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Ma X, Wang J, Su Z, Ma H. Developmentally dependent reprogramming of the Arabidopsis floral transcriptome under sufficient and limited water availability. BMC PLANT BIOLOGY 2024; 24:273. [PMID: 38605371 PMCID: PMC11007919 DOI: 10.1186/s12870-024-04916-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Environmental stresses negatively impact reproductive development and yield. Drought stress, in particular, has been examined during Arabidopsis reproductive development at morphological and transcriptomic levels. However, drought-responsive transcriptomic changes at different points in reproductive development remain unclear. Additionally, an investigation of the entire transcriptome at various stages during flower development is of great interest. RESULTS Here, we treat Arabidopsis plants with well-watered and moderately and severely limiting water amounts when the first flowers reach maturity and generate RNA-seq datasets for early, middle, and late phases during flower development at 5, 6, and 7 days following treatment. Under different drought conditions, flowers in different developmental phases display differential sets of drought-responsive genes (DTGs), including those that are enriched in different GO functional categories, such as transcriptional regulation and response to stresses (early phase), lipid storage (middle phase), and pollen and seed development and metabolic processes (late phase). Some gene families have different members induced at different floral phases, suggesting that similar biochemical functions are carried out by distinct members. Developmentally-regulated genes (DVGs) with differential expression among the three floral phases belong to GO terms that are similar between water conditions, such as development and reproduction, metabolism and transport, and signaling and stress response. However, for different water conditions, such similar GO terms correspond to either distinct gene families or different members of a gene family, suggesting that drought affects the expression of distinct families or family members during reproductive development. A further comparison among transcriptomes of tissues collected on different days after treatment identifies differential gene expression, suggesting age-related genes (ARGs) might reflect the changes in the overall plant physiology in addition to drought response and development. CONCLUSION Together, our study provides new insights into global transcriptome reprogramming and candidate genes for drought response, flower development, aging and coordination among these complex biological processes.
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Affiliation(s)
- Xinwei Ma
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jun Wang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Zhao Su
- Laboratory of Plant Stress and Development, College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hong Ma
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
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2
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Sinha R, Induri SP, Peláez-Vico MÁ, Tukuli A, Shostak B, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1064-1080. [PMID: 37006191 DOI: 10.1111/tpj.16222] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Global warming and climate change are driving an alarming increase in the frequency and intensity of extreme climate events, such as droughts, heat waves, and their combination, inflicting heavy losses to agricultural production. Recent studies revealed that the transcriptomic responses of different crops to water deficit (WD) or heat stress (HS) are very different from that to a combination of WD + HS. In addition, it was found that the effects of WD, HS, and WD + HS are significantly more devastating when these stresses occur during the reproductive growth phase of crops, compared to vegetative growth. As the molecular responses of different reproductive and vegetative tissues of plants to WD, HS, or WD + HS could be different from each other and these differences could impact many current and future attempts to enhance the resilience of crops to climate change through breeding and/or engineering, we conducted a transcriptomic analysis of different soybean (Glycine max) tissues to WD, HS, and WD + HS. Here we present a reference transcriptomic dataset that includes the response of soybean leaf, pod, anther, stigma, ovary, and sepal to WD, HS, and WD + HS conditions. Mining this dataset for the expression pattern of different stress response transcripts revealed that each tissue had a unique transcriptomic response to each of the different stress conditions. This finding is important as it suggests that enhancing the overall resilience of crops to climate change could require a coordinated approach that simultaneously alters the expression of different groups of transcripts in different tissues in a stress-specific manner.
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Affiliation(s)
- Ranjita Sinha
- Division of Plant Science and Technology, College of Agriculture Food and Natural Resources and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
| | - Sai Preethi Induri
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - María Ángeles Peláez-Vico
- Division of Plant Science and Technology, College of Agriculture Food and Natural Resources and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
| | - Adama Tukuli
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Benjamin Shostak
- Division of Plant Science and Technology, College of Agriculture Food and Natural Resources and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
| | - Sara I Zandalinas
- Department of Biology, Biochemistry and Environmental Sciences, University Jaume I, Av. de Vicent Sos Baynat, s/n, Castelló de la Plana, 12071, Spain
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
- Institute for Data Science and Informatics and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
- Department of Health Management and Informatics, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Felix B Fritschi
- Division of Plant Science and Technology, College of Agriculture Food and Natural Resources and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
| | - Ron Mittler
- Division of Plant Science and Technology, College of Agriculture Food and Natural Resources and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA
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Nagatoshi Y, Ikazaki K, Kobayashi Y, Mizuno N, Sugita R, Takebayashi Y, Kojima M, Sakakibara H, Kobayashi NI, Tanoi K, Fujii K, Baba J, Ogiso-Tanaka E, Ishimoto M, Yasui Y, Oya T, Fujita Y. Phosphate starvation response precedes abscisic acid response under progressive mild drought in plants. Nat Commun 2023; 14:5047. [PMID: 37598175 PMCID: PMC10439899 DOI: 10.1038/s41467-023-40773-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 08/09/2023] [Indexed: 08/21/2023] Open
Abstract
Drought severely damages crop production, even under conditions so mild that the leaves show no signs of wilting. However, it is unclear how field-grown plants respond to mild drought. Here, we show through six years of field trials that ridges are a useful experimental tool to mimic mild drought stress in the field. Mild drought reduces inorganic phosphate levels in the leaves to activate the phosphate starvation response (PSR) in soybean plants in the field. Using Arabidopsis thaliana and its mutant plants grown in pots under controlled environments, we demonstrate that PSR occurs before abscisic acid response under progressive mild drought and that PSR plays a crucial role in plant growth under mild drought. Our observations in the field and laboratory using model crop and experimental plants provide insight into the molecular response to mild drought in field-grown plants and the relationship between nutrition and drought stress response.
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Affiliation(s)
- Yukari Nagatoshi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Kenta Ikazaki
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki, 305-8686, Japan
| | - Yasufumi Kobayashi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Nobuyuki Mizuno
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, 305-8518, Japan
| | - Ryohei Sugita
- Radioisotope Research Center, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Natsuko I Kobayashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Kenichiro Fujii
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, 305-8604, Japan
| | - Junya Baba
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Eri Ogiso-Tanaka
- Institute of Crop Science, National Agricultuetre and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agricultuetre and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Tetsuji Oya
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki, 305-8686, Japan
| | - Yasunari Fujita
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan.
- Graduate School of Life Environmental Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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4
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Choudhary A, Senthil-Kumar M. Drought attenuates plant defence against bacterial pathogens by suppressing the expression of CBP60g/SARD1 during combined stress. PLANT, CELL & ENVIRONMENT 2022; 45:1127-1145. [PMID: 35102557 DOI: 10.1111/pce.14275] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
In nature, plants are frequently exposed to drought and bacterial pathogens simultaneously. However, information on how the drought and defence pathways interact and orchestrate global transcriptional regulation is limited. Here, we show that moderate drought stress enhances the susceptibility of Arabidopsis thaliana to Pseudomonas syringae pv. tomato DC3000. Using transcriptome meta-analysis, we found that drought and bacterial stress antagonistically modulate a large set of genes predominantly involved in salicylic acid (SA) and abscisic acid (ABA) signalling networks. We identified that the levels of SA and ABA are dynamically regulated during the course of stress. Importantly, under combined stress, drought through the ABA pathway downregulates the induction of Calmodulin-binding Protein 60 g (CBP60g) and Systemic Acquired Resistance Deficient 1 (SARD1), two transcription factors crucial for SA production upon bacterial infection. We also identified an important role of NPR1-LIKE PROTEIN 3 and 4 (NPR3/4) transcriptional repressors in the drought-mediated negative regulation of CBP60g/SARD1 expression. Using a genetic approach, we show that CBP60g/SARD1 expression is the key determinant of plant defence against bacterial pathogens under combined stress. Thus, these transcription factors act as critical nodes for the crosstalk between drought and bacterial stress signalling under combined stress in plants.
