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Ilyas M, Irfan M, Mahmood T, Hussain H, Latif-ur-Rehman, Naeem I, Khaliq-ur-Rahman. Analysis of Germin-like Protein Genes (OsGLPs) Family in Rice Using Various In silico Approaches. Curr Bioinform 2020. [DOI: 10.2174/1574893614666190722165130] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background:
Germin-like Proteins (GLPs) play an important role in various stresses.
Rice contains 43 GLPs, among which many remain functionally unexplored. The computational
analysis will provide significant insight into their function.
Objective:
To find various structural properties, functional importance, phylogeny and expression
pattern of all OsGLPs using various bioinformatics tools.
Methods:
Physiochemical properties, sub-cellular localization, domain composition, Nglycosylation
and Phosphorylation sites, and 3D structural models of the OsGLPs were predicted
using various bioinformatics tools. Functional analysis was carried out with the Search Tool for
the Retrieval of Interacting Genes/Proteins (STRING) and Blast2GO servers. The expression
profile of the OsGLPs was predicted by retrieving the data for expression values from tissuespecific
and hormonal stressed array libraries of RiceXPro. Their phylogenetic relationship was
computed using Molecular and Evolutionary Genetic Analysis (MEGA6) tool.
Results:
Most of the OsGLPs are stable in the cellular environment with a prominent expression in
the extracellular region (57%) and plasma membrane (33%). Besides, 3 basic cupin domains, 7
more were reported, among which NTTNKVGSNVTLINV, FLLAALLALASWQAI, and
MASSSF were common to 99% of the sequences, related to bacterial pathogenicity, peroxidase
activity, and peptide signal activity, respectively. Structurally, OsGLPs are similar but functionally
they are diverse with novel enzymatic activities of oxalate decarboxylase, lyase, peroxidase, and
oxidoreductase. Expression analysis revealed prominent activities in the root, endosperm, and
leaves. OsGLPs were strongly expressed by abscisic acid, auxin, gibberellin, cytokinin, and
brassinosteroid. Phylogenetically they showed polyphyletic origin with a narrow genetic
background of 0.05%. OsGLPs of chromosome 3, 8, and 12 are functionally more important due to
their defensive role against various stresses through co-expression strategy.
Conclusion:
The analysis will help to utilize OsGLPs in future food programs.
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Affiliation(s)
- Muhammad Ilyas
- Department of Botany, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Irfan
- Department of Botany, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Tariq Mahmood
- Department of Botany, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan
| | - Hazrat Hussain
- Department of Biotechnology, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Latif-ur-Rehman
- Department of Biotechnology, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Ijaz Naeem
- Department of Biotechnology, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
| | - Khaliq-ur-Rahman
- Department of Chemistry, University of Swabi, Swabi-23561, Khyber Pakhtunkhwa, Pakistan
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Hu B, Deng F, Chen G, Chen X, Gao W, Long L, Xia J, Chen ZH. Evolution of Abscisic Acid Signaling for Stress Responses to Toxic Metals and Metalloids. FRONTIERS IN PLANT SCIENCE 2020; 11:909. [PMID: 32765540 PMCID: PMC7379394 DOI: 10.3389/fpls.2020.00909] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/03/2020] [Indexed: 05/02/2023]
Abstract
Toxic heavy metals and metalloids in agricultural ecosystems are crucial factors that limit global crop productivity and food safety. Industrial toxic heavy metals and metalloids such as cadmium, lead, and arsenic have contaminated large areas of arable land in the world and their accumulation in the edible parts of crops is causing serious health risks to humans and animals. Plants have co-evolved with various concentrations of these toxic metals and metalloids in soil and water. Some green plant species have significant innovations in key genes for the adaptation of abiotic stress tolerance pathways that are able to tolerate heavy metals and metalloids. Increasing evidence has demonstrated that phytohormone abscisic acid (ABA) plays a vital role in the alleviation of heavy metal and metalloid stresses in plants. Here, we trace the evolutionary origins of the key gene families connecting ABA signaling with tolerance to heavy metals and metalloids in green plants. We also summarize the molecular and physiological aspects of ABA in the uptake, root-to-shoot translocation, chelation, sequestration, reutilization, and accumulation of key heavy metals and metalloids in plants. The molecular evolution and interaction between the ABA signaling pathway and mechanisms for heavy metal and metalloid tolerance are highlighted in this review. Therefore, we propose that it is promising to manipulate ABA signaling in plant tissues to reduce the uptake and accumulation of toxic heavy metals and metalloids in crops through the application of ABA-producing bacteria or ABA analogues. This may lead to improvements in tolerance of major crops to heavy metals and metalloids.
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Affiliation(s)
- Beibei Hu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, China
| | - Fenglin Deng
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, China
- *Correspondence: Fenglin Deng, ; Zhong-Hua Chen,
| | - Guang Chen
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, China
| | - Xuan Chen
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, China
| | - Wei Gao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Lu Long
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Jixing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- *Correspondence: Fenglin Deng, ; Zhong-Hua Chen,
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Zhao Z, Zhang Z, Ding Z, Meng H, Shen R, Tang H, Liu YG, Chen L. Public-transcriptome-database-assisted selection and validation of reliable reference genes for qRT-PCR in rice. SCIENCE CHINA. LIFE SCIENCES 2020; 63:92-101. [PMID: 31709495 DOI: 10.1007/s11427-019-1553-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 09/26/2019] [Indexed: 01/05/2023]
Abstract
Accurate quantitative reverse transcription PCR (qRT-PCR) requires reliable reference genes whose expression does not vary in different tissues and developmental stages. However, few reliable reference genes are available for qRT-PCR in rice (Oryza sativa). Here, we established an effective strategy for identifying novel reference genes (NRGs) for reliable normalization of qRT-PCR data in various rice organs and developmental stages. We selected candidate NRGs using the Information Commons for Rice Database and confirmed their expression in Rice Expression Profile Database (RiceXPro) data. Genes with low variation (<2.5 cycle quantification) across tissues and developmental stages, and little fluctuation in expression in heatmaps from RiceXPro data were considered stable NRGs. To validate this strategy, we selected 11 candidate NRGs and calculated their expression stability in different spatio-temporal conditions using five programs, and compared these genes with five established reference genes (ERGs). Only one of the ERGs (UBQ5) was reliable and 10 of the candidate NRGs were more stable than the four remaining ERGs. Therefore, public transcriptomic databases are useful for identifying NRGs. We selected two NRGs, UFC1 (Homolog of UFM1-Conjugating Enzyme 1) and FhaB (Homolog of Adhesin FhaB) for qRT-PCR analysis in rice; their homologs might be suitable for other monocot plants.
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Affiliation(s)
- Zhe Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zixu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhi Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Hengjun Meng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huiwu Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China.
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China.
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Guo ZH, Haslam RP, Michaelson LV, Yeung EC, Lung SC, Napier JA, Chye ML. The overexpression of rice ACYL-CoA-BINDING PROTEIN2 increases grain size and bran oil content in transgenic rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1132-1147. [PMID: 31437323 DOI: 10.1111/tpj.14503] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 07/27/2019] [Accepted: 08/05/2019] [Indexed: 05/18/2023]
Abstract
As Oryza sativa (rice) seeds represent food for over three billion people worldwide, the identification of genes that enhance grain size and composition is much desired. Past reports have indicated that Arabidopsis thaliana acyl-CoA-binding proteins (ACBPs) are important in seed development but did not affect seed size. Herein, rice OsACBP2 was demonstrated not only to play a role in seed development and germination, but also to influence grain size. OsACBP2 mRNA accumulated in embryos and endosperm of germinating seeds in qRT-PCR analysis, while β-glucuronidase (GUS) assays on OsACBP2pro::GUS rice transformants showed GUS expression in embryos, as well as the scutellum and aleurone layer of germinating seeds. Deletion analysis of the OsACBP2 5'-flanking region revealed five copies of the seed cis-element, Skn-I-like motif (-1486/-1482, -956/-952, -939/-935, -826/-822, and -766/-762), and the removal of any adversely affected expression in seeds, thereby providing a molecular basis for OsACBP2 expression in seeds. When OsACBP2 function was investigated using osacbp2 mutants and transgenic rice overexpressing OsACBP2 (OsACBP2-OE), osacbp2 was retarded in germination, while OsACBP2-OEs performed better than the wild-type and vector-transformed controls, in germination, seedling growth, grain size and grain weight. Transmission electron microscopy of OsACBP2-OE mature seeds revealed an accumulation of oil bodies in the scutellum cells, while confocal laser scanning microscopy indicated oil accumulation in OsACBP2-OE aleurone tissues. Correspondingly, OsACBP2-OE seeds showed gain in triacylglycerols and long-chain fatty acids over the vector-transformed control. As dietary rice bran contains beneficial bioactive components, OsACBP2 appears to be a promising candidate for enriching seed nutritional value.
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Affiliation(s)
- Ze-Hua Guo
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Richard P Haslam
- Department of Plant Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Louise V Michaelson
- Department of Plant Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Edward C Yeung
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4,, Canada
| | - Shiu-Cheung Lung
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Johnathan A Napier
- Department of Plant Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Mee-Len Chye
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
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Kobayashi T, Ozu A, Kobayashi S, An G, Jeon JS, Nishizawa NK. OsbHLH058 and OsbHLH059 transcription factors positively regulate iron deficiency responses in rice. PLANT MOLECULAR BIOLOGY 2019; 101:471-486. [PMID: 31552586 PMCID: PMC6814640 DOI: 10.1007/s11103-019-00917-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/07/2019] [Indexed: 05/03/2023]
Abstract
Subgroup IVc basic helix-loop-helix transcription factors OsbHLH058 and OsbHLH059 positively regulate major iron deficiency responses in rice in a similar but distinct manner, putatively under partial control by OsHRZs. Under low iron availability, plants transcriptionally induce the expression of genes involved in iron uptake and translocation. OsHRZ1 and OsHRZ2 ubiquitin ligases negatively regulate this iron deficiency response in rice. The basic helix-loop-helix (bHLH) transcription factor OsbHLH060 interacts with OsHRZ1, and positively regulates iron deficiency-inducible genes. However, the functions of three other subgroup IVc bHLH transcription factors in rice, OsbHLH057, OsbHLH058, and OsbHLH059, have not yet been characterized. In the present study, we investigated the functions of OsbHLH058 and OsbHLH059 related to iron deficiency response. OsbHLH058 expression was repressed under iron deficiency, whereas the expression of OsbHLH057 and OsbHLH060 was moderately induced. Yeast two-hybrid analysis indicated that OsbHLH058 interacts with OsHRZ1 and OsHRZ2 more strongly than OsbHLH060, whereas OsbHLH059 showed no interaction. An in vitro ubiquitination assay detected no OsbHLH058 and OsbHLH060 ubiquitination by OsHRZ1 and OsHRZ2. Transgenic rice lines overexpressing OsbHLH058 showed tolerance for iron deficiency and higher iron concentration in seeds. These lines also showed enhanced expression of many iron deficiency-inducible genes involved in iron uptake and translocation under iron-sufficient conditions. Conversely, OsbHLH058 knockdown lines showed susceptibility to iron deficiency and reduced expression of many iron deficiency-inducible genes. OsbHLH059 knockdown lines were also susceptible to iron deficiency, and formed characteristic brownish regions in iron-deficient new leaves. OsbHLH059 knockdown lines also showed reduced expression of many iron deficiency-inducible genes. These results indicate that OsbHLH058 and OsbHLH059 positively regulate major iron deficiency responses in a similar but distinct manner, and that this function may be partially controlled by OsHRZs.
