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Voothuluru P, Wu Y, Sharp RE. Not so hidden anymore: Advances and challenges in understanding root growth under water deficits. THE PLANT CELL 2024; 36:1377-1409. [PMID: 38382086 PMCID: PMC11062450 DOI: 10.1093/plcell/koae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Limited water availability is a major environmental factor constraining plant development and crop yields. One of the prominent adaptations of plants to water deficits is the maintenance of root growth that enables sustained access to soil water. Despite early recognition of the adaptive significance of root growth maintenance under water deficits, progress in understanding has been hampered by the inherent complexity of root systems and their interactions with the soil environment. We highlight selected milestones in the understanding of root growth responses to water deficits, with emphasis on founding studies that have shaped current knowledge and set the stage for further investigation. We revisit the concept of integrated biophysical and metabolic regulation of plant growth and use this framework to review central growth-regulatory processes occurring within root growth zones under water stress at subcellular to organ scales. Key topics include the primary processes of modifications of cell wall-yielding properties and osmotic adjustment, as well as regulatory roles of abscisic acid and its interactions with other hormones. We include consideration of long-recognized responses for which detailed mechanistic understanding has been elusive until recently, for example hydrotropism, and identify gaps in knowledge, ongoing challenges, and opportunities for future research.
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Affiliation(s)
- Priya Voothuluru
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | - Yajun Wu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Robert E Sharp
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
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2
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Kalra A, Goel S, Elias AA. Understanding role of roots in plant response to drought: Way forward to climate-resilient crops. THE PLANT GENOME 2024; 17:e20395. [PMID: 37853948 DOI: 10.1002/tpg2.20395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/26/2023] [Accepted: 09/18/2023] [Indexed: 10/20/2023]
Abstract
Drought stress leads to a significant amount of agricultural crop loss. Thus, with changing climatic conditions, it is important to develop resilience measures in agricultural systems against drought stress. Roots play a crucial role in regulating plant development under drought stress. In this review, we have summarized the studies on the role of roots and root-mediated plant responses. We have also discussed the importance of root system architecture (RSA) and the various structural and anatomical changes that it undergoes to increase survival and productivity under drought. Various genes, transcription factors, and quantitative trait loci involved in regulating root growth and development are also discussed. A summarization of various instruments and software that can be used for high-throughput phenotyping in the field is also provided in this review. More comprehensive studies are required to help build a detailed understanding of RSA and associated traits for breeding drought-resilient cultivars.
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Affiliation(s)
- Anmol Kalra
- Department of Botany, University of Delhi, North Campus, Delhi, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, North Campus, Delhi, India
| | - Ani A Elias
- ICFRE - Institute of Forest Genetics and Tree Breeding (ICFRE - IFGTB), Coimbatore, India
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3
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Xia K, Wu Q, Yang Y, Liu Q, Wang Z, Zhao Z, Li J, He J, Chai S, Qiu S. Drought Stress Induced Different Response Mechanisms in Three Dendrobium Species under Different Photosynthetic Pathways. Int J Mol Sci 2024; 25:2731. [PMID: 38473979 DOI: 10.3390/ijms25052731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/16/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
Many Dendrobium species, which hold a high status and value in traditional Chinese medicine, grow on barks and rocks in the wild, often encountering harsh environments and facing droughts. However, the molecular mechanisms underlying the shift in the photosynthetic pathway induced by drought remain unclear. To address this issue, three Dendrobium species with different photosynthetic pathways were selected for sequencing and transcriptome data analysis after drought treatment. The findings included 134.43 GB of sequencing data, with numerous Differentially Expressed Genes (DEGs) exhibiting different response mechanisms under drought stress. Gene Ontology (GO)-KEGG-based enrichment analysis of DEGs revealed that metabolic pathways contributed to drought tolerance and alterations in photosynthetic pathways. Phosphoenolpyruvate Carboxylase (PEPC) was subjected to phylogenetic tree construction, sequence alignment, and domain analysis. Under drought stress, variations were observed in the PEPC gene structure and expression among different Dendrobium species; the upregulation of Dc_gene2609 expression may be caused by dof-miR-384, which resulted in the shift from C3 photosynthesis to CAM, thereby improving drought tolerance in Dendrobium. This study revealed the expression patterns and roles of PEPC genes in enhancing plant drought tolerance and will provide an important basis for in-depth research on Dendrobium's adaptation mechanisms in arid environments.
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Affiliation(s)
- Ke Xia
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Qiaofen Wu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Yanni Yang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Qiao Liu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Zaihua Wang
- Guangdong Provincial Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhiguo Zhao
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jinxiang He
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Shengfeng Chai
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Shuo Qiu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
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4
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Klaus A, Marcon C, Hochholdinger F. Spatiotemporal transcriptomic plasticity in barley roots: unravelling water deficit responses in distinct root zones. BMC Genomics 2024; 25:79. [PMID: 38243200 PMCID: PMC10799489 DOI: 10.1186/s12864-024-10002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Drought poses a major threat to agricultural production and thus food security. Understanding the processes shaping plant responses to water deficit is essential for global food safety. Though many studies examined the effect of water deficit on the whole-root level, the distinct functions of each root zone and their specific stress responses remain masked by this approach. RESULTS In this study, we investigated the effect of water deficit on root development of the spring barley (Hordeum vulgare L.) cultivar Morex and examined transcriptomic responses at the level of longitudinal root zones. Water deficit significantly reduced root growth rates after two days of treatment. RNA-sequencing revealed root zone and temporal gene expression changes depending on the duration of water deficit treatment. The majority of water deficit-regulated genes were unique for their respective root zone-by-treatment combination, though they were associated with commonly enriched gene ontology terms. Among these, we found terms associated with transport, detoxification, or cell wall formation affected by water deficit. Integration of weighted gene co-expression analyses identified differential hub genes, that highlighted the importance of modulating energy and protein metabolism and stress response. CONCLUSION Our findings provide new insights into the highly dynamic and spatiotemporal response cascade triggered by water deficit and the underlying genetic regulations on the level of root zones in the barley cultivar Morex, providing potential targets to enhance plant resilience against environmental constraints. This study further emphasizes the importance of considering spatial and temporal resolution when examining stress responses.
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Affiliation(s)
- Alina Klaus
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Caroline Marcon
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany.
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Sharma N, Raman H, Wheeler D, Kalenahalli Y, Sharma R. Data-driven approaches to improve water-use efficiency and drought resistance in crop plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111852. [PMID: 37659733 DOI: 10.1016/j.plantsci.2023.111852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
With the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits.
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Affiliation(s)
- Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia.
| | - Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia
| | - Yogendra Kalenahalli
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324, India
| | - Rita Sharma
- Department of Biological Sciences, BITS Pilani, Pilani Campus, Rajasthan 333031, India
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Wang R, Zhang Z, Wang H, Chen Y, Zhang M. Soil Water Deficit Reduced Root Hydraulic Conductivity of Common Reed ( Phragmites australis). PLANTS (BASEL, SWITZERLAND) 2023; 12:3543. [PMID: 37896007 PMCID: PMC10610267 DOI: 10.3390/plants12203543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023]
Abstract
Alterations in root hydraulics in response to varying moisture conditions remain a subject of debate. In our investigation, we subjected common reeds (Phragmites australis) to a 45-day treatment with four distinct soil moisture levels. The findings unveiled that, in response to drought stress, the total root length, surface area, volume, and average diameter exhibited varying degrees of reduction. Anatomically, drought caused a reduction in root diameter (RD), cortex thickness (CT), vessel diameter (VD), and root cross-sectional area (RCA). A decrease in soil moisture significantly reduced both whole- and single-root hydraulic conductivity (Lpwr, Lpsr). The total length, surface area, volume, and average diameter of the reed root system were significantly correlated with Lpwr, while RD, CT, and RCA were significantly correlated with Lpsr. A decrease in soil moisture content significantly influenced root morphological and anatomical characteristics, which, in turn, altered Lpr, and the transcriptome results suggest that this may be associated with the variation in the expression of abscisic acid (ABA) and aquaporins (AQPs) genes. Our initial findings address a gap in our understanding of reed hydraulics, offering fresh theoretical insights into how herbaceous plants respond to external stressors.
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Affiliation(s)
- Ruiqing Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (R.W.); (H.W.)
- The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing 100083, China
- Wetland Research Centre, Beijing Forestry University, Beijing 100083, China
| | - Zhenming Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (R.W.); (H.W.)
- The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing 100083, China
- Wetland Research Centre, Beijing Forestry University, Beijing 100083, China
| | - Haoyue Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (R.W.); (H.W.)
- The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing 100083, China
- Wetland Research Centre, Beijing Forestry University, Beijing 100083, China
| | - Yinglong Chen
- The UWA Institute of Agriculture, School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia;
| | - Mingxiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (R.W.); (H.W.)
- The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing 100083, China
- State Key Laboratory of Efficient Production of Forest Resources, Beijing 100083, China
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7
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Yang Z, Cao Y, Shi Y, Qin F, Jiang C, Yang S. Genetic and molecular exploration of maize environmental stress resilience: Toward sustainable agriculture. MOLECULAR PLANT 2023; 16:1496-1517. [PMID: 37464740 DOI: 10.1016/j.molp.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/03/2023] [Accepted: 07/15/2023] [Indexed: 07/20/2023]
Abstract
Global climate change exacerbates the effects of environmental stressors, such as drought, flooding, extreme temperatures, salinity, and alkalinity, on crop growth and grain yield, threatening the sustainability of the food supply. Maize (Zea mays) is one of the most widely cultivated crops and the most abundant grain crop in production worldwide. However, the stability of maize yield is highly dependent on environmental conditions. Recently, great progress has been made in understanding the molecular mechanisms underlying maize responses to environmental stresses and in developing stress-resilient varieties due to advances in high-throughput sequencing technologies, multi-omics analysis platforms, and automated phenotyping facilities. In this review, we summarize recent advances in dissecting the genetic factors and networks that contribute to maize abiotic stress tolerance through diverse strategies. We also discuss future challenges and opportunities for the development of climate-resilient maize varieties.