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Affiliation(s)
- Aanchal Choudhary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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5
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Terletskaya NV, Seitimova GA, Kudrina NO, Meduntseva ND, Ashimuly K. The Reactions of Photosynthetic Capacity and Plant Metabolites of Sedum hybridum L. in Response to Mild and Moderate Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060828. [PMID: 35336710 PMCID: PMC8955115 DOI: 10.3390/plants11060828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/26/2022] [Accepted: 03/06/2022] [Indexed: 05/17/2023]
Abstract
In this article, for the first time, an experimental study of the effect of mild and moderate osmotic stress, NaCl content and the effect of low positive temperature on photosynthetic activity and composition of metabolites of immature plants Sedum hybridum L. is reported. In this representative of the genus Sedum adapted to arid conditions and having the properties of a succulent, a change in photosynthetic activity and an increase in the level of protective metabolites in the shoots were revealed when exposed to mild and moderate stress factors. The results of this study can be used in work on the adaptation of succulent plants to arid conditions, environmental monitoring and work on the directed induction of valuable secondary metabolites in succulents to obtain new herbal medicines.
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Affiliation(s)
- Nina V. Terletskaya
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan
- Correspondence: (N.V.T.); (N.O.K.); Tel.: +7-(777)-2993-335 (N.V.T.); +7-(705)-1811-440 (N.O.K.)
| | - Gulnaz A. Seitimova
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan
| | - Nataliya O. Kudrina
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan
- Correspondence: (N.V.T.); (N.O.K.); Tel.: +7-(777)-2993-335 (N.V.T.); +7-(705)-1811-440 (N.O.K.)
| | - Nataliya D. Meduntseva
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
| | - Kazhybek Ashimuly
- Faculty of Biology and Biotechnology and Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan; (G.A.S.); (N.D.M.); (K.A.)
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan
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6
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Sinha R, Fritschi FB, Zandalinas SI, Mittler R. The impact of stress combination on reproductive processes in crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 311:111007. [PMID: 34482910 DOI: 10.1016/j.plantsci.2021.111007] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Historically, extended droughts combined with heat waves caused severe reductions in crop yields estimated at billions of dollars annually. Because global warming and climate change are driving an increase in the frequency and intensity of combined water-deficit and heat stress episodes, understanding how these episodes impact yield is critical for our efforts to develop climate change-resilient crops. Recent studies demonstrated that a combination of water-deficit and heat stress exacerbates the impacts of water-deficit or heat stress on reproductive processes of different cereals and legumes, directly impacting grain production. These studies identified several different mechanisms potentially underlying the effects of stress combination on anthers, pollen, and stigma development and function, as well as fertilization. Here we review some of these findings focusing on unbalanced reactive oxygen accumulation, altered sugar concentrations, and conflicting functions of different hormones, as contributing to the reduction in yield during a combination of water-deficit and heat stress. Future studies focused on the effects of water-deficit and heat stress combination on reproduction of different crops are likely to unravel additional mechanisms, as well as reveal novel ways to develop stress combination-resilient crops. These could mitigate some of the potentially devastating impacts of this stress combination on agriculture.
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Affiliation(s)
- Ranjita Sinha
- Division of Plant Sciences, College of Agriculture Food and Natural Resources, and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Felix B Fritschi
- Division of Plant Sciences, College of Agriculture Food and Natural Resources, and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Sara I Zandalinas
- Division of Plant Sciences, College of Agriculture Food and Natural Resources, and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Ron Mittler
- Division of Plant Sciences, College of Agriculture Food and Natural Resources, and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO, 65201, USA.
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7
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Leaf Age-Dependent Photosystem II Photochemistry and Oxidative Stress Responses to Drought Stress in Arabidopsis thaliana Are Modulated by Flavonoid Accumulation. Molecules 2021; 26:molecules26144157. [PMID: 34299433 PMCID: PMC8307756 DOI: 10.3390/molecules26144157] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 11/17/2022] Open
Abstract
We investigated flavonoid accumulation and lipid peroxidation in young leaves (YL) and mature leaves (ML) of Arabidopsis thaliana plants, whose watering stopped 24 h before sampling, characterized as onset of drought stress (OnDS), six days before sampling, characterized as mild drought stress (MiDS), and ten days before sampling, characterized as moderate drought stress (MoDS). The response to drought stress (DS) of photosystem II (PSII) photochemistry, in both leaf types, was evaluated by estimating the allocation of absorbed light to photochemistry (ΦPSII), to heat dissipation by regulated non-photochemical energy loss (ΦNPQ) and to non-regulated energy dissipated in PSII (ΦNO). Young leaves were better protected at MoDS than ML leaves, by having higher concentration of flavonoids that promote acclimation of YL PSII photochemistry to MoDS, showing lower lipid peroxidation and excitation pressure (1 - qp). Young leaves at MoDS possessed lower 1 - qp values and lower excess excitation energy (EXC), not only compared to MoDS ML, but even to MiDS YL. They also possessed a higher capacity to maintain low ΦNO, suggesting a lower singlet oxygen (1O2) generation. Our results highlight that leaves of different developmental stage may display different responses to DS, due to differential accumulation of metabolites, and imply that PSII photochemistry in Arabidopsis thaliana may not show a dose dependent DS response.
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8
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Chen Y, Dubois M, Vermeersch M, Inzé D, Vanhaeren H. Distinct cellular strategies determine sensitivity to mild drought of Arabidopsis natural accessions. PLANT PHYSIOLOGY 2021; 186:1171-1185. [PMID: 33693949 PMCID: PMC8195540 DOI: 10.1093/plphys/kiab115] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/14/2021] [Indexed: 05/18/2023]
Abstract
The worldwide distribution of Arabidopsis (Arabidopsis thaliana) accessions imposes different types of evolutionary pressures, which contributes to various responses of these accessions to environmental stresses. Responses to drought stress have mostly been studied in the Columbia accession, which is predominantly used in plant research. However, the reactions to drought stress are complex and our understanding of the responses that contribute to maintaining plant growth during mild drought (MD) is very limited. Here, we studied the mechanisms with which natural accessions react to MD at a physiological and molecular level during early leaf development. We documented variations in MD responses among natural accessions and used transcriptome sequencing of a drought-sensitive accession, ICE163, and a drought-insensitive accession, Yeg-1, to gain insights into the mechanisms underlying this discrepancy. This revealed that ICE163 preferentially induces jasmonate- and anthocyanin-related pathways, which are beneficial in biotic stress defense, whereas Yeg-1 has a more pronounced activation of abscisic acid signaling, the classical abiotic stress response. Related physiological traits, including the content of proline, anthocyanins, and reactive oxygen species, stomatal closure, and cellular leaf parameters, were investigated and linked to the transcriptional responses. We can conclude that most of these processes constitute general drought response mechanisms that are regulated similarly in drought-insensitive and -sensitive accessions. However, the capacity to close stomata and maintain cell expansion under MD appeared to be major factors that allow to better sustain leaf growth under MD.