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Affiliation(s)
- Takanori Kobayashi
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan.
| | - Asami Ozu
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
| | - Subaru Kobayashi
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, Korea
| | - Jong-Seong Jeon
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, Korea
| | - Naoko K Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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Suppression of Melatonin 2-Hydroxylase Increases Melatonin Production Leading to the Enhanced Abiotic Stress Tolerance against Cadmium, Senescence, Salt, and Tunicamycin in Rice Plants. Biomolecules 2019; 9:biom9100589. [PMID: 31597397 PMCID: PMC6843340 DOI: 10.3390/biom9100589] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/01/2019] [Accepted: 10/04/2019] [Indexed: 12/15/2022] Open
Abstract
Melatonin 2-hydroxylase (M2H) catalyzes the conversion of melatonin into 2hydroxymelatonin (2OHM), which is present in plants at a higher concentration than melatonin. Although M2H has been cloned, the in vivo function of its product is unknown. Here, we generated stable T2 homozygous transgenic rice plants in which expression of endogenous M2H was suppressed (RNAi lines). However, we failed to generate M2H overexpression transgenic rice due to failure of somatic embryogenesis. The M2H transcript level showed a diurnal rhythm with a peak at night concomitantly with the peak concentration of 2OHM. RNAi rice showed a reduced M2H mRNA level and 2OHM and melatonin concentrations. The unexpected decrease in the melatonin concentration was caused by redirection of melatonin into cyclic 3hydroxymelatonin via a detour catabolic pathway. Thus, the decrease in the melatonin concentration in M2H RNAi rice led to slowed seedling growth and delayed germination. By contrast, the transient increase in the melatonin concentration was of greater magnitude in the M2H RNAi than the wild-type rice upon cadmium treatment due to possible suppression of melatonin degradation. Due to its higher concentration of melatonin, the M2H RNAi rice displayed tolerance to senescence, salt, and tunicamycin stresses. Therefore, the increase in the melatonin concentration caused by suppression of melatonin degradation or by overexpression of melatonin biosynthetic genes enhances stress tolerance in rice.
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Song Y, Li G, Nowak J, Zhang X, Xu D, Yang X, Huang G, Liang W, Yang L, Wang C, Bulone V, Nikoloski Z, Hu J, Persson S, Zhang D. The Rice Actin-Binding Protein RMD Regulates Light-Dependent Shoot Gravitropism. PLANT PHYSIOLOGY 2019; 181:630-644. [PMID: 31416828 PMCID: PMC6776841 DOI: 10.1104/pp.19.00497] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/30/2019] [Indexed: 05/25/2023]
Abstract
Light and gravity are two key determinants in orientating plant stems for proper growth and development. The organization and dynamics of the actin cytoskeleton are essential for cell biology and critically regulated by actin-binding proteins. However, the role of actin cytoskeleton in shoot negative gravitropism remains controversial. In this work, we report that the actin-binding protein Rice Morphology Determinant (RMD) promotes reorganization of the actin cytoskeleton in rice (Oryza sativa) shoots. The changes in actin organization are associated with the ability of the rice shoots to respond to negative gravitropism. Here, light-grown rmd mutant shoots exhibited agravitropic phenotypes. By contrast, etiolated rmd shoots displayed normal negative shoot gravitropism. Furthermore, we show that RMD maintains an actin configuration that promotes statolith mobility in gravisensing endodermal cells, and for proper auxin distribution in light-grown, but not dark-grown, shoots. RMD gene expression is diurnally controlled and directly repressed by the phytochrome-interacting factor-like protein OsPIL16. Consequently, overexpression of OsPIL16 led to gravisensing and actin patterning defects that phenocopied the rmd mutant. Our findings outline a mechanism that links light signaling and gravity perception for straight shoot growth in rice.
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Affiliation(s)
- Yu Song
- The University of Adelaide-Shanghai Jiao Tong University Joint Laboratory for Plant Science and Breeding, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 China
| | - Gang Li
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Jacqueline Nowak
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Xiaoqing Zhang
- The University of Adelaide-Shanghai Jiao Tong University Joint Laboratory for Plant Science and Breeding, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 China
| | - Dongbei Xu
- The University of Adelaide-Shanghai Jiao Tong University Joint Laboratory for Plant Science and Breeding, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 China
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Guoqiang Huang
- The University of Adelaide-Shanghai Jiao Tong University Joint Laboratory for Plant Science and Breeding, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 China
| | - Wanqi Liang
- The University of Adelaide-Shanghai Jiao Tong University Joint Laboratory for Plant Science and Breeding, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 China
| | - Litao Yang
- The University of Adelaide-Shanghai Jiao Tong University Joint Laboratory for Plant Science and Breeding, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 China
| | - Canhua Wang
- The University of Adelaide-Shanghai Jiao Tong University Joint Laboratory for Plant Science and Breeding, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 China
| | - Vincent Bulone
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Jianping Hu
- School of Biosciences, University of Melbourne, Parkville Victoria 3010, Melbourne, Australia
| | - Staffan Persson
- The University of Adelaide-Shanghai Jiao Tong University Joint Laboratory for Plant Science and Breeding, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 China
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Dabing Zhang
- The University of Adelaide-Shanghai Jiao Tong University Joint Laboratory for Plant Science and Breeding, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 China
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
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58
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Luo Y, Fang B, Wang W, Yang Y, Rao L, Zhang C. Genome-wide analysis of the rice J-protein family: identification, genomic organization, and expression profiles under multiple stresses. 3 Biotech 2019; 9:358. [PMID: 31544012 PMCID: PMC6730974 DOI: 10.1007/s13205-019-1880-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/20/2019] [Indexed: 12/17/2022] Open
Abstract
J-proteins which function as molecular chaperone played critical roles in plant growth, development, and response to various environment stresses, but little was reported on this gene family in rice. Here, we identified 115 putative rice J-proteins and classified them into nine major clades (I–IX) according to their phylogenetic relationships. Gene-structure analysis revealed that each member of the same clade has same or similar exon–intron structure, and most rice J-protein genes of clade VII were intronless. Chromosomes mapping suggested that tandem duplication was occurred in evolution. Expression profile showed that the 61 rice J-protein genes were expressed in at least one tissue. The result implied that they could be involved in the process of rice growth and development. The RNA-sequencing data identified 96 differentially expressed genes, 59.38% (57/96), 67.71% (65/96), and 62.50% (60/96) genes were induced by heat stress, drought stress, and salt stress, respectively. The results indicated that J-protein genes could participated in rice response to different stresses. The findings in this study would provide a foundation for further analyzing the function of J-proteins in rice.
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Affiliation(s)
- Ying Luo
- College of Bioscience and Biotechnology, Hunan Agricultural University, 410125 Changsha, China
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, China
| | - Baohua Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, 410125 Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture, 410125 Changsha, China
| | - Weiping Wang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 410125 Changsha, China
| | - Ying Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, 410125 Changsha, China
| | - Liqun Rao
- College of Bioscience and Biotechnology, Hunan Agricultural University, 410125 Changsha, China
| | - Chao Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, 410125 Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 410125 Changsha, China
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59
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Mahender A, Ali J, Prahalada GD, Sevilla MAL, Balachiranjeevi CH, Md J, Maqsood U, Li Z. Genetic dissection of developmental responses of agro-morphological traits under different doses of nutrient fertilizers using high-density SNP markers. PLoS One 2019; 14:e0220066. [PMID: 31335882 PMCID: PMC6650078 DOI: 10.1371/journal.pone.0220066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/07/2019] [Indexed: 11/19/2022] Open
Abstract
The production and productivity of rice (Oryza sativa L.) are primarily influenced by the application of the critical nutrients nitrogen (N), phosphorus (P), and potassium (K). However, excessive application of these fertilizers is detrimental to the environment and increases the cost of production. Hence, there is a need to develop varieties that simultaneously increase yields under both optimal and suboptimal rates of fertilizer application by maximizing nutrient use efficiency (NuUE). To unravel the hidden genetic variation and understand the molecular and physiological mechanisms of NuUE, three different mapping populations (MPs; BC1F5) derived from three donors (Haoannong, Cheng-Hui 448, and Zhong 413) and recipient Weed Tolerant Rice 1 were developed. A total of three favorable agronomic traits (FATs) were considered as the measure of NuUE. Analysis of variance and descriptive statistics indicated the existence of genetic variation for NuUE and quantitative inheritance of FATs. The genotypic data from single-nucleotide polymorphism (SNP) markers from Tunable Genotyping-By-Sequencing (tGBS) and phenotypic values were used for locating the genomic regions conferring NuUE. A total of 19 quantitative trait loci (QTLs) were detected, out of which 11 QTLs were putative on eight chromosomes, which individually explained 17.02% to 34.85% of the phenotypic variation. Notably, qLC-II_1 and qLC-II_11 detected at zero fertilizer application showed higher performance for LC under zero percentage of NPK fertilizer. The remarkable findings of the present study are that the detected QTLs were associated in building tolerance to low/no nutrient application and six candidate genes on chromosomes 2 and 5 within these putative QTLs were found associated with low nutrient tolerance and related to several physiological and metabolic pathways involved in abiotic stress tolerance. The identified superior introgressed lines (ILs) and trait-associated genetic regions can be effectively used in marker-assisted selection (MAS) for NuUE breeding programs.
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Affiliation(s)
- Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
- * E-mail:
| | - G. D. Prahalada
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Ma. Anna Lynn Sevilla
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - C. H. Balachiranjeevi
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jamaloddin Md
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Umer Maqsood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan
| | - Zhikang Li
- Chinese Academy of Agricultural Sciences, Haidian District, P.R. China
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60
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Yamaguchi T, Yamakawa H, Nakata M, Kuroda M, Hakata M. Suppression of phospholipase D genes improves chalky grain production by high temperature during the grain-filling stage in rice. Biosci Biotechnol Biochem 2019; 83:1102-1110. [DOI: 10.1080/09168451.2019.1580137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
ABSTRACT
High temperature (HT) during the grain developing stage causes deleterious effects on rice quality resulting in mature grains with a chalky appearance. Phospholipase D (PLD) plays an important role in plants, including responses to environmental stresses. OsPLDα1, α3 and β2-knockdown (KD) plants showed decreased production of chalky grains at HT. HT ripening increased H2O2 accumulated in the developing grains. However, the increase was canceled by the knockdown of OsPLDβ2. Expression levels of OsCATA which is one of three rice catalase genes, in developing grains of OsPLDβ2-KD plants at 10 DAF were increased compared with that in vector-controls in HT growth conditions. Overexpression of OsCATA markedly suppressed the production of chalky grains in HT growth conditions. These results suggested that OsPLDβ2 functions as a negative regulator of the induction of OsCATA and is involved in the production of chalky grains in HT growth conditions.
