbin, 150025, People's Republic of China
| | - Chao Chen
- Department of Chemistry and Molecular biology, School of Life Science and Technology, Harbin Normal University, Harbin, 150025, People's Republic of China.
| | - Hosam O Elansary
- Department of Plant Production, College of Food & Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
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Leung HS, Chan LY, Law CH, Li MW, Lam HM. Twenty years of mining salt tolerance genes in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:45. [PMID: 37313223 PMCID: PMC10248715 DOI: 10.1007/s11032-023-01383-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/12/2023] [Indexed: 06/15/2023]
Abstract
Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01383-3.
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Affiliation(s)
- Hoi-Sze Leung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Long-Yiu Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Cheuk-Hin Law
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Man-Wah Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000 People’s Republic of China
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Huang P, Lu M, Li X, Sun H, Cheng Z, Miao Y, Fu Y, Zhang X. An Efficient Agrobacterium rhizogenes-Mediated Hairy Root Transformation Method in a Soybean Root Biology Study. Int J Mol Sci 2022; 23:ijms232012261. [PMID: 36293115 PMCID: PMC9603872 DOI: 10.3390/ijms232012261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
The stable genetic transformation of soybean is time-consuming and inefficient. As a simple and practical alternative method, hairy root transformation mediated by Agrobacterium rhizogenes is widely applied in studying root-specific processes, nodulation, biochemical and molecular functions of genes of interest, gene editing efficiency of CRISPR/Cas9, and biological reactors and producers. Therefore, many laboratories have developed unique protocols to obtain hairy roots in composite plants composed of transgenic roots and wild-type shoots. However, these protocols still suffer from the shortcomings of low efficiency and time, space, and cost consumption. To address this issue, we developed a new protocol efficient regeneration and transformation of hairy roots (eR&T) in soybean, by integrating and optimizing the main current methods to achieve high efficiency in both hairy root regeneration and transformation within a shorter period and using less space. By this eR&T method, we obtained 100% regeneration of hairy roots for all explants, with an average 63.7% of transformation frequency, which promoted the simultaneous and comparative analysis of the function of several genes. The eR&T was experimentally verified Promoter:GUS reporters, protein subcellular localization, and CRISPR/Cas9 gene editing experiments. Employing this approach, we identified several novel potential regulators of nodulation, and nucleoporins of the Nup107-160 sub-complex, which showed development-dependent and tissue-dependent expression patterns, indicating their important roles in nodulation in soybean. Thus, the new eR&T method is an efficient and economical approach for investigating not only root and nodule biology, but also gene function.
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Affiliation(s)
- Penghui Huang
- Moa Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingyang Lu
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in the Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Xiangbei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Huiyu Sun
- Moa Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Cheng
- CAS Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yuchen Miao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yongfu Fu
- Moa Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (Y.F.); (X.Z.)
| | - Xiaomei Zhang
- Moa Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (Y.F.); (X.Z.)
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Wang X, Chen K, Zhou M, Gao Y, Huang H, Liu C, Fan Y, Fan Z, Wang Y, Li X. GmNAC181 promotes symbiotic nodulation and salt tolerance of nodulation by directly regulating GmNINa expression in soybean. THE NEW PHYTOLOGIST 2022; 236:656-670. [PMID: 35751548 DOI: 10.1111/nph.18343] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Soybean (Glycine max) is one of the most important crops world-wide. Under low nitrogen (N) condition, soybean can form a symbiotic relationship with rhizobia to acquire sufficient N for their growth and production. Nodulation signaling controls soybean symbiosis with rhizobia. The soybean Nodule Inception (GmNINa) gene is a central regulator of soybean nodulation. However, the transcriptional regulation of GmNINa remains largely unknown. Nodulation is sensitive to salt stress, but the underlying mechanisms are unclear. Here, we identified an NAC transcription factor designated GmNAC181 (also known as GmNAC11) as the interacting protein of GmNSP1a. GmNAC181 overexpression or knockdown in soybean resulted in increased or decreased numbers of nodules, respectively. Accordingly, the expression of GmNINa was greatly up- and downregulated, respectively. Furthermore, we showed that GmNAC181 can directly bind to the GmNINa promoter to activate its gene expression. Intriguingly, GmNAC181 was highly induced by salt stress during nodulation and promoted symbiotic nodulation under salt stress. We identified a new transcriptional activator of GmNINa in the nodulation pathway and revealed a mechanism by which GmNAC181 acts as a network node orchestrating the expression of GmNINa and symbiotic nodulation under salt stress conditions.
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Affiliation(s)
- Xiaodi Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Road, Guangzhou, Guangdong, 510642, China
| | - Kuan Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Miaomiao Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongkang Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Huimei Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yuanyuan Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zihui Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Youning Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Road, Guangzhou, Guangdong, 510642, China
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Han X, Wang D, Song GQ. Expression of a maize SOC1 gene enhances soybean yield potential through modulating plant growth and flowering. Sci Rep 2021; 11:12758. [PMID: 34140602 PMCID: PMC8211702 DOI: 10.1038/s41598-021-92215-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/07/2021] [Indexed: 11/08/2022] Open
Abstract
Yield enhancement is a top priority for soybean (Glycine max Merr.) breeding. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) is a major integrator in flowering pathway, and it is anticipated to be capable of regulating soybean reproductive stages through its interactions with other MADS-box genes. Thus, we produced transgenic soybean for a constitutive expression of a maize SOC1 (ZmSOC1). T1 transgenic plants, in comparison with the nontransgenic plants, showed early flowering, reduced height of mature plants, and no significant impact on grain quality. The transgenic plants also had a 13.5-23.2% of higher grain weight per plant than the nontransgenic plants in two experiments. Transcriptome analysis in the leaves of 34-day old plants revealed 58 differentially expressed genes (DEGs) responding to the expression of the ZmSOC1, of which the upregulated FRUITFULL MADS-box gene, as well as the transcription factor VASCULAR PLANT ONE-ZINC FINGER1, contributed to the promoted flowering. The downregulated gibberellin receptor GID1B could play a major role in reducing the plant height. The remaining DEGs suggested broader effects on the other unmeasured traits (e.g., photosynthesis efficiency and abiotic tolerance), which could contribute to yield increase. Overall, modulating expression of SOC1 in soybean provides a novel and promising approach to regulate plant growth and reproductive development and thus has a potential either to enhance grain yield or to change plant adaptability.
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Affiliation(s)
- Xue Han
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Dechun Wang
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Guo-Qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
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Mandozai A, Moussa AA, Zhang Q, Qu J, Du Y, Anwari G, Al Amin N, Wang P. Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean ( Glycine max L.) at Seedling Stages Using SLAF-Seq. FRONTIERS IN PLANT SCIENCE 2021; 12:568995. [PMID: 34394134 PMCID: PMC8355526 DOI: 10.3389/fpls.2021.568995] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/08/2021] [Indexed: 05/19/2023]
Abstract
Root systems can display variable genetic architectures leading to nutrient foraging or improving abiotic stress tolerance. Breeding for new soybean varieties with efficient root systems has tremendous potential in enhancing resource use efficiency and plant adaptation for challenging climates. In this study, root related traits were analyzed in a panel of 260 spring soybean with genome-wide association study (GWAS). Genotyping was done with specific locus amplified fragment sequencing (SLAF-seq), and five GWAS models (GLM, MLM, CMLM, FaST-LMM, and EMMAX) were used for analysis. A total of 179,960 highly consistent SNP markers distributed over the entire genome with an inter-marker distance of 2.36 kb was used for GWAS analysis. Overall, 27 significant SNPs with a phenotypic contribution ranging from 20 to 72% and distributed on chromosomes 2, 6, 8, 9, 13, 16 and 18 were identified and two of them were found to be associated with multiple root-related traits. Based on the linkage disequilibrium (LD) distance of 9.5 kb for the different chromosomes, 11 root and shoot regulating genes were detected based on LD region of a maximum 55-bp and phenotypic contribution greater than 22%. Expression analysis revealed an association between expression levels of those genes and the degree of root branching number. The current study provides new insights into the genetic architecture of soybean roots, and the underlying SNPs/genes could be critical for future breeding of high-efficient root system in soybean.
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Prince SJ, Vuong TD, Wu X, Bai Y, Lu F, Kumpatla SP, Valliyodan B, Shannon JG, Nguyen HT. Mapping Quantitative Trait Loci for Soybean Seedling Shoot and Root Architecture Traits in an Inter-Specific Genetic Population. FRONTIERS IN PLANT SCIENCE 2020; 11:1284. [PMID: 32973843 PMCID: PMC7466435 DOI: 10.3389/fpls.2020.01284] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/06/2020] [Indexed: 05/27/2023]
Abstract
Wild soybean species (Glycine soja Siebold & Zucc.) comprise a unique resource to widen the genetic base of cultivated soybean [Glycine max (L.) Merr.] for various agronomic traits. An inter-specific mapping population derived from a cross of cultivar Williams 82 and PI 483460B, a wild soybean accession, was utilized for genetic characterization of root architecture traits. The objectives of this study were to identify and characterize quantitative trait loci (QTL) for seedling shoot and root architecture traits, as well as to determine additive/epistatic interaction effects of identified QTLs. A total of 16,469 single nucleotide polymorphisms (SNPs) developed for the Illumina beadchip genotyping platform were used to construct a high resolution genetic linkage map. Among the 11 putative QTLs identified, two significant QTLs on chromosome 7 were determined to be associated with total root length (RL) and root surface area (RSA) with favorable alleles from the wild soybean parent. These seedling root traits, RL (BARC_020495_04641 ~ BARC_023101_03769) and RSA (SNP02285 ~ SNP18129_Magellan), could be potential targets for introgression into cultivated soybean background to improve both tap and lateral roots. The RL QTL region harbors four candidate genes with higher expression in root tissues: Phosphofructokinase (Glyma.07g126400), Snf7 protein (Glyma.07g127300), unknown functional gene (Glyma.07g127900), and Leucine Rich-Repeat protein (Glyma.07g127100). The novel alleles inherited from the wild soybean accession could be used as molecular markers to improve root system architecture and productivity in elite soybean lines.