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Affiliation(s)
- Ying Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Marieke Dubois
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Address for communication:
| | - Hannes Vanhaeren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
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Fernández Nevyl S, Battaglia ME. Developmental plasticity in Arabidopsis thaliana under combined cold and water deficit stresses during flowering stage. PLANTA 2021; 253:50. [PMID: 33506329 DOI: 10.1007/s00425-021-03575-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/19/2021] [Indexed: 05/02/2023]
Abstract
Morpho-physiological changes were observed in Arabidopsis plants acclimated to long-term combined cold and water deficit stresses. Limiting growth and differences in bolting, flowering, and silique development were evidenced. In nature, plants are exposed to multiple and simultaneous abiotic stresses that influence their growth, development, and reproduction. In the last years, the study of combined stresses has aroused the interest to know the physiological and molecular responses, because these new stress conditions are probed to be different from the sum of the individual stress. We are interested in the study of the acclimation of plants growing under the combination of cold and water deficit stresses prevalent in cold-arid or semi-arid climates worldwide. We hypothesized that the reproduction of the acclimated plants will be compromised and affected. Arabidopsis plants were submitted to long-term combined stress from the beginning to the reproductive stage, when floral bud was visible, until the silique development. Our results demonstrate severe morpho-anatomical changes after acclimation to combined stress. Inflorescence stem morphology was altered having a delayed bolting and a limited growth. Flowering and silique formation were delayed, and a higher size in the corolla and the petals was observed. Flower and silique number were severely diminished as a result of combined stress, unlike acclimated plants to individual cold stress. These traits were recovered after deacclimation to optimal conditions and plants achieved similar silique production as control plants. The long-term stress results suggest that there is not a single dominant stress, but there is an alternating dominance depending on the structure or the plant stage development evaluated.
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Affiliation(s)
- Solange Fernández Nevyl
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación Para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, 7600, Mar del Plata, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (FCEyN, UNMdP), Funes 3250, 7600, Mar del Plata, Argentina
| | - Marina E Battaglia
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación Para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, 7600, Mar del Plata, Argentina.
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Choudhary A, Senthil‐Kumar M. An efficient, high-throughput method for the simultaneous exposure of drought stress and bacterial infection in plants. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11399. [PMID: 33304662 PMCID: PMC7705336 DOI: 10.1002/aps3.11399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/11/2020] [Indexed: 06/12/2023]
Abstract
PREMISE We developed a systematic protocol for the easy, high-throughput, qualitative, and quantitative assessment of the patho-morphological, physiological, and molecular responses of Arabidopsis thaliana plants simultaneously subjected to drought and bacterial infection. This approach will assist studies elucidating plant adaptation strategies to combat combined stresses. METHODS AND RESULTS Plants were grown in small screw-capped containers, individual pots, or pot strips. Watering was withheld from 30-day-old plants, which were subsequently infected with Pseudomonas syringae pv. tomato DC3000 using a dip inoculation. The natural development of both drought and bacterial infection was successfully and rapidly replicated in large numbers of plants, which is difficult to achieve with existing protocols. CONCLUSIONS Our protocol offers a simple, low-cost, high-throughput strategy for the rapid and easy bacterial infection of large numbers of plants. It can be used in large-scale mutant and ecotype screenings under combined stresses and for other foliar pathogens in different plant species.
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Affiliation(s)
- Aanchal Choudhary
- National Institute of Plant Genome ResearchAruna Asaf Ali MargNew Delhi110067India
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11
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Lu J, Fu Y, Li M, Wang S, Wang J, Yang Q, Ye J, Zhang X, Ma H, Chang F. Global Quantitative Proteomics Studies Revealed Tissue-Preferential Expression and Phosphorylation of Regulatory Proteins in Arabidopsis. Int J Mol Sci 2020; 21:ijms21176116. [PMID: 32854314 PMCID: PMC7503369 DOI: 10.3390/ijms21176116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022] Open
Abstract
Organogenesis in plants occurs across all stages of the life cycle. Although previous studies have identified many genes as important for either vegetative or reproductive development at the RNA level, global information on translational and post-translational levels remains limited. In this study, six Arabidopsis stages/organs were analyzed using quantitative proteomics and phosphoproteomics, identifying 2187 non-redundant proteins and evidence for 1194 phosphoproteins. Compared to the expression observed in cauline leaves, the expression of 1445, 1644, and 1377 proteins showed greater than 1.5-fold alterations in stage 1–9 flowers, stage 10–12 flowers, and open flowers, respectively. Among these, 294 phosphoproteins with 472 phosphorylation sites were newly uncovered, including 275 phosphoproteins showing differential expression patterns, providing molecular markers and possible candidates for functional studies. Proteins encoded by genes preferentially expressed in anther (15), meiocyte (4), or pollen (15) were enriched in reproductive organs, and mutants of two anther-preferentially expressed proteins, acos5 and mee48, showed obviously reduced male fertility with abnormally organized pollen exine. In addition, more phosphorylated proteins were identified in reproductive stages (1149) than in the vegetative organs (995). The floral organ-preferential phosphorylation of GRP17, CDC2/CDKA.1, and ATSK11 was confirmed with western blot analysis. Moreover, phosphorylation levels of CDPK6 and MAPK6 and their interacting proteins were elevated in reproductive tissues. Overall, our study yielded extensive data on protein expression and phosphorylation at six stages/organs and provides an important resource for future studies investigating the regulatory mechanisms governing plant development.
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Affiliation(s)
- Jianan Lu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Ying Fu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Mengyu Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Shuangshuang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Jingya Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Qi Yang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Juanying Ye
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (H.M.); (F.C.); Tel.: +86-021-51630534 (H.M.); +1-814-865-5343 (F.C.)
| | - Fang Chang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; (J.L.); (Y.F.); (M.L.); (S.W.); (J.W.); (Q.Y.); (J.Y.); (X.Z.)
- Correspondence: (H.M.); (F.C.); Tel.: +86-021-51630534 (H.M.); +1-814-865-5343 (F.C.)
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12
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Ma X, Su Z, Ma H. Molecular genetic analyses of abiotic stress responses during plant reproductive development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2870-2885. [PMID: 32072177 PMCID: PMC7260722 DOI: 10.1093/jxb/eraa089] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/12/2020] [Indexed: 05/20/2023]
Abstract
Plant responses to abiotic stresses during vegetative growth have been extensively studied for many years. Daily environmental fluctuations can have dramatic effects on plant vegetative growth at multiple levels, resulting in molecular, cellular, physiological, and morphological changes. Plants are even more sensitive to environmental changes during reproductive stages. However, much less is known about how plants respond to abiotic stresses during reproduction. Fortunately, recent advances in this field have begun to provide clues about these important processes, which promise further understanding and a potential contribution to maximize crop yield under adverse environments. Here we summarize information from several plants, focusing on the possible mechanisms that plants use to cope with different types of abiotic stresses during reproductive development, and present a tentative molecular portrait of plant acclimation during reproductive stages. Additionally, we discuss strategies that plants use to balance between survival and productivity, with some comparison among different plants that have adapted to distinct environments.