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Affiliation(s)
| | | | - Masaru Nakata
- Central Region Agricultural Research Center, NARO, Joetsu, Japan
| | - Masaharu Kuroda
- Central Region Agricultural Research Center, NARO, Joetsu, Japan
| | - Makoto Hakata
- Central Region Agricultural Research Center, NARO, Joetsu, Japan
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61
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Oshima M, Taniguchi Y, Akasaka M, Abe K, Ichikawa H, Tabei Y, Tanaka J. Development of a visible marker trait based on leaf sheath-specific anthocyanin pigmentation applicable to various genotypes in rice. BREEDING SCIENCE 2019; 69:244-254. [PMID: 31481833 PMCID: PMC6711742 DOI: 10.1270/jsbbs.18151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/14/2019] [Indexed: 05/20/2023]
Abstract
To overcome a limitation to the breeding of autogamous crops, recurrent selection using transgenic male sterility (RSUTMS) has been proposed. In this system, negatively or positively selectable marker traits are required along with dominant transgenic male sterility. Anthocyanin pigmentation is an excellent marker trait. Two regulatory genes for MYB and bHLH and a structural gene for DFR are required for anthocyanin pigmentation in rice. Therefore, to apply anthocyanin pigmentation as a marker trait in various rice genotypes, coordinated expression of the three genes is required. In this study, we developed a leaf sheath-specific promoter and introduced three genes-DFR and C1/Myb, driven by the 35S promoter, and OsB2/bHLH, driven by the leaf sheath-specific promoter-into the rice genome. Leaf sheath-specific pigmentation was confirmed in all seven genotypes tested, which included japonica and indica cultivars. Analysis of genome sequence data from 25 cultivars showed that the strategy of conferring leaf sheath-specific anthocyanin pigmentation by introduction of these three genes would be effective for a wide range of genotypes and will be applicable to RSUTMS.
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Affiliation(s)
- Masao Oshima
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Yojiro Taniguchi
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Maiko Akasaka
- Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Kiyomi Abe
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Hiroaki Ichikawa
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Yutaka Tabei
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Junichi Tanaka
- Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Graduate School of Life and Environmental Science, University of Tsukuba,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Corresponding author (e-mail: )
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62
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Bashir K, Matsui A, Rasheed S, Seki M. Recent advances in the characterization of plant transcriptomes in response to drought, salinity, heat, and cold stress. F1000Res 2019; 8:F1000 Faculty Rev-658. [PMID: 31131087 PMCID: PMC6518435 DOI: 10.12688/f1000research.18424.1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/09/2019] [Indexed: 11/28/2022] Open
Abstract
Despite recent advancements in plant molecular biology and biotechnology, providing food security for an increasing world population remains a challenge. Drought (water scarcity), salinity, heat, and cold stress are considered major limiting factors that affect crop production both qualitatively and quantitatively. Therefore, the development of cost-effective and environmentally friendly strategies will be needed to resolve these agricultural problems. This will require a comprehensive understanding of transcriptomic alterations that occur in plants in response to varying levels of environmental stresses, singly and in combination. Here, we briefly discuss the current status and future challenges in plant research related to understanding transcriptional changes that occur in response to drought, salinity, heat, and cold stress.
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Affiliation(s)
- Khurram Bashir
- Plant Genomic Network Research Team, CSRS, RIKEN, Yokohama, Tsurumi-ku, Kanagawa, 230-0045, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, CSRS, RIKEN, Yokohama, Tsurumi-ku, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, CPR, RIKEN, Wako, Saitama, 351-0198, Japan
| | - Sultana Rasheed
- Plant Genomic Network Research Team, CSRS, RIKEN, Yokohama, Tsurumi-ku, Kanagawa, 230-0045, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, CSRS, RIKEN, Yokohama, Tsurumi-ku, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, CPR, RIKEN, Wako, Saitama, 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Core Research for Evolutionary Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
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63
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Lenka SK, Singh AK, Muthusamy SK, Smita S, Chinnusamy V, Bansal KC. Heterologous expression of rice RNA-binding glycine-rich (RBG) gene OsRBGD3 in transgenic Arabidopsis thaliana confers cold stress tolerance. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:482-491. [PMID: 30940336 DOI: 10.1071/fp18241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Imparting cold stress tolerance to crops is a major challenge in subtropical agriculture. New genes conferring cold tolerance needs to be identified and characterised for sustainable crop production in low-temperature stress affected areas. Here we report functional characterisation of OsRBGD3, classified previously as a class D glycine-rich RNA recognition motif (RRM) containing proteins from a drought-tolerant Indica rice cultivar N22. The gene was isolated by screening yeast one-hybrid library using the minimal promoter region of the OsMYB38 that is necessary for cold stress-responsive expression. OsRBGD3 exhibited cold, drought and salt stress inductive expression in a drought tolerant N22 rice cultivar as compared with susceptible variety IR64. OsRBGD3 was found to be localised to both nuclear and cytoplasmic subcellular destinations. Constitutive overexpression of the OsRBGD3 in transgenic Arabidopsis conferred tolerance to cold stress. ABA sensitivity was also observed in transgenic lines suggesting the regulatory role of this gene in the ABA signalling pathway. OsRBGD3 overexpression also attributed to significant root development and early flowering in transgenics. Hence, OsRBGD3 could be an important target for developing cold tolerant early flowering rice and other crops' genotypes for increasing production in low temperature affected areas.
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Affiliation(s)
- Sangram K Lenka
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India
| | - Amit K Singh
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Senthilkumar K Muthusamy
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, 695017, India
| | - Shuchi Smita
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and Department of Immunology, School of Medicine, University of Pittsburgh, PA 15261, USA
| | - Viswanathan Chinnusamy
- ICAR-Indian Agricultural Research Institute, Division of Plant Physiology, New Delhi, 110012, India
| | - Kailash C Bansal
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India; and Corresponding author.
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64
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Chattopadhyay K, Behera L, Bagchi TB, Sardar SS, Moharana N, Patra NR, Chakraborti M, Das A, Marndi BC, Sarkar A, Ngangkham U, Chakraborty K, Bose LK, Sarkar S, Ray S, Sharma S. Detection of stable QTLs for grain protein content in rice (Oryza sativa L.) employing high throughput phenotyping and genotyping platforms. Sci Rep 2019; 9:3196. [PMID: 30824776 PMCID: PMC6397320 DOI: 10.1038/s41598-019-39863-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Lack of appropriate donors, non-utilization of high throughput phenotyping and genotyping platforms with high genotype × environment interaction restrained identification of robust QTLs for grain protein content (GPC) in rice. In the present investigation a BC3F4 mapping population was developed using grain protein donor, ARC10075 and high-yielding cultivar Naveen and 190 lines were genotyped using 40 K Affimetrix custom SNP array with the objective to identify stable QTLs for protein content. Three of the identified QTLs, one for GPC (qGPC1.1) and the other two for single grain protein content (qSGPC2.1, qSGPC7.1) were stable over the environments explaining 13%, 14% and 7.8% of the phenotypic variances, respectively. Stability and repeatability of these additive QTLs were supported by the synergistic additive effects of multi-environmental-QTLs. One epistatic-QTL, independent of the main effect QTL was detected over the environment for SGPC. A few functional genes governing seed storage protein were hypothesised inside these identified QTLs. The qGPC1.1 was validated by NIR Spectroscopy-based high throughput phenotyping in BC3F5 population. Higher glutelin content was estimated in high-protein lines with the introgression of qGPC1.1 in telomeric region of short arm of chromosome 1. This was supported by the postulation of probable candidate gene inside this QTL region encoding glutelin family proteins.
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Affiliation(s)
| | | | | | | | | | | | | | - Avijit Das
- ICAR-National Institute of Natural Fibre Engineering and Technology, Kolkata, India
| | | | - Ananta Sarkar
- ICAR- Central Institute for Women in Agriculture, Bhubaneswar, India
| | | | | | | | - Sutapa Sarkar
- ICAR-National Rice Research Institute, Cuttack, India
| | - Soham Ray
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
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65
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Takehisa H, Sato Y. Transcriptome monitoring visualizes growth stage-dependent nutrient status dynamics in rice under field conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1048-1060. [PMID: 30481387 DOI: 10.1111/tpj.14176] [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: 01/25/2018] [Revised: 11/09/2018] [Accepted: 11/16/2018] [Indexed: 05/24/2023]
Abstract
Crop plants undergo morpho-physiological changes throughout the growth process in response to both the internal and the external environment, and that eventually determine the yield. The system-level adjustment of the morpho-physiological changes has remained largely unclear, however, especially in field conditions. Here, we reveal changes in nutrient status associated with tiller development and soil conditions based on the leaf transcriptome profile of rice (Oryza sativa) throughout the entire period of growth. We performed gene co-expression network analysis and identified three gene sets as indicators for monitoring the internal nitrogen and phosphorus status. Expression profiling reveals that the phosphorus starvation response is expressed during the tillering stage and is then switched off with the transition to nitrogen deficiency. Coincident with phosphorus status dynamics, the level of phosphate in the leaf is demonstrated to be low during the tillering stage and subsequently increases drastically. The phosphorus dynamics are genetically validated by analysing mutants with a defect in phosphorus homeostasis. Notably, we show that nitrogen limitation directly suppresses the phosphorus starvation response. Finally, the phosphorus starvation response is demonstrated to be activated in soil with a high phosphate retention capacity, without the visible phenotypes associated with phosphorus starvation. Our results reveal a growth stage- and soil condition-dependent reaction that requires phosphorus, which is expressed to promote the phosphorus uptake required for developing tillers and is directly adjusted by nitrogen status. A molecular framework for elucidating nutrient status dynamics under field conditions would provide insights into improving crop productivity.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
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66
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Damaris RN, Lin Z, Yang P, He D. The Rice Alpha-Amylase, Conserved Regulator of Seed Maturation and Germination. Int J Mol Sci 2019; 20:E450. [PMID: 30669630 PMCID: PMC6359163 DOI: 10.3390/ijms20020450] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 11/29/2022] Open
Abstract
Alpha-amylase, the major form of amylase with secondary carbohydrate binding sites, is a crucial enzyme throughout the growth period and life cycle of angiosperm. In rice, alpha-amylase isozymes are critical for the formation of the storage starch granule during seed maturation and motivate the stored starch to nourish the developing seedling during seed germination which will directly affect the plant growth and field yield. Alpha-amylase has not yet been studied intensely to understand its classification, structure, expression trait, and expression regulation in rice and other crops. Among the 10-rice alpha-amylases, most were exclusively expressed in the developing seed embryo and induced in the seed germination process. During rice seed germination, the expression of alpha-amylase genes is known to be regulated negatively by sugar in embryos, however positively by gibberellin (GA) in endosperm through competitively binding to the specific promoter domain; besides, it is also controlled by a series of other abiotic or biotic factors, such as salinity. In this review, we overviewed the research progress of alpha-amylase with focus on seed germination and reflected on how in-depth work might elucidate its regulation and facilitate crop breeding as an efficient biomarker.
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Affiliation(s)
- Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhongyuan Lin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Pingfang Yang
- School of Life Sciences, Hubei University, Wuhan 430070, China.
| | - Dongli He
- School of Life Sciences, Hubei University, Wuhan 430070, China.
