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Naveenarani M, Swamy HKM, Surya Krishna S, Mahadevaiah C, Valarmathi R, Manickavasagam M, Arun M, Hemaprabha G, Appunu C. Isolation and Characterization of Erianthus arundinaceus Phosphate Transporter 1 (PHT1) Gene Promoter and 5' Deletion Analysis of Transcriptional Regulation Regions under Phosphate Stress in Transgenic Tobacco. PLANTS (BASEL, SWITZERLAND) 2023; 12:3760. [PMID: 37960116 PMCID: PMC10650210 DOI: 10.3390/plants12213760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023]
Abstract
Phosphorus deficiency highly interferes with plant growth and development. Plants respond to persistent P deficiency by coordinating the expression of genes involved in the alleviation of stress. Promoters of phosphate transporter genes are a great choice for the development of genetically modified plants with enhanced phosphate uptake abilities, which improve crop yields in phosphate-deficient soils. In our previous study, the sugarcane phosphate transporter PHT1;2 gene showed a significantly high expression under salinity stress. In this study, the Erianthus arundinaceus EaPHT1;2 gene was isolated and characterized using various in silico tools. The deduced 542 amino acid residues have 10 transmembrane domains, with a molecular weight and isoelectric point of 58.9 kDa and 9.80, respectively. They