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Affiliation(s)
- Xinwei Ma
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Zhao Su
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Correspondence:
| | - Hong Ma
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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13
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Dubois M, Inzé D. Plant growth under suboptimal water conditions: early responses and methods to study them. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1706-1722. [PMID: 31967643 DOI: 10.1093/jxb/eraa037] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 05/03/2023]
Abstract
Drought stress forms a major environmental constraint during the life cycle of plants, often decreasing plant yield and in extreme cases threatening survival. The molecular and physiological responses induced by drought have been the topic of extensive research during the past decades. Because soil-based approaches to studying drought responses are often challenging due to low throughput and insufficient control of the conditions, osmotic stress assays in plates were developed to mimic drought. Addition of compounds such as polyethylene glycol, mannitol, sorbitol, or NaCl to controlled growth media has become increasingly popular since it offers the advantage of accurate control of stress level and onset. These osmotic stress assays enabled the discovery of very early stress responses, occurring within seconds or minutes following osmotic stress exposure. In this review, we construct a detailed timeline of early responses to osmotic stress, with a focus on how they initiate plant growth arrest. We further discuss the specific responses triggered by different types and severities of osmotic stress. Finally, we compare short-term plant responses under osmotic stress versus in-soil drought and discuss the advantages, disadvantages, and future of these plate-based proxies for drought.
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Affiliation(s)
- Marieke Dubois
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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14
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Borghi M, Perez de Souza L, Yoshida T, Fernie AR. Flowers and climate change: a metabolic perspective. THE NEW PHYTOLOGIST 2019; 224:1425-1441. [PMID: 31257600 DOI: 10.1111/nph.16031] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 06/24/2019] [Indexed: 05/18/2023]
Abstract
Adverse climatic conditions at the time of flowering severely hinder crop yields and threaten the interactions between plants and their pollinators. These features depend on a common trait: the metabolism of flowers. In this Viewpoint article, we aim to provide insight into the metabolic changes that occur in flowers in response to changes in climate and emphasize that these changes severely impact the fitness of autogamous and allogamous species, plant-pollinator interactions, and overall ecosystem health. We review the biochemical processes that lead to failure of gamete development and to alterations of color, scent and nectar secretion. Then, making use of open access expression data, we examine the expression of genes that may drive these changes in response to heat and drought. Finally, we present measurements of metabolites from flowers exposed to a heat wave and discuss how the results of this short-term experiment may give rise to misleading conclusions regarding the positive effect of heat on flower fitness. We hope this article draws attention to this often-neglected dynamic and its important consequences.
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Affiliation(s)
- Monica Borghi
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | | | - Takuya Yoshida
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
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15
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Laxa M, Liebthal M, Telman W, Chibani K, Dietz KJ. The Role of the Plant Antioxidant System in Drought Tolerance. Antioxidants (Basel) 2019; 8:E94. [PMID: 30965652 PMCID: PMC6523806 DOI: 10.3390/antiox8040094] [Citation(s) in RCA: 247] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 03/30/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022] Open
Abstract
Water deficiency compromises plant performance and yield in many habitats and in agriculture. In addition to survival of the acute drought stress period which depends on plant-genotype-specific characteristics, stress intensity and duration, also the speed and efficiency of recovery determine plant performance. Drought-induced deregulation of metabolism enhances generation of reactive oxygen species (ROS) and reactive nitrogen species (RNS) which in turn affect the redox regulatory state of the cell. Strong correlative and analytical evidence assigns a major role in drought tolerance to the redox regulatory and antioxidant system. This review compiles current knowledge on the response and function of superoxide, hydrogen peroxide and nitric oxide under drought stress in various species and drought stress regimes. The meta-analysis of reported changes in transcript and protein amounts, and activities of components of the antioxidant and redox network support the tentative conclusion that drought tolerance is more tightly linked to up-regulated ascorbate-dependent antioxidant activity than to the response of the thiol-redox regulatory network. The significance of the antioxidant system in surviving severe phases of dehydration is further supported by the strong antioxidant system usually encountered in resurrection plants.
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Affiliation(s)
- Miriam Laxa
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, North Rhine Westphalia, Germany.
| | - Michael Liebthal
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, North Rhine Westphalia, Germany.
| | - Wilena Telman
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, North Rhine Westphalia, Germany.
| | - Kamel Chibani
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, North Rhine Westphalia, Germany.
| | - Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, North Rhine Westphalia, Germany.
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16
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Sukiran NL, Ma JC, Ma H, Su Z. ANAC019 is required for recovery of reproductive development under drought stress in Arabidopsis. PLANT MOLECULAR BIOLOGY 2019; 99:161-174. [PMID: 30604322 DOI: 10.1007/s11103-018-0810-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 12/10/2018] [Indexed: 05/02/2023]
Abstract
Morphological and transcriptomic evidences provide us strong support for the function of ANAC019 in reproductive development under drought stress. Plants are sensitive to drought conditions, particularly at the reproductive stage. Several studies have reported drought effects on crop reproductive development, but the molecular mechanism underlying drought response during reproduction is still unclear. A recent study showed that drought induces in Arabidopsis inflorescence increased expression of many genes, including ANAC019. However, the function of ANAC019 in drought response during reproductive development has not been characterized. Here, we report an investigation of the ANAC019 function in the response to drought during reproduction. ANAC019 is preferentially expressed in the inflorescence compared with the leaf, suggesting possible roles in regulating both stress response and flower development. The anac019 mutant was more sensitive to drought than WT plant, and exhibited a delay in recovery of floral organ development under prolonged drought stress. Moreover, many fewer genes were differentially expressed in the anac019 inflorescence under drought than that of WT, suggesting that the mutant was impaired in drought-induced gene expression. The genes affected by ANAC019 were associated with stress and hormone responses as well as floral development. In particular, the expression levels of several key drought-induced genes, DREB2A, DREB2B, ARF2, MYB21 and MYB24, were dramatically reduced in the absence of ANAC019, suggesting that ANAC019 is an upstream regulator these genes for drought response and flower development. These results provide strong support for the potential function of ANAC019 in reproductive development under drought stress.
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Affiliation(s)
- Noor Liyana Sukiran
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Center of Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Julia C Ma
- State College Area High School, State College, PA, 16801, USA
| | - Hong Ma
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Zhao Su
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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17
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Castelán-Muñoz N, Herrera J, Cajero-Sánchez W, Arrizubieta M, Trejo C, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. MADS-Box Genes Are Key Components of Genetic Regulatory Networks Involved in Abiotic Stress and Plastic Developmental Responses in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:853. [PMID: 31354752 PMCID: PMC6636334 DOI: 10.3389/fpls.2019.00853] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 06/13/2019] [Indexed: 05/05/2023]
Abstract
Plants, as sessile organisms, adapt to different stressful conditions, such as drought, salinity, extreme temperatures, and nutrient deficiency, via plastic developmental and growth responses. Depending on the intensity and the developmental phase in which it is imposed, a stress condition may lead to a broad range of responses at the morphological, physiological, biochemical, and molecular levels. Transcription factors are key components of regulatory networks that integrate environmental cues and concert responses at the cellular level, including those that imply a stressful condition. Despite the fact that several studies have started to identify various members of the MADS-box gene family as important molecular components involved in different types of stress responses, we still lack an integrated view of their role in these processes. In this review, we analyze the function and regulation of MADS-box gene family members in response to drought, salt, cold, heat, and oxidative stress conditions in different developmental processes of several plants. In addition, we suggest that MADS-box genes are key components of gene regulatory networks involved in plant responses to stress and plant developmental plasticity in response to seasonal changes in environmental conditions.