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Affiliation(s)
- Silvas J. Prince
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
- Plant Biology Division, Noble Research Institute, LLC, Ardmore, OK, United States
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Xiaolei Wu
- BASF Agricultural Solutions, Morrisville, NC, United States
| | - Yonghe Bai
- Nuseed Americas, Woodland, CA, United States
| | - Fang Lu
- Amgen Inc., Thousand Oaks, CA, United States
| | | | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO, United States
| | - J. Grover Shannon
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
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Fan YL, Zhang XH, Zhong LJ, Wang XY, Jin LS, Lyu SH. One-step generation of composite soybean plants with transgenic roots by Agrobacterium rhizogenes-mediated transformation. BMC PLANT BIOLOGY 2020; 20:208. [PMID: 32397958 PMCID: PMC7333419 DOI: 10.1186/s12870-020-02421-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 04/29/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Agrobacterium rhizogenes-mediated (ARM) transformation is a highly efficient technique for generating composite plants composed of transgenic roots and wild-type shoot, providing a powerful tool for studying root biology. The ARM transformation has been established in many plant species, including soybean. However, traditional transformation of soybean, transformation efficiency is low. Additionally, the hairy roots were induced in a medium, and then the generated composite plants were transplanted into another medium for growth. This two-step operation is not only time-consuming, but aggravates contamination risk in the study of plant-microbe interactions. RESULTS Here, we report a one-step ARM transformation method with higher transformation efficiency for generating composite soybean plants. Both the induction of hairy roots and continuous growth of the composite plants were conducted in a single growth medium. The primary root of a 7-day-old seedling was decapitated with a slanted cut, the residual hypocotyl (maintained 0.7-1 cm apical portion) was inoculated with A. rhizogenes harboring the gene construct of interest. Subsequently, the infected seedling was planted into a pot with wet sterile vermiculite. Almost 100% of the infected seedlings could produce transgenic positive roots 16 days post-inoculation in 7 tested genotypes. Importantly, the transgenic hairy roots in each composite plant are about three times more than those of the traditional ARM transformation, indicating that the one-step method is simpler in operation and higher efficiency in transformation. The reliability of the one-step method was verified by CRISPR/Cas9 system to knockout the soybean Rfg1, which restricts nodulation in Williams 82 (Nod-) by Sinorhizobium fredii USDA193. Furthermore, we applied this method to analyze the function of Arabidopsis YAO promoter in soybean. The activity of YAO promoter was detected in whole roots and stronger in the root tips. We also extended the protocol to tomato. CONCLUSIONS We established a one-step ARM transformation method, which is more convenient in operation and higher efficiency (almost 100%) in transformation for generating composite soybean plants. This method has been validated in promoter functional analysis and rhizobia-legume interactions. We anticipate a broad application of this method to analyze root-related events in tomato and other plant species besides soybean.
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Affiliation(s)
- Ying-lun Fan
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Xing-hui Zhang
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Li-jing Zhong
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Xiu-yuan Wang
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Liang-shen Jin
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
| | - Shan-hua Lyu
- College of Agriculture, Liaocheng University, Liaocheng, 252000 China
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Chen L, Fang Y, Li X, Zeng K, Chen H, Zhang H, Yang H, Cao D, Hao Q, Yuan S, Zhang C, Guo W, Chen S, Yang Z, Shan Z, Zhang X, Qiu D, Zhan Y, Zhou XA. Identification of soybean drought-tolerant genotypes and loci correlated with agronomic traits contributes new candidate genes for breeding. PLANT MOLECULAR BIOLOGY 2020; 102:109-122. [PMID: 31820285 DOI: 10.1007/s11103-019-00934-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE Drought tolerance level of 136 soybean genotypes, the correlations among traits were evaluated, and several important drought-tolerant genotypes, traits, SNPs and genes were possibly useful for soybean genetic breeding. Drought is an adverse environmental factor affecting crops growth, development, and yield. Promising genotypes and genes with improved tolerance to drought are probably effective ways to alleviate the situation. In this study, our main task was to determine drought tolerance level of 136 soybean genotypes, the correlations among physiological and agronomic traits under drought, and drought-tolerant single nucleotide polymorphism (SNPs) and genes. In this study, twenty-six varieties were identified as excellent tolerant genotypes to stress among which S14, S93 and S135 with high drought-tolerant index (DTI > 1.3) and yield (Y > 300 kg). Fourteen varieties were identified as drought-sensitive genotypes, such as S25, S45 and S58, with low drought-tolerant index (DTI < 0.5). 422 SNPs and 302 genes correlated with seed number per plant (SNPP), maturity (M), number of seeds per pod (NSPP), node number of main stem (NNMS), Stem diameter (SD) and pull stem (PS) were detected under well-watered and drought conditions by genome-wide association study (GWAS). Among them, we found SNPs (Chr 3:1758920-1958934) between drought-tolerant and sensitive genotypes. 13 genes (Glyma.03G017800, Glyma.03G018000, Glyma.03G018200, Glyma.03G018400, Glyma.03G018500, Glyma.03G018600, Glyma.03G018700, Glyma.03G018800, Glyma.03G018900, Glyma.03G019000, Glyma.03G019100, Glyma.03G019200, Glyma.03G019300) correlated with NNMS were detected. By qRT-PCR, the expression level of Glyma.03G018000 and Glyma.03G018900 in drought-tolerant varieties was significantly increased, but low or no expression in sensitive varieties under drought stress. This study provides important drought-tolerant genotypes, traits, SNPs and potential genes, possibly useful for soybean genetic breeding.
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Affiliation(s)
- Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Yisheng Fang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Xiangyong Li
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Kai Zeng
- Crop Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Key Lab of Cereal Quality Research and Genetic Improvement, Xinjiang Production and Construction Crops, Shihezi, 832000, China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Hengbin Zhang
- Crop Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Key Lab of Cereal Quality Research and Genetic Improvement, Xinjiang Production and Construction Crops, Shihezi, 832000, China
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Qingnan Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Shuilian Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Zhonglu Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Zhihui Shan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Xiaojuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Dezhen Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China
| | - Yong Zhan
- Crop Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Key Lab of Cereal Quality Research and Genetic Improvement, Xinjiang Production and Construction Crops, Shihezi, 832000, China.
| | - Xin-An Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, China.
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Cordell GA. Cyberecoethnopharmacolomics. JOURNAL OF ETHNOPHARMACOLOGY 2019; 244:112134. [PMID: 31377262 DOI: 10.1016/j.jep.2019.112134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Development of a new term which describes the contemporary, composite, constituent sciences of ethnopharmacology. AIM OF THE STUDY To discuss the polysyllabic term cyberecoethnopharmacolomics in the context of the future of ethnopharmacology in global health care. MATERIALS AND METHODS Literature background and assessment from the prior literature, diverse databases, and personal discussions. RESULTS The profiles and literature background with contemporary and future thoughts regarding the concepts and practices of cyber-, eco-, ethno-, pharmacol-, and -omics, and their impact in ethnopharmacology for the future are presented in the context of integrated health care systems. CONCLUSIONS Ethnopharmacology has a major role to play in global health care if the relevant sciences and cutting-edge technologies can coalesce synergistically as a responsive, evidence-based health care practice.
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Affiliation(s)
- Geoffrey A Cordell
- Natural Products Inc., Evanston, IL, USA; Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
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Chang C, Tian L, Ma L, Li W, Nasir F, Li X, Tran LSP, Tian C. Differential responses of molecular mechanisms and physiochemical characters in wild and cultivated soybeans against invasion by the pathogenic Fusarium oxysporum Schltdl. PHYSIOLOGIA PLANTARUM 2019; 166:1008-1025. [PMID: 30430602 DOI: 10.1111/ppl.12870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 05/07/2023]
Abstract
Cultivated soybean (Glycine max) was derived from the wild soybean (Glycine soja), which has genetic resources that can be critically important for improving plant stress resistance. However, little information is available pertaining to the molecular and physiochemical comparison between the cultivated and wild soybeans in response to the pathogenic Fusarium oxysporum Schltdl. In this study, we first used comparative phenotypic and paraffin section analyses to indicate that wild soybean is indeed more resistant to F. oxysporum than cultivated soybean. Genome-wide RNA-sequencing approach was then used to elucidate the genetic mechanisms underlying the differential physiological and biochemical responses of the cultivated soybean, and its relative, to F. oxysporum. A greater number of genes related to cell wall synthesis and hormone metabolism were significantly altered in wild soybean than in cultivated soybean under F. oxysporum infection. Accordingly, a higher accumulation of lignins was observed in wild soybean than cultivated soybean under F. oxysporum infection. Collectively, these results indicated that secondary metabolites and plant hormones may play a vital role in differentiating the response between cultivated and wild soybeans against the pathogen. These important findings may provide future direction to breeding programs to improve resistance to F. oxysporum in the elite soybean cultivars by taking advantage of the genetic resources within wild soybean germplasm.
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Affiliation(s)
- Chunling Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiqiang Li
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
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Tian L, Shi S, Ma L, Nasir F, Li X, Tran LSP, Tian C. Co-evolutionary associations between root-associated microbiomes and root transcriptomes in wild and cultivated rice varieties. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 128:134-141. [PMID: 29777991 DOI: 10.1016/j.plaphy.2018.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/26/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
The plants and root-associated microbiomes are closely related. Plant metabolic substances can serve as a nutrient source for the microbiome, and in return, the microbiome can regulate the production of plant metabolic substances. Wild rice (Oryza rufipogon), as the ancestor of cultivated rice (Oryza sativa), has changed several metabolic pathways and root-associated microbiome during evolution. Thus, the study of the different associations between metabolic pathways and root-associated microbiomes in wild and cultivated rice varieties is important for rice breeding. In this article, the co-evolutionary association between metabolic pathways, which are based on transcriptome data, and root-associated microbiomes, which are based on 16S rRNA and internal transcribed spacer (ITS) amplicon data, in wild and cultivated rice was studied. The results showed that the enriched pathways were differentially correlated with the enriched microbiomes in wild and cultivated rice varieties. Pathways for 'Glutathione metabolism', 'Plant-pathogen interaction', 'Protein processing in endoplasmic reticulum' and 'Tyrosine metabolism' were positively associated with the improved relative abundance of bacterial and fungal operational taxonomic units (OTUs) in wild rice. On the other hand, 'Glycolysis/Gluconeogenesis', 'Brassinosteroid biosynthesis', 'Carbon metabolism', 'Phenylpropanoid biosynthesis' and 'Caffeine metabolism' were positively correlated with the improved relative abundance of bacterial and fungal OTUs in cultivated rice. Redundancy analysis showed that certain bacterial and fungal species could positively and significantly affect plant gene expression; for instance, Streptomyces, with 8.7% relative abundance in bacterial community, significantly affected plant gene expression in wild rice. This study can provide the theoretical basis for recognizing the associations between root-associated microbiomes and root transcriptomes in wild and cultivated rice varieties, and can provide practical significance for developing useful bacterial and fungal resources in wild rice.
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Affiliation(s)
- Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Fahad Nasir
- School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Xiujun Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Lam-Son Phan Tran
- Plant Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China.