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67
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Chandran AKN, Moon S, Yoo YH, Gho YS, Cao P, Sharma R, Sharma MK, Ronald PC, Jung KH. A web-based tool for the prediction of rice transcription factor function. Database (Oxford) 2019; 2019:baz061. [PMID: 31169887 PMCID: PMC6553503 DOI: 10.1093/database/baz061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/15/2019] [Indexed: 11/14/2022]
Abstract
Transcription factors (TFs) are an important class of regulatory molecules. Despite their importance, only a small number of genes encoding TFs have been characterized in Oryza sativa (rice), often because gene duplication and functional redundancy complicate their analysis. To address this challenge, we developed a web-based tool called the Rice Transcription Factor Phylogenomics Database (RTFDB) and demonstrate its application for predicting TF function. The RTFDB hosts transcriptome and co-expression analyses. Sources include high-throughput data from oligonucleotide microarray (Affymetrix and Agilent) as well as RNA-Seq-based expression profiles. We used the RTFDB to identify tissue-specific and stress-related gene expression. Subsequently, 273 genes preferentially expressed in specific tissues or organs, 455 genes showing a differential expression pattern in response to 4 abiotic stresses, 179 genes responsive to infection of various pathogens and 512 genes showing differential accumulation in response to various hormone treatments were identified through the meta-expression analysis. Pairwise Pearson correlation coefficient analysis between paralogous genes in a phylogenetic tree was used to assess their expression collinearity and thereby provides a hint on their genetic redundancy. Integrating transcriptome with the gene evolutionary information reveals the possible functional redundancy or dominance played by paralog genes in a highly duplicated genome such as rice. With this method, we estimated a predominant role for 83.3% (65/78) of the TF or transcriptional regulator genes that had been characterized via loss-of-function studies. In this regard, the proposed method is applicable for functional studies of other plant species with annotated genome.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Yoon-Shil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, China
| | - Rita Sharma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manoj K Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
- Feedstocks Division, The Joint Bioenergy Institute, Emeryville, CA, USA
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
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68
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Tanaka N, Uraguchi S, Kajikawa M, Saito A, Ohmori Y, Fujiwara T. A rice PHD-finger protein OsTITANIA, is a growth regulator that functions through elevating expression of transporter genes for multiple metals. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:997-1006. [PMID: 30194869 DOI: 10.1111/tpj.14085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 06/08/2023]
Abstract
Essential metal absorption for plant growth is mediated predominantly by metal-specific transporters, with expression that responds to the environmental or cellular conditions of specific metals. Differing from metal-specific regulation, we describe a constitutively expressed transcription factor that regulates the transport of several metals in rice. We characterized the rice mutant LOW CADMIUM 5 (LC5), which exhibited reduced growth and accumulation of essential metals (e.g., copper [Cu], zinc [Zn] and manganese [Mn]) in shoots. LC5 was dwarf and developed less tillers than the wild type, but the structure of vasculature was apparently normal. Molecular genetic analysis revealed that the causal gene of LC5 is an ortholog of the transcriptional regulator Arabidopsis thaliana TITANIA (TTA), known as a transcriptional regulator. Expression analyses demonstrated that the OsTTA gene encodes a nucleus-localized protein containing a plant homeodomain-finger (PHD-finger) domain and is expressed ubiquitously in rice plants. RNA sequencing and quantitative PCR analyses revealed that the mRNA accumulation of transporter genes for essential metals, including iron (Fe), Zn, or Mn, were substantially lower in LC5 roots than in the wild type. Unlike known transcription factors of metal transport regulation, OsTTA transcript accumulation was not affected by metal availability. In addition, the growth defect of LC5 was partially rescued by Fe, Zn, or Mn supplementation, respectively. Taken together, OsTTA is a constitutively expressed regulator of multiple metal transporter genes responsible for essential metals delivery to shoots for their normal growth.
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Affiliation(s)
- Nobuhiro Tanaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shimpei Uraguchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masataka Kajikawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Akihiro Saito
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Ohmori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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69
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Abe K, Araki E, Suzuki Y, Toki S, Saika H. Production of high oleic/low linoleic rice by genome editing. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:58-62. [PMID: 29735369 DOI: 10.1016/j.plaphy.2018.04.033] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 05/24/2023]
Abstract
Rice bran oil (RBO) contains many valuable healthy constituents, including oleic acid. Improvement of the fatty acid composition in RBO, including an increase in the content of oleic acid, which helps suppress lifestyle disease, would increase health benefits. The enzyme fatty acid desaturase 2 (FAD2) catalyzes the conversion of oleic acid to linoleic acid in plants, and FAD2 mutants exhibit altered oleic and linoleic acid content in many crops. There are three functional FAD2 genes in the genome of rice (Oryza sativa L.), and, of these, expression of the OsFAD2-1 gene is highest in rice seeds. In order to produce high oleic/low linoleic RBO, we attempted to disrupt the OsFAD2-1 gene by CRISPR/Cas9-mediated targeted mutagenesis. We succeeded in the production of homozygous OsFAD2-1 knockout rice plants. The content of oleic acid increased to more than twice that of wild type, and, surprisingly, linoleic acid, a catabolite of oleic acid by FAD2, decreased dramatically to undetectable levels in fad2-1 mutant brown rice seeds. In this study, by genome editing based on genome information, we succeeded in the production of rice whose fatty acid composition is greatly improved. We suggest that CRISPR/Cas9-mediated mutagenesis of a major gene that shows dominant expression in the target tissue could be a powerful tool to improve target traits in a tissue-specific manner.
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Affiliation(s)
- Kiyomi Abe
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Etsuko Araki
- Rice Quality Research Unit, Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yasuhiro Suzuki
- Bio-oriented Technology Research Advancement Institution, National Agriculture and Food Research Organization, 1-40-2, Nissinmachi, Kita-ku, Saitama, Saitama, 331-8537, Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Yokohama, Kanagawa, 244-0813, Japan
| | - Hiroaki Saika
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
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Akasaka M, Taniguchi Y, Oshima M, Abe K, Tabei Y, Tanaka J. Development of transgenic male-sterile rice by using anther-specific promoters identified by comprehensive screening of the gene expression profile database 'RiceXPro'. BREEDING SCIENCE 2018; 68:420-431. [PMID: 30369816 PMCID: PMC6198903 DOI: 10.1270/jsbbs.18019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/24/2018] [Indexed: 05/29/2023]
Abstract
Because genomic selection is designed for the population breeding of allogamous species, a successive outcrossing system is required for efficient use of genomic selection in autogamous crops, such as Oryza sativa L. (rice). Transgenic and dominant male-sterility is a suitable tool for efficient outcrossing of autogamous crops. Though there have been some reports of dominant male-sterile rice developed using transgenic technology, the flowering habit was substandard. Here, to isolate promoters that, when linked to a lethal gene, induce dominant male-sterility while retaining a good flowering habit, we identified 38 candidate genes with anther-specific expression by using the 'RiceXPro' database. We then evaluated the abilities of the near-upstream regions of these genes to induce male-sterility when linked to the lethal gene barnase and introduced into the rice cultivar 'Nipponbare'. Seven of the 38 promoters induced clear dominant male-sterility; promoters expressed in the later stage of anther development induced male-sterility while retaining better flowering habits when compared to ones expressed in the early stage. These seven promoters could potentially be used to facilitate development of an efficient outcross-based breeding system in rice.
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Affiliation(s)
- Maiko Akasaka
- Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Yojiro Taniguchi
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masao Oshima
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kiyomi Abe
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Yutaka Tabei
- Institute of Agrobiological Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Junichi Tanaka
- Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Graduate School of Life and Environmental Science, University of Tsukuba,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
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71
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Shahan R, Zawora C, Wight H, Sittmann J, Wang W, Mount SM, Liu Z. Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry. PLANT PHYSIOLOGY 2018; 178:202-216. [PMID: 29991484 PMCID: PMC6130042 DOI: 10.1104/pp.18.00086] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/27/2018] [Indexed: 05/19/2023]
Abstract
The diploid strawberry, Fragaria vesca, is a developing model system for the economically important Rosaceae family. Strawberry fleshy fruit develops from the floral receptacle and its ripening is nonclimacteric. The external seed configuration of strawberry fruit facilitates the study of seed-to-fruit cross tissue communication, particularly phytohormone biosynthesis and transport. To investigate strawberry fruit development, we previously generated spatial and temporal transcriptome data profiling F. vesca flower and fruit development pre- and postfertilization. In this study, we combined 46 of our existing RNA-seq libraries to generate coexpression networks using the Weighted Gene Co-Expression Network Analysis package in R. We then applied a post-hoc consensus clustering approach and used bootstrapping to demonstrate consensus clustering's ability to produce robust and reproducible clusters. Further, we experimentally tested hypotheses based on the networks, including increased iron transport from the receptacle to the seed postfertilization and characterized a F. vesca floral mutant and its candidate gene. To increase their utility, the networks are presented in a web interface (www.fv.rosaceaefruits.org) for easy exploration and identification of coexpressed genes. Together, the work reported here illustrates ways to generate robust networks optimized for the mining of large transcriptome data sets, thereby providing a useful resource for hypothesis generation and experimental design in strawberry and related Rosaceae fruit crops.
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Affiliation(s)
- Rachel Shahan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Christopher Zawora
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Haley Wight
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - John Sittmann
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Wanpeng Wang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
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Hwang OJ, Back K. Melatonin is involved in skotomorphogenesis by regulating brassinosteroid biosynthesis in rice plants. J Pineal Res 2018; 65:e12495. [PMID: 29607549 DOI: 10.1111/jpi.12495] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/25/2018] [Indexed: 12/30/2022]
Abstract
Serotonin N-acetyltransferase (SNAT) is the penultimate enzyme in melatonin biosynthesis catalyzing the conversion of serotonin into N-acetylserotonin. In plants, SNAT is encoded by 2 isogenes of which SNAT1 is constitutively expressed and its overexpression confers increased yield in rice. However, the role of SNAT2 remains to be clarified. In contrast to SNAT1, the diurnal rhythm of SNAT2 mRNA expression peaks at night. In this study, transgenic rice plants in which SNAT2 expression were suppressed by RNAi technology showed a decrease in melatonin and a dwarf phenotype with erect leaves, reminiscent of brassinosteroids (BR)-deficient mutants. Of note, the dwarf phenotype was dependent on the presence of dark, suggesting that melatonin is involved in dark growth (skotomorphogenesis). In support of this suggestion, SNAT2 RNAi lines exhibited photomorphogenic phenotypes such as inhibition of internodes and increased expression of light-inducible CAB genes in the dark. The causative gene for the melatonin-mediated BR biosynthetic gene was DWARF4, a rate-limiting BR biosynthetic gene. Exogenous melatonin treatment induced several BR biosynthetic genes, including DWARF4, D11, and RAVL1. As expected from the erect leaves, the SNAT2 RNAi lines produced less BR than the wild type. Our results show for the first time that melatonin is a positive regulator of dark growth or shade outgrowth by regulating BR biosynthesis in plants.
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Affiliation(s)
- Ok Jin Hwang
- Department of Biotechnology, Bioenergy Research Center, Chonnam National University, Gwangju, South Korea
| | - Kyoungwhan Back
- Department of Biotechnology, Bioenergy Research Center, Chonnam National University, Gwangju, South Korea
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73
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Global analysis of threonine metabolism genes unravel key players in rice to improve the abiotic stress tolerance. Sci Rep 2018; 8:9270. [PMID: 29915249 PMCID: PMC6006157 DOI: 10.1038/s41598-018-27703-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/08/2018] [Indexed: 12/13/2022] Open
Abstract
The diversity in plant metabolites with improved phytonutrients is essential to achieve global food security and sustainable crop yield. Our study using computational metabolomics genome wide association study (cmGWAS) reports on a comprehensive profiling of threonine (Thr) metabolite in rice. Sixteen abiotic stress responsive (AbSR) – Thr metabolite producing genes (ThrMPG), modulate metabolite levels and play a significant role determining both physiological and nutritional importance of rice. These AbSR-ThrMPG were computationally analysed for their protein properties using OryzaCyc through plant metabolic network analyser. A total of 1373 and 1028 SNPs were involved in complex traits and genomic variations. Comparative mapping of AbSR-ThrMPG revealed the chromosomal colinearity with C4 grass species. Further, computational expression pattern of these genes predicted a differential expression profiling in diverse developmental tissues. Protein interaction of protein coding gene sequences revealed that the abiotic stresses (AbS) are multigenic in nature. In silico expression of AbSR-ThrMPG determined the putative involvement in response to individual AbS. This is the first comprehensive genome wide study reporting on AbSR –ThrMPG analysis in rice. The results of this study provide a pivotal resource for further functional investigation of these key genes in the vital areas of manipulating AbS signaling in rice improvement.