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Affiliation(s)
- Natalia Castelán-Muñoz
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Postgrado en Recursos Genéticos y Productividad-Fisiología Vegetal, Colegio de Postgraduados, Texcoco, Mexico
| | - Joel Herrera
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wendy Cajero-Sánchez
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Maite Arrizubieta
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Trejo
- Postgrado en Botánica, Colegio de Postgraduados, Texcoco, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Adriana Garay-Arroyo
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18
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Minh-Thu PT, Kim JS, Chae S, Jun KM, Lee GS, Kim DE, Cheong JJ, Song SI, Nahm BH, Kim YK. A WUSCHEL Homeobox Transcription Factor, OsWOX13, Enhances Drought Tolerance and Triggers Early Flowering in Rice. Mol Cells 2018; 41:781-798. [PMID: 30078233 PMCID: PMC6125423 DOI: 10.14348/molcells.2018.0203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 12/14/2022] Open
Abstract
Plants have evolved strategies to cope with drought stress by maximizing physiological capacity and adjusting developmental processes such as flowering time. The WOX13 orthologous group is the most conserved among the clade of WOX homeodomain-containing proteins and is found to function in both drought stress and flower development. In this study, we isolated and characterized OsWOX13 from rice. OsWOX13 was regulated spatially in vegetative organs but temporally in flowers and seeds. Overexpression of OsWOX13 (OsWOX13-ov) in rice under the rab21 promoter resulted in drought resistance and early flowering by 7-10 days. Screening of gene expression profiles in mature leaf and panicles of OsWOX13-ov showed a broad spectrum of effects on biological processes, such as abiotic and biotic stresses, exerting a cross-talk between responses. Protein binding microarray and electrophoretic mobility shift assay analyses supported ATTGATTG as the putative cis-element binding of OsWOX13. OsDREB1A and OsDREB1F, drought stress response transcription factors, contain ATTGATTG motif(s) in their promoters and are preferentially expressed in OsWOX13-ov. In addition, Heading date 3a and OsMADS14, regulators in the flowering pathway and development, were enhanced in OsWOX13-ov. These results suggest that OsWOX13 mediates the stress response and early flowering and, thus, may be a regulator of genes involved in drought escape.
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Affiliation(s)
- Pham-Thi Minh-Thu
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Joung Sug Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Songhwa Chae
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Kyong Mi Jun
- Genomics Genetics Institute, GreenGene Biotech Inc., Yongin 17058,
Korea
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54875,
Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029,
Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826,
Korea
| | - Sang Ik Song
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Baek Hie Nahm
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
- Genomics Genetics Institute, GreenGene Biotech Inc., Yongin 17058,
Korea
| | - Yeon-Ki Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
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19
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Dubois M, Selden K, Bediée A, Rolland G, Baumberger N, Noir S, Bach L, Lamy G, Granier C, Genschik P. SIAMESE-RELATED1 Is Regulated Posttranslationally and Participates in Repression of Leaf Growth under Moderate Drought. PLANT PHYSIOLOGY 2018; 176:2834-2850. [PMID: 29472278 PMCID: PMC5884595 DOI: 10.1104/pp.17.01712] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/10/2018] [Indexed: 05/06/2023]
Abstract
The plant cell cycle is tightly regulated by factors that integrate endogenous cues and environmental signals to adapt plant growth to changing conditions. Under drought, cell division in young leaves is blocked by an active mechanism, reducing the evaporative surface and conserving energy resources. The molecular function of cyclin-dependent kinase-inhibitory proteins (CKIs) in regulating the cell cycle has already been well studied, but little is known about their involvement in cell cycle regulation under adverse growth conditions. In this study, we show that the transcript of the CKI gene SIAMESE-RELATED1 (SMR1) is quickly induced under moderate drought in young Arabidopsis (Arabidopsis thaliana) leaves. Functional characterization further revealed that SMR1 inhibits cell division and affects meristem activity, thereby restricting the growth of leaves and roots. Moreover, we demonstrate that SMR1 is a short-lived protein that is degraded by the 26S proteasome after being ubiquitinated by a Cullin-RING E3 ubiquitin ligase. Consequently, overexpression of a more stable variant of the SMR1 protein leads to a much stronger phenotype than overexpression of the native SMR1. Under moderate drought, both the SMR1 transcript and SMR1 protein accumulate. Despite this induction, smr1 mutants do not show overall tolerance to drought stress but do show less growth inhibition of young leaves under drought. Surprisingly, the growth-repressive hormone ethylene promotes SMR1 induction, but the classical drought hormone abscisic acid does not.
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Affiliation(s)
- Marieke Dubois
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Katia Selden
- Biochimie et Physiologie Moléculaire des Plantes, Université de Montpellier, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Alexis Bediée
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Université de Montpellier, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Gaëlle Rolland
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Université de Montpellier, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Nicolas Baumberger
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Sandra Noir
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Lien Bach
- Biochimie et Physiologie Moléculaire des Plantes, Université de Montpellier, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Geneviève Lamy
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Christine Granier
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Université de Montpellier, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
- Biochimie et Physiologie Moléculaire des Plantes, Université de Montpellier, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
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20
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Abraham PE, Garcia BJ, Gunter LE, Jawdy SS, Engle N, Yang X, Jacobson DA, Hettich RL, Tuskan GA, Tschaplinski TJ. Quantitative proteome profile of water deficit stress responses in eastern cottonwood (Populus deltoides) leaves. PLoS One 2018; 13:e0190019. [PMID: 29447168 PMCID: PMC5813909 DOI: 10.1371/journal.pone.0190019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/06/2017] [Indexed: 12/26/2022] Open
Abstract
Drought stress is a recurring feature of world climate and the single most important factor influencing agricultural yield worldwide. Plants display highly variable, species-specific responses to drought and these responses are multifaceted, requiring physiological and morphological changes influenced by genetic and molecular mechanisms. Moreover, the reproducibility of water deficit studies is very cumbersome, which significantly impedes research on drought tolerance, because how a plant responds is highly influenced by the timing, duration, and intensity of the water deficit. Despite progress in the identification of drought-related mechanisms in many plants, the molecular basis of drought resistance remains to be fully understood in trees, particularly in poplar species because their wide geographic distribution results in varying tolerances to drought. Herein, we aimed to better understand this complex phenomenon in eastern cottonwood (Populus deltoides) by performing a detailed contrast of the proteome changes between two different water deficit experiments to identify functional intersections and divergences in proteome responses. We investigated plants subjected to cyclic water deficit and compared these responses to plants subjected to prolonged acute water deficit. In total, we identified 108,012 peptide sequences across both experiments that provided insight into the quantitative state of 22,737 Populus gene models and 8,199 functional protein groups in response to drought. Together, these datasets provide the most comprehensive insight into proteome drought responses in poplar to date and a direct proteome comparison between short period dehydration shock and cyclic, post-drought re-watering. Overall, this investigation provides novel insights into drought avoidance mechanisms that are distinct from progressive drought stress. Additionally, we identified proteins that have been associated as drought-relevant in previous studies. Importantly, we highlight the RD26 transcription factor as a gene regulated at both the transcript and protein level, regardless of species and drought condition, and, thus, represents a key, universal drought marker for Populus species.