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Tian L, Shi S, Nasir F, Chang C, Li W, Tran LSP, Tian C. Comparative analysis of the root transcriptomes of cultivated and wild rice varieties in response to Magnaporthe oryzae infection revealed both common and species-specific pathogen responses. RICE (NEW YORK, N.Y.) 2018; 11:26. [PMID: 29679239 PMCID: PMC5910329 DOI: 10.1186/s12284-018-0211-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/20/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Magnaporthe oryzae, the causal fungus of rice blast disease, negatively impacts global rice production. Wild rice (Oryza rufipogon), a relative of cultivated rice (O. sativa), possesses unique attributes that enable it to resist pathogen invasion. Although wild rice represents a major resource for disease resistance, relative to current cultivated rice varieties, no prior studies have compared the immune and transcriptional responses in the roots of wild and cultivated rice to M. oryzae. RESULTS In this study, we showed that M. oryzae could act as a typical root-infecting pathogen in rice, in addition to its common infection of leaves, and wild rice roots were more resistant to M. oryzae than cultivated rice roots. Next, we compared the differential responses of wild and cultivated rice roots to M. oryzae using RNA-sequencing (RNA-seq) to unravel the molecular mechanisms underlying the enhanced resistance of the wild rice roots. Results indicated that both common and genotype-specific mechanisms exist in both wild and cultivated rice that are associated with resistance to M. oryzae. In wild rice, resistance mechanisms were associated with lipid metabolism, WRKY transcription factors, chitinase activities, jasmonic acid, ethylene, lignin, and phenylpropanoid and diterpenoid metabolism; while the pathogen responses in cultivated rice were mainly associated with phenylpropanoid, flavone and wax metabolism. Although modulations in primary metabolism and phenylpropanoid synthesis were common to both cultivated and wild rice, the modulation of secondary metabolism related to phenylpropanoid synthesis was associated with lignin synthesis in wild rice and flavone synthesis in cultivated rice. Interestingly, while the expression of fatty acid and starch metabolism-related genes was altered in both wild and cultivated rice in response to the pathogen, changes in lipid acid synthesis and lipid acid degradation were dominant in cultivated and wild rice, respectively. CONCLUSIONS The response mechanisms to M. oryzae were more complex in wild rice than what was observed in cultivated rice. Therefore, this study may have practical implications for controlling M. oryzae in rice plantings and will provide useful information for incorporating and assessing disease resistance to M. oryzae in rice breeding programs.
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Affiliation(s)
- Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
- School of Life Sciences, Northeast Normal University, Changchun City, Jilin China
| | - Chunling Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Weiqiang Li
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam; Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
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Zhang M, Liu Y, Shi H, Guo M, Chai M, He Q, Yan M, Cao D, Zhao L, Cai H, Qin Y. Evolutionary and expression analyses of soybean basic Leucine zipper transcription factor family. BMC Genomics 2018; 19:159. [PMID: 29471787 PMCID: PMC5824455 DOI: 10.1186/s12864-018-4511-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/31/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Soybean, a major legume crop native to East Asia, presents a wealth of resources for utilization. The basic leucine zipper (bZIP) transcription factors play important roles in various biological processes including developmental regulation and responses to environmental stress stimuli. Currently, little information is available regarding the bZIP family in the legume crop soybean. RESULTS Using a genome-wide domain analysis, we identified 160 GmbZIP genes in soybean genome, named from GmbZIP1 to GmbZIP160. These 160GmbZIP genes, distributed unevenly across 20 chromosomes, were grouped into 12 subfamilies based on phylogenetic analysis. Gene structure and conserved motif analyses showed that GmbZIP within the same subfamily shared similar intron-exon organizations and motif composition. Syntenic and phylogenetic analyses identified 40 Arabidopsis bZIP genes and 83 soybean bZIP genes as orthologs. By investigating the expression profiling of GmbZIP in different tissues and under drought and flooding stresses, we showed that a majority of GmbZIP (83.44%) exhibited transcript abundance in all examined tissues and 75.6% displayed transcript changes after drought and flooding treatment, suggesting that GmbZIP may play a broad role in soybean development and response to water stress. CONCLUSIONS One hundred sixty GmbZIP genes were identified in soybean genome. Our results provide insights for the evolutionary history of bZIP family in soybean and shed light on future studies on the function of bZIP genes in response to water stress in soybean.
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Affiliation(s)
- Man Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Yanhui Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Hang Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Mingliang Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Mengnan Chai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Qing He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Maokai Yan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Du Cao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Lihua Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Hanyang Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
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16
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Lu L, Dong C, Liu R, Zhou B, Wang C, Shou H. Roles of Soybean Plasma Membrane Intrinsic Protein GmPIP2;9 in Drought Tolerance and Seed Development. FRONTIERS IN PLANT SCIENCE 2018; 9:530. [PMID: 29755491 PMCID: PMC5932197 DOI: 10.3389/fpls.2018.00530] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/05/2018] [Indexed: 05/21/2023]
Abstract
Aquaporins play an essential role in water uptake and transport in vascular plants. The soybean genome contains a total of 22 plasma membrane intrinsic protein (PIP) genes. To identify candidate PIPs important for soybean yield and stress tolerance, we studied the transcript levels of all 22 soybean PIPs. We found that a GmPIP2 subfamily member, GmPIP2;9, was predominately expressed in roots and developing seeds. Here, we show that GmPIP2;9 localized to the plasma membrane and had high water channel activity when expressed in Xenopus oocytes. Using transgenic soybean plants expressing a native GmPIP2;9 promoter driving a GUS-reporter gene, it was found high GUS expression in the roots, in particular, in the endoderm, pericycle, and vascular tissues of the roots of transgenic plants. In addition, GmPIP2;9 was also highly expressed in developing pods. GmPIP2;9 expression significantly increased in short term of polyethylene glycol (PEG)-mediated drought stress treatment. GmPIP2;9 overexpression increased tolerance to drought stress in both solution cultures and soil plots. Drought stress in combination with GmPIP2;9 overexpression increased net CO2 assimilation of photosynthesis, stomata conductance, and transpiration rate, suggesting that GmPIP2;9-overexpressing transgenic plants were less stressed than wild-type (WT) plants. Furthermore, field experiments showed that GmPIP2;9-overexpressing plants had significantly more pod numbers and larger seed sizes than WT plants. In summary, the study demonstrated that GmPIP2;9 has water transport activity. Its relative high expression levels in roots and developing pods are in agreement with the phenotypes of GmPIP2;9-overexpressing plants in drought stress tolerance and seed development.
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Affiliation(s)
- Linghong Lu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Changhe Dong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ruifang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Bin Zhou
- Institute of Crop Science, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Chuang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Huixia Shou,
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Ghosh Dasgupta M, Dharanishanthi V. Identification of PEG-induced water stress responsive transcripts using co-expression network in Eucalyptus grandis. Gene 2017; 627:393-407. [DOI: 10.1016/j.gene.2017.06.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/12/2017] [Accepted: 06/28/2017] [Indexed: 12/23/2022]
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Li Y, Chen Q, Nan H, Li X, Lu S, Zhao X, Liu B, Guo C, Kong F, Cao D. Overexpression of GmFDL19 enhances tolerance to drought and salt stresses in soybean. PLoS One 2017; 12:e0179554. [PMID: 28640834 PMCID: PMC5480881 DOI: 10.1371/journal.pone.0179554] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/30/2017] [Indexed: 01/17/2023] Open
Abstract
The basic leucine zipper (bZIP) family of transcription factors plays an important role in the growth and developmental process as well as responds to various abiotic stresses, such as drought and high salinity. Our previous work identified GmFDL19, a bZIP transcription factor, as a flowering promoter in soybean, and the overexpression of GmFDL19 caused early flowering in transgenic soybean plants. Here, we report that GmFDL19 also enhances tolerance to drought and salt stress in soybean. GmFDL19 was determined to be a group A member, and its transcription expression was highly induced by abscisic acid (ABA), polyethylene glycol (PEG 6000) and high salt stresses. Overexpression of GmFDL19 in soybean enhanced drought and salt tolerance at the seedling stage. The relative plant height (RPH) and relative shoot dry weight (RSDW) of transgenic plants were significantly higher than those of the WT after PEG and salt treatments. In addition, the germination rate and plant height of the transgenic soybean were also significantly higher than that of WT plants after various salt treatments. Furthermore, we also found that GmFDL19 could reduce the accumulation of Na+ ion content and up-regulate the expression of several ABA/stress-responsive genes in transgenic soybean. We also found that GmFDL19 overexpression increased the activities of several antioxidative enzyme and chlorophyll content but reduced malondialdehyde content. These results suggested that GmFDL19 is involved in soybean abiotic stress responses and has potential utilization to improve multiple stress tolerance in transgenic soybean.
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Affiliation(s)
- Yuanyuan Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Quanzhen Chen
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Haiyang Nan
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaoming Li
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sijia Lu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaohui Zhao
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Dong Cao
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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19
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Zeng H, Zhang Y, Zhang X, Pi E, Zhu Y. Analysis of EF-Hand Proteins in Soybean Genome Suggests Their Potential Roles in Environmental and Nutritional Stress Signaling. FRONTIERS IN PLANT SCIENCE 2017; 8:877. [PMID: 28596783 PMCID: PMC5443154 DOI: 10.3389/fpls.2017.00877] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/10/2017] [Indexed: 05/23/2023]
Abstract
Calcium ion (Ca2+) is a universal second messenger that plays a critical role in plant responses to diverse physiological and environmental stimuli. The stimulus-specific signals are perceived and decoded by a series of Ca2+ binding proteins serving as Ca2+ sensors. The majority of Ca2+ sensors possess the EF-hand motif, a helix-loop-helix structure which forms a turn-loop structure. Although EF-hand proteins in model plant such as Arabidopsis have been well described, the identification, classification, and the physiological functions of EF-hand-containing proteins from soybean are not systemically reported. In this study, a total of at least 262 genes possibly encoding proteins containing one to six EF-hand motifs were identified in soybean genome. These genes include 6 calmodulins (CaMs), 144 calmodulin-like proteins (CMLs), 15 calcineurin B-like proteins, 50 calcium-dependent protein kinases (CDPKs), 13 CDPK-related protein kinases, 2 Ca2+- and CaM-dependent protein kinases, 17 respiratory burst oxidase homologs, and 15 unclassified EF-hand proteins. Most of these genes (87.8%) contain at least one kind of hormonal signaling- and/or stress response-related cis-elements in their -1500 bp promoter regions. Expression analyses by exploring the published microarray and Illumina transcriptome sequencing data revealed that the expression of these EF-hand genes were widely detected in different organs of soybean, and nearly half of the total EF-hand genes were responsive to various environmental or nutritional stresses. Quantitative RT-PCR was used to confirm their responsiveness to several stress treatments. To confirm the Ca2+-binding ability of these EF-hand proteins, four CMLs (CML1, CML13, CML39, and CML95) were randomly selected for SDS-PAGE mobility-shift assay in the presence and absence of Ca2+. Results showed that all of them have the ability to bind Ca2+. This study provided the first comprehensive analyses of genes encoding for EF-hand proteins in soybean. Information on the classification, phylogenetic relationships and expression profiles of soybean EF-hand genes in different tissues and under various environmental and nutritional stresses will be helpful for identifying candidates with potential roles in Ca2+ signal-mediated physiological processes including growth and development, plant-microbe interactions and responses to biotic and abiotic stresses.