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Affiliation(s)
- Zhirui Yang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yibo Cao
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiting Shi
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Caifu Jiang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Shuhua Yang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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8
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Murphy KM, Dowd T, Khalil A, Char SN, Yang B, Endelman BJ, Shih PM, Topp C, Schmelz EA, Zerbe P. A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize. PLANT PHYSIOLOGY 2023; 192:1338-1358. [PMID: 36896653 PMCID: PMC10231366 DOI: 10.1093/plphys/kiad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 06/01/2023]
Abstract
Two major groups of specialized metabolites in maize (Zea mays), termed kauralexins and dolabralexins, serve as known or predicted diterpenoid defenses against pathogens, herbivores, and other environmental stressors. To consider the physiological roles of the recently discovered dolabralexin pathway, we examined dolabralexin structural diversity, tissue-specificity, and stress-elicited production in a defined biosynthetic pathway mutant. Metabolomics analyses support a larger number of dolabralexin pathway products than previously known. We identified dolabradienol as a previously undetected pathway metabolite and characterized its enzymatic production. Transcript and metabolite profiling showed that dolabralexin biosynthesis and accumulation predominantly occur in primary roots and show quantitative variation across genetically diverse inbred lines. Generation and analysis of CRISPR-Cas9-derived loss-of-function Kaurene Synthase-Like 4 (Zmksl4) mutants demonstrated dolabralexin production deficiency, thus supporting ZmKSL4 as the diterpene synthase responsible for the conversion of geranylgeranyl pyrophosphate precursors into dolabradiene and downstream pathway products. Zmksl4 mutants further display altered root-to-shoot ratios and root architecture in response to water deficit. Collectively, these results demonstrate dolabralexin biosynthesis via ZmKSL4 as a committed pathway node biochemically separating kauralexin and dolabralexin metabolism, and suggest an interactive role of maize dolabralexins in plant vigor during abiotic stress.
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Affiliation(s)
- Katherine M Murphy
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
| | - Tyler Dowd
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Ahmed Khalil
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Si Nian Char
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Bing Yang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Benjamin J Endelman
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
| | - Patrick M Shih
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720, USA
| | | | - Eric A Schmelz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
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9
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Liu L, Liu S, Lu H, Tian Z, Zhao H, Wei D, Wang S, Huang Z. Integration of transcriptome and metabolome analyses reveals key lodging-resistance-related genes and metabolic pathways in maize. Front Genet 2022; 13:1001195. [PMID: 36299597 PMCID: PMC9588961 DOI: 10.3389/fgene.2022.1001195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Stalk lodging, or breakage of the stalk at or below the ear, is one of the vital factors causing substantial yield losses in maize (Zea mays. L). Lodging affects maize plants’ physiological and molecular processes, eventually impacting plant growth and productivity. Despite this known fact, few researchers have investigated the genetic architecture underlying lodging in maize. Herein, through integrated transcriptome, metabolome, and phenotypic analyses of stalks of three diverse hybrid cultivars (highly resistant JNK738, mildly resistant JNK728, and lowly resistant XY335) at the tasseling (10 days to silking, 10 DTS) stage, we identified key genes and metabolic pathways modulating lodging resistance in maize. Based on the RNA-Seq analysis, a total of 10093 differentially expressed genes (DEGs) were identified from the comparison of the three varieties in pairs. Additionally, key lodging resistance–related metabolic pathways were obtained by KEGG enrichment analysis, and the DEGs were found predominantly enriched in phenylpropanoid and secondary metabolites biosynthesis pathways in the L_vs._H and M_vs._H comparison groups. Moreover, K-means analysis clustered the DEGs into clear and distinct expression profiles for each cultivar, with several functional and regulatory genes involved in the cell wall assembly, lignin biosynthetic process and hormone metabolic process being identified in the special clusters related to lodging resistance. Subsequently, integrating metabolome and transcriptome analyses revealed nine key lignin-associated metabolites that showed different expression trends in the three hybrid cultivars, among which L-phenylalanine and p-coumaric acid were regarded as differentially changed metabolites (DCMs). These two DCMs belonged to phenylalanine metabolism and biosynthesis pathways and were also supported by the RNA-Seq data. Furthermore, plant hormone signal transduction pathway–related genes encoding auxin, abscisic acid, jasmonates, and salicylic acid were differentially expressed in the three comparisons of lodging resistance, indicating these DEGs were valuable potential targets for improving maize lodging resistance. Finally, comparative physiological and qRT-PCR analyses results supported our transcriptome-based findings. Our research not only provides a preliminary theoretical basis and experimental ideas for an in-depth study of the regulatory networks involved in maize lodging resistance regulation but also opens up new avenues for molecular maize stalk lodging resistance breeding.
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Affiliation(s)
- Lei Liu
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Songtao Liu
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Haibo Lu
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Zaimin Tian
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Haichao Zhao
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Dong Wei
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Shuo Wang
- School of Medicine, Nankai University, Tianjin, China
| | - Zhihong Huang
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
- *Correspondence: Zhihong Huang,
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10
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Yang B, Fu P, Lu J, Ma F, Sun X, Fang Y. Regulated deficit irrigation: an effective way to solve the shortage of agricultural water for horticulture. STRESS BIOLOGY 2022; 2:28. [PMID: 37676363 PMCID: PMC10441918 DOI: 10.1007/s44154-022-00050-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/06/2022] [Indexed: 09/08/2023]
Abstract
The deficient agricultural water caused by water shortage is a crucial limiting factor of horticultural production. Among many agricultural water-saving technologies, regulated deficit irrigation (RDI) has been proven to be one of the effective technologies to improve water use efficiency and reduce water waste on the premise of maintaining the quality of agricultural products. RDI was first reported more than 40 years ago, although it has been applied in some areas, little is known about understanding of the implementation method, scope of application and detailed mechanism of RDI, resulting in the failure to achieve the effect that RDI should have. This review refers to the research on RDI in different crops published in recent years, summarizes the definition, equipment condition, function, theory illumination, plant response and application in different crops of RDI, and looks forward to its prospect. We expect that this review will provide valuable guidance for researchers and producers concerned, and support the promotion of RDI in more horticultural crops.
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Affiliation(s)
- Bohan Yang
- College of Enology, Shaanxi Provincial Key Laboratory of Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-viniculture Station, Ningxia Eastern Foot of Helan Mountain Wine Station, Northwest A&F University, Yangling, 712100, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peining Fu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiang Lu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China.
| | - Xiangyu Sun
- College of Enology, Shaanxi Provincial Key Laboratory of Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-viniculture Station, Ningxia Eastern Foot of Helan Mountain Wine Station, Northwest A&F University, Yangling, 712100, China.
| | - Yulin Fang
- College of Enology, Shaanxi Provincial Key Laboratory of Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-viniculture Station, Ningxia Eastern Foot of Helan Mountain Wine Station, Northwest A&F University, Yangling, 712100, China.
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11
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Zhang Z, Jatana BS, Campbell BJ, Gill J, Suseela V, Tharayil N. Cross-inoculation of rhizobiome from a congeneric ruderal plant imparts drought tolerance in maize (Zea mays) through changes in root morphology and proteome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:54-71. [PMID: 35426964 PMCID: PMC9542220 DOI: 10.1111/tpj.15775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Rhizobiome confer stress tolerance to ruderal plants, yet their ability to alleviate stress in crops is widely debated, and the associated mechanisms are poorly understood. We monitored the drought tolerance of maize (Zea mays) as influenced by the cross-inoculation of rhizobiota from a congeneric ruderal grass Andropogon virginicus (andropogon-inoculum), and rhizobiota from organic farm maintained under mesic condition (organic-inoculum). Across drought treatments (40% field capacity), maize that received andropogon-inoculum produced two-fold greater biomass. This drought tolerance translated to a similar leaf metabolomic composition as that of the well-watered control (80% field capacity) and reduced oxidative damage, despite a lower activity of antioxidant enzymes. At a morphological-level, drought tolerance was associated with an increase in specific root length and surface area facilitated by the homeostasis of phytohormones promoting root branching. At a proteome-level, the drought tolerance was associated with upregulation of proteins related to glutathione metabolism and endoplasmic reticulum-associated degradation process. Fungal taxa belonging to Ascomycota, Mortierellomycota, Archaeorhizomycetes, Dothideomycetes, and Agaricomycetes in andropogon-inoculum were identified as potential indicators of drought tolerance. Our study provides a mechanistic understanding of the rhizobiome-facilitated drought tolerance and demonstrates a better path to utilize plant-rhizobiome associations to enhance drought tolerance in crops.
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Affiliation(s)
- Ziliang Zhang
- Department of Plant & Environmental SciencesClemson UniversityClemsonSCUSA
| | | | | | - Jasmine Gill
- Department of Plant & Environmental SciencesClemson UniversityClemsonSCUSA
| | - Vidya Suseela
- Department of Plant & Environmental SciencesClemson UniversityClemsonSCUSA
| | - Nishanth Tharayil
- Department of Plant & Environmental SciencesClemson UniversityClemsonSCUSA
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12
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Identifying Signal-Crosstalk Mechanism in Maize Plants during Combined Salinity and Boron Stress Using Integrative Systems Biology Approaches. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1027288. [PMID: 35505877 PMCID: PMC9057046 DOI: 10.1155/2022/1027288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/19/2022] [Indexed: 01/04/2023]
Abstract
Combined stress has been seen as a major threat to world agriculture production. Maize is one of the leading cereal crops of the world due to its wide spectrum of growth conditions and is moderately sensitive to salt stress. A saline soil environment is a major factor that hinders its growth and overall yield and causes an increase in the concentration of micronutrients like boron, leading to excess over the requirement of the plant. Boron toxicity combined with salinity has been reported to be a serious threat to the yield and quality of maize. The response signatures of the maize plants to the combined effect of salinity and boron stress have not been studied well. We carried out an integrative systems-level analysis of the publicly available transcriptomic data generated on tolerant maize (Lluteño maize from the Atacama Desert, Chile) landrace under combined salt and boron stress. We identified significant biological processes that are differentially regulated in combined salt and boron stress in the leaves and roots of maize, respectively. Protein-protein interaction network analysis identified important roles of aldehyde dehydrogenase (ALDH), galactinol synthase 2 (GOLS2) proteins of leaf and proteolipid membrane potential regulator (pmpm4), metallothionein lea protein group 3 (mlg3), and cold regulated 410 (COR410) proteins of root in salt tolerance and regulating boron toxicity in maize. Identification of transcription factors coupled with regulatory network analysis using machine learning approach identified a few heat shock factors (HSFs) and NAC (NAM (no apical meristem, Petunia), ATAF1–2 (Arabidopsis thaliana activating factor), and CUC2 (cup-shaped cotyledon, Arabidopsis)) family transcription factors (TFs) to play crucial roles in salt tolerance, maintaining reactive oxygen species (ROS) levels and minimizing oxidative damage to the cells. These findings will provide new ways to design targeted functional validation experiments for developing multistress-resistant maize crops.