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Affiliation(s)
- Paul E. Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Benjamin J. Garcia
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Lee E. Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Sara S. Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Nancy Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Daniel A. Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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21
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Coutinho ID, Moraes TB, Mertz-Henning LM, Nepomuceno AL, Giordani W, Marcolino-Gomes J, Santagneli S, Colnago LA. Integrating High-Resolution and Solid-State Magic Angle Spinning NMR Spectroscopy and a Transcriptomic Analysis of Soybean Tissues in Response to Water Deficiency. PHYTOCHEMICAL ANALYSIS : PCA 2017; 28:529-540. [PMID: 28722224 DOI: 10.1002/pca.2702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 05/18/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Solid-state NMR (SSNMR) spectroscopy methods provide chemical environment and ultrastructural details that are not easily accessible by other non-destructive, high-resolution spectral techniques. High-resolution magic angle spinning (HR-MAS) has been widely used to obtain the metabolic profile of a heterogeneous sample, combining the resolution enhancement provided by MAS in SSNMR with the shimming and locking procedures in liquid-state NMR. OBJECTIVE In this work, we explored the feasibility of using the HR-MAS and SSNMR techniques to identify metabolic changes in soybean leaves subjected to water-deficient conditions. METHODOLOGY Control and water-deficient soybean leaves were analysed using one-dimensional (1D) HR-MAS and SSNMR. Total RNA was extracted from the leaves for the transcriptomic analysis. RESULTS The 1 H HR-MAS and CP-MAS 13 C{1 H} spectra of soybean leaves grown with and without water deficiency stress revealed striking differences in metabolites. A total of 30 metabolites were identified, and the impact of water deficiency on the metabolite profile of soybean leaves was to induce amino acid synthesis. High expression levels of genes required for amino acid biosynthesis were highly correlated with the compounds identified by 1 H HR-MAS. CONCLUSIONS The integration of the 1 H HR-MAS and SSNMR spectra with the transcriptomic data provided a complete picture of the major changes in the metabolic profile of soybeans in response to water deficiency. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Isabel D Coutinho
- Embrapa Instrumentação, XV de Novembro, 1452, Centro, 13560-970, São Carlos, São Carlos, Brazil
| | - Tiago Bueno Moraes
- Embrapa Instrumentação, XV de Novembro, 1452, Centro, 13560-970, São Carlos, São Carlos, Brazil
| | | | | | - Willian Giordani
- Londrina State University, Rodovia Celso Garcia Cid, Km 380, 86051-900, Londrina, Paraná, Brazil
| | - Juliana Marcolino-Gomes
- Embrapa Soja, Rodovia Carlos João Strass, Distrito de Warta, 86001-970, Londrina, Paraná, Brazil
| | - Silvia Santagneli
- Institute of Chemistry, University of São Paulo State, Rua Prof. Francisco Degni, 55, 14800-060, Araraquara, São Paulo, Brazil
| | - Luiz Alberto Colnago
- Embrapa Soja, Rodovia Carlos João Strass, Distrito de Warta, 86001-970, Londrina, Paraná, Brazil
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22
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Campbell LG, Shukla K, Sneck ME, Chaplin C, Mercer KL. The Effect of Altered Soil Moisture on Hybridization Rate in a Crop-Wild System (Raphanus spp.). PLoS One 2016; 11:e0166802. [PMID: 27936159 PMCID: PMC5147839 DOI: 10.1371/journal.pone.0166802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/03/2016] [Indexed: 11/18/2022] Open
Abstract
Since plant mating choices are flexible and responsive to the environment, rates of spontaneous hybridization may vary across ecological clines. Developing a robust and predictive framework for rates of plant gene flow requires assessing the role of environmental sensitivity on plant reproductive traits, relative abundance, and pollen vectors. Therefore, across a soil moisture gradient, we quantified pollinator movement, life-history trait variation, and unidirectional hybridization rates from crop (Raphanus sativus) to wild (Raphanus raphanistrum) radish populations. Both radish species were grown together in relatively dry (no rain), relatively wet (double rain), or control soil moisture conditions in Ohio, USA. We measured wild and crop radish life-history, phenology and pollinator visitation patterns. To quantify hybridization rates from crop-to-wild species, we used a simply inherited morphological marker to detect F1 hybrid progeny. Although crop-to-wild hybridization did not respond to watering treatments, the abundance of hybrid offspring was higher in fruits produced late in the period of phenological overlap, when both species had roughly equal numbers of open flowers. Therefore, the timing of fruit production and its relationship to flowering overlap may be more important to hybrid zone formation in Raphanus spp. than soil moisture or pollen vector movements.
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Affiliation(s)
- Lesley G. Campbell
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Kruti Shukla
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Michelle E. Sneck
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Colleen Chaplin
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Kristin L. Mercer
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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23
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Smith AR, Zhao D. Sterility Caused by Floral Organ Degeneration and Abiotic Stresses in Arabidopsis and Cereal Grains. FRONTIERS IN PLANT SCIENCE 2016; 7:1503. [PMID: 27790226 PMCID: PMC5064672 DOI: 10.3389/fpls.2016.01503] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 09/21/2016] [Indexed: 05/18/2023]
Abstract
Natural floral organ degeneration or abortion results in unisexual or fully sterile flowers, while abiotic stresses lead to sterility after initiation of floral reproductive organs. Since normal flower development is essential for plant sexual reproduction and crop yield, it is imperative to have a better understanding of plant sterility under regular and stress conditions. Here, we review the functions of ABC genes together with their downstream genes in floral organ degeneration and the formation of unisexual flowers in Arabidopsis and several agriculturally significant cereal grains. We further explore the roles of hormones, including auxin, brassinosteroids, jasmonic acid, gibberellic acid, and ethylene, in floral organ formation and fertility. We show that alterations in genes affecting hormone biosynthesis, hormone transport and perception cause loss of stamens/carpels, abnormal floral organ development, poor pollen production, which consequently result in unisexual flowers and male/female sterility. Moreover, abiotic stresses, such as heat, cold, and drought, commonly affect floral organ development and fertility. Sterility is induced by abiotic stresses mostly in male floral organ development, particularly during meiosis, tapetum development, anthesis, dehiscence, and fertilization. A variety of genes including those involved in heat shock, hormone signaling, cold tolerance, metabolisms of starch and sucrose, meiosis, and tapetum development are essential for plants to maintain normal fertility under abiotic stress conditions. Further elucidation of cellular, biochemical, and molecular mechanisms about regulation of fertility will improve yield and quality for many agriculturally valuable crops.