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Affiliation(s)
- Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yaxian Zhang
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Xiajun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yiyong Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China
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20
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Conforte AJ, Guimarães-Dias F, Neves-Borges AC, Bencke-Malato M, Felix-Whipps D, Alves-Ferreira M. Isolation and characterization of a promoter responsive to salt, osmotic and dehydration stresses in soybean. Genet Mol Biol 2017; 40:226-237. [PMID: 28350037 PMCID: PMC5452143 DOI: 10.1590/1678-4685-gmb-2016-0052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 11/21/2016] [Indexed: 11/22/2022] Open
Abstract
Drought stress is the main limiting factor of soybean yield. Currently, genetic
engineering has been one important tool in the development of drought-tolerant
cultivars. A widely used strategy is the fusion of genes that confer tolerance under
the control of the CaMV35S constitutive promoter; however,
stress-responsive promoters would constitute the best alternative to the generation
of drought-tolerant crops. We characterized the promoter of α-galactosidase soybean
(GlymaGAL) gene that was previously identified as highly
up-regulated by drought stress. The β-glucuronidase (GUS) activity
of Arabidopsis transgenic plants bearing 1000- and 2000-bp fragments of the
GlymaGAL promoter fused to the uidA gene was
evaluated under air-dried, polyethylene glycol (PEG) and salt stress treatments.
After 24 h of air-dried and PEG treatments, the pGAL-2kb led to an
increase in GUS expression in leaf and root samples when compared to
the control samples. These results were corroborated by qPCR expression analysis of
the uidA gene. The pGAL-1kb showed no difference in
GUS activity between control and treated samples. The
pGAL-2kb promoter was evaluated in transgenic soybean roots,
leading to an increase in EGFP expression under air-dried treatment.
Our data indicates that pGAL-2kb could be a useful tool in
developing drought-tolerant cultivars by driving gene expression.
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Affiliation(s)
| | - Fábia Guimarães-Dias
- Department of Genetics. Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Anna Cristina Neves-Borges
- Department of Botany. Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ, Brazil
| | - Marta Bencke-Malato
- Department of Genetics. Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Durvalina Felix-Whipps
- Department of Genetics. Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Márcio Alves-Ferreira
- Department of Genetics. Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
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21
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Rai AN, Tamirisa S, Rao KV, Kumar V, Suprasanna P. Brassica RNA binding protein ERD4 is involved in conferring salt, drought tolerance and enhancing plant growth in Arabidopsis. PLANT MOLECULAR BIOLOGY 2016; 90:375-87. [PMID: 26711633 DOI: 10.1007/s11103-015-0423-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 12/22/2015] [Indexed: 05/24/2023]
Abstract
'Early responsive to dehydration' (ERD) genes are a group of plant genes having functional roles in plant stress tolerance and development. In this study, we have isolated and characterized a Brassica juncea 'ERD' gene (BjERD4) which encodes a novel RNA binding protein. The expression pattern of ERD4 analyzed under different stress conditions showed that transcript levels were increased with dehydration, sodium chloride, low temperature, heat, abscisic acid and salicylic acid treatments. The BjERD4 was found to be localized in the chloroplasts as revealed by Confocal microscopy studies. To study the function, transgenic Arabidopsis plants were generated and analyzed for various morphological and physiological parameters. The overexpressing transgenic lines showed significant increase in number of leaves with more leaf area and larger siliques as compared to wild type plants, whereas RNAi:ERD4 transgenic lines showed reduced leaf number, leaf area, dwarf phenotype and delayed seed germination. Transgenic Arabidopsis plants overexpressing BjERD4 gene also exhibited enhanced tolerance to dehydration and salt stresses, while the knockdown lines were susceptible as compared to wild type plants under similar stress conditions. It was observed that BjERD4 protein could bind RNA as evidenced by the gel-shift assay. The overall results of transcript analysis, RNA gel-shift assay, and transgenic expression, for the first time, show that the BjERD4 is involved in abiotic stress tolerance besides offering new clues about the possible roles of BjERD4 in plant growth and development.
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Affiliation(s)
- Archana N Rai
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Srinath Tamirisa
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500007, India
| | - K V Rao
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500007, India
| | - Vinay Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - P Suprasanna
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
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22
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Tiwari LD, Mittal D, Chandra Mishra R, Grover A. Constitutive over-expression of rice chymotrypsin protease inhibitor gene OCPI2 results in enhanced growth, salinity and osmotic stress tolerance of the transgenic Arabidopsis plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 92:48-55. [PMID: 25910649 DOI: 10.1016/j.plaphy.2015.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 03/31/2015] [Indexed: 05/01/2023]
Abstract
Protease inhibitors are involved primarily in defense against pathogens. In recent years, these proteins have also been widely implicated in response of plants to diverse abiotic stresses. Rice chymotrypsin protease inhibitor gene OCPI2 is highly induced under salt and osmotic stresses. The construct containing the complete coding sequence of OCPI2 cloned downstream to CaMV35S promoter was transformed in Arabidopsis and single copy, homozygous transgenic lines were produced. The transgenic plants exhibited significantly enhanced tolerance to NaCl, PEG and mannitol stress as compared to wild type plants. Importantly, the vegetative and reproductive growth of transgenic plants under unstressed, control conditions was also enhanced: transgenic plants were more vigorous than wild type, resulting into higher yield in terms of silique number. The RWC values and membrane stability index of transgenic in comparison to wild type plants was higher. Higher proline content was observed in the AtOCPI2 lines, which was associated with higher transcript expression of pyrroline-5-carboxylate synthase and lowered levels of proline dehydrogenase genes. The chymotrypsin protease activities were lower in the transgenic as against wild type plants, under both unstressed, control as well as stressed conditions. It thus appears that rice chymotrypsin protease inhibitor gene OCPI2 is a useful candidate gene for genetic improvement of plants against salt and osmotic stress.
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Affiliation(s)
- Lalit Dev Tiwari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Dheeraj Mittal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Ratnesh Chandra Mishra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
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23
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Manavalan LP, Prince SJ, Musket TA, Chaky J, Deshmukh R, Vuong TD, Song L, Cregan PB, Nelson JC, Shannon JG, Specht JE, Nguyen HT. Identification of novel QTL governing root architectural traits in an interspecific soybean population. PLoS One 2015; 10:e0120490. [PMID: 25756528 PMCID: PMC4355624 DOI: 10.1371/journal.pone.0120490] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/22/2015] [Indexed: 11/25/2022] Open
Abstract
Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibited significant differences in root architecture and root-related traits. In this study, phenotypic variability for root traits among 251 BC2F5 backcross inbred lines (BILs) developed from the cross Dunbar/PI 326582A were identified. The root systems of the parents and BILs were evaluated in controlled environmental conditions using a cone system at seedling stage. The G. max parent Dunbar contributed phenotypically favorable alleles at a major quantitative trait locus on chromosome 8 (Satt315-I locus) that governed root traits (tap root length and lateral root number) and shoot length. This QTL accounted for >10% of the phenotypic variation of both tap root and shoot length. This QTL region was found to control various shoot- and root-related traits across soybean genetic backgrounds. Within the confidence interval of this region, eleven transcription factors (TFs) were identified. Based on RNA sequencing and Affymetrix expression data, key TFs including MYB, AP2-EREBP and bZIP TFs were identified in this QTL interval with high expression in roots and nodules. The backcross inbred lines with different parental allelic combination showed different expression pattern for six transcription factors selected based on their expression pattern in root tissues. It appears that the marker interval Satt315-I locus on chromosome 8 contain an essential QTL contributing to early root and shoot growth in soybean.
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Affiliation(s)
- Lakshmi P. Manavalan
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Silvas J. Prince
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Theresa A. Musket
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Julian Chaky
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Rupesh Deshmukh
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Li Song
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Perry B. Cregan
- Soybean Genomics and Improvement Lab, USDA-ARS, Beltsville, Maryland, United States of America
| | - James C. Nelson
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - J. Grover Shannon
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - James E. Specht
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
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24
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Ha CV, Watanabe Y, Tran UT, Le DT, Tanaka M, Nguyen KH, Seki M, Nguyen DV, Tran LSP. Comparative analysis of root transcriptomes from two contrasting drought-responsive Williams 82 and DT2008 soybean cultivars under normal and dehydration conditions. FRONTIERS IN PLANT SCIENCE 2015; 6:551. [PMID: 26300889 PMCID: PMC4528160 DOI: 10.3389/fpls.2015.00551] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/06/2015] [Indexed: 05/04/2023]
Abstract
The economically important DT2008 and the model Williams 82 (W82) soybean cultivars were reported to have differential drought-tolerant degree to dehydration and drought, which was associated with root trait. Here, we used 66K Affymetrix Soybean Array GeneChip to compare the root transcriptomes of DT2008 and W82 seedlings under normal, as well as mild (2 h treatment) and severe (10 h treatment) dehydration conditions. Out of the 38172 soybean genes annotated with high confidence, 822 (2.15%) and 632 (1.66%) genes showed altered expression by dehydration in W82 and DT2008 roots, respectively, suggesting that a larger machinery is required to be activated in the drought-sensitive W82 cultivar to cope with the stress. We also observed that long-term dehydration period induced expression change of more genes in soybean roots than the short-term one, independently of the genotypes. Furthermore, our data suggest that the higher drought tolerability of DT2008 might be attributed to the higher number of genes induced in DT2008 roots than in W82 roots by early dehydration, and to the expression changes of more genes triggered by short-term dehydration than those by prolonged dehydration in DT2008 roots vs. W82 roots. Differentially expressed genes (DEGs) that could be predicted to have a known function were further analyzed to gain a basic understanding on how soybean plants respond to dehydration for their survival. The higher drought tolerability of DT2008 vs. W82 might be attributed to differential expression in genes encoding osmoprotectant biosynthesis-, detoxification- or cell wall-related proteins, kinases, transcription factors and phosphatase 2C proteins. This research allowed us to identify genetic components that contribute to the improved drought tolerance of DT2008, as well as provide a useful genetic resource for in-depth functional analyses that ultimately leads to development of soybean cultivars with improved tolerance to drought.