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74
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Mani A, Sankaranarayanan K. In Silico Analysis of Natural Resistance-Associated Macrophage Protein (NRAMP) Family of Transporters in Rice. Protein J 2018; 37:237-247. [DOI: 10.1007/s10930-018-9773-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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75
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Sanan-Mishra N, Tripathi A, Goswami K, Shukla RN, Vasudevan M, Goswami H. ARMOUR - A Rice miRNA: mRNA Interaction Resource. FRONTIERS IN PLANT SCIENCE 2018; 9:602. [PMID: 29868062 PMCID: PMC5952065 DOI: 10.3389/fpls.2018.00602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/16/2018] [Indexed: 05/09/2023]
Abstract
ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.
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Affiliation(s)
- Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Anita Tripathi
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kavita Goswami
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rohit N. Shukla
- Genome Informatics Research Group, Bionivid Technology Private Limited, Bengaluru, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Private Limited, Bengaluru, India
| | - Hitesh Goswami
- Genome Informatics Research Group, Bionivid Technology Private Limited, Bengaluru, India
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Liu C, Zheng S, Gui J, Fu C, Yu H, Song D, Shen J, Qin P, Liu X, Han B, Yang Y, Li L. Shortened Basal Internodes Encodes a Gibberellin 2-Oxidase and Contributes to Lodging Resistance in Rice. MOLECULAR PLANT 2018; 11:288-299. [PMID: 29253619 DOI: 10.1016/j.molp.2017.12.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 05/05/2023]
Abstract
Breeding semi-dwarf varieties to improve lodging resistance has been proven to be enormously successful in increasing grain yield since the advent of the "green revolution." However, the breeding of the majority of semi-dwarf rice varieties in Asia has been dependent mainly on genetic introduction of the mutant alleles of SD1, which encodes a gibberellin (GA) 20-oxidase, OsGA20ox2, for catalyzing GA biosynthesis. Here, we report a new rice lodging-resistance gene, Shortened Basal Internodes (SBI), which encodes a gibberellin 2-oxidase and specifically controls the elongation of culm basal internodes through deactivating GA activity. SBI is predominantly expressed in culm basal internodes. Genetic analyses indicate that SBI is a semi-dominant gene affecting rice height and lodging resistance. SBI allelic variants display different activities and are associated with the height of rice varieties. Breeding with higher activity of the SBI allele generates new rice varieties with improved lodging resistance and increased yield. The discovery of the SBI provides a desirable gene resource for producing semi-dwarf rice phenotypes and offers an effective strategy for breeding rice varieties with enhanced lodging resistance and high yield.
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Affiliation(s)
- Chang Liu
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Zheng
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jinshan Gui
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chenjian Fu
- Yuan Longping Agriculture High-Tech Co., Ltd., Hunan 410001, China
| | - Hasi Yu
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Dongliang Song
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junhui Shen
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Qin
- Yuan Longping Agriculture High-Tech Co., Ltd., Hunan 410001, China
| | | | - Bin Han
- National Center of Plant Gene Research and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yuanzhu Yang
- Yuan Longping Agriculture High-Tech Co., Ltd., Hunan 410001, China; Hunan Ava Seed Research Institute, Hunan 410119, China; Hunan Engineering Laboratory for Disease and Insect-Resistant Rice Breeding, Hunan 410119, China.
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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77
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Hwang SG, Lee CY, Tseng CS. Heterologous expression of rice 9-cis-epoxycarotenoid dioxygenase 4 (OsNCED4) in Arabidopsis confers sugar oversensitivity and drought tolerance. BOTANICAL STUDIES 2018; 59:2. [PMID: 29335785 PMCID: PMC5768580 DOI: 10.1186/s40529-018-0219-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/10/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND The 9-cis-epoxycarotenoid dioxygenases OsNCED4 was cloned from rice in conjunction with OsNCED 1-3 and 5, of which 3 has been shown to function in ABA biosynthesis and alteration of leaf morphology. In higher plants, NCEDs have been shown to be key enzymes controlling ABA biosynthesis and belong to a differentially expressed gene family. Aside from OsNCED3, it remains largely unknown if other OsNCED genes are involved in ABA biosynthesis in rice. Thus, transgenic Arabidopsis plants overexpressing OsNCED4 were generated in the 129B08/nced3 mutant background to explore OsNCED4 function in ABA biosynthesis. RESULTS Heterologous expression of OsNCED4 in Arabidopsis increased ABA levels and altered plant size and leaf shape, delayed seed germination, caused sugar oversensitivity in post-germination growth, and enhanced tolerance to drought. The native OsNCED3 and OsNCED4 promoters were expressed in an overlapping pattern in rice seeds and young seedlings, suggesting possible functional redundancy between OsNCED3 and OsNCED4. At the one-leaf stage, similar regulation of OsNCED3 and OsNCED4 gene expression in roots or leaves in response to moderate salt stress (150 mM NaCl) was observed. CONCLUSION Like OsNCED3, OsNCED4 is functionally active in ABA biosynthesis in rice. OsNCED3 and OsNCED4 might play redundant roles in controlling ABA biosynthesis in rice, as suggested by GUS staining assay, but this should be further analyzed through complementation of rice NCED knockout mutants.
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Affiliation(s)
- San-Gwang Hwang
- Department of Horticulture, National Chung Hsing University, 145 Xingda Road, South District, Taichung, 40227 Taiwan, ROC
| | - Chia-Yun Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, ROC
| | - Ching-Shan Tseng
- Taiwan Agricultural Research Institute, Council of Agriculture, Executive Yuan, No.189, Zhongzheng Road, Wufeng District, Taichung, 41362 Taiwan, ROC
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Chandran AKN, Bhatnagar N, Yoo YH, Moon S, Park SA, Hong WJ, Kim BG, An G, Jung KH. Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles. PLANT MOLECULAR BIOLOGY 2018; 96:17-34. [PMID: 29086189 DOI: 10.1007/s11103-017-0675-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
This work suggests 2020 potential candidates in rice for the functional annotation of unannotated genes using meta-analysis of anatomical samples derived from microarray and RNA-seq technologies and this information will be useful to identify novel morphological agronomic traits. Although the genome of rice (Oryza sativa) has been sequenced, 14,365 genes are considered unannotated because they lack putative annotation information. According to the Rice Genome Annotation Project Database ( http://rice.plantbiology.msu.edu/ ), the proportion of functionally characterized unannotated genes (0.35%) is quite limited when compared with the approximately 3.9% of annotated genes with assigned putative functions. Researchers require additional information to help them investigate the molecular mechanisms associated with those unannotated genes. To determine which of them might regulate morphological or physiological traits in the rice genome, we conducted a meta-analysis of expression data that covered a wide range of tissue/organ samples. Overall, 2020 genes showed cultivar-, tissue-, or organ-preferential patterns of expression. Representative candidates from featured groups were validated by RT-PCR, and the GUS reporter system was used to validate the expression of genes that were clustered according to their leaf or root preference. Taking a molecular and genetics approach, we examined meta-expression data and found that 127 genes were differentially expressed between japonica and indica rice cultivars. This is potentially significant for future agronomic applications. We also used a T-DNA insertional mutant and performed a co-expression network analysis of Sword shape dwarf1 (SSD1), a gene that regulates cell division. This network was refined via RT-PCR analysis. Our results suggested that SSD1 represses the expression of four genes related to the processes of DNA replication or cell division and provides insight into possible molecular mechanisms. Together, these strategies present a valuable tool for in-depth characterization of currently unannotated genes.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Nikita Bhatnagar
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sun-Ah Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Beom-Gi Kim
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea.
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79
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Moon S, Chandran AKN, Gho YS, Park SA, Kim SR, Yoo YH, Jung KH. Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:11-23. [PMID: 29132026 DOI: 10.1016/j.jplph.2017.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles. The expression patterns of four candidate genes were confirmed in vivo by monitoring expression of β-glucuronidase under control of the candidate-gene promoters, providing new tools to manipulate agronomic traits associated with roots. We also utilized real-time PCR to examine the root-preferential expression of 14 genes across four rice varieties, including japonica and indica cultivars. Using a database of rice genes with known functions, we identified the reported functions of 39 out of the 684 candidate genes. Sixteen genes are directly involved in root development, while the remaining are involved in processes indirectly related to root development (i.e., soil-stress tolerance or growth retardation). This indicates the importance of our candidate genes for studies on root development and function. Gene ontology enrichment analysis in the 'biological processes' category revealed that root-preferred genes in rice are closely associated with nutrient transport-related genes, indicating that the primary role of roots is the uptake of nutrients from soil. In addition, predicted protein-protein interaction analysis suggested a molecular network for root development composed of 215 interactions associated with 44 root-preferred or root development-related genes. Taken together, our data provide an important foundation for future research on root development in rice.
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Affiliation(s)
- Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Yun-Shil Gho
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sun-A Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sung-Ryul Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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Minhas AP, Tuli R, Puri S. Pathway Editing Targets for Thiamine Biofortification in Rice Grains. FRONTIERS IN PLANT SCIENCE 2018; 9:975. [PMID: 30042775 PMCID: PMC6048418 DOI: 10.3389/fpls.2018.00975] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has been partially elucidated and the effect of overexpression of a few genes such as thi1 and thiC, on thiamine accumulation in rice has been reported. Based on current knowledge, this review focuses on the potential of gene editing in metabolic engineering of thiamine biosynthesis pathway to improve thiamine in rice grains. Candidate genes, suitable for modification of the structural part to evolve more efficient versions of enzymes in the pathway, are discussed. For example, adjacent cysteine residues may be introduced in the catalytic domain of thi4 to improve the turn over activity of thiamine thiazole synthase 2. Motif specific editing to modify promoter regulatory regions of genes is discussed to modulate gene expression. Editing cis acting regulatory elements in promoter region can shift the expression of transporters and thiamine binding proteins to endosperm. This can enhance dietary availability of thiamine from rice grains. Differential transcriptomics on rice varieties with contrasting grain thiamine and functional genomic studies will identify more strategic targets for editing in future. Developing functionally enhanced foods by biofortification is a sustainable approach to make diets wholesome.
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81
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Wambugu P, Ndjiondjop M, Furtado A, Henry R. Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:100-110. [PMID: 28499072 PMCID: PMC5785344 DOI: 10.1111/pbi.12752] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/25/2017] [Accepted: 05/01/2017] [Indexed: 05/03/2023]
Abstract
Amylose content (AC) is a key quality trait in rice. A cross between Oryza glaberrima (African rice) and Oryza sativa (Asian rice) segregating for AC was analysed by sequencing bulks of individuals with high and low AC. SNP associated with the granule bound starch synthase (GBSS1) locus on chromosome 6 were polymorphic between the bulks. In particular, a G/A SNP that would result in an Asp to Asn mutation was identified. This amino acid substitution may be responsible for differences in GBSS activity as it is adjacent to a disulphide linkage conserved in all grass GBSS proteins. Other polymorphisms in genomic regions closely surrounding this variation may be the result of linkage drag. In addition to the variant in the starch biosynthesis gene, SNP on chromosomes 1 and 11 linked to AC was also identified. SNP was found in the genes encoding the NAC and CCAAT-HAP5 transcription factors that have previously been linked to starch biosynthesis. This study has demonstrated that the approach of sequencing bulks was able to identify genes on different chromosomes associated with this complex trait.