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Affiliation(s)
| | - Dazhong Zhao
- Department of Biological Sciences, University of Wisconsin-Milwaukee, MilwaukeeWI, USA
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24
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Gray SB, Brady SM. Plant developmental responses to climate change. Dev Biol 2016; 419:64-77. [PMID: 27521050 DOI: 10.1016/j.ydbio.2016.07.023] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/30/2016] [Accepted: 07/31/2016] [Indexed: 02/02/2023]
Abstract
Climate change is multi-faceted, and includes changing concentrations of greenhouse gases in the atmosphere, rising temperatures, changes in precipitation patterns, and increasing frequency of extreme weather events. Here, we focus on the effects of rising atmospheric CO2 concentrations, rising temperature, and drought stress and their interaction on plant developmental processes in leaves, roots, and in reproductive structures. While in some cases these responses are conserved across species, such as decreased root elongation, perturbation of root growth angle and reduced seed yield in response to drought, or an increase in root biomass in shallow soil in response to elevated CO2, most responses are variable within and between species and are dependent on developmental stage. These variable responses include species-specific thresholds that arrest development of reproductive structures, reduce root growth rate and the rate of leaf initiation and expansion in response to elevated temperature. Leaf developmental responses to elevated CO2 vary by cell type and by species. Variability also exists between C3 and C4 species in response to elevated CO2, especially in terms of growth and seed yield stimulation. At the molecular level, significantly less is understood regarding conservation and variability in molecular mechanisms underlying these traits. Abscisic acid-mediated changes in cell wall expansion likely underlie reductions in growth rate in response to drought, and changes in known regulators of flowering time likely underlie altered reproductive transitions in response to elevated temperature and CO2. Genes that underlie most other organ or tissue-level responses have largely only been identified in a single species in response to a single stress and their level of conservation is unknown. We conclude that there is a need for further research regarding the molecular mechanisms of plant developmental responses to climate change factors in general, and that this lack of data is particularly prevalent in the case of interactive effects of multiple climate change factors. As future growing conditions will likely expose plants to multiple climate change factors simultaneously, with a sum negative influence on global agriculture, further research in this area is critical.
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Affiliation(s)
- Sharon B Gray
- Department of Plant Biology, University of California, Davis, 2243 Life Sciences Addition, One Shields Avenue, Davis, CA 95616, USA.
| | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, 2243 Life Sciences Addition, One Shields Avenue, Davis, CA 95616, USA; Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.
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25
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Das A, Eldakak M, Paudel B, Kim DW, Hemmati H, Basu C, Rohila JS. Leaf Proteome Analysis Reveals Prospective Drought and Heat Stress Response Mechanisms in Soybean. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6021047. [PMID: 27034942 PMCID: PMC4808539 DOI: 10.1155/2016/6021047] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/01/2016] [Indexed: 12/26/2022]
Abstract
Drought and heat are among the major abiotic stresses that affect soybean crops worldwide. During the current investigation, the effect of drought, heat, and drought plus heat stresses was compared in the leaves of two soybean varieties, Surge and Davison, combining 2D-DIGE proteomic data with physiology and biochemical analyses. We demonstrated how 25 differentially expressed photosynthesis-related proteins affect RuBisCO regulation, electron transport, Calvin cycle, and carbon fixation during drought and heat stress. We also observed higher abundance of heat stress-induced EF-Tu protein in Surge. It is possible that EF-Tu might have activated heat tolerance mechanisms in the soybean. Higher level expressions of heat shock-related protein seem to be regulating the heat tolerance mechanisms. This study identifies the differential expression of various abiotic stress-responsive proteins that regulate various molecular processes and signaling cascades. One inevitable outcome from the biochemical and proteomics assays of this study is that increase of ROS levels during drought stress does not show significant changes at the phenotypic level in Davison and this seems to be due to a higher amount of carbonic anhydrase accumulation in the cell which aids the cell to become more resistant to cytotoxic concentrations of H2O2.
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Affiliation(s)
- Aayudh Das
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD 57007, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840, USA
| | - Moustafa Eldakak
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Bimal Paudel
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Dea-Wook Kim
- National Institute of Crop Science, Rural Development Administration (RDA), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Homa Hemmati
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
| | - Chhandak Basu
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
| | - Jai S. Rohila
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD 57007, USA
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26
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Bechtold U, Penfold CA, Jenkins DJ, Legaie R, Moore JD, Lawson T, Matthews JSA, Vialet-Chabrand SRM, Baxter L, Subramaniam S, Hickman R, Florance H, Sambles C, Salmon DL, Feil R, Bowden L, Hill C, Baker NR, Lunn JE, Finkenstädt B, Mead A, Buchanan-Wollaston V, Beynon J, Rand DA, Wild DL, Denby KJ, Ott S, Smirnoff N, Mullineaux PM. Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis. THE PLANT CELL 2016; 28:345-66. [PMID: 26842464 PMCID: PMC4790877 DOI: 10.1105/tpc.15.00910] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/14/2016] [Accepted: 02/02/2016] [Indexed: 05/18/2023]
Abstract
In Arabidopsis thaliana, changes in metabolism and gene expression drive increased drought tolerance and initiate diverse drought avoidance and escape responses. To address regulatory processes that link these responses, we set out to identify genes that govern early responses to drought. To do this, a high-resolution time series transcriptomics data set was produced, coupled with detailed physiological and metabolic analyses of plants subjected to a slow transition from well-watered to drought conditions. A total of 1815 drought-responsive differentially expressed genes were identified. The early changes in gene expression coincided with a drop in carbon assimilation, and only in the late stages with an increase in foliar abscisic acid content. To identify gene regulatory networks (GRNs) mediating the transition between the early and late stages of drought, we used Bayesian network modeling of differentially expressed transcription factor (TF) genes. This approach identified AGAMOUS-LIKE22 (AGL22), as key hub gene in a TF GRN. It has previously been shown that AGL22 is involved in the transition from vegetative state to flowering but here we show that AGL22 expression influences steady state photosynthetic rates and lifetime water use. This suggests that AGL22 uniquely regulates a transcriptional network during drought stress, linking changes in primary metabolism and the initiation of stress responses.
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Affiliation(s)
- Ulrike Bechtold
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | | | - Dafyd J Jenkins
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Roxane Legaie
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jonathan D Moore
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tracy Lawson
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Jack S A Matthews
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | | | - Laura Baxter
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sunitha Subramaniam
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Richard Hickman
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Hannah Florance
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Christine Sambles
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Deborah L Salmon
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Laura Bowden
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Claire Hill
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Neil R Baker
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Bärbel Finkenstädt
- Department of Statistics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew Mead
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vicky Buchanan-Wollaston
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jim Beynon
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David A Rand
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David L Wild
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Katherine J Denby
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sascha Ott
- Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Nicholas Smirnoff
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Philip M Mullineaux
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
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27
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DuanMu H, Wang Y, Bai X, Cheng S, Deyholos MK, Wong GKS, Li D, Zhu D, Li R, Yu Y, Cao L, Chen C, Zhu Y. Wild soybean roots depend on specific transcription factors and oxidation reduction related genesin response to alkaline stress. Funct Integr Genomics 2015; 15:651-60. [PMID: 25874911 DOI: 10.1007/s10142-015-0439-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 03/21/2015] [Accepted: 04/06/2015] [Indexed: 01/08/2023]
Abstract
Soil alkalinity is an important environmental problem limiting agricultural productivity. Wild soybean (Glycine soja) shows strong alkaline stress tolerance, so it is an ideal plant candidate for studying the molecular mechanisms of alkaline tolerance and identifying alkaline stress-responsive genes. However, limited information is available about G. soja responses to alkaline stress on a genomic scale. Therefore, in the present study, we used RNA sequencing to compare transcript profiles of G. soja root responses to sodium bicarbonate (NaHCO3) at six time points, and a total of 68,138,478 pairs of clean reads were obtained using the Illumina GAIIX. Expression patterns of 46,404 G. soja genes were profiled in all six samples based on RNA-seq data using Cufflinks software. Then, t12 transcription factors from MYB, WRKY, NAC, bZIP, C2H2, HB, and TIFY families and 12 oxidation reduction related genes were chosen and verified to be induced in response to alkaline stress by using quantitative real-time polymerase chain reaction (qRT-PCR). The GO functional annotation analysis showed that besides "transcriptional regulation" and "oxidation reduction," these genes were involved in a variety of processes, such as "binding" and "response to stress." This is the first comprehensive transcriptome profiling analysis of wild soybean root under alkaline stress by RNA sequencing. Our results highlight changes in the gene expression patterns and identify a set of genes induced by NaHCO3 stress. These findings provide a base for the global analyses of G. soja alkaline stress tolerance mechanisms.