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Affiliation(s)
- Chien Van Ha
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Uyen Thi Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Dung Tien Le
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Kien Huu Nguyen
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- CREST, Japan Science and Technology AgencyKawaguchi, Japan
| | - Dong Van Nguyen
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- *Correspondence: Lam-Son Phan Tran, Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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25
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Guttikonda SK, Valliyodan B, Neelakandan AK, Tran LSP, Kumar R, Quach TN, Voothuluru P, Gutierrez-Gonzalez JJ, Aldrich DL, Pallardy SG, Sharp RE, Ho THD, Nguyen HT. Overexpression of AtDREB1D transcription factor improves drought tolerance in soybean. Mol Biol Rep 2014; 41:7995-8008. [PMID: 25192890 DOI: 10.1007/s11033-014-3695-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
Drought is one of the major abiotic stresses that affect productivity in soybean (Glycine max L.) Several genes induced by drought stress include functional genes and regulatory transcription factors. The Arabidopsis thaliana DREB1D transcription factor driven by the constitutive and ABA-inducible promoters was introduced into soybean through Agrobacterium tumefaciens-mediated gene transfer. Several transgenic lines were generated and molecular analysis was performed to confirm transgene integration. Transgenic plants with an ABA-inducible promoter showed a 1.5- to two-fold increase of transgene expression under severe stress conditions. Under well-watered conditions, transgenic plants with constitutive and ABA-inducible promoters showed reduced total leaf area and shoot biomass compared to non-transgenic plants. No significant differences in root length or root biomass were observed between transgenic and non-transgenic plants under non-stress conditions. When subjected to gradual water deficit, transgenic plants maintained higher relative water content because the transgenic lines used water more slowly as a result of reduced total leaf area. This caused them to wilt slower than non-transgenic plants. Transgenic plants showed differential drought tolerance responses with a significantly higher survival rate compared to non-transgenic plants when subjected to comparable severe water-deficit conditions. Moreover, the transgenic plants also showed improved drought tolerance by maintaining 17-24 % greater leaf cell membrane stability compared to non-transgenic plants. The results demonstrate the feasibility of engineering soybean for enhanced drought tolerance by expressing stress-responsive genes.
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Affiliation(s)
- Satish K Guttikonda
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
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26
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Sherman-Broyles S, Bombarely A, Powell AF, Doyle JL, Egan AN, Coate JE, Doyle JJ. The wild side of a major crop: soybean's perennial cousins from Down Under. AMERICAN JOURNAL OF BOTANY 2014; 101:1651-65. [PMID: 25326613 DOI: 10.3732/ajb.1400121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The accumulation of over 30 years of basic research on the biology, genetic variation, and evolution of the wild perennial relatives of soybean (Glycine max) provides a foundation to improve cultivated soybean. The cultivated soybean and its wild progenitor, G. soja, have a center of origin in eastern Asia and are the only two species in the annual subgenus Soja. Systematic and evolutionary studies of the ca. 30 perennial species of subgenus Glycine, native to Australia, have benefited from the availability of the G. max genomic sequence. The perennial species harbor many traits of interest to soybean breeders, among them resistance to major soybean pathogens such as cyst nematode and leaf rust. New species in the Australian subgenus continue to be described, due to the collection of new material and to insights gleaned through systematic studies of accessions in germplasm collections. Ongoing studies in perennial species focus on genomic regions that contain genes for key traits relevant to soybean breeding. These comparisons also include the homoeologous regions that are the result of polyploidy in the common ancestor of all Glycine species. Subgenus Glycine includes a complex of recently formed allopolyploids that are the focus of studies aimed at elucidating genomic, transcriptomic, physiological, taxonomic, morphological, developmental, and ecological processes related to polyploid evolution. Here we review what has been learned over the past 30 years and outline ongoing work on photosynthesis, nitrogen fixation, and floral biology, much of it drawing on new technologies and resources.
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Affiliation(s)
| | | | - Adrian F Powell
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| | - Jane L Doyle
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| | - Ashley N Egan
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington D.C. 20013-7012 USA
| | - Jeremy E Coate
- Reed College, Department of Biology, 3203 SE Woodstock Blvd., Portland, Oregon 97202 USA
| | - Jeff J Doyle
- Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
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27
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Yu Y, Huang W, Chen H, Wu G, Yuan H, Song X, Kang Q, Zhao D, Jiang W, Liu Y, Wu J, Cheng L, Yao Y, Guan F. Identification of differentially expressed genes in flax (Linum usitatissimum L.) under saline-alkaline stress by digital gene expression. Gene 2014; 549:113-22. [PMID: 25058012 DOI: 10.1016/j.gene.2014.07.053] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/17/2014] [Accepted: 07/19/2014] [Indexed: 01/04/2023]
Abstract
The salinization and alkalization of soil are widespread environmental problems, and alkaline salt stress is more destructive than neutral salt stress. Therefore, understanding the mechanism of plant tolerance to saline-alkaline stress has become a major challenge. However, little attention has been paid to the mechanism of plant alkaline salt tolerance. In this study, gene expression profiling of flax was analyzed under alkaline-salt stress (AS2), neutral salt stress (NSS) and alkaline stress (AS) by digital gene expression. Three-week-old flax seedlings were placed in 25 mM Na2CO3 (pH11.6) (AS2), 50mM NaCl (NSS) and NaOH (pH11.6) (AS) for 18 h. There were 7736, 1566 and 454 differentially expressed genes in AS2, NSS and AS compared to CK, respectively. The GO category gene enrichment analysis revealed that photosynthesis was particularly affected in AS2, carbohydrate metabolism was particularly affected in NSS, and the response to biotic stimulus was particularly affected in AS. We also analyzed the expression pattern of five categories of genes including transcription factors, signaling transduction proteins, phytohormones, reactive oxygen species proteins and transporters under these three stresses. Some key regulatory gene families involved in abiotic stress, such as WRKY, MAPKKK, ABA, PrxR and ion channels, were differentially expressed. Compared with NSS and AS, AS2 triggered more differentially expressed genes and special pathways, indicating that the mechanism of AS2 was more complex than NSS and AS. To the best of our knowledge, this was the first transcriptome analysis of flax in response to saline-alkaline stress. These data indicate that common and diverse features of saline-alkaline stress provide novel insights into the molecular mechanisms of plant saline-alkaline tolerance and offer a number of candidate genes as potential markers of tolerance to saline-alkaline stress.
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Affiliation(s)
- Ying Yu
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin 150086, PR China; Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Wengong Huang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Hongyu Chen
- College of Life Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Guangwen Wu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Hongmei Yuan
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin 150086, PR China; Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Xixia Song
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Qinghua Kang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Dongsheng Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Weidong Jiang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Yan Liu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Jianzhong Wu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Lili Cheng
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Yubo Yao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Fengzhi Guan
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin 150086, PR China; Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China.
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Thu NBA, Nguyen QT, Hoang XLT, Thao NP, Tran LSP. Evaluation of drought tolerance of the Vietnamese soybean cultivars provides potential resources for soybean production and genetic engineering. BIOMED RESEARCH INTERNATIONAL 2014; 2014:809736. [PMID: 24804248 PMCID: PMC3997955 DOI: 10.1155/2014/809736] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 11/18/2022]
Abstract
Drought is one of the greatest constraints to soybean production in many countries, including Vietnam. Although a wide variety of the newly produced cultivars have been produced recently in Vietnam through classical breeding to cope with water shortage, little knowledge of their molecular and physiological responses to drought has been discovered. This study was conducted to quickly evaluate drought tolerance of thirteen local soybean cultivars for selection of the best drought-tolerant cultivars for further field test. Differences in drought tolerance of cultivars were assessed by root and shoot lengths, relative water content, and drought-tolerant index under both normal and drought conditions. Our data demonstrated that DT51 is the strongest drought-tolerant genotype among all the tested cultivars, while the highest drought-sensitive phenotype was observed with MTD720. Thus, DT51 could be subjected to further yield tests in the field prior to suggesting it for use in production. Due to their contrasting drought-tolerant phenotypes, DT51 and MTD720 provide excellent genetic resources for further studies underlying mechanisms regulating drought responses and gene discovery. Our results provide vital information to support the effort of molecular breeding and genetic engineering to improve drought tolerance of soybean.
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Affiliation(s)
- Nguyen Binh Anh Thu
- School of Biotechnology, International University, Vietnam National University HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 70000, Vietnam
| | - Quang Thien Nguyen
- School of Biotechnology, International University, Vietnam National University HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 70000, Vietnam
| | - Xuan Lan Thi Hoang
- School of Biotechnology, International University, Vietnam National University HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 70000, Vietnam
| | - Nguyen Phuong Thao
- School of Biotechnology, International University, Vietnam National University HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 70000, Vietnam
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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Osakabe Y, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. ABA control of plant macroelement membrane transport systems in response to water deficit and high salinity. THE NEW PHYTOLOGIST 2014; 202:35-49. [PMID: 24283512 DOI: 10.1111/nph.12613] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/21/2013] [Indexed: 05/18/2023]
Abstract
Plant growth and productivity are adversely affected by various abiotic stressors and plants develop a wide range of adaptive mechanisms to cope with these adverse conditions, including adjustment of growth and development brought about by changes in stomatal activity. Membrane ion transport systems are involved in the maintenance of cellular homeostasis during exposure to stress and ion transport activity is regulated by phosphorylation/dephosphorylation networks that respond to stress conditions. The phytohormone abscisic acid (ABA), which is produced rapidly in response to drought and salinity stress, plays a critical role in the regulation of stress responses and induces a series of signaling cascades. ABA signaling involves an ABA receptor complex, consisting of an ABA receptor family, phosphatases and kinases: these proteins play a central role in regulating a variety of diverse responses to drought stress, including the activities of membrane-localized factors, such as ion transporters. In this review, recent research on signal transduction networks that regulate the function ofmembrane transport systems in response to stress, especially water deficit and high salinity, is summarized and discussed. The signal transduction networks covered in this review have central roles in mitigating the effect of stress by maintaining plant homeostasis through the control of membrane transport systems.