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Affiliation(s)
- Peterson Wambugu
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQldAustralia
- Present address:
Kenya Agricultural and Livestock Research Organization (KALRO)Genetic Resources Research InstituteNairobiKenya
| | | | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQldAustralia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQldAustralia
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Sandhu M, Sureshkumar V, Prakash C, Dixit R, Solanke AU, Sharma TR, Mohapatra T, S V AM. RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. BMC Bioinformatics 2017; 18:432. [PMID: 28964253 PMCID: PMC5622590 DOI: 10.1186/s12859-017-1846-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Background Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. Results RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. Conclusions The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201 Electronic supplementary material The online version of this article (10.1186/s12859-017-1846-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maninder Sandhu
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | - V Sureshkumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Rekha Dixit
- Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India.,Current address: Department of biotechnology, Keralverma faculty of science, Swami Vivekanand Subharti University, Meerut, 250005, Uttar Pradesh, India
| | - Amolkumar U Solanke
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India
| | - Amitha Mithra S V
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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83
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Huang J, Vendramin S, Shi L, McGinnis KM. Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data. PLANT PHYSIOLOGY 2017; 175:568-583. [PMID: 28768814 PMCID: PMC5580776 DOI: 10.1104/pp.17.00825] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/31/2017] [Indexed: 05/22/2023]
Abstract
With the emergence of massively parallel sequencing, genomewide expression data production has reached an unprecedented level. This abundance of data has greatly facilitated maize research, but may not be amenable to traditional analysis techniques that were optimized for other data types. Using publicly available data, a gene coexpression network (GCN) can be constructed and used for gene function prediction, candidate gene selection, and improving understanding of regulatory pathways. Several GCN studies have been done in maize (Zea mays), mostly using microarray datasets. To build an optimal GCN from plant materials RNA-Seq data, parameters for expression data normalization and network inference were evaluated. A comprehensive evaluation of these two parameters and a ranked aggregation strategy on network performance, using libraries from 1266 maize samples, were conducted. Three normalization methods and 10 inference methods, including six correlation and four mutual information methods, were tested. The three normalization methods had very similar performance. For network inference, correlation methods performed better than mutual information methods at some genes. Increasing sample size also had a positive effect on GCN. Aggregating single networks together resulted in improved performance compared to single networks.
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Affiliation(s)
- Ji Huang
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - Stefania Vendramin
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - Lizhen Shi
- Department of Computer Science, Florida State University, Tallahassee, Florida 32306
| | - Karen M McGinnis
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
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84
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Lee S, Jeong H, Lee S, Lee J, Kim SJ, Park JW, Woo HR, Lim PO, An G, Nam HG, Hwang D. Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice. Sci Rep 2017; 7:8792. [PMID: 28821707 PMCID: PMC5562787 DOI: 10.1038/s41598-017-07035-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/21/2017] [Indexed: 01/31/2023] Open
Abstract
Flag leaves (FL) and second leaves (SL) in rice show differential aging patterns during monocarpic senescence. Coordination of aging programs between FL and SL is important for grain yield and quality. However, the molecular bases for differential aging programs between FL and SL have not been systematically explored in rice. Here, we performed mRNA-sequencing of FL and SL at six time points during grain-filling and identified four molecular bases for differential aging programs between FL and SL: phenylpropanoid biosynthesis, photosynthesis, amino acid (AA) transport, and hormone response. Of them, photosynthesis (carbon assimilation) and AA transport (nitrogen remobilization) predominantly occurred in FL and SL, respectively, during grain-filling. Unlike other molecular bases, AA transport showed consistent differential expression patterns between FL and SL in independent samples. Moreover, long-distance AA transporters showed invariant differential expression patterns between FL and SL after panicle removal, which was consistent to invariant differential nitrogen contents between FL and SL after panicle removal. Therefore, our results suggest that the supplies of carbon and nitrogen to seeds is functionally segregated between FL and SL and that long-distance AA transport is an invariant core program for high nitrogen remobilization in SL.
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Affiliation(s)
- Shinyoung Lee
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Hyobin Jeong
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Sichul Lee
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Jinwon Lee
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Sun-Ji Kim
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Ji-Won Park
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Pyung Ok Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Hong Gil Nam
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea. .,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea.
| | - Daehee Hwang
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea. .,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea.
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85
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Feng H, Guo Z, Yang W, Huang C, Chen G, Fang W, Xiong X, Zhang H, Wang G, Xiong L, Liu Q. An integrated hyperspectral imaging and genome-wide association analysis platform provides spectral and genetic insights into the natural variation in rice. Sci Rep 2017; 7:4401. [PMID: 28667309 PMCID: PMC5493659 DOI: 10.1038/s41598-017-04668-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/17/2017] [Indexed: 01/24/2023] Open
Abstract
With progress of genetic sequencing technology, plant genomics has experienced rapid development and subsequently triggered the progress of plant phenomics. In this study, a high-throughput hyperspectral imaging system (HHIS) was developed to obtain 1,540 hyperspectral indices at whole-plant level during tillering, heading, and ripening stages. These indices were used to quantify traditional agronomic traits and to explore genetic variation. We performed genome-wide association study (GWAS) of these indices and traditional agronomic traits in a global rice collection of 529 accessions. With the genome-level suggestive P-value threshold, 989 loci were identified. Of the 1,540 indices, we detected 502 significant indices (designated as hyper-traits) that exhibited phenotypic and genetic relationship with traditional agronomic traits and had high heritability. Many hyper-trait-associated loci could not be detected using traditional agronomic traits. For example, we identified a candidate gene controlling chlorophyll content (Chl). This gene, which was not identified based on Chl, was significantly associated with a chlorophyll-related hyper-trait in GWAS and was demonstrated to control Chl. Moreover, our study demonstrates that red edge (680-760 nm) is vital for rice research for phenotypic and genetic insights. Thus, combination of HHIS and GWAS provides a novel platform for dissection of complex traits and for crop breeding.
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Affiliation(s)
- Hui Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China.,Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zilong Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chenglong Huang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guoxing Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Fang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiong Xiong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongyu Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qian Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China. .,MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
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86
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Jiang W, Zhou S, Zhang Q, Song H, Zhou DX, Zhao Y. Transcriptional regulatory network of WOX11 is involved in the control of crown root development, cytokinin signals, and redox in rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2787-2798. [PMID: 28830102 PMCID: PMC5853245 DOI: 10.1093/jxb/erx153] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The rice root system is mainly composed of post-embryonic shoot-borne roots called crown roots. WOX11, encoding a WUSCHEL-related homeobox domain transcription factor, is a key regulator of crown root growth and development in rice (Oryza sativa. L). In addition to specifically activating crown root development, WOX11 is also involved in lateral root initiation, root hair formation, and abiotic stresses. However, the gene regulatory network downstream of WOX11 remains largely unknown. Here, we studied the transcriptome of wox11 root tips by RNA-Seq and determined direct WOX11-binding targets by bioinformatic and biochemical analysis. The transcriptomic analysis revealed 664 differentially expressed genes, which covered a wide range of functions related to root development, cytokinin homeostasis/signaling, stress response, and redox metabolic processes. Bioinformatic analysis also revealed that the WOX11-binding motif was distributed over 41% (273/664) of the differentially expressed genes, and was mostly enriched in the promoter and intron regions. We used qRT-PCR and/or in situ hybridization to confirm co-expression of some of the WOX11-regulated genes in crown root development. We also used electrophoretic mobility shift assay and chromatin immunoprecipitation with anti-WOX11 antibody to validate direct regulation of these genes by WOX11. The analysis identified several genes that acted downstream of WOX11 in controlling crown root formation, cytokinin signaling, stress response, and redox metabolism. This work built a hierarchical regulatory model of WOX11 in rice crown root development.
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Affiliation(s)
- Wei Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shaoli Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qian Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Huazhi Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Université Paris-Sud, Orsay, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Correspondence:
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87
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Xia L, Zou D, Sang J, Xu X, Yin H, Li M, Wu S, Hu S, Hao L, Zhang Z. Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice. J Genet Genomics 2017; 44:235-241. [PMID: 28529082 DOI: 10.1016/j.jgg.2017.05.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 04/24/2017] [Accepted: 05/02/2017] [Indexed: 10/19/2022]
Abstract
Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community. Here, we present RED (Rice Expression Database; http://expression.ic4r.org), an integrated database of rice gene expression profiles derived entirely from RNA-Seq data. RED features a comprehensive collection of 284 high-quality RNA-Seq experiments, integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments. Based on massive expression profiles, RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest. Besides, it provides user-friendly web interfaces for querying, browsing and visualizing expression profiles of concerned genes. Together, as a core resource in BIG Data Center, RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.
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Affiliation(s)
- Lin Xia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Sang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingjian Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyan Yin
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengwei Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuangyang Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Lili Hao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China.
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88
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Nakata M, Fukamatsu Y, Miyashita T, Hakata M, Kimura R, Nakata Y, Kuroda M, Yamaguchi T, Yamakawa H. High Temperature-Induced Expression of Rice α-Amylases in Developing Endosperm Produces Chalky Grains. FRONTIERS IN PLANT SCIENCE 2017; 8:2089. [PMID: 29270189 PMCID: PMC5723670 DOI: 10.3389/fpls.2017.02089] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/23/2017] [Indexed: 05/05/2023]
Abstract
Global warming impairs grain filling in rice and reduces starch accumulation in the endosperm, leading to chalky-appearing grains, which damages their market value. We found previously that high temperature-induced expression of starch-lytic α-amylases during ripening is crucial for grain chalkiness. Because the rice genome carries at least eight functional α-amylase genes, identification of the α-amylase(s) that contribute most strongly to the production of chalky grains could accelerate efficient breeding. To identify α-amylase genes responsible for the production of chalky grains, we characterized the histological expression pattern of eight α-amylase genes and the influences of their overexpression on grain appearance and carbohydrate components through a series of experiments with transgenic rice plants. The promoter activity of most α-amylase genes was elevated to various extents at high temperature. Among them, the expression of Amy1A and Amy3C was induced in the internal, especially basal to dorsal, region of developing endosperm, whereas that of Amy3D was confined near the ventral aleurone. These regions coincided with the site of occurrence of chalkiness, which was in clear contrast to conventionally known expression patterns of the enzyme in the scutellum and aleurone during seed germination. Furthermore, overexpression of α-amylase genes, except for Amy3E, in developing endosperm produced various degrees of chalky grains without heat exposure, whereas that of Amy3E yielded normal translucent grains, as was the case in the vector control, even though Amy3E-overexpressing grains contained enhanced α-amylase activities. The weight of the chalky grains was decreased due to reduced amounts of starch, and microscopic observation of the chalky part of these grains revealed that their endosperm consisted of loosely packed round starch granules that had numerous pits on their surface, confirming the hydrolysis of the starch reserve by α-amylases. Moreover, the chalky grains contained increased amounts of soluble sugars including maltooligosaccharides at the expense of starch. The integrated analyses proposed that expression of Amy1A, Amy3C, and Amy3D at the specific regions of the developing endosperm could generate the chalkiness. This finding provides the fundamental knowledge to narrow down the targets for the development of high temperature-tolerant premium rice.