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Affiliation(s)
- Huizi DuanMu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Wang
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Xi Bai
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Shufei Cheng
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, T6G2E9, Canada
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, T6G2E9, Canada
| | - Dan Li
- BGI-Shenzen, Shenzhen, 518083, China
| | - Dan Zhu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Ran Li
- BGI-Shenzen, Shenzhen, 518083, China
| | - Yang Yu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Lei Cao
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Chao Chen
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Yanming Zhu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
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28
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Krannich CT, Maletzki L, Kurowsky C, Horn R. Network Candidate Genes in Breeding for Drought Tolerant Crops. Int J Mol Sci 2015; 16:16378-400. [PMID: 26193269 PMCID: PMC4519955 DOI: 10.3390/ijms160716378] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 01/09/2023] Open
Abstract
Climate change leading to increased periods of low water availability as well as increasing demands for food in the coming years makes breeding for drought tolerant crops a high priority. Plants have developed diverse strategies and mechanisms to survive drought stress. However, most of these represent drought escape or avoidance strategies like early flowering or low stomatal conductance that are not applicable in breeding for crops with high yields under drought conditions. Even though a great deal of research is ongoing, especially in cereals, in this regard, not all mechanisms involved in drought tolerance are yet understood. The identification of candidate genes for drought tolerance that have a high potential to be used for breeding drought tolerant crops represents a challenge. Breeding for drought tolerant crops has to focus on acceptable yields under water-limited conditions and not on survival. However, as more and more knowledge about the complex networks and the cross talk during drought is available, more options are revealed. In addition, it has to be considered that conditioning a crop for drought tolerance might require the production of metabolites and might cost the plants energy and resources that cannot be used in terms of yield. Recent research indicates that yield penalty exists and efficient breeding for drought tolerant crops with acceptable yields under well-watered and drought conditions might require uncoupling yield penalty from drought tolerance.
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Affiliation(s)
- Christoph Tim Krannich
- Institute of Biological Sciences, Department of Plant Genetics, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany.
| | - Lisa Maletzki
- Institute of Biological Sciences, Department of Plant Genetics, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany.
| | - Christina Kurowsky
- Institute of Biological Sciences, Department of Plant Genetics, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany.
| | - Renate Horn
- Institute of Biological Sciences, Department of Plant Genetics, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany.
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29
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Pushpavalli R, Krishnamurthy L, Thudi M, Gaur PM, Rao MV, Siddique KHM, Colmer TD, Turner NC, Varshney RK, Vadez V. Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines. BMC PLANT BIOLOGY 2015; 15:124. [PMID: 25994494 PMCID: PMC4440540 DOI: 10.1186/s12870-015-0491-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/09/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although chickpea (Cicer arietinum L.), an important food legume crop, is sensitive to salinity, considerable variation for salinity tolerance exists in the germplasm. To improve any existing cultivar, it is important to understand the genetic and physiological mechanisms underlying this tolerance. RESULTS In the present study, 188 recombinant inbred lines (RILs) derived from the cross ICCV 2 × JG 11 were used to assess yield and related traits in a soil with 0 mM NaCl (control) and 80 mM NaCl (salinity) over two consecutive years. Salinity significantly (P < 0.05) affected almost all traits across years and yield reduction was in large part related to a reduction in seed number but also a reduction in above ground biomass. A genetic map was constructed using 56 polymorphic markers (28 simple sequence repeats; SSRs and 28 single nucleotide polymorphisms; SNPs). The QTL analysis revealed two key genomic regions on CaLG05 (28.6 cM) and on CaLG07 (19.4 cM), that harboured QTLs for six and five different salinity tolerance associated traits, respectively, and imparting either higher plant vigour (on CaLG05) or higher reproductive success (on CaLG07). Two major QTLs for yield in the salinity treatment (explaining 12 and 17% of the phenotypic variation) were identified within the two key genomic regions. Comparison with already published chickpea genetic maps showed that these regions conferred salinity tolerance across two other populations and the markers can be deployed for enhancing salinity tolerance in chickpea. Based on the gene ontology annotation, forty eight putative candidate genes responsive to salinity stress were found on CaLG05 (31 genes) and CaLG07 (17 genes) in a distance of 11.1 Mb and 8.2 Mb on chickpea reference genome. Most of the genes were known to be involved in achieving osmoregulation under stress conditions. CONCLUSION Identification of putative candidate genes further strengthens the idea of using CaLG05 and CaLG07 genomic regions for marker assisted breeding (MAB). Further fine mapping of these key genomic regions may lead to novel gene identification for salinity stress tolerance in chickpea.
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Affiliation(s)
- Raju Pushpavalli
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
- Department of Plant Science, Bharathidasan University, 620024, Tiruchirappalli, Tamil Nadu, India.
| | - Laxmanan Krishnamurthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
| | - Mandali V Rao
- Department of Plant Science, Bharathidasan University, 620024, Tiruchirappalli, Tamil Nadu, India.
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, 6009, Crawley, WA, Australia.
| | - Timothy D Colmer
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, 6009, , Crawley, WA, Australia.
| | - Neil C Turner
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, 6009, Crawley, WA, Australia.
- Centre for Plant Genetics and Breeding, M080, The University of Western Australia, 35 Stirling Highway, 6009, Crawley, WA, Australia.
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, 6009, , Crawley, WA, Australia.
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
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Yang C, Wei H. Designing microarray and RNA-Seq experiments for greater systems biology discovery in modern plant genomics. MOLECULAR PLANT 2015; 8:196-206. [PMID: 25680773 DOI: 10.1016/j.molp.2014.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/31/2014] [Accepted: 11/02/2014] [Indexed: 05/07/2023]
Abstract
Microarray and RNA-seq experiments have become an important part of modern genomics and systems biology. Obtaining meaningful biological data from these experiments is an arduous task that demands close attention to many details. Negligence at any step can lead to gene expression data containing inadequate or composite information that is recalcitrant for pattern extraction. Therefore, it is imperative to carefully consider experimental design before launching a time-consuming and costly experiment. Contemporarily, most genomics experiments have two objectives: (1) to generate two or more groups of comparable data for identifying differentially expressed genes, gene families, biological processes, or metabolic pathways under experimental conditions; (2) to build local gene regulatory networks and identify hierarchically important regulators governing biological processes and pathways of interest. Since the first objective aims to identify the active molecular identities and the second provides a basis for understanding the underlying molecular mechanisms through inferring causality relationships mediated by treatment, an optimal experiment is to produce biologically relevant and extractable data to meet both objectives without substantially increasing the cost. This review discusses the major issues that researchers commonly face when embarking on microarray or RNA-seq experiments and summarizes important aspects of experimental design, which aim to help researchers deliberate how to generate gene expression profiles with low background noise but with more interaction to facilitate novel biological discoveries in modern plant genomics.
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Affiliation(s)
- Chuanping Yang
- State Key Laboratory of Forest Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Hairong Wei
- State Key Laboratory of Forest Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China; Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
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