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Affiliation(s)
- Yuriko Osakabe
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Kouyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Kouyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
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30
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Quach TN, Tran LSP, Valliyodan B, Nguyen HTM, Kumar R, Neelakandan AK, Guttikonda SK, Sharp RE, Nguyen HT. Functional analysis of water stress-responsive soybean GmNAC003 and GmNAC004 transcription factors in lateral root development in arabidopsis. PLoS One 2014; 9:e84886. [PMID: 24465446 PMCID: PMC3900428 DOI: 10.1371/journal.pone.0084886] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 11/27/2013] [Indexed: 12/22/2022] Open
Abstract
In Arabidopsis, NAC (NAM, ATAF and CUC) transcription factors have been found to promote lateral root number through the auxin signaling pathway. In the present study, the role of water stress-inducible soybean GmNAC003 and GmNAC004 genes in the enhancement of lateral root development under water deficit conditions was investigated. Both genes were highly expressed in roots, leaves and flowers of soybean and were strongly induced by water stress and moderately induced by a treatment with abscisic acid (ABA). They showed a slight response to treatment with 2,4-dichlorophenoxyacetic acid (2,4-D). The transgenic Arabidopsis plants overexpressing GmNAC004 showed an increase in lateral root number and length under non-stress conditions and maintained higher lateral root number and length under mild water stress conditions compared to the wild-type (WT), while the transgenic plants overexpressing GmNAC003 did not show any response. However, LR development of GmNAC004 transgenic Arabidopsis plants was not enhanced in the water-stressed compared to the well-watered treatment. In the treatment with ABA, LR density of the GmNAC004 transgenic Arabidopsis was less suppressed than that of the WT, suggesting that GmNAC004 counteracts ABA-induced inhibition of lateral root development. In the treatment with 2,4-D, lateral root density was enhanced in both GmNAC004 transgenic Arabidopsis and WT plants but the promotion was higher in the transgenic plants. Conversely, in the treatment with naphthylphthalamic acid (NPA), lateral root density was inhibited and there was no difference in the phenotype of the GmNAC004 transgenic Arabidopsis and WT plants, indicating that auxin is required for the action of GmNAC004. Transcript analysis for a number of known auxin and ABA related genes showed that GmNAC004's role may suppress ABA signaling but promote auxin signaling to increase lateral root development in the Arabidopsis heterologous system.
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Affiliation(s)
- Truyen N. Quach
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Lam-Son Phan Tran
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Babu Valliyodan
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Hanh TM. Nguyen
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Rajesh Kumar
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Anjanasree K. Neelakandan
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Satish Kumar Guttikonda
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Robert E. Sharp
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Henry T. Nguyen
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
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Chen LM, Zhou XA, Li WB, Chang W, Zhou R, Wang C, Sha AH, Shan ZH, Zhang CJ, Qiu DZ, Yang ZL, Chen SL. Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions. BMC Genomics 2013; 14:687. [PMID: 24093224 PMCID: PMC3827939 DOI: 10.1186/1471-2164-14-687] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 09/25/2013] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Soybean is an important crop that provides valuable proteins and oils for human use. Because soybean growth and development is extremely sensitive to water deficit, quality and crop yields are severely impacted by drought stress. In the face of limited water resources, drought-responsive genes are therefore of interest. Identification and analysis of dehydration- and rehydration-inducible differentially expressed genes (DEGs) would not only aid elucidation of molecular mechanisms of stress response, but also enable improvement of crop stress tolerance via gene transfer. Using Digital Gene Expression Tag profiling (DGE), a new technique based on Illumina sequencing, we analyzed expression profiles between two soybean genotypes to identify drought-responsive genes. RESULTS Two soybean genotypes - drought-tolerant Jindou21 and drought-sensitive Zhongdou33 - were subjected to dehydration and rehydration conditions. For analysis of DEGs under dehydration conditions, 20 cDNA libraries were generated from roots and leaves at two different time points under well-watered and dehydration conditions. We also generated eight libraries for analysis under rehydration conditions. Sequencing of the 28 libraries produced 25,000-33,000 unambiguous tags, which were mapped to reference sequences for annotation of expressed genes. Many genes exhibited significant expression differences among the libraries. DEGs in the drought-tolerant genotype were identified by comparison of DEGs among treatments and genotypes. In Jindou21, 518 and 614 genes were differentially expressed under dehydration in leaves and roots, respectively, with 24 identified both in leaves and roots. The main functional categories enriched in these DEGs were metabolic process, response to stresses, plant hormone signal transduction, protein processing, and plant-pathogen interaction pathway; the associated genes primarily encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significantly expressed (|log2 ratio| ≥ 8) genes - Glyma15g03920, Glyma05g02470, Glyma15g15010, Glyma05g09070, Glyma06g35630, Glyma08g12590, and Glyma11g16000 - are more likely to determine drought stress tolerance. The expression patterns of eight randomly-selected genes were confirmed by quantitative RT-PCR; the results of QRT-PCR analysis agreed with transcriptional profile data for 96 out of 128 (75%) data points. CONCLUSIONS Many soybean genes were differentially expressed between drought-tolerant and drought-sensitive genotypes. Based on GO functional annotation and pathway enrichment analysis, some of these genes encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significant DEGs are candidates for improving soybean drought tolerance. These findings will be helpful for analysis and elucidation of molecular mechanisms of drought tolerance; they also provide a basis for cultivating new varieties of drought-tolerant soybean.
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Affiliation(s)
- Li M Chen
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Harbin 150030, China
| | - Xin A Zhou
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Wen B Li
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Harbin 150030, China
| | - Wei Chang
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Harbin 150030, China
| | - Rong Zhou
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Cheng Wang
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Ai H Sha
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Zhi H Shan
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Chan J Zhang
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - De Z Qiu
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Zhong L Yang
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Shui L Chen
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
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Van Ha C, Le DT, Nishiyama R, Watanabe Y, Sulieman S, Tran UT, Mochida K, Van Dong N, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. The auxin response factor transcription factor family in soybean: genome-wide identification and expression analyses during development and water stress. DNA Res 2013; 20:511-24. [PMID: 23810914 PMCID: PMC3789561 DOI: 10.1093/dnares/dst027] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/28/2013] [Indexed: 12/20/2022] Open
Abstract
In plants, the auxin response factor (ARF) transcription factors play important roles in regulating diverse biological processes, including development, growth, cell division and responses to environmental stimuli. An exhaustive search of soybean genome revealed 51 GmARFs, many of which were formed by genome duplications. The typical GmARFs (43 members) contain a DNA-binding domain, an ARF domain and an auxin/indole acetic acid (AUX/IAA) dimerization domain, whereas the remaining eight members lack the dimerization domain. Phylogenetic analysis of the ARFs from soybean and Arabidopsis revealed both similarity and divergence between the two ARF families, as well as enabled us to predict the functions of the GmARFs. Using quantitative real-time polymerase chain reaction (qRT-PCR) and available soybean Affymetrix array and Illumina transcriptome sequence data, a comprehensive expression atlas of GmARF genes was obtained in various organs and tissues, providing useful information about their involvement in defining the precise nature of individual tissues. Furthermore, expression profiling using qRT-PCR and microarray data revealed many water stress-responsive GmARFs in soybean, albeit with different patterns depending on types of tissues and/or developmental stages. Our systematic analysis has identified excellent tissue-specific and/or stress-responsive candidate GmARF genes for in-depth in planta functional analyses, which would lead to potential applications in the development of genetically modified soybean cultivars with enhanced drought tolerance.
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Affiliation(s)
- Chien Van Ha
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, Vietnam
- Post-Graduate Program, Vietnamese Academy of Agricultural Science, Thanhtri, Hanoi, Vietnam
| | - Dung Tien Le
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, Vietnam
| | - Rie Nishiyama
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Saad Sulieman
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Uyen Thi Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiichi Mochida
- Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan
| | - Nguyen Van Dong
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, Vietnam
| | | | - Kazuo Shinozaki
- Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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33
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The Cysteine Protease–Cysteine Protease Inhibitor System Explored in Soybean Nodule Development. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3030550] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Mittler R, Shulaev V. Functional genomics, challenges and perspectives for the future. PHYSIOLOGIA PLANTARUM 2013; 148:317-321. [PMID: 23582101 DOI: 10.1111/ppl.12060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/07/2013] [Indexed: 06/02/2023]
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35
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Cabreira C, Cagliari A, Bücker-Neto L, Wiebke-Strohm B, de Freitas LB, Marcelino-Guimarães FC, Nepomuceno AL, Margis-Pinheiro MMAN, Bodanese-Zanettini MH. The Lesion Simulating Disease (LSD) gene family as a variable in soybean response to Phakopsora pachyrhizi infection and dehydration. Funct Integr Genomics 2013; 13:323-38. [DOI: 10.1007/s10142-013-0326-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/20/2013] [Accepted: 05/27/2013] [Indexed: 12/13/2022]
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Ha S, Tran LS. Understanding plant responses to phosphorus starvation for improvement of plant tolerance to phosphorus deficiency by biotechnological approaches. Crit Rev Biotechnol 2013; 34:16-30. [PMID: 23586682 DOI: 10.3109/07388551.2013.783549] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In both prokaryotes and eukaryotes, including plants, phosphorus (P) is an essential nutrient that is involved in various biochemical processes, such as lipid metabolism and the biosynthesis of nucleic acids and cell membranes. P also contributes to cellular signaling cascades by function as mediators of signal transduction and it also serves as a vital energy source for a wide range of biological functions. Due to its intensive use in agriculture, P resources have become limited. Therefore, it is critically important in the future to develop scientific strategies that aim to increase P use efficiency and P recycling. In addition, the biologically available soluble form of P for uptake (phosphate; Pi) is readily washed out of topsoil layers, resulting in serious environmental pollution. In addition to this environmental concern, the wash out of Pi from topsoil necessitates a continuous Pi supply to maintain adequate levels of fertilization, making the situation worse. As a coping mechanism to P stress, plants are known to undergo drastic cellular changes in metabolism, physiology, hormonal balance and gene expression. Understanding these molecular, physiological and biochemical responses developed by plants will play a vital role in improving agronomic practices, resource conservation and environmental protection as well as serving as a foundation for the development of biotechnological strategies, which aim to improve P use efficiency in crops. In this review, we will discuss a variety of plant responses to low P conditions and various molecular mechanisms that regulate these responses. In addition, we also discuss the implication of this knowledge for the development of plant biotechnological applications.
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Affiliation(s)
- Sukbong Ha
- Department of Plant Biotechnology, Chonnam National University , Buk-Gu, Gwangju , Korea and
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37
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Teh HF, Neoh BK, Hong MPL, Low JYS, Ng TLM, Ithnin N, Thang YM, Mohamed M, Chew FT, Yusof HM, Kulaveerasingam H, Appleton DR. Differential metabolite profiles during fruit development in high-yielding oil palm mesocarp. PLoS One 2013; 8:e61344. [PMID: 23593468 PMCID: PMC3623811 DOI: 10.1371/journal.pone.0061344] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/07/2013] [Indexed: 01/02/2023] Open
Abstract
To better understand lipid biosynthesis in oil palm mesocarp, in particular the differences in gene regulation leading to and including de novo fatty acid biosynthesis, a multi-platform metabolomics technology was used to profile mesocarp metabolites during six critical stages of fruit development in comparatively high- and low-yielding oil palm populations. Significantly higher amino acid levels preceding lipid biosynthesis and nucleosides during lipid biosynthesis were observed in a higher yielding commercial palm population. Levels of metabolites involved in glycolysis revealed interesting divergence of flux towards glycerol-3-phosphate, while carbon utilization differences in the TCA cycle were proven by an increase in malic acid/citric acid ratio. Apart from insights into the regulation of enhanced lipid production in oil palm, these results provide potentially useful metabolite yield markers and genes of interest for use in breeding programmes.