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89
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Ishikawa-Sakurai J, Murai-Hatano M, Hayashi H, Matsunami M, Kuwagata T. Rice aquaporins and their responses to environmental stress. ACTA ACUST UNITED AC 2017. [DOI: 10.3117/rootres.26.39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Junko Ishikawa-Sakurai
- Tohoku Agricultural Research Center, NARO
- Institute of Crop Science, NARO
- United Graduate School of Agricultural Sciences, Iwate University
| | | | - Hidehiro Hayashi
- Tohoku Agricultural Research Center, NARO
- United Graduate School of Agricultural Sciences, Iwate University
| | - Maya Matsunami
- Tohoku Agricultural Research Center, NARO
- JSPS Research Fellow
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90
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Schläppi MR, Jackson AK, Eizenga GC, Wang A, Chu C, Shi Y, Shimoyama N, Boykin DL. Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection. FRONTIERS IN PLANT SCIENCE 2017; 8:957. [PMID: 28642772 PMCID: PMC5463297 DOI: 10.3389/fpls.2017.00957] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/22/2017] [Indexed: 05/21/2023]
Abstract
Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC) collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association study (GWAS) based quantitative trait loci (QTL) mapping. For young seedling stage indices, japonica and indica subspecies clustered into chilling tolerant and chilling sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. Indica subspecies were shown to have chilling acclimation potential. GWAS mapping uncovered 48 QTL at 39 chromosome regions distributed across all 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 18 QTL and 32 QTL were in regions discovered in previously reported bi-parental and GWAS based QTL mapping studies, respectively. Two novel low temperature seedling survivability (LTSS)-QTL, qLTSS3-4 and qLTSS4-1, were not in a previously reported QTL region. QTL with strong effect alleles identified in this study will be useful for marker assisted breeding efforts to improve chilling tolerance in rice cultivars and enhance gene discovery for chilling tolerance.
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Affiliation(s)
- Michael R. Schläppi
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
- *Correspondence: Michael R. Schläppi,
| | - Aaron K. Jackson
- Dale Bumpers National Rice Research Center, United States Department of Agriculture – Agricultural Research Service, StuttgartAR, United States
| | - Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, United States Department of Agriculture – Agricultural Research Service, StuttgartAR, United States
| | - Aiju Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yao Shi
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
| | - Naoki Shimoyama
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
| | - Debbie L. Boykin
- United States Department of Agriculture – Agricultural Research Service, StonevilleMS, United States
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91
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Hibara KI, Isono M, Mimura M, Sentoku N, Kojima M, Sakakibara H, Kitomi Y, Yoshikawa T, Itoh JI, Nagato Y. Jasmonate regulates juvenile-to-adult phase transition in rice. Development 2016; 143:3407-16. [PMID: 27578792 DOI: 10.1242/dev.138602] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/04/2016] [Indexed: 12/15/2022]
Abstract
Juvenile-to-adult phase transition is an important shift for the acquisition of adult vegetative characteristics and subsequent reproductive competence. We identified a recessive precocious (pre) mutant exhibiting a long leaf phenotype in rice. The long leaf phenotype is conspicuous in the second to the fourth leaves, which are juvenile and juvenile-to-adult transition leaves. We found that morphological and physiological traits, such as midrib formation, shoot meristem size, photosynthetic rate and plastochron, in juvenile and juvenile-to-adult transition stages of the pre mutant have precociously acquired adult characteristics. In agreement with these results, expression patterns of miR156 and miR172, which are microRNAs regulating phase change, support the accelerated juvenile-to-adult phase change in the pre mutant. The mutated gene encodes an allene oxide synthase (OsAOS1), which is a key enzyme for the biosynthesis of jasmonic acid (JA). The pre mutant showed a low level of JA and enhanced sensitivity to gibberellic acid, which promotes the phase change in some plant species. We also show that prolonged plastochron in the pre mutant is caused by accelerated PLASTOCHRON1 (PLA1) function. The present study reveals a substantial role of JA as a negative regulator of vegetative phase change.
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Affiliation(s)
- Ken-Ichiro Hibara
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Miyako Isono
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Manaki Mimura
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Naoki Sentoku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Ibaraki 305-8602, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yuka Kitomi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Takanori Yoshikawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Jun-Ichi Itoh
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Yasuo Nagato
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
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92
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Shimono H, Abe A, Aoki N, Koumoto T, Sato M, Yokoi S, Kuroda E, Endo T, Saeki KI, Nagano K. Combining mapping of physiological quantitative trait loci and transcriptome for cold tolerance for counteracting male sterility induced by low temperatures during reproductive stage in rice. PHYSIOLOGIA PLANTARUM 2016; 157:175-92. [PMID: 26607766 DOI: 10.1111/ppl.12410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/06/2015] [Accepted: 10/21/2015] [Indexed: 05/18/2023]
Abstract
Male sterility induced by low temperatures (LTs) during the reproductive stage is a major constraint for temperate zone rice. To detect physiological quantitative trait loci (QTLs), we modeled genotypic variation in the physiological processes involved in low temperature spikelet sterility on the basis of anther length (AL), a proxy for microspore and pollen grain number per anther. The model accounted for 83% of the genotypic variation in potential AL at normal temperature and the ability to maintain AL at LT. We tested the model on 208 recombinant inbred lines of cold-tolerant 'Tohoku-PL3' (PL3) × cold-sensitive 'Akihikari' (AH) for 2 years. QTLs for spikelet fertility (FRT) at LT were detected on chromosomes 5 (QTL for Cold Tolerance at Reproductive stage, qCTR5) and 12 (qCTR12). qCTR12 was annotated with the ability to maintain AL under LTs. qCTR5 was in a region shared with QTLs for culm length and heading date. Genome-wide expression analysis showed 798 genes differentially expressed in the spikelets between the parents at LTs. Of these, 12 were near qCTR5 and 23 were near qCTR12. Gene expression analysis confirmed two candidate genes for qCTR5 (O-methyltransferase ZRP4, Os05g0515600; beta-1,3-glucanase-like protein, Os05g0535100) and one for qCTR12 (conserved hypothetical protein, Os12g0550600). Nucleotide polymorphisms (21 deletions, 2 insertions and 10 single nucleotide polymorphisms) in PL3 were found near the candidate conserved hypothetical protein (Os12g0550600) and upstream in PL3, but not in AH. Haplotype analysis revealed that this gene came from 'Kuchum'. The combination of mapping physiological QTLs with gene expression analysis can be extended to identify other genes for abiotic stress response in cereals.
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Affiliation(s)
- Hiroyuki Shimono
- Crop Science Laboratory, Faculty of Agriculture, Iwate University, 3-18-8, Ueda, Morioka, Iwate, 020-8850, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, 22-174-4, Narita, Kitakami, Iwate, 024-0003, Japan
| | - Naohiro Aoki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 989-6227, Japan
| | - Takemasa Koumoto
- Crop Science Laboratory, Faculty of Agriculture, Iwate University, 3-18-8, Ueda, Morioka, Iwate, 020-8850, Japan
| | - Masahiro Sato
- Crop Science Laboratory, Faculty of Agriculture, Iwate University, 3-18-8, Ueda, Morioka, Iwate, 020-8850, Japan
| | - Shuji Yokoi
- Crop Science Laboratory, Faculty of Agriculture, Iwate University, 3-18-8, Ueda, Morioka, Iwate, 020-8850, Japan
| | - Eiki Kuroda
- Crop Science Laboratory, Faculty of Agriculture, Iwate University, 3-18-8, Ueda, Morioka, Iwate, 020-8850, Japan
| | - Takashi Endo
- Miyagi Prefectural Furukawa Agricultural Experiment Station, 88 Fukoku, Oosaki, Furukawa, Miyagi, 989-6227, Japan
| | - Ken-Ich Saeki
- Miyagi Prefectural Furukawa Agricultural Experiment Station, 88 Fukoku, Oosaki, Furukawa, Miyagi, 989-6227, Japan
| | - Kuniaki Nagano
- Miyagi Prefectural Furukawa Agricultural Experiment Station, 88 Fukoku, Oosaki, Furukawa, Miyagi, 989-6227, Japan
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93
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Sugano S, Hayashi N, Kawagoe Y, Mochizuki S, Inoue H, Mori M, Nishizawa Y, Jiang CJ, Matsui M, Takatsuji H. Rice OsVAMP714, a membrane-trafficking protein localized to the chloroplast and vacuolar membrane, is involved in resistance to rice blast disease. PLANT MOLECULAR BIOLOGY 2016; 91:81-95. [PMID: 26879413 DOI: 10.1007/s11103-016-0444-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 01/26/2016] [Indexed: 06/05/2023]
Abstract
Membrane trafficking plays pivotal roles in many cellular processes including plant immunity. Here, we report the characterization of OsVAMP714, an intracellular SNARE protein, focusing on its role in resistance to rice blast disease caused by the fungal pathogen Magnaporthe oryzae. Disease resistance tests using OsVAMP714 knockdown and overexpressing rice plants demonstrated the involvement of OsVAMP714 in blast resistance. The overexpression of OsVAMP7111, whose product is highly homologous to OsVAMP714, did not enhance blast resistance to rice, implying a potential specificity of OsVAMP714 to blast resistance. OsVAMP714 was localized to the chloroplast in mesophyll cells and to the cellular periphery in epidermal cells of transgenic rice plant leaves. We showed that chloroplast localization is critical for the normal OsVAMP714 functioning in blast resistance by analyzing the rice plants overexpressing OsVAMP714 mutants whose products did not localize in the chloroplast. We also found that OsVAMP714 was located in the vacuolar membrane surrounding the invasive hyphae of M. oryzae. Furthermore, we showed that OsVAMP714 overexpression promotes leaf sheath elongation and that the first 19 amino acids, which are highly conserved between animal and plant VAMP7 proteins, are crucial for normal rice plant growths. Our studies imply that the OsVAMP714-mediated trafficking pathway plays an important role in rice blast resistance as well as in the vegetative growth of rice.
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Affiliation(s)
- Shoji Sugano
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Nagao Hayashi
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yasushi Kawagoe
- Functional Plant Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Susumu Mochizuki
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School and Faculty of Agriculture, Kagawa University, Miki, Kagawa, 761-0795, Japan
| | - Haruhiko Inoue
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Masaki Mori
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yoko Nishizawa
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Chang-Jie Jiang
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Minami Matsui
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiroshi Takatsuji
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
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94
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Minamisawa K, Imaizumi-Anraku H, Bao Z, Shinoda R, Okubo T, Ikeda S. Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root? Microbes Environ 2016; 31:4-10. [PMID: 26960961 PMCID: PMC4791114 DOI: 10.1264/jsme2.me15180] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH4–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of 15N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation).
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95
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Matsushima R, Maekawa M, Kusano M, Tomita K, Kondo H, Nishimura H, Crofts N, Fujita N, Sakamoto W. Amyloplast Membrane Protein SUBSTANDARD STARCH GRAIN6 Controls Starch Grain Size in Rice Endosperm. PLANT PHYSIOLOGY 2016; 170:1445-59. [PMID: 26792122 PMCID: PMC4775137 DOI: 10.1104/pp.15.01811] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/18/2016] [Indexed: 05/18/2023]
Abstract
Starch is a biologically and commercially important polymer of glucose. Starch is organized into starch grains (SGs) inside amyloplasts. The SG size differs depending on the plant species and is one of the most important factors for industrial applications of starch. There is limited information on genetic factors regulating SG sizes. In this study, we report the rice (Oryza sativa) mutant substandard starch grain6 (ssg6), which develops enlarged SGs in endosperm. Enlarged SGs are observed starting at 3 d after flowering. During endosperm development, a number of smaller SGs appear and coexist with enlarged SGs in the same cells. The ssg6 mutation also affects SG morphologies in pollen. The SSG6 gene was identified by map-based cloning and microarray analysis. SSG6 encodes a protein homologous to aminotransferase. SSG6 differs from other rice homologs in that it has a transmembrane domain. SSG6-green fluorescent protein is localized in the amyloplast membrane surrounding SGs in rice endosperm, pollen, and pericarp. The results of this study suggest that SSG6 is a novel protein that controls SG size. SSG6 will be a useful molecular tool for future starch breeding and applications.