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13
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Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing. Int J Mol Sci 2022; 23:ijms23073840. [PMID: 35409200 PMCID: PMC8998571 DOI: 10.3390/ijms23073840] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
In this study, we characterized the gene expression profile in the roots of Populus ussuriensis at 0, 6, 12, 24, 48 and 120 h after the start of polyethylene glycol (PEG)-induced drought stress using PacBio single-molecule real-time sequencing (SMRT-seq) and Illumina RNA sequencing. Compared to the control, 2244 differentially expressed genes (DEGs) were identified, and many of these DEGs were associated with the signal transduction, antioxidant system, ion accumulation and drought-inducing proteins. Changes in certain physiological and biochemical indexes, such as antioxidant activity and the contents of Ca2+, proline, and total soluble sugars, were further confirmed in P. ussuriensis roots. Furthermore, most of the differentially expressed transcription factors were members of the AP2/ERF, C2H2, MYB, NAC, C2C2 and WRKY families. Additionally, based on PacBio SMRT-seq results, 5955 long non-coding RNAs and 700 alternative splicing events were identified. Our results provide a global view of the gene expression profile that contributes to drought resistance in P. ussuriensis and meaningful information for genetic engineering research in the future.
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14
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Tas T, Mutlu A. Morpho-physiological effects of environmental stress on yield and quality of sweet corn varieties (Zea mays L.). PeerJ 2021; 9:e12613. [PMID: 35003926 PMCID: PMC8684323 DOI: 10.7717/peerj.12613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/18/2021] [Indexed: 11/20/2022] Open
Abstract
Sweet corn is cultivated in different climatic regions of the world, and consumed either fresh or processed. Morpho-physiological effects of environmental stress on yield, yield components and quality of some sweet corn varieties were investigated in field experiments conducted at Southeastern Anatolia Region of Turkey during 2019 and 2020 growing seasons. The experimental lay out was randomized blocks with three replicates. Eight candidates and two control sweet corn varieties classified as moderate maturity (FAO 650–700) were used in field experiment. Mean values of pollen fertility rate (PFR, %), total soluble solids (TSS, °Brix), abscisic acid (ABA, nmol/g DW), ear length (EL, cm), plant height (PH, cm), number of grains per cob (CGN, grain) and fresh cob yield (FCY, t ha−1) were significantly different between years and sweet corn varieties. The PFR, TSS, ABA, EL, PH, CGN and FCY ranged from 40.29–67.65%, 13.24–20.09 °brix, 7.74–21.04 nmol/g DW, 9.69–15.98 cm, 97.80–171.34 cm, 289.15–420.33 grain and 4.15–10.23 t ha−1 respectively. The FCY, yield components and PFR values in the second year that had a higher temperature and lower relative humidity were lower compared to the first year, while ABA and TSS values were higher in the second year. Statistically significant correlations were recorded between the parameters investigated except FCY and TSS. The FCY and other parameters of sweet corn varieties, which produced high ABA phytohormone, were high, and the ABA hormone significantly contributed to plant growth under stress conditions. The results revealed that the PFR physiological parameter and ABA hormone in the plants provide important information about stress level and stress tolerance level of the cultivars, respectively. Despite adverse environmental stress conditions, the FCY of ŞADA-18.7 variety, one of the candidate varieties, was higher than that of the control and the mean value of the experiment.
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Affiliation(s)
- Timucin Tas
- Kepsut Vocational High School, Balikesir University, Balikesir, Marmara Region, Turkey
| | - Arzu Mutlu
- Akcakale Vocational High School, Harran University, Sanliurfa, Turkey
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15
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Ortiz-Ramírez C, Guillotin B, Xu X, Rahni R, Zhang S, Yan Z, Coqueiro Dias Araujo P, Demesa-Arevalo E, Lee L, Van Eck J, Gingeras TR, Jackson D, Gallagher KL, Birnbaum KD. Ground tissue circuitry regulates organ complexity in maize and Setaria. Science 2021; 374:1247-1252. [PMID: 34855479 DOI: 10.1126/science.abj2327] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Carlos Ortiz-Ramírez
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.,UGA Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Guanajuato 36821, México
| | - Bruno Guillotin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Xiaosa Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ramin Rahni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Sanqiang Zhang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Zhe Yan
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 1904, USA
| | | | | | - Laura Lee
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kimberly L Gallagher
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 1904, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
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16
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Santos TDO, do Amaral Junior AT, Bispo RB, de Lima VJ, Kamphorst SH, Leite JT, dos Santos Júnior DR, Santos PHAD, de Oliveira UA, Schmitt KFM, Campostrini E, Moulin MM, Viana AP, Gravina GDA, Corrêa CCG, Gonçalves GMB. Phenotyping Latin American Open-Pollinated Varieties of Popcorn for Environments with Low Water Availability. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10061211. [PMID: 34203591 PMCID: PMC8232228 DOI: 10.3390/plants10061211] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 06/12/2023]
Abstract
Drought is a common abiotic stress in tropical and subtropical regions that limits the growth and development of agricultural crops, mainly impacting grain yield. Acting through plant breeding is the most viable alternative for obtaining genotypes more tolerant of environments with stress. This work aims to select popcorn genotypes for environments with drought and to identify discriminating traits for the evaluation of drought tolerance in popcorn germplasm. Fifteen Latin American populations of popcorn were evaluated in water stress (WS) and well-watered (WW) conditions. The evaluated traits were based in morpho-agronomic, physiological and radicular descriptors. Data were submitted to individual and joint ANOVA and GT Biplot analysis. Variability was detected between populations for all traits in both conditions. The drought caused a reduction of 30.61% and 3.5% in grain yield and popping expansion, respectively. Based in GT biplot analysis, 880POP was the most stable in WS and WW, being indicated as a promising population for cultivation in environments with water limitation. This study is going to allow the establishment of a collection of great importance to maize germplasm and to provide information to facilitate the process of selection in breeding programs focused on drought tolerance.
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Affiliation(s)
- Talles de Oliveira Santos
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Antônio Teixeira do Amaral Junior
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Rosimeire Barboza Bispo
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Valter Jário de Lima
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Samuel Henrique Kamphorst
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Jhean Torres Leite
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Divino Rosa dos Santos Júnior
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Pedro Henrique Araújo Diniz Santos
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Uéliton Alves de Oliveira
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Kátia Fabiane Medeiros Schmitt
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Eliemar Campostrini
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Monique Moreira Moulin
- Laboratory of Genetics and Molecular Biology, Instituto Federal do Espírito Santo—Campus de Alegre (IFES), Alegre 29500-000, ES, Brazil;
| | - Alexandre Pio Viana
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Geraldo de Amaral Gravina
- Laboratory of Agricultural Engineering, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil;
| | - Caio Cezar Guedes Corrêa
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
| | - Gabriel Moreno Bernardo Gonçalves
- Laboratory of Genetics and Plant Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (R.B.B.); (V.J.d.L.); (S.H.K.); (J.T.L.); (D.R.d.S.J.); (P.H.A.D.S.); (U.A.d.O.); (K.F.M.S.); (E.C.); (A.P.V.); (C.C.G.C.); (G.M.B.G.)
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17
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Integration of QTL, Transcriptome and Polymorphism Studies Reveals Candidate Genes for Water Stress Response in Tomato. Genes (Basel) 2020; 11:genes11080900. [PMID: 32784535 PMCID: PMC7465520 DOI: 10.3390/genes11080900] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 11/22/2022] Open
Abstract
Water deficit (WD) leads to significant phenotypic changes in crops resulting from complex stress regulation mechanisms involving responses at the physiological, biochemical and molecular levels. Tomato growth and fruit quality have been shown to be significantly affected by WD stress. Understanding the molecular mechanism underlying response to WD is crucial to develop tomato cultivars with relatively high performance under low watering conditions. Transcriptome response to WD was investigated through the RNA sequencing of fruit and leaves in eight accessions grown under two irrigation conditions, in order to get insight into the complex genetic regulation of WD response in tomato. Significant differences in genotype WD response were first observed at the phenotypic level for fruit composition and plant development traits. At the transcriptome level, a total of 14,065 differentially expressed genes (DEGs) in response to WD were detected, among which 7393 (53%) and 11,059 (79%) were genotype- and organ-specific, respectively. Water deficit induced transcriptome variations much stronger in leaves than in fruit. A significant effect of the genetic background on expression variation was observed compared to the WD effect, along with the presence of a set of genes showing a significant genotype × watering regime interaction. Integrating the DEGs with previously identified WD response quantitative trait loci (QTLs) mapped in a multi-parental population derived from the crossing of the eight genotypes narrowed the candidate gene lists to within the confidence intervals surrounding the QTLs. The results present valuable resources for further study to decipher the genetic determinants of tomato response to WD.
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18
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Liu G, Zenda T, Liu S, Wang X, Jin H, Dong A, Yang Y, Duan H. Comparative transcriptomic and physiological analyses of contrasting hybrid cultivars ND476 and ZX978 identify important differentially expressed genes and pathways regulating drought stress tolerance in maize. Genes Genomics 2020; 42:937-955. [PMID: 32623576 DOI: 10.1007/s13258-020-00962-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/21/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Drought is the major abiotic stress factor that negatively influences growth and yield in cereal grain crops such as maize (Zea mays L.). A multitude of genes and pathways tightly modulate plant growth, development and responses to environmental stresses including drought. Therefore, crop breeding efforts for enhanced drought resistance require improved knowledge of plant drought responses. OBJECTIVE Here, we sought to elucidate the molecular and physiological mechanisms underpinning maize drought stress tolerance. METHODS We therefore applied a 12-day water-deficit stress treatment to maize plants of two contrasting (drought tolerant ND476 and drought sensitive ZX978) hybrid cultivars at the late vegetative (V12) growth stage and performed a large-scale RNA sequencing (RNA-seq) transcriptome analysis of the leaf tissues. RESULTS A comparative analysis of the two genotypes leaf transcriptomes and physiological parameters revealed the key differentially expressed genes (DEGs) and metabolic pathways that respond to drought in a genotype-specific manner. A total of 3114 DEGs were identified, with 21 DEGs being specifically expressed in tolerant genotype ND476 in response to drought stress. Of these, genes involved in secondary metabolites biosynthesis, transcription factor regulation, detoxification and stress defense were highly expressed in ND476. Physiological analysis results substantiated our RNA-seq data, with ND476 exhibiting better cell water retention, higher soluble protein content and guaiacol peroxidase activity, along with low lipid peroxidation extent than the sensitive cultivar ZX978 under drought conditions. CONCLUSION Our findings enrich the maize genetic resources and enhance our further understanding of the molecular mechanisms regulating drought stress tolerance in maize. Additionally, the DEGs screened in this study may provide a foundational basis for our future targeted cloning studies.
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Affiliation(s)
- Guo Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Xuan Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Hongyu Jin
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Anyi Dong
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Yatong Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China. .,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China.
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19
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Zhang Q, Liu H, Wu X, Wang W. Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses. BMC PLANT BIOLOGY 2020; 20:315. [PMID: 32620139 PMCID: PMC7350183 DOI: 10.1186/s12870-020-02526-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/25/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Frequently occurring drought stress negatively affects the production of maize worldwide. Numerous efforts have been made to develop drought-tolerant maize lines and to explore drought tolerant mechanisms in maize. However, there is a lack of comparative studies on transcriptomic changes between drought-tolerant and control maize lines. RESULTS In the present study, we have developed a drought-tolerant maize mutant (C7-2t) by irradiating the seeds of maize inbred line ChangC7-2 (C7-2) with 60Co-γ. Compared to its wild type C7-2, C7-2t exhibited a significantly delayed wilting and higher drought tolerance under both the controlled and field conditions, indicating its high water-holding ability. Transcriptomic profiling was performed to identify differentially expressed genes (DEGs) between C7-2 and C7-2t during drought. As a result, a total of 4552 DEGs were implied in drought tolerance of C7-2 and C7-2t. In particular, the expression of photosynthesis-related genes in C7-2 was inhibited, whereas these genes in C7-2t were almost unaffected under drought. Moreover, a specific set of the DEGs were involved in phenylpropanoid biosynthesis and taurine (hypotaurine) metabolism in C7-2t; these DEGs were enriched in cell components associated with membrane systems and cell wall biosynthesis. CONCLUSIONS The drought tolerance of C7-2t was largely due to its high water-holding ability, stable photosynthesis (for supporting osmoregulation) and strengthened biosynthesis of cell walls under drought conditions.
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Affiliation(s)
- Qinbin Zhang
- College of Life Sciences, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Hui Liu
- College of Life Sciences, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Xiaolin Wu
- College of Life Sciences, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- College of Life Sciences, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China.
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20
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Dwivedi SL, Stoddard FL, Ortiz R. Genomic-based root plasticity to enhance abiotic stress adaptation and edible yield in grain crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 295:110365. [PMID: 32534611 DOI: 10.1016/j.plantsci.2019.110365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/15/2019] [Accepted: 12/01/2019] [Indexed: 06/11/2023]
Abstract
Phenotypic plasticity refers to changes expressed by a genotype across different environments and is one of the major means by which plants cope with environmental variability. Multi-fold differences in phenotypic plasticity have been noted across crops, with wild ancestors and landraces being more plastic than crops when under stress. Plasticity in response to abiotic stress adaptation, plant architecture, physio-reproductive and quality traits are multi-genic (QTL). Plasticity QTL (pQTL) were either collocated with main effect QTL and QEI (QTL × environment interaction) or located independently from the main effect QTL. For example, variations in root plasticity have been successfully introgressed to enhance abiotic stress adaptation in rice. The independence of genetic control of a trait and of its plasticity suggests that breeders may select for high or low plasticity in combination with high or low performance of economically important traits. Trait plasticity in stressful environments may be harnessed through breeding stress-tolerant crops. There exists a genetic cost associated with plasticity, so a better understanding of the trade-offs between plasticity and productivity is warranted prior to undertaking breeding for plasticity traits together with productivity in stress environments.
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Affiliation(s)
| | | | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Sundsvagen, 14 Box 101, SE 23053, Alnarp, Sweden.
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21
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Frey FP, Pitz M, Schön CC, Hochholdinger F. Transcriptomic diversity in seedling roots of European flint maize in response to cold. BMC Genomics 2020; 21:300. [PMID: 32293268 PMCID: PMC7158136 DOI: 10.1186/s12864-020-6682-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/17/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Low temperatures decrease the capacity for biomass production and lead to growth retardation up to irreversible cellular damage in modern maize cultivars. European flint landraces are an untapped genetic resource for genes and alleles conferring cold tolerance which they acquired during their adaptation to the agroecological conditions in Europe. RESULTS Based on a phenotyping experiment of 276 doubled haploid lines derived from the European flint landrace "Petkuser Ferdinand Rot" diverging for cold tolerance, we selected 21 of these lines for an RNA-seq experiment. The different genotypes showed highly variable transcriptomic responses to cold. We identified 148, 3254 and 563 genes differentially expressed with respect to cold treatment, cold tolerance and growth rate at cold, respectively. Gene ontology (GO) term enrichment demonstrated that the detoxification of reactive oxygen species is associated with cold tolerance, whereas amino acids might play a crucial role as antioxidant precursors and signaling molecules. CONCLUSION Doubled haploids representing a European maize flint landrace display genotype-specific transcriptome patterns associated with cold response, cold tolerance and seedling growth rate at cold. Identification of cold regulated genes in European flint germplasm, could be a starting point for introgressing such alleles in modern breeding material for maize improvement.
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Affiliation(s)
- Felix P. Frey
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Marion Pitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Chris-Carolin Schön
- Department of Plant Breeding, Technische Universität München, Freising, Germany
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
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22
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Guo J, Li C, Zhang X, Li Y, Zhang D, Shi Y, Song Y, Li Y, Yang D, Wang T. Transcriptome and GWAS analyses reveal candidate gene for seminal root length of maize seedlings under drought stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110380. [PMID: 32005385 DOI: 10.1016/j.plantsci.2019.110380] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 05/21/2023]
Abstract
Water deficits are a major constraint on maize growth and yield, and deep roots are one of the major mechanisms of drought tolerance. In this study, four root and shoot traits were evaluated within an association panel consisting of 209 diverse maize accessions under well-watered (WW) and water-stressed (WS) conditions. A significant positive correlation was observed between seminal root length (SRL) under WS treatment and the drought tolerance index (DI) of maize seedlings. The transcriptome profiles of maize seminal roots were compared between four drought-tolerant lines and four drought-sensitive lines under both water conditions to identify genes associated with the drought stress response. After drought stress, 343 and 177 common differentially expressed genes (DEGs) were identified in the drought-tolerant group and drought-sensitive group, respectively. In parallel, a coexpression network underlying SRL was constructed on the basis of transcriptome data, and 10 hub genes involved in two significant associated modules were identified. Additionally, a genome-wide association study (GWAS) of the SRL revealed 62 loci for the two water treatments. By integrating the results of the GWAS, the common DEGs and the coexpression network analysis, 7 promising candidate genes were prioritized for further research. Together, our results provide a foundation for the enhanced understanding of seminal root changes in response to drought stress in maize.
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Affiliation(s)
- Jian Guo
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | | | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Deguang Yang
- College of Agriculture, Northeast Agricultural University, Harbin, China.
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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23
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Yang Y, Guo Y, Zhong J, Zhang T, Li D, Ba T, Xu T, Chang L, Zhang Q, Sun M. Root Physiological Traits and Transcriptome Analyses Reveal that Root Zone Water Retention Confers Drought Tolerance to Opisthopappus taihangensis. Sci Rep 2020; 10:2627. [PMID: 32060321 PMCID: PMC7021704 DOI: 10.1038/s41598-020-59399-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022] Open
Abstract
Opisthopappus taihangensis (Ling) Shih, as a relative of chrysanthemum, mainly survives on the cracks of steep slopes and cliffs. Due to the harsh environment in which O. taihangensis lives, it has evolved strong adaptive traits to drought stress. The root system first perceives soil water deficiency, triggering a multi-pronged response mechanism to maintain water potential; however, the drought tolerance mechanism of O. taihangensis roots remains unclear. Therefore, roots were selected as materials to explore the physiological and molecular responsive mechanisms. We found that the roots had a stronger water retention capacity than the leaves. This result was attributed to ABA accumulation, which promoted an increased accumulation of proline and trehalose to maintain cell osmotic pressure, activated SOD and POD to scavenge ROS to protect root cell membrane structure and induced suberin depositions to minimize water backflow to dry soil. Transcriptome sequencing analyses further confirmed that O. taihangensis strongly activated genes involved in the ABA signalling pathway, osmolyte metabolism, antioxidant enzyme activity and biosynthesis of suberin monomer. Overall, these results not only will provide new insights into the drought response mechanisms of O. taihangensis but also will be helpful for future drought breeding programmes of chrysanthemum.
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Affiliation(s)
- Yongjuan Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yanhong Guo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Jian Zhong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tengxun Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Dawei Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tingting Ba
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Ting Xu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Lina Chang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Ming Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
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24
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Lang Y, Liu Z, Zheng Z. Retracted Article: Investigation of yellow horn ( Xanthoceras sorbifolia Bunge) transcriptome in response to different abiotic stresses: a comparative RNA-Seq study. RSC Adv 2020; 10:6512-6519. [PMID: 35496033 PMCID: PMC9049705 DOI: 10.1039/c9ra09535g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/05/2020] [Indexed: 01/23/2023] Open
Abstract
Yellow horn (Xanthoceras sorbifolia Bunge) is a well-known oil-rich seed shrub which can grow well in barren and arid environments in the northern part of China. Yellow horn has received worldwide attention because of its excellent economic and environmental value. However, because of its limited genetic data, little information can be found regarding the molecular defense mechanisms of yellow horn exposed to various abiotic stresses. In view of this, the current study aims to investigate the impact of different abiotic stresses (i.e. NaCl, ABA and low temperature) on the transcriptome of yellow horn using RNA-Seq. Based on the transcriptome sequencing data, approximately 27% to 45% of stress-responsive genes were found highly expressed after stress treatment for 24 h. In addition, these genes were found to be still expressed after stress treatment for 48 h. However, many additional genes were stress-regulated after 48 h treatment compared with the 24 h treatment. GO enrichment analysis revealed that the expression patterns of the stress-responsive, type-specific terms were generally down-regulated. Most shared GO terms were primarily involved in protein folding, unfolding protein binding, protein transport and protein modification. Further, transcription factors (TFs), such as ERFs, bHLH, GRAS and NAC, were found to be enriched only in the low temperature treatment group, particularly the ERF TFs families. These combined results suggested that yellow horn may have developed specific molecular defense systems against diverse abiotic stresses.
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Affiliation(s)
- Yanhe Lang
- State Key Laboratory of Tree Genetics and Breeding Laboratory, Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), College of Life Science, Northeast Forestry University Harbin Heilongjiang Province China +86-151-0453-8096
| | - Zhi Liu
- State Key Laboratory of Tree Genetics and Breeding Laboratory, Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), College of Life Science, Northeast Forestry University Harbin Heilongjiang Province China +86-151-0453-8096
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding Laboratory, Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), College of Life Science, Northeast Forestry University Harbin Heilongjiang Province China +86-151-0453-8096
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25
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Moisseyev G, Park K, Cui A, Freitas D, Rajagopal D, Konda AR, Martin-Olenski M, Mcham M, Liu K, Du Q, Schnable JC, Moriyama EN, Cahoon EB, Zhang C. RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5851117. [PMID: 32500918 PMCID: PMC7273057 DOI: 10.1093/database/baaa038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/02/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022]
Abstract
Root-associated genes play an important role in plants. Despite the fact that there have been studies on root biology, information on genes that are specifically expressed or upregulated in roots is poorly collected. There exist very few databases dedicated to genes and promoters associated with root biology, preventing effective root-related studies. Therefore, we analyzed multiple types of omics data to identify root-associated genes in maize, soybean, and sorghum and constructed a comprehensive online database of these genes and their promoter sequences. This database creates a pivotal platform capable of stimulating and facilitating further studies on manipulating root growth and development.
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Affiliation(s)
- Gleb Moisseyev
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kiyoul Park
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Alix Cui
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Daniel Freitas
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Divith Rajagopal
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Anji Reddy Konda
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | | | - Mackenzie Mcham
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kan Liu
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Qian Du
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Etsuko N Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Edgar B Cahoon
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
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26
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Seeve CM, Sunkar R, Zheng Y, Liu L, Liu Z, McMullen M, Nelson S, Sharp RE, Oliver MJ. Water-deficit responsive microRNAs in the primary root growth zone of maize. BMC PLANT BIOLOGY 2019; 19:447. [PMID: 31651253 PMCID: PMC6814125 DOI: 10.1186/s12870-019-2037-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/12/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNA-mediated gene regulatory networks play a significant role in plant growth and development and environmental stress responses. RESULTS We identified 79 microRNAs (miRNAs) and multiple miRNA variants (isomiRs) belonging to 26 miRNA families in the primary root growth zone of maize seedlings grown at one of three water potentials: well-watered (- 0.02 MPa), mild water deficit stress (- 0.3 MPa), and severe water deficit stress (- 1.6 MPa). The abundances of 3 miRNAs (mild stress) and 34 miRNAs representing 17 families (severe stress) were significantly different in water-deficit stressed relative to well-watered controls (FDR < 0.05 and validated by stem loop RT-qPCR). Degradome sequencing revealed 213 miRNA-regulated transcripts and trancriptome profiling revealed that the abundance of 77 (miRNA-regulated) were regulated by water-defecit stress. miR399e,i,j-3p was strongly regulated by water-defcit stress implicating the possibility of nutrient deficiency during stress. CONCLUSIONS We have identified a number of maize miRNAs that respond to specific water deficits applied to the primary root growth zone. We have also identified transcripts that are targets for miRNA regulation in the root growth zone under water-deficit stress. The miR399e,i,j-3p that is known to regulate phosphate uptake in response to nutrient deficiencies responds to water-deficit stress, however, at the seedling stage the seed provides adequate nutrients for root growth thus miR399e,i,j-3p may play a separate role in water-deficit responses. A water-deficit regulated maize transcript, similar to known miR399 target mimics, was identified and we hypothesized that it is another regulatory player, moderating the role of miR399e,i,j-3p, in primary root growth zone water deficit responses.
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Affiliation(s)
- Candace M. Seeve
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, 650500 Yunnan China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500 Yunnan China
| | - Zhijie Liu
- Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Michael McMullen
- Division of Plant Sciences, Columbia, University of Missouri, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Sven Nelson
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Robert E. Sharp
- Division of Plant Sciences, Columbia, University of Missouri, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Melvin J. Oliver
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
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27
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Dowd TG, Braun DM, Sharp RE. Maize lateral root developmental plasticity induced by mild water stress. I: Genotypic variation across a high-resolution series of water potentials. PLANT, CELL & ENVIRONMENT 2019; 42:2259-2273. [PMID: 29981147 DOI: 10.1111/pce.13399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
Lateral root developmental plasticity induced by mild water stress was examined across a high-resolution series of growth media water potentials (Ψw ) in two genotypes of maize. The suitability of several media for imposing near-stable Ψw treatments on transpiring plants over prolonged growth periods was assessed. Genotypic differences specific to responses of lateral root growth from the primary root system occurred between cultivars FR697 and B73 over a narrow series of water stress treatments ranging in Ψw from -0.25 to -0.40 MPa. In FR697, both the average length and number of first-order lateral roots were substantially enhanced at a Ψw of -0.25 MPa compared with well-watered controls. These effects were separated spatially, occurring primarily in the upper and lower regions of the axial root, respectively. Furthermore, first-order lateral roots progressively increased in diameter with increasing water stress, resulting in a maximum 2.3-fold increase in root volume at a Ψw of -0.40 MPa. In B73, in contrast, the length, diameter, nor number of lateral roots was increased in any of the water stress treatments. The genotype-specific responses observed over this narrow range of Ψw demonstrate the necessity of high-resolution studies at mild stress levels for characterization of lateral root developmental plasticity.
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Affiliation(s)
- Tyler G Dowd
- Divisions of Plant Sciences, University of Missouri, Columbia, Missouri, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri
| | - David M Braun
- Biological Sciences, University of Missouri, Columbia, Missouri
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri
| | - Robert E Sharp
- Divisions of Plant Sciences, University of Missouri, Columbia, Missouri, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri
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28
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Osthoff A, Donà Dalle Rose P, Baldauf JA, Piepho HP, Hochholdinger F. Transcriptomic reprogramming of barley seminal roots by combined water deficit and salt stress. BMC Genomics 2019; 20:325. [PMID: 31035922 PMCID: PMC6489292 DOI: 10.1186/s12864-019-5634-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/21/2019] [Indexed: 12/21/2022] Open
Abstract
Background Water deficit and soil salinity substantially influence plant growth and productivity. When occurring individually, plants often exhibit reduced growth resulting in yield losses. The simultaneous occurrence of these stresses enhances their negative effects. Unraveling the molecular mechanisms of combined abiotic stress responses is essential to secure crop productivity under unfavorable environmental conditions. Results This study examines the effects of water deficit, salinity and a combination of both on growth and transcriptome plasticity of barley seminal roots by RNA-Seq. Exposure to water deficit and combined stress for more than 4 days significantly reduced total seminal root length. Transcriptome sequencing demonstrated that 60 to 80% of stress type-specific gene expression responses observed 6 h after treatment were also present after 24 h of stress application. However, after 24 h of stress application, hundreds of additional genes were stress-regulated compared to the short 6 h treatment. Combined salt and water deficit stress application results in a unique transcriptomic response that cannot be predicted from individual stress responses. Enrichment analyses of gene ontology terms revealed stress type-specific adjustments of gene expression. Further, global reprogramming mediated by transcription factors and consistent over-representation of basic helix-loop-helix (bHLH) transcription factors, heat shock factors (HSF) and ethylene response factors (ERF) was observed. Conclusion This study reveals the complex transcriptomic responses regulating the perception and signaling of multiple abiotic stresses in barley. Electronic supplementary material The online version of this article (10.1186/s12864-019-5634-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alina Osthoff
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Petra Donà Dalle Rose
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Jutta A Baldauf
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Hans-Peter Piepho
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599, Stuttgart, Germany
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany.
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29
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Nagaraju M, Kumar SA, Reddy PS, Kumar A, Rao DM, Kavi Kishor PB. Genome-scale identification, classification, and tissue specific expression analysis of late embryogenesis abundant (LEA) genes under abiotic stress conditions in Sorghum bicolor L. PLoS One 2019; 14:e0209980. [PMID: 30650107 PMCID: PMC6335061 DOI: 10.1371/journal.pone.0209980] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 12/14/2018] [Indexed: 12/20/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins, the space fillers or molecular shields, are the hydrophilic protective proteins which play an important role during plant development and abiotic stress. The systematic survey and characterization revealed a total of 68 LEA genes, belonging to 8 families in Sorghum bicolor. The LEA-2, a typical hydrophobic family is the most abundant family. All of them are evenly distributed on all 10 chromosomes and chromosomes 1, 2, and 3 appear to be the hot spots. Majority of the S. bicolor LEA (SbLEA) genes are intron less or have fewer introns. A total of 22 paralogous events were observed and majority of them appear to be segmental duplications. Segmental duplication played an important role in SbLEA-2 family expansion. A total of 12 orthologs were observed with Arabidopsis and 13 with Oryza sativa. Majority of them are basic in nature, and targeted by chloroplast subcellular localization. Fifteen miRNAs targeted to 25 SbLEAs appear to participate in development, as well as in abiotic stress tolerance. Promoter analysis revealed the presence of abiotic stress-responsive DRE, MYB, MYC, and GT1, biotic stress-responsive W-Box, hormone-responsive ABA, ERE, and TGA, and development-responsive SKn cis-elements. This reveals that LEA proteins play a vital role during stress tolerance and developmental processes. Using microarray data, 65 SbLEA genes were analyzed in different tissues (roots, pith, rind, internode, shoot, and leaf) which show clear tissue specific expression. qRT-PCR analysis of 23 SbLEA genes revealed their abundant expression in various tissues like roots, stems and leaves. Higher expression was noticed in stems compared to roots and leaves. Majority of the SbLEA family members were up-regulated at least in one tissue under different stress conditions. The SbLEA3-2 is the regulator, which showed abundant expression under diverse stress conditions. Present study provides new insights into the formation of LEAs in S. bicolor and to understand their role in developmental processes under stress conditions, which may be a valuable source for future research.
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Affiliation(s)
- M Nagaraju
- Department of Genetics, Osmania University, Hyderabad, India
| | - S Anil Kumar
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Silk Park, Prem Nagar, Dehradun, India
| | - D Manohar Rao
- Department of Genetics, Osmania University, Hyderabad, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad, India
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Kreszies T, Shellakkutti N, Osthoff A, Yu P, Baldauf JA, Zeisler‐Diehl VV, Ranathunge K, Hochholdinger F, Schreiber L. Osmotic stress enhances suberization of apoplastic barriers in barley seminal roots: analysis of chemical, transcriptomic and physiological responses. THE NEW PHYTOLOGIST 2019; 221:180-194. [PMID: 30055115 PMCID: PMC6586163 DOI: 10.1111/nph.15351] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/18/2018] [Indexed: 05/08/2023]
Abstract
Barley (Hordeum vulgare) is more drought tolerant than other cereals, thus making it an excellent model for the study of the chemical, transcriptomic and physiological effects of water deficit. Roots are the first organ to sense soil water deficit. Therefore, we studied the response of barley seminal roots to different water potentials induced by polyethylene glycol (PEG) 8000. We investigated changes in anatomical parameters by histochemistry and microscopy, quantitative and qualitative changes in suberin composition by analytical chemistry, transcript changes by RNA-sequencing (RNA-Seq), and the radial water and solute movement of roots using a root pressure probe. In response to osmotic stress, genes in the suberin biosynthesis pathway were upregulated that correlated with increased suberin amounts in the endodermis and an overall reduction in hydraulic conductivity (Lpr ). In parallel, transcriptomic data indicated no or only weak effects of osmotic stress on aquaporin expression. These results indicate that osmotic stress enhances cell wall suberization and markedly reduces Lpr of the apoplastic pathway, whereas Lpr of the cell-to-cell pathway is not altered. Thus, the sealed apoplast markedly reduces the uncontrolled backflow of water from the root to the medium, whilst keeping constant water flow through the highly regulated cell-to-cell path.
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Affiliation(s)
- Tino Kreszies
- Department of EcophysiologyInstitute of Cellular and Molecular BotanyUniversity of BonnKirschallee 153115BonnGermany
| | - Nandhini Shellakkutti
- Department of EcophysiologyInstitute of Cellular and Molecular BotanyUniversity of BonnKirschallee 153115BonnGermany
| | - Alina Osthoff
- Crop Functional GenomicsInstitute of Crop Science and Resource Conservation (INRES)University of Bonn53113BonnGermany
| | - Peng Yu
- Crop Functional GenomicsInstitute of Crop Science and Resource Conservation (INRES)University of Bonn53113BonnGermany
| | - Jutta A. Baldauf
- Crop Functional GenomicsInstitute of Crop Science and Resource Conservation (INRES)University of Bonn53113BonnGermany
| | - Viktoria V. Zeisler‐Diehl
- Department of EcophysiologyInstitute of Cellular and Molecular BotanyUniversity of BonnKirschallee 153115BonnGermany
| | - Kosala Ranathunge
- School of Biological SciencesUniversity of Western Australia35 Stirling HighwayCrawley6009PerthAustralia
| | - Frank Hochholdinger
- Crop Functional GenomicsInstitute of Crop Science and Resource Conservation (INRES)University of Bonn53113BonnGermany
| | - Lukas Schreiber
- Department of EcophysiologyInstitute of Cellular and Molecular BotanyUniversity of BonnKirschallee 153115BonnGermany
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31
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Del Bianco M, Kepinski S. Building a future with root architecture. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5319-5323. [PMID: 30445468 PMCID: PMC6255693 DOI: 10.1093/jxb/ery390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Affiliation(s)
- Marta Del Bianco
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Stefan Kepinski
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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Ma H, Liu C, Li Z, Ran Q, Xie G, Wang B, Fang S, Chu J, Zhang J. ZmbZIP4 Contributes to Stress Resistance in Maize by Regulating ABA Synthesis and Root Development. PLANT PHYSIOLOGY 2018; 178:753-770. [PMID: 30126870 PMCID: PMC6181033 DOI: 10.1104/pp.18.00436] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/07/2018] [Indexed: 05/11/2023]
Abstract
In plants, bZIP (basic leucine zipper) transcription factors regulate diverse processes such as development and stress responses. However, few of these transcription factors have been functionally characterized in maize (Zea mays). In this study, we characterized the bZIP transcription factor gene ZmbZIP4 from maize. ZmbZIP4 was differentially expressed in various organs of maize and was induced by high salinity, drought, heat, cold, and abscisic acid treatment in seedlings. A transactivation assay in yeast demonstrated that ZmbZIP4 functioned as a transcriptional activator. A genome-wide screen for ZmbZIP4 targets by immunoprecipitation sequencing revealed that ZmbZIP4 could positively regulate a number of stress response genes, such as ZmLEA2, ZmRD20, ZmRD21, ZmRab18, ZmNHX3, ZmGEA6, and ZmERD, and some abscisic acid synthesis-related genes, including NCED, ABA1, AAO3, and LOS5 In addition, ZmbZIP4 targets some root development-related genes, including ZmLRP1, ZmSCR, ZmIAA8, ZmIAA14, ZmARF2, and ZmARF3, and overexpression of ZmbZIP4 resulted in an increased number of lateral roots, longer primary roots, and an improved root system. Increased abscisic acid synthesis by overexpression of ZmbZIP4 also can increase the plant's ability to resist abiotic stress. Thus, ZmbZIP4 is a positive regulator of plant abiotic stress responses and is involved in root development in maize.
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Affiliation(s)
- Haizhen Ma
- School of Life Sciences, Shandong University, Jinan 250100, Shandong, China
| | - Can Liu
- School of Life Sciences, Shandong University, Jinan 250100, Shandong, China
| | - Zhaoxia Li
- School of Life Sciences, Shandong University, Jinan 250100, Shandong, China
| | - Qijun Ran
- School of Life Sciences, Shandong University, Jinan 250100, Shandong, China
| | - Guangning Xie
- School of Life Sciences, Shandong University, Jinan 250100, Shandong, China
| | - Baomei Wang
- School of Life Sciences, Shandong University, Jinan 250100, Shandong, China
| | - Shuang Fang
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Juren Zhang
- School of Life Sciences, Shandong University, Jinan 250100, Shandong, China
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MCENet: A database for maize conditional co-expression network and network characterization collaborated with multi-dimensional omics levels. J Genet Genomics 2018; 45:351-360. [DOI: 10.1016/j.jgg.2018.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/30/2018] [Accepted: 05/25/2018] [Indexed: 01/09/2023]
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Mittal S, Banduni P, Mallikarjuna MG, Rao AR, Jain PA, Dash PK, Thirunavukkarasu N. Structural, Functional, and Evolutionary Characterization of Major Drought Transcription Factors Families in Maize. Front Chem 2018; 6:177. [PMID: 29876347 PMCID: PMC5974147 DOI: 10.3389/fchem.2018.00177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 05/03/2018] [Indexed: 01/22/2023] Open
Abstract
Drought is one of the major threats to the maize yield especially in subtropical production systems. Understanding the genes and regulatory mechanisms of drought tolerance is important to sustain the yield. Transcription factors (TFs) play a major role in gene regulation under drought stress. In the present study, a set of 15 major TF families comprising 1,436 genes was structurally and functionally characterized. The functional annotation indicated that the genes were involved in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed for individual TF and combined TF families. Phylogenetic analysis clustered the genes into specific and mixed groups. Gene structure analysis revealed that more number of genes were intron-rich as compared to intron-less. Drought-responsive cis-regulatory elements such as ABREA, ABREB, DRE1, and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. Protein-protein interaction network of 269 drought-responsive genes belonging to different TFs has been provided. The information generated on structural and functional characteristics, expression, and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to breed drought-tolerant genotypes in maize.
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Affiliation(s)
- Shikha Mittal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pooja Banduni
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Atmakuri R Rao
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prashant A Jain
- Department of Computational Biology & Bioinformatics, J.I.B.B., Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India
| | - Prasanta K Dash
- National Research Centre on Plant Biotechnology, New Delhi, India
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Wong DCJ, Zhang L, Merlin I, Castellarin SD, Gambetta GA. Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine. BMC Genomics 2018; 19:248. [PMID: 29642857 PMCID: PMC5896048 DOI: 10.1186/s12864-018-4638-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/29/2018] [Indexed: 12/05/2022] Open
Abstract
Background The major intrinsic protein (MIP) family is a family of proteins, including aquaporins, which facilitate water and small molecule transport across plasma membranes. In plants, MIPs function in a huge variety of processes including water transport, growth, stress response, and fruit development. In this study, we characterize the structure and transcriptional regulation of the MIP family in grapevine, describing the putative genome duplication events leading to the family structure and characterizing the family’s tissue and developmental specific expression patterns across numerous preexisting microarray and RNAseq datasets. Gene co-expression network (GCN) analyses were carried out across these datasets and the promoters of each family member were analyzed for cis-regulatory element structure in order to provide insight into their transcriptional regulation. Results A total of 29 Vitis vinifera MIP family members (excluding putative pseudogenes) were identified of which all but two were mapped onto Vitis vinifera chromosomes. In this study, segmental duplication events were identified for five plasma membrane intrinsic protein (PIP) and four tonoplast intrinsic protein (TIP) genes, contributing to the expansion of PIPs and TIPs in grapevine. Grapevine MIP family members have distinct tissue and developmental expression patterns and hierarchical clustering revealed two primary groups regardless of the datasets analyzed. Composite microarray and RNA-seq gene co-expression networks (GCNs) highlighted the relationships between MIP genes and functional categories involved in cell wall modification and transport, as well as with other MIPs revealing a strong co-regulation within the family itself. Some duplicated MIP family members have undergone sub-functionalization and exhibit distinct expression patterns and GCNs. Cis-regulatory element (CRE) analyses of the MIP promoters and their associated GCN members revealed enrichment for numerous CREs including AP2/ERFs and NACs. Conclusions Combining phylogenetic analyses, gene expression profiling, gene co-expression network analyses, and cis-regulatory element enrichment, this study provides a comprehensive overview of the structure and transcriptional regulation of the grapevine MIP family. The study highlights the duplication and sub-functionalization of the family, its strong coordinated expression with genes involved in growth and transport, and the putative classes of TFs responsible for its regulation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4638-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Darren Chern Jan Wong
- Wine Research Centre, University of British Columbia, 2205 East Mall, Vancouver, BC, V6T 0Z4, Canada
| | - Li Zhang
- Bordeaux Science Agro, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F- 33140, Villenave d'Ornon, France
| | - Isabelle Merlin
- Bordeaux Science Agro, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F- 33140, Villenave d'Ornon, France
| | - Simone D Castellarin
- Wine Research Centre, University of British Columbia, 2205 East Mall, Vancouver, BC, V6T 0Z4, Canada
| | - Gregory A Gambetta
- Bordeaux Science Agro, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F- 33140, Villenave d'Ornon, France.
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Magwanga RO, Lu P, Kirungu JN, Lu H, Wang X, Cai X, Zhou Z, Zhang Z, Salih H, Wang K, Liu F. Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton. BMC Genet 2018; 19:6. [PMID: 29334890 PMCID: PMC5769447 DOI: 10.1186/s12863-017-0596-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/29/2017] [Indexed: 12/20/2022] Open
Abstract
Background Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton. Increased cotton production in the face of declining precipitation and availability of fresh water for agriculture use is the focus for breeders, cotton being the backbone of textile industries and a cash crop for many countries globally. Results In this work, a total of 242, 136 and 142 LEA genes were identified in G. hirsutum, G. arboreum and G. raimondii respectively. The identified genes were classified into eight groups based on their conserved domain and phylogenetic tree analysis. LEA 2 were the most abundant, this could be attributed to their hydrophobic character. Upland cotton LEA genes have fewer introns and are distributed in all chromosomes. Majority of the duplicated LEA genes were segmental. Syntenic analysis showed that greater percentages of LEA genes are conserved. Segmental gene duplication played a key role in the expansion of LEA genes. Sixty three miRNAs were found to target 89 genes, such as miR164, ghr-miR394 among others. Gene ontology analysis revealed that LEA genes are involved in desiccation and defense responses. Almost all the LEA genes in their promoters contained ABRE, MBS, W-Box and TAC-elements, functionally known to be involved in drought stress and other stress responses. Majority of the LEA genes were involved in secretory pathways. Expression profile analysis indicated that most of the LEA genes were highly expressed in drought tolerant cultivars Gossypium tomentosum as opposed to drought susceptible, G. hirsutum. The tolerant genotypes have a greater ability to modulate genes under drought stress than the more susceptible upland cotton cultivars. Conclusion The finding provides comprehensive information on LEA genes in upland cotton, G. hirsutum and possible function in plants under drought stress. Electronic supplementary material The online version of this article (10.1186/s12863-017-0596-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard Odongo Magwanga
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.,School of physical and biological sciences (SPBS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Pu Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Joy Nyangasi Kirungu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Hejun Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Xingxing Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Xiaoyan Cai
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Zhongli Zhou
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Zhenmei Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Haron Salih
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Kunbo Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.
| | - Fang Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.
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37
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Magwanga RO, Lu P, Kirungu JN, Lu H, Wang X, Cai X, Zhou Z, Zhang Z, Salih H, Wang K, Liu F. Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton. BMC Genet 2018; 19:6. [PMID: 29334890 PMCID: PMC5769447 DOI: 10.1007/s11033-012-2250-3fang 10.1186/s12863-017-0596-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/29/2017] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton. Increased cotton production in the face of declining precipitation and availability of fresh water for agriculture use is the focus for breeders, cotton being the backbone of textile industries and a cash crop for many countries globally. RESULTS In this work, a total of 242, 136 and 142 LEA genes were identified in G. hirsutum, G. arboreum and G. raimondii respectively. The identified genes were classified into eight groups based on their conserved domain and phylogenetic tree analysis. LEA 2 were the most abundant, this could be attributed to their hydrophobic character. Upland cotton LEA genes have fewer introns and are distributed in all chromosomes. Majority of the duplicated LEA genes were segmental. Syntenic analysis showed that greater percentages of LEA genes are conserved. Segmental gene duplication played a key role in the expansion of LEA genes. Sixty three miRNAs were found to target 89 genes, such as miR164, ghr-miR394 among others. Gene ontology analysis revealed that LEA genes are involved in desiccation and defense responses. Almost all the LEA genes in their promoters contained ABRE, MBS, W-Box and TAC-elements, functionally known to be involved in drought stress and other stress responses. Majority of the LEA genes were involved in secretory pathways. Expression profile analysis indicated that most of the LEA genes were highly expressed in drought tolerant cultivars Gossypium tomentosum as opposed to drought susceptible, G. hirsutum. The tolerant genotypes have a greater ability to modulate genes under drought stress than the more susceptible upland cotton cultivars. CONCLUSION The finding provides comprehensive information on LEA genes in upland cotton, G. hirsutum and possible function in plants under drought stress.
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Affiliation(s)
- Richard Odongo Magwanga
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
- School of physical and biological sciences (SPBS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Pu Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Joy Nyangasi Kirungu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Hejun Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Xingxing Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Xiaoyan Cai
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Zhongli Zhou
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Zhenmei Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Haron Salih
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Kunbo Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Fang Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
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38
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Jia H, Sun W, Li M, Zhang Z. Integrated Analysis of Protein Abundance, Transcript Level, and Tissue Diversity To Reveal Developmental Regulation of Maize. J Proteome Res 2018; 17:822-833. [DOI: 10.1021/acs.jproteome.7b00586] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Haitao Jia
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Wei Sun
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Manfei Li
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Zuxin Zhang
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
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39
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Hochholdinger F, Yu P, Marcon C. Genetic Control of Root System Development in Maize. TRENDS IN PLANT SCIENCE 2018; 23:79-88. [PMID: 29170008 DOI: 10.1016/j.tplants.2017.10.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/21/2017] [Accepted: 10/25/2017] [Indexed: 05/21/2023]
Abstract
The maize root system comprises structurally and functionally different root types. Mutant analyses have revealed that root-type-specific genetic regulators intrinsically determine the maize root system architecture. Molecular cloning of these genes has demonstrated that key elements of auxin signal transduction, such as LOB domain (LBD) and Aux/IAA proteins, are instrumental for seminal, shoot-borne, and lateral root initiation. Moreover, genetic analyses have demonstrated that genes related to exocytotic vesicle docking, cell wall loosening, and cellulose synthesis and organization control root hair elongation. The identification of upstream regulators, protein interaction partners, and downstream targets of these genes together with cell-type-specific transcriptome analyses have provided novel insights into the regulatory networks controlling root development and architecture in maize.
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Affiliation(s)
- Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany.
| | - Peng Yu
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | - Caroline Marcon
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
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40
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Abstract
Promoters regulate gene expression, and are essential biotechnology tools. Since its introduction in the mid-1990s, biotechnology has greatly enhanced maize productivity primarily through the development of insect control and herbicide tolerance traits. Additional biotechnology applications include improving seed nutrient composition, industrial protein production, therapeutic production, disease resistance, abiotic stress resistance, and yield enhancement. Biotechnology has also greatly expanded basic research into important mechanisms that govern plant growth and reproduction. Many novel promoters have been developed to facilitate this work, but only a few are widely used. Transgene optimization includes a variety of strategies some of which effect promoter structure. Recent reviews examine the state of the art with respect to transgene design for biotechnology applications. This chapter examines the use of transgene technology in maize, focusing on the way promoters are selected and used. The impact of new developments in genomic technology on promoter structure is also discussed.
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41
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Dossa K, Li D, Wang L, Zheng X, Liu A, Yu J, Wei X, Zhou R, Fonceka D, Diouf D, Liao B, Cissé N, Zhang X. Transcriptomic, biochemical and physio-anatomical investigations shed more light on responses to drought stress in two contrasting sesame genotypes. Sci Rep 2017; 7:8755. [PMID: 28821876 PMCID: PMC5562740 DOI: 10.1038/s41598-017-09397-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/26/2017] [Indexed: 11/09/2022] Open
Abstract
Sesame is an important oilseed crop with a high oil quality. It is prone to drought stress in the arid and semi-arid areas where it is widely grown. This study aims to decipher the response of tolerant (DT) and sensitive (DS) genotypes to progressive drought based on transcriptome, biochemical and physio-anatomical characterizations. Results indicated that under severe stress, DT relied on a well-functioning taproot while DS displayed a disintegrated root due to collapsed cortical cells. This was attributed to a higher accumulation of osmoprotectants and strong activity of antioxidant enzymes especially peroxidases in DT. From roots, DT could supply water to the aboveground tissues to ensure photosynthetic activities and improve endurance under stress. Temporal transcriptome sequencing under drought further confirmed that DT strongly activated genes related to antioxidant activity, osmoprotection and hormonal signaling pathways including abscisic acid and Ethylene. Furthermore, DT displayed unique differentially expressed genes in root functioning as peroxidases, interleukin receptor-associated kinase, heat shock proteins, APETALA2/ethylene-responsive element-binding protein and mitogen activated protein kinase, to effectively scavenge reactive oxygen species and preserve root cell integrity. Finally, 61 candidate genes conferring higher drought tolerance in DT were discovered and may constitute useful resources for drought tolerance improvement in sesame.
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Affiliation(s)
- Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China.,Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Senegal.,Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal, 107000, Dakar, Senegal
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | | | - Aili Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Jingyin Yu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Xin Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Daniel Fonceka
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Senegal.,Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR AGAP, F-34398, Montpellier, France
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal, 107000, Dakar, Senegal
| | - Boshou Liao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Ndiaga Cissé
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Senegal
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China.
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42
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Zhang X, Liu X, Zhang D, Tang H, Sun B, Li C, Hao L, Liu C, Li Y, Shi Y, Xie X, Song Y, Wang T, Li Y. Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance. PLoS One 2017; 12:e0179477. [PMID: 28700592 PMCID: PMC5507481 DOI: 10.1371/journal.pone.0179477] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/31/2017] [Indexed: 11/19/2022] Open
Abstract
Drought is a major threat to maize growth and production. Understanding the molecular regulation network of drought tolerance in maize is of great importance. In this study, two maize inbred lines with contrasting drought tolerance were tested in the field under natural soil drought and well-watered conditions. In addition, the transcriptomes of their leaves was analyzed by RNA-Seq. In total, 555 and 2,558 genes were detected to specifically respond to drought in the tolerant and the sensitive line, respectively, with a more positive regulation tendency in the tolerant genotype. Furthermore, 4,700, 4,748, 4,403 and 4,288 genes showed differential expression between the two lines under moderate drought, severe drought and their well-watered controls, respectively. Transcription factors were enriched in both genotypic differentially expressed genes and specifically responsive genes of the tolerant line. It was speculated that the genotype-specific response of 20 transcription factors in the tolerance line and the sustained genotypically differential expression of 22 transcription factors might enhance tolerance to drought in maize. Our results provide new insight into maize drought tolerance-related regulation systems and provide gene resources for subsequent studies and drought tolerance improvement.
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Affiliation(s)
- Xiaojing Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaijun Tang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Baocheng Sun
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luyang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Liu
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoqing Xie
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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43
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Savoi S, Wong DCJ, Degu A, Herrera JC, Bucchetti B, Peterlunger E, Fait A, Mattivi F, Castellarin SD. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries ( Vitis vinifera L.) Exposed to Water Deficit. FRONTIERS IN PLANT SCIENCE 2017; 8:1124. [PMID: 28740499 DOI: 10.2174/9781608059300117010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/12/2017] [Indexed: 05/24/2023]
Abstract
Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.
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Affiliation(s)
- Stefania Savoi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Darren C J Wong
- Wine Research Centre, The University of British Columbia, VancouverBC, Canada
| | - Asfaw Degu
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSede Boqer, Israel
| | - Jose C Herrera
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Barbara Bucchetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Enrico Peterlunger
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Aaron Fait
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSede Boqer, Israel
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
- Center Agriculture Food Environment, University of TrentoSan Michele all'Adige, Italy
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44
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Savoi S, Wong DCJ, Degu A, Herrera JC, Bucchetti B, Peterlunger E, Fait A, Mattivi F, Castellarin SD. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries ( Vitis vinifera L.) Exposed to Water Deficit. FRONTIERS IN PLANT SCIENCE 2017; 8:1124. [PMID: 28740499 PMCID: PMC5502274 DOI: 10.3389/fpls.2017.01124] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.
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Affiliation(s)
- Stefania Savoi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Darren C. J. Wong
- Wine Research Centre, The University of British Columbia, VancouverBC, Canada
| | - Asfaw Degu
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSede Boqer, Israel
| | - Jose C. Herrera
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Barbara Bucchetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Enrico Peterlunger
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Aaron Fait
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSede Boqer, Israel
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund MachSan Michele all’Adige, Italy
- Center Agriculture Food Environment, University of TrentoSan Michele all’Adige, Italy
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45
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Seeve CM, Cho IJ, Hearne LB, Srivastava GP, Joshi T, Smith DO, Sharp RE, Oliver MJ. Water-deficit-induced changes in transcription factor expression in maize seedlings. PLANT, CELL & ENVIRONMENT 2017; 40:686-701. [PMID: 28039925 DOI: 10.1111/pce.12891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 05/15/2023]
Abstract
Plants tolerate water deficits by regulating gene networks controlling cellular and physiological traits to modify growth and development. Transcription factor (TF)-directed regulation of transcription within these gene networks is key to eliciting appropriate responses. In this study, reverse transcription quantitative PCR (RT-qPCR) was used to examine the abundance of 618 transcripts from 536 TF genes in individual root and shoot tissues of maize seedlings grown in vermiculite under well-watered (water potential of -0.02 MPa) and water-deficit conditions (water potentials of -0.3 and -1.6 MPa). A linear mixed model identified 433 TF transcripts representing 392 genes that differed significantly in abundance in at least one treatment, including TFs that intersect growth and development and environmental stress responses. TFs were extensively differentially regulated across stressed maize seedling tissues. Hierarchical clustering revealed TFs with stress-induced increased abundance in primary root tips that likely regulate root growth responses to water deficits, possibly as part of abscisic acid and/or auxin-dependent signaling pathways. Ten of these TFs were selected for validation in nodal root tips of drought-stressed field-grown plants (late V1 to early V2 stage). Changes in abundance of these TF transcripts under a field drought were similar to those observed in the seedling system.
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Affiliation(s)
- Candace M Seeve
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO, 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
| | - In-Jeong Cho
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO, 65211, USA
| | - Leonard B Hearne
- Statistics Department, University of Missouri, Columbia, MO, 65211, USA
| | | | - Trupti Joshi
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
- Informatics Institute and Christopher S Bond Life Science Center, Columbia, MO, 65211, USA
| | - Dante O Smith
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Robert E Sharp
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Melvin J Oliver
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
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46
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Hey S, Baldauf J, Opitz N, Lithio A, Pasha A, Provart N, Nettleton D, Hochholdinger F. Complexity and specificity of the maize (Zea mays L.) root hair transcriptome. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2175-2185. [PMID: 28398587 PMCID: PMC5447894 DOI: 10.1093/jxb/erx104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Root hairs are tubular extensions of epidermis cells. Transcriptome profiling demonstrated that the single cell-type root hair transcriptome was less complex than the transcriptome of multiple cell-type primary roots without root hairs. In total, 831 genes were exclusively and 5585 genes were preferentially expressed in root hairs [false discovery rate (FDR) ≤1%]. Among those, the most significantly enriched Gene Ontology (GO) functional terms were related to energy metabolism, highlighting the high energy demand for the development and function of root hairs. Subsequently, the maize homologs for 138 Arabidopsis genes known to be involved in root hair development were identified and their phylogenetic relationship and expression in root hairs were determined. This study indicated that the genetic regulation of root hair development in Arabidopsis and maize is controlled by common genes, but also shows differences which need to be dissected in future genetic experiments. Finally, a maize root view of the eFP browser was implemented including the root hair transcriptome of the present study and several previously published maize root transcriptome data sets. The eFP browser provides color-coded expression levels for these root types and tissues for any gene of interest, thus providing a novel resource to study gene expression and function in maize roots.
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Affiliation(s)
- Stefan Hey
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Jutta Baldauf
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Nina Opitz
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
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47
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Tardieu F, Varshney RK, Tuberosa R. Improving crop performance under drought - cross-fertilization of disciplines. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1393-1398. [PMID: 28338855 PMCID: PMC5444440 DOI: 10.1093/jxb/erx042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Affiliation(s)
| | - Rajeev K Varshney
- Research Programme - Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru-502 324, India
| | - Roberto Tuberosa
- Department of Agricultural Sciences, Viale Fanin 44, 40127 Bologna, Italy
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48
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Marcon C, Paschold A, Malik WA, Lithio A, Baldauf JA, Altrogge L, Opitz N, Lanz C, Schoof H, Nettleton D, Piepho HP, Hochholdinger F. Stability of Single-Parent Gene Expression Complementation in Maize Hybrids upon Water Deficit Stress. PLANT PHYSIOLOGY 2017; 173:1247-1257. [PMID: 27999083 PMCID: PMC5291719 DOI: 10.1104/pp.16.01045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/18/2016] [Indexed: 05/24/2023]
Abstract
Heterosis is the superior performance of F1 hybrids compared with their homozygous, genetically distinct parents. In this study, we monitored the transcriptomic divergence of the maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrid progeny in primary roots under control and water deficit conditions simulated by polyethylene glycol treatment. Single-parent expression (SPE) of genes is an extreme instance of gene expression complementation, in which genes are active in only one of two parents but are expressed in both reciprocal hybrids. In this study, 1,997 genes only expressed in B73 and 2,024 genes only expressed in Mo17 displayed SPE complementation under control and water deficit conditions. As a consequence, the number of active genes in hybrids exceeded the number of active genes in the parental inbred lines significantly independent of treatment. SPE patterns were substantially more stable to expression changes by water deficit treatment than other genotype-specific expression profiles. While, on average, 75% of all SPE patterns were not altered in response to polyethylene glycol treatment, only 17% of the remaining genotype-specific expression patterns were not changed by water deficit. Nonsyntenic genes that lack syntenic orthologs in other grass species, and thus evolved late in the grass lineage, were significantly overrepresented among SPE genes. Hence, the significant overrepresentation of nonsyntenic genes among SPE patterns and their stability under water limitation might suggest a function of these genes during the early developmental manifestation of heterosis under fluctuating environmental conditions in hybrid progeny of the inbred lines B73 and Mo17.
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Affiliation(s)
- Caroline Marcon
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Anja Paschold
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Waqas Ahmed Malik
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Andrew Lithio
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Jutta A Baldauf
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Lena Altrogge
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Christa Lanz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Heiko Schoof
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Dan Nettleton
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Hans-Peter Piepho
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany;
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.);
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
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49
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Ali F, Ahsan M, Ali Q, Kanwal N. Phenotypic Stability of Zea mays Grain Yield and Its Attributing Traits under Drought Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:1397. [PMID: 28878785 PMCID: PMC5572255 DOI: 10.3389/fpls.2017.01397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/26/2017] [Indexed: 05/21/2023]
Abstract
Phenotypic stability under stress environment facilitate the fitness of genotype and opens new horizons to explore the cryptic genetic variation. Variation in tolerance to drought stress, a major grain yield constraint to global maize production, was identified, at the phenotypic and genotypic level. Here we found a prominent hybrid H9 that showed fitness over four growing seasons for grain yield under water stress conditions. Genotypic and phenotypic correlation of yield attributing traits over four seasons demonstrated that cobs per plant, 100 seed weight, number of grains rows per cob, total dry matter, cob diameter had positive association (r2 = 0.3-0.9) to grain yield. The perturbation was found for chlorophyll content as it showed moderate to strong association (P < 0.01) over four seasons, might be due to environment or genotype dependent. Highest heritability (95%) and genetic advance (79%) for grain yield was found in H9 over four consecutive crop growing seasons. Combined analysis over four seasons showed that studied variables together explained 85% of total variation in dependent structure (grain yield) obtained by Principal component analysis. This significant finding is the best example of phenotypic stability of grain yield in H9 and made it best fitted for grain yield under drought stress scenario. Detailed genetic analysis of H9 will help us to identify significant loci and alleles that made H9 the best fitted and it could serve as a potential source to generate novel transgressive levels of tolerance for drought stress in arid/semiarid regions.
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Affiliation(s)
- Fawad Ali
- Department of Plant Breeding and Genetics, University of Agriculture FaisalabadFaisalabad, Pakistan
- *Correspondence: Fawad Ali
| | - Muhammad Ahsan
- Department of Plant Breeding and Genetics, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, University of Agriculture FaisalabadFaisalabad, Pakistan
- Centre of Excellence in Molecular Biology, University of the PunjabLahore, Pakistan
- Qurban Ali
| | - Naila Kanwal
- Department of Plant Breeding and Genetics, University of Agriculture FaisalabadFaisalabad, Pakistan
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Chen W, Li J, Zhu H, Xu P, Chen J, Yao Q. Arbuscular Mycorrhizal Fungus Enhances Lateral Root Formation in Poncirus trifoliata (L.) as Revealed by RNA-Seq Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:2039. [PMID: 29238356 PMCID: PMC5713035 DOI: 10.3389/fpls.2017.02039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/14/2017] [Indexed: 05/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) establish symbiosis with most terrestrial plants, and greatly regulate lateral root (LR) formation. Phosphorus (P), sugar, and plant hormones are proposed being involved in this regulation, however, no global evidence regarding these factors is available so far, especially in woody plants. In this study, we inoculated trifoliate orange seedlings (Poncirus trifoliata L. Raf) with an AMF isolate, Rhizophagus irregularis BGC JX04B. After 4 months of growth, LR formation was characterized, and sugar contents in roots were determined. RNA-Seq analysis was performed to obtain the transcriptomes of LR root tips from non-mycorrhizal and mycorrhizal seedlings. Quantitative real time PCR (qRT-PCR) of selected genes was also conducted for validation. The results showed that AMF significantly increased LR number, as well as plant biomass and shoot P concentration. The contents of glucose and fructose in primary root, and sucrose content in LR were also increased. A total of 909 differentially expressed genes (DEGs) were identified in response to AMF inoculation, and qRT-PCR validated the transcriptomic data. The numbers of DEGs related to P, sugar, and plant hormones were 31, 32, and 25, respectively. For P metabolism, the most up-regulated DEGs mainly encoded phosphate transporter, and the most down-regulated DEGs encoded acid phosphatase. For sugar metabolism, the most up-regulated DEGs encoded polygalacturonase and chitinase. For plant hormones, the most up-regulated DEGs were related to auxin signaling, and the most down-regulated DEGs were related to ethylene signaling. PLS-SEM analysis indicates that P metabolism was the most important pathway by which AMF regulates LR formation in this study. These data reveal the changes of genome-wide gene expression in responses to AMF inoculation in trifoliate orange and provide a solid basis for the future identification and characterization of key genes involved in LR formation induced by AMF.
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Affiliation(s)
- Weili Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Juan Li
- Department of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China
| | - Pengyang Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiezhong Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
- *Correspondence: Qing Yao
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