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Affiliation(s)
- Huey Fang Teh
- Sime Darby Technology Centre, Lebuh Silikon, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
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38
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Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics. DNA Res 2013; 20:151-62. [PMID: 23284086 PMCID: PMC3628445 DOI: 10.1093/dnares/dss040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 12/10/2012] [Indexed: 12/11/2022] Open
Abstract
Crop plants, whose productivity is affected by a wide range of growing and environmental conditions, are grown for economic purposes. Transcription factors (TFs) play central role in regulation of many biological processes, including plant development and responses to environmental stimuli, by activating or repressing spatiotemporal gene expression. Here, we describe the TreeTFDB (http://treetfdb.bmep.riken.jp/index.pl) that houses the TF repertoires of six economically important tree crop species: Jatropha curcas, papaya, cassava, poplar, castor bean and grapevine. Among these, the TF repertoire of J. curcas has not been reported by any other TF databases. In addition to their basic information, such as sequence and domain features, domain alignments, gene ontology assignment and sequence comparison, information on available full-length cDNAs, identity and positions of all types of known cis-motifs found in the promoter regions, gene expression data are provided. With its newly designed and friendly interface and its unique features, TreeTFDB will enable research community to predict the functions and provide access to available genetic resources for performing comparative and functional genomics of the crop TFs, either individually or at whole family level, in a comprehensive and convenient manner.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan
| | - Takuhiro Yoshida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | - Kazuo Shinozaki
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Lam-Son Phan Tran
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Osakabe Y, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. Sensing the environment: key roles of membrane-localized kinases in plant perception and response to abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:445-58. [PMID: 23307915 DOI: 10.1093/jxb/ers354] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Adverse environmental conditions have negative effects on plant growth and development. Receptor proteins on the plasma membrane sense various environmental stimuli and transduce them to downstream intra- and intercellular signalling networks. Receptor-like kinases (RLKs) play important roles in perceiving the extracellular ligands and activating the downstream pathway via phosphorylation of intracellular serine/threonine kinase domains. The Arabidopsis genome possesses >600 RLK-encoding genes, some of which are implicated in the perception of environmental signals during the life cycle of the sessile plants. Histidine kinases are also membrane-localized kinases and perceive osmotic stress and plant hormones. In this review, we focus on the RLKs and histidine kinases that play a role in plant response to abiotic stresses. We summarize our recent understanding of their specific roles in stress responses and absicisic acid (ABA) regulation. Elucidation of the functions of these kinases in the osmotic stress response will provide a better understanding of stress-sensing mechanisms in plants and help to identify potential candidate genes for genetic engineering of improved stress-tolerant crops.
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Affiliation(s)
- Yuriko Osakabe
- Gene Discovery Research Group, RIKEN Plant Science Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
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Ha CV, Le DT, Nishiyama R, Watanabe Y, Tran UT, Dong NV, Tran LSP. Characterization of the newly developed soybean cultivar DT2008 in relation to the model variety W82 reveals a new genetic resource for comparative and functional genomics for improved drought tolerance. BIOMED RESEARCH INTERNATIONAL 2012; 2013:759657. [PMID: 23509774 PMCID: PMC3591244 DOI: 10.1155/2013/759657] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/20/2012] [Indexed: 01/09/2023]
Abstract
Soybean (Glycine max) productivity is adversely affected by drought stress worldwide, including Vietnam. In the last few years, we have made a great effort in the development of drought-tolerant soybean cultivars by breeding and/or radiation-induced mutagenesis. One of the newly developed cultivars, the DT2008, showed enhanced drought tolerance and stable yield in the field conditions. The purpose of this study was to compare the drought-tolerant phenotype of DT2008 and Williams 82 (W82) by assessing their water loss and growth rate under dehydration and/or drought stress conditions as a means to provide genetic resources for further comparative and functional genomics. We found that DT2008 had reduced water loss under both dehydration and drought stresses in comparison with W82. The examination of root and shoot growths of DT2008 and W82 under both normal and drought conditions indicated that DT2008 maintains a better shoot and root growth rates than W82 under both two growth conditions. These results together suggest that DT2008 has better drought tolerance degree than W82. Our results open the way for further comparison of DT2008 and W82 at molecular levels by advanced omic approaches to identify mutation(s) involved in the enhancement of drought tolerance of DT2008, contributing to our understanding of drought tolerance mechanisms in soybean. Mutation(s) identified are potential candidates for genetic engineering of elite soybean varieties to improve drought tolerance and biomass.
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Affiliation(s)
- Chien Van Ha
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham Van Dong Street, Hanoi, Vietnam
- Post-Graduate Program, Vietnamese Academy of Agricultural Science, Thanhtri, Hanoi, Vietnam
| | - Dung Tien Le
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham Van Dong Street, Hanoi, Vietnam
| | - Rie Nishiyama
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Uyen Thi Tran
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Nguyen Van Dong
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham Van Dong Street, Hanoi, Vietnam
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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Hossain Z, Hajika M, Komatsu S. Comparative proteome analysis of high and low cadmium accumulating soybeans under cadmium stress. Amino Acids 2012; 43:2393-416. [PMID: 22588482 DOI: 10.1007/s00726-012-1319-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 05/02/2012] [Indexed: 10/28/2022]
Abstract
A comparative proteomic study was performed to unravel the protein networks involved in cadmium stress response in soybean. Ten-day-old seedlings of contrasting cadmium accumulating soybean cultivars-Harosoy (high cadmium accumulator), Fukuyutaka (low cadmium accumulator), and their recombinant inbred line CDH-80 (high cadmium accumulator) were exposed to 100 μM CdCl(2) treatment for 3 days. Root growth was found to be affected under cadmium stress in all. Varietal differences at root protein level were evaluated. NADP-dependent alkenal double bond reductase P1 was found to be more abundant in low cadmium accumulating Fukuyutaka. Leaf proteome analysis revealed that differentially expressed proteins were primarily involved in metabolism and energy production. The results indicate that both high and low cadmium accumulating cultivars and CDH-80 share some common defense strategies to cope with the cadmium stress. High abundance of enzymes involved in glycolysis and TCA cycle might help cadmium challenged cells to produce more energy necessary to meet the high energy demand. Moreover, enhanced expressions of photosynthesis related proteins indicate quick utilization of photoassimilates in energy generation. Increased abundance of glutamine synthetase in all might be involved in phytochelatin mediated detoxification of cadmium ions. In addition, increased abundance of antioxidant enzymes, namely superoxide dismutase, ascorbate peroxidase, catalase, ensures cellular protection from reactive oxygen species mediated damages under cadmium stress. Enhanced expression of molecular chaperones in high cadmium accumulating cultivar might be another additional defense mechanism for refolding of misfolded proteins and to stabilize protein structure and function, thus maintain cellular homeostasis.
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Affiliation(s)
- Zahed Hossain
- National Institute of Crop Science, Kannondai 2-1-18, Tsukuba, 305-8518, Japan
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Abstract
Soybean (Glycine max) is one of the most important crops in legume family. Soybean and soybean-based products are also considered as popular food for human and animal husbandry. With its high oil content, soybean has become a potential resource for the production of renewable fuel. However, soybean is considered one of the most drought-sensitive crops, with approximately 40% reduction of the yield in the worst years. Recent research progresses in elucidation of biochemical, morphological and physiological responses as well as molecular mechanisms of plant adaptation to drought stress in model plants have provided a solid foundation for translational genomics of soybean toward drought tolerance. In this review, we will summarize the recent advances in development of drought-tolerant soybean cultivars by gene transfer.
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Affiliation(s)
- Nguyen Phuong Thao
- International University, Vietnam National University-HCMC, St block 6, Linh Trung ward, Thu Duc district, HCM city, Vietnam
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Homrich MS, Wiebke-Strohm B, Weber RLM, Bodanese-Zanettini MH. Soybean genetic transformation: A valuable tool for the functional study of genes and the production of agronomically improved plants. Genet Mol Biol 2012; 35:998-1010. [PMID: 23412849 PMCID: PMC3571417 DOI: 10.1590/s1415-47572012000600015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Transgenic plants represent an invaluable tool for molecular, genetic, biochemical and physiological studies by gene overexpression or silencing, transposon-based mutagenesis, protein sub-cellular localization and/or promoter characterization as well as a breakthrough for breeding programs, allowing the production of novel and genetically diverse genotypes. However, the stable transformation of soybean cannot yet be considered to be routine because it depends on the ability to combine efficient transformation and regeneration techniques. Two methods have been used with relative success to produce completely and stably transformed plants: particle bombardment and the Agrobacterium tumefaciens system. In addition, transformation by Agrobacterium rhizogenes has been used as a powerful tool for functional studies. Most available information on gene function is based on heterologous expression systems. However, as the activity of many promoters or proteins frequently depends on specific interactions that only occur in homologous backgrounds, a final confirmation based on a homologous expression system is desirable. With respect to soybean biotech improvement, transgenic lines with agronomical, nutritional and pharmaceutical traits have been obtained, including herbicide-tolerant soybeans, which represented the principal biotech crop in 2011, occupying 47% of the global biotech area.
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Affiliation(s)
- Milena Schenkel Homrich
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Beatriz Wiebke-Strohm
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Centro de Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ricardo Luís Mayer Weber
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Helena Bodanese-Zanettini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Le DT, Nishiyama R, Watanabe Y, Tanaka M, Seki M, Ham LH, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. Differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis. PLoS One 2012; 7:e49522. [PMID: 23189148 PMCID: PMC3505142 DOI: 10.1371/journal.pone.0049522] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 10/09/2012] [Indexed: 12/15/2022] Open
Abstract
The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to drought stress from late vegetative V6 and from full bloom reproductive R2 stages. Our data analyses showed that out of 46,093 soybean genes, which were predicted with high confidence among approximately 66,000 putative genes, 41,059 genes could be assigned with a known function. Using the criteria of a ratio change > = 2 and a q-value<0.05, we identified 1458 and 1818 upregulated and 1582 and 1688 downregulated genes in drought-stressed V6 and R2 leaves, respectively. These datasets were classified into 19 most abundant biological categories with similar proportions. There were only 612 and 463 genes that were overlapped among the upregulated and downregulated genes, respectively, in both stages, suggesting that both conserved and unconserved pathways might be involved in regulation of drought response in different stages of plant development. A comparative expression analysis using our datasets and that of drought stressed Arabidopsis leaves revealed the existence of both conserved and species-specific mechanisms that regulate drought responses. Many upregulated genes encode either regulatory proteins, such as transcription factors, including those with high homology to Arabidopsis DREB, NAC, AREB and ZAT/STZ transcription factors, kinases and two-component system members, or functional proteins, e.g. late embryogenesis-abundant proteins, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins. A detailed analysis of the GmNAC family and the hormone-related gene category showed that expression of many GmNAC and hormone-related genes was altered by drought in V6 and/or R2 leaves. Additionally, the downregulation of many photosynthesis-related genes, which contribute to growth retardation under drought stress, may serve as an adaptive mechanism for plant survival. This study has identified excellent drought-responsive candidate genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans.
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Affiliation(s)
- Dung Tien Le
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
- National Key Laboratory of Plant Cell Biotechnology and Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Hanoi, Vietnam
| | - Rie Nishiyama
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Le Huy Ham
- National Key Laboratory of Plant Cell Biotechnology and Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Hanoi, Vietnam
| | | | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
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Hakeem KR, Chandna R, Ahmad P, Iqbal M, Ozturk M. Relevance of Proteomic Investigations in Plant Abiotic Stress Physiology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:621-35. [DOI: 10.1089/omi.2012.0041] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Khalid Rehman Hakeem
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Ruby Chandna
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Parvaiz Ahmad
- Department of Botany, Amar Singh College, University of Kashmir, Srinagar, India
| | - Muhammad Iqbal
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Munir Ozturk
- Department of Botany, Ege University, Bornova, Izmir, Turkey
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Le DT, Aldrich DL, Valliyodan B, Watanabe Y, Ha CV, Nishiyama R, Guttikonda SK, Quach TN, Gutierrez-Gonzalez JJ, Tran LSP, Nguyen HT. Evaluation of candidate reference genes for normalization of quantitative RT-PCR in soybean tissues under various abiotic stress conditions. PLoS One 2012; 7:e46487. [PMID: 23029532 PMCID: PMC3460875 DOI: 10.1371/journal.pone.0046487] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 09/02/2012] [Indexed: 12/16/2022] Open
Abstract
Quantitative RT-PCR can be a very sensitive and powerful technique for measuring differential gene expression. Changes in gene expression induced by abiotic stresses are complex and multifaceted, which make determining stably expressed genes for data normalization difficult. To identify the most suitable reference genes for abiotic stress studies in soybean, 13 candidate genes collected from literature were evaluated for stability of expression under dehydration, high salinity, cold and ABA (abscisic acid) treatments using delta CT and geNorm approaches. Validation of reference genes indicated that the best reference genes are tissue- and stress-dependent. With respect to dehydration treatment, the Fbox/ABC, Fbox/60s gene pairs were found to have the highest expression stability in the root and shoot tissues of soybean seedlings, respectively. Fbox and 60s genes are the most suitable reference genes across dehydrated root and shoot tissues. Under salt stress the ELF1b/IDE and Fbox/ELF1b are the most stably expressed gene pairs in roots and shoots, respectively, while 60s/Fbox is the best gene pair in both tissues. For studying cold stress in roots or shoots, IDE/60s and Fbox/Act27 are good reference gene pairs, respectively. With regard to gene expression analysis under ABA treatment in either roots, shoots or across these tissues, 60s/ELF1b, ELF1b/Fbox and 60s/ELF1b are the most suitable reference genes, respectively. The expression of ELF1b/60s, 60s/Fbox and 60s/Fbox genes was most stable in roots, shoots and both tissues, respectively, under various stresses studied. Among the genes tested, 60s was found to be the best reference gene in different tissues and under various stress conditions. The highly ranked reference genes identified from this study were proved to be capable of detecting subtle differences in expression rates that otherwise would be missed if a less stable reference gene was used.
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Affiliation(s)
- Dung Tien Le
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Donavan L. Aldrich
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Chien Van Ha
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Rie Nishiyama
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Satish K. Guttikonda
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Truyen N. Quach
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Juan J. Gutierrez-Gonzalez
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
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Le DT, Nishiyama R, Watanabe Y, Vankova R, Tanaka M, Seki M, Ham LH, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. Identification and expression analysis of cytokinin metabolic genes in soybean under normal and drought conditions in relation to cytokinin levels. PLoS One 2012; 7:e42411. [PMID: 22900018 PMCID: PMC3416864 DOI: 10.1371/journal.pone.0042411] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/04/2012] [Indexed: 01/15/2023] Open
Abstract
Cytokinins (CKs) mediate cellular responses to drought stress and targeted control of CK metabolism can be used to develop drought-tolerant plants. Aiming to manipulate CK levels to improve drought tolerance of soybean cultivars through genetic engineering of CK metabolic genes, we surveyed the soybean genome and identified 14 CK biosynthetic (isopentenyltransferase, GmIPT) and 17 CK degradative (CK dehydrogenase, GmCKX) genes. Comparative analyses of GmIPTs and GmCKXs with Arabidopsis counterparts revealed their similar architecture. The average numbers of abiotic stress-inducible cis-elements per promoter were 0.4 and 1.2 for GmIPT and GmCKX genes, respectively, suggesting that upregulation of GmCKXs, thereby reduction of CK levels, maybe the major events under abiotic stresses. Indeed, the expression of 12 GmCKX genes was upregulated by dehydration in R2 roots. Overall, the expressions of soybean CK metabolic genes in various tissues at various stages were highly responsive to drought. CK contents in various organs at the reproductive (R2) stage were also determined under well-watered and drought stress conditions. Although tRNA-type GmIPT genes were highly expressed in soybean, cis-zeatin and its derivatives were found at low concentrations. Moreover, reduction of total CK content in R2 leaves under drought was attributable to the decrease in dihydrozeatin levels, suggesting a role of this molecule in regulating soybean's responses to drought stress. Our systematic analysis of the GmIPT and GmCKX families has provided an insight into CK metabolism in soybean under drought stress and a solid foundation for in-depth characterization and future development of improved drought-tolerant soybean cultivars by manipulation of CK levels via biotechnological approach.
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Affiliation(s)
- Dung Tien Le
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
- National Key Laboratory of Plant Cell Biotechnology and Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Hanoi, Vietnam
| | - Rie Nishiyama
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Le Huy Ham
- National Key Laboratory of Plant Cell Biotechnology and Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Hanoi, Vietnam
| | | | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
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Sulieman S, Tran LSP. Asparagine: an amide of particular distinction in the regulation of symbiotic nitrogen fixation of legumes. Crit Rev Biotechnol 2012; 33:309-27. [DOI: 10.3109/07388551.2012.695770] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Choudhary SP, Kanwar M, Bhardwaj R, Yu JQ, Tran LSP. Chromium stress mitigation by polyamine-brassinosteroid application involves phytohormonal and physiological strategies in Raphanus sativus L. PLoS One 2012; 7:e33210. [PMID: 22479371 PMCID: PMC3315560 DOI: 10.1371/journal.pone.0033210] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 02/13/2012] [Indexed: 01/01/2023] Open
Abstract
Brassinosteroids (BRs) and polyamines (PAs) are well-established growth regulators playing key roles in stress management among plants. In the present study, we evaluated the effects of epibrassinolide (EBL, an active BR) and spermidine (Spd, an active PA) on the tolerance of radish to oxidative stress induced by Cr (VI) metal. Our investigation aimed to study the impacts of EBL (10(-9) M) and/or Spd (1 mM) on the biochemical and physiological responses of radish (Raphanus sativus L.) under Cr-stress. Applications of EBL and/or Spd were found to improve growth of Cr-stressed seedlings in terms of root length, shoot length and fresh weight. Our data also indicated that applications of EBL and Spd have significant impacts, particularly when applied together, on the endogenous titers of PAs, free and bound forms of IAA and ABA in seedlings treated with Cr-stress. Additionally, co-applications of EBL and Spd modulated more remarkably the titers of antioxidants (glutathione, ascorbic acid, proline, glycine betaine and total phenol) and activities of antioxidant enzymes (guaicol peroxidase, catalase, superoxide dismutase and glutathione reductase) in Cr-stressed plants than their individual applications. Attenuation of Cr-stress by EBL and/or Spd (more efficient with EBL and Spd combination) was also supported by enhanced values of stress indices, such as phytochelatins, photosynthetic pigments and total soluble sugars, and reduction in malondialdehyde and H(2)O(2) levels in Cr-treated seedlings. Diminution of ROS production and enhanced ROS scavenging capacities were also noted for EBL and/or Spd under Cr-stress. However, no significant reduction in Cr uptake was observed for co-application of EBL and Spd when compared to their individual treatments in Cr-stressed seedlings. Taken together, our results demonstrate that co-applications of EBL and Spd are more effective than their independent treatments in lowering the Cr-induced oxidative stress in radish, leading to improved growth of radish seedlings under Cr-stress.
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Affiliation(s)
- Sikander Pal Choudhary
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Botany, University of Jammu, Jammu, India
- * E-mail: (SPC); (LPT)
| | - Mukesh Kanwar
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Jing-Quan Yu
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
- * E-mail: (SPC); (LPT)
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50
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Jogaiah S, Govind SR, Tran LSP. Systems biology-based approaches toward understanding drought tolerance in food crops. Crit Rev Biotechnol 2012; 33:23-39. [PMID: 22364373 DOI: 10.3109/07388551.2012.659174] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Economically important crops, such as maize, wheat, rice, barley, and other food crops are affected by even small changes in water potential at important growth stages. Developing a comprehensive understanding of host response to drought requires a global view of the complex mechanisms involved. Research on drought tolerance has generally been conducted using discipline-specific approaches. However, plant stress response is complex and interlinked to a point where discipline-specific approaches do not give a complete global analysis of all the interlinked mechanisms. Systems biology perspective is needed to understand genome-scale networks required for building long-lasting drought resistance. Network maps have been constructed by integrating multiple functional genomics data with both model plants, such as Arabidopsis thaliana, Lotus japonicus, and Medicago truncatula, and various food crops, such as rice and soybean. Useful functional genomics data have been obtained from genome-wide comparative transcriptome and proteome analyses of drought responses from different crops. This integrative approach used by many groups has led to identification of commonly regulated signaling pathways and genes following exposure to drought. Combination of functional genomics and systems biology is very useful for comparative analysis of other food crops and has the ability to develop stable food systems worldwide. In addition, studying desiccation tolerance in resurrection plants will unravel how combination of molecular genetic and metabolic processes interacts to produce a resurrection phenotype. Systems biology-based approaches have helped in understanding how these individual factors and mechanisms (biochemical, molecular, and metabolic) "interact" spatially and temporally. Signaling network maps of such interactions are needed that can be used to design better engineering strategies for improving drought tolerance of important crop species.
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Affiliation(s)
- Sudisha Jogaiah
- Downy Mildew Research Laboratory, Department of Studies in Biotechnology, University of Mysore, Mysore, Karnataka, India
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