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Affiliation(s)
- Ryo Matsushima
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Masahiko Maekawa
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Miyako Kusano
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Katsura Tomita
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Hideki Nishimura
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Naoko Crofts
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Naoko Fujita
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
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96
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Endo T, Chiba B, Wagatsuma K, Saeki K, Ando T, Shomura A, Mizubayashi T, Ueda T, Yamamoto T, Nishio T. Detection of QTLs for cold tolerance of rice cultivar 'Kuchum' and effect of QTL pyramiding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:631-40. [PMID: 26747044 DOI: 10.1007/s00122-015-2654-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/11/2015] [Indexed: 05/03/2023]
Abstract
A QTL for cold tolerance at the booting stage of rice cultivar 'Kuchum' was detected and delimited into a 1.36 Mb region, and a cold-tolerant line was developed by QTL pyramiding. Low temperature in summer causes pollen sterility in rice, resulting in a serious loss of yield. The second most widely grown rice cultivar in Japan, 'Hitomebore', has been developed as a cultivar highly tolerant to low temperature at the booting stage. However, even 'Hitomebore' exhibits sterility at a temperature lower than 18.5 °C. Further improvement of cold tolerance of rice is required. In the present study, QTLs for cold tolerance in a Bhutanese rice variety, 'Kuchum', were analyzed using backcrossed progenies and a major QTL, named qCT-4, was detected on chromosome 4. Evaluating cold tolerance of seven types of near isogenic lines having 'Kuchum' alleles around qCT-4 with a 'Hitomebore' genetic background, qCT-4 was delimited to a region of ca. 1.36 Mb between DNA markers 9_1 and 10_13. Homozygous 'Kuchum' alleles at qCT-4 showed an effect of increasing seed fertility by ca. 10 % under cold-water treatment. Near isogenic lines of 'Hitomebore' having 'Silewah' alleles of Ctb1 and Ctb2 and a 'Hokkai PL9' allele of qCTB8 did not exhibit higher cold tolerance than that of 'Hitomebore'. On the other hand, a qLTB3 allele derived from a Chinese cultivar 'Lijiangxintuanheigu' increased cold tolerance of 'Hitomebore', and pyramiding of the qCT-4 allele and the qLTB3 allele further increased seed fertility under cold-water treatment. Since NILs of 'Hitomebore' with the 'Kuchum' allele of qCT-4 were highly similar to 'Hitomebore' in other agronomic traits, the qCT-4 allele is considered to be useful for developing a cold-tolerant cultivar.
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Affiliation(s)
- Takashi Endo
- Miyagi Prefectural Furukawa Agricultural Experiment Station, Osaki, Miyagi, 989-6227, Japan
| | - Bunya Chiba
- Miyagi Prefectural Furukawa Agricultural Experiment Station, Osaki, Miyagi, 989-6227, Japan
- Miyagi Pref. Northern Regional Promotion Office Kurihara Regional Office, Fujiki,Tsukidate, Kurihara, Miyagi, 987-2251, Japan
| | - Kensuke Wagatsuma
- Miyagi Prefectural Furukawa Agricultural Experiment Station, Osaki, Miyagi, 989-6227, Japan
- Earthquake Reconstruction and Planning Department, Miyagi Prefectural Office, Honcho, Aoba-ku, Sendai, Miyagi, 980-8570, Japan
| | - Kenichi Saeki
- Miyagi Prefectural Furukawa Agricultural Experiment Station, Osaki, Miyagi, 989-6227, Japan
| | - Tsuyu Ando
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Ayahiko Shomura
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Tatsumi Mizubayashi
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Tadamasa Ueda
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Toshio Yamamoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi, 981-8555, Japan.
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97
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Itoh JI, Sato Y, Sato Y, Hibara KI, Shimizu-Sato S, Kobayashi H, Takehisa H, Sanguinet KA, Namiki N, Nagamura Y. Genome-wide analysis of spatiotemporal gene expression patterns during early embryogenesis in rice. Development 2016; 143:1217-27. [PMID: 26903508 DOI: 10.1242/dev.123661] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 02/15/2016] [Indexed: 12/11/2022]
Abstract
Embryogenesis in rice is different from that of most dicotolydonous plants in that it shows a non-stereotypic cell division pattern, formation of dorsal-ventral polarity, and endogenous initiation of the radicle. To reveal the transcriptional features associated with developmental events during rice early embryogenesis, we used microarray analysis coupled with laser microdissection to obtain both spatial and temporal transcription profiles. Our results allowed us to determine spatial expression foci for each expressed gene in the globular embryo, which revealed the importance of phytohormone-related genes and a suite of transcription factors to early embryogenesis. Our analysis showed the polarized expression of a small number of genes along the apical-basal and dorsal-ventral axes in the globular embryo, which tended to fluctuate in later developmental stages. We also analyzed gene expression patterns in the early globular embryo and how this relates to expression in embryonic organs at later stages. We confirmed the accuracy of the expression patterns found by microarray analysis of embryo subdomains using in situ hybridization. Our study identified homologous genes from Arabidopsis thaliana with known functions in embryogenesis in addition to unique and uncharacterized genes that show polarized expression patterns during embryogenesis. The results of this study are presented in a database to provide a framework for spatiotemporal gene expression during rice embryogenesis, to serve as a resource for future functional analysis of genes, and as a basis for comparative studies of plant embryogenesis.
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Affiliation(s)
- Jun-Ichi Itoh
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Yutaka Sato
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Yutaka Sato
- Department of Bioresource Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Ken-Ichiro Hibara
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Sae Shimizu-Sato
- Department of Bioresource Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hiromi Kobayashi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Hinako Takehisa
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Nobukazu Namiki
- Genome Informatics Department, Mitsubishi Space Software Co., Ltd., Takezono 1-6-1, Tsukuba, Ibaraki 305-0032, Japan
| | - Yoshiaki Nagamura
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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98
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Wang D, Qin B, Li X, Tang D, Zhang Y, Cheng Z, Xue Y. Nucleolar DEAD-Box RNA Helicase TOGR1 Regulates Thermotolerant Growth as a Pre-rRNA Chaperone in Rice. PLoS Genet 2016; 12:e1005844. [PMID: 26848586 PMCID: PMC4743921 DOI: 10.1371/journal.pgen.1005844] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/13/2016] [Indexed: 11/18/2022] Open
Abstract
Plants have evolved a considerable number of intrinsic tolerance strategies to acclimate to ambient temperature increase. However, their molecular mechanisms remain largely obscure. Here we report a DEAD-box RNA helicase, TOGR1 (Thermotolerant Growth Required1), prerequisite for rice growth themotolerance. Regulated by both temperature and the circadian clock, its expression is tightly coupled to daily temperature fluctuations and its helicase activities directly promoted by temperature increase. Located in the nucleolus and associated with the small subunit (SSU) pre-rRNA processome, TOGR1 maintains a normal rRNA homeostasis at high temperature. Natural variation in its transcript level is positively correlated with plant height and its overexpression significantly improves rice growth under hot conditions. Our findings reveal a novel molecular mechanism of RNA helicase as a key chaperone for rRNA homeostasis required for rice thermotolerant growth and provide a potential strategy to breed heat-tolerant crops by modulating the expression of TOGR1 and its orthologs. Global warming is increasingly posing negative impacts on crop productivity. In this study, we report a nucleolar-located RNA helicase TOGR1 for thermotolerant growth in rice. TOGR1 maintains pre-rRNA homeostasis under high temperature by securing a proper pre-rRNA structure via elevating its helicase activity. Its expression is high temperature inducible with an afternoon peak expression, consistent with a high temperature anticipation of the circadian clock. Transcriptome analysis revealed that TOGR1 is essential in coordinating primary metabolisms to support thermotolerant growth. Importantly, an enhanced expression of TOGR1 significantly increased biomass of rice. Our findings reveal a novel role of a RNA helicase in thermotolerance and provide a potential strategy to breed heat-tolerant rice cultivars and possibly other heat-tolerant crops.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Baoxiang Qin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Xiang Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Yu’e Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Yongbiao Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Regulatory role of FZP in the determination of panicle branching and spikelet formation in rice. Sci Rep 2016; 6:19022. [PMID: 26744119 PMCID: PMC4705600 DOI: 10.1038/srep19022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/02/2015] [Indexed: 11/22/2022] Open
Abstract
FRIZZLE PANICLE (FZP) and RFL/ABERRANT PANICLE ORGANIZATION 2 (APO2) play important roles in regulating the ABCDE floral organ identity genes. However, the relationships among FZP and these floral identity genes in the regulation of panicle formation remain unclear. Here, we used the novel mutant fzp-11, wild-type and FZP-overexpressing plants to compare the expression of these genes during panicle development by real-time PCR and in situ hybridization. The results indicate that FZP is a major negative regulator of RFL/APO2 and determines the transition from panicle branching to spikelet formation. Moreover, overexpression of FZP severely represses axillary meristem formation in both the vegetative and reproductive phases and the outgrowth of secondary branches in panicle. FZP overexpression positively regulates the expression of a subset of the class B genes, AGL6 genes (OsMADS6 and OsMADS17) as well as class E genes (OsMADS1, OsMADS7 and OsMADS8) in floral meristem (FM). Thus, it suggested that FZP could specify floral organ identity by regulating the related OsMADS-box genes.
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Wei Y, Zeng H, Hu W, Chen L, He C, Shi H. Comparative Transcriptional Profiling of Melatonin Synthesis and Catabolic Genes Indicates the Possible Role of Melatonin in Developmental and Stress Responses in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:676. [PMID: 27242875 PMCID: PMC4870392 DOI: 10.3389/fpls.2016.00676] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/02/2016] [Indexed: 05/17/2023]
Abstract
As a well-known animal hormone, melatonin (N-acetyl-5-methoxytryptamine) is also involved in multiple plant biological processes, especially in various stress responses. Rice is one of the most important crops, and melatonin is taken in by many people everyday from rice. However, the transcriptional profiling of melatonin-related genes in rice is largely unknown. In this study, the expression patterns of 11 melatonin related genes in rice in different periods, tissues, in response to different treatments were synthetically analyzed using published microarray data. These results suggest that the melatonin-related genes may play important and dual roles in rice developmental stages. We highlight the commonly regulation of rice melatonin-related genes by abscisic acid (ABA), jasmonic acid (JA), various abiotic stresses and pathogen infection, indicating the possible role of these genes in multiple stress responses and underlying crosstalks of plant hormones, especially ABA and JA. Taken together, this study may provide insight into the association among melatonin biosynthesis and catabolic pathway, plant development and stress responses in rice. The profile analysis identified candidate genes for further functional characterization in circadian rhythm and specific stress responses.
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Affiliation(s)
- Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHaikou, China
| | - Hongqiu Zeng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHaikou, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Lanzhen Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural SciencesBeijing, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHaikou, China
- *Correspondence: Haitao Shi, ; Chaozu He,
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHaikou, China
- *Correspondence: Haitao Shi, ; Chaozu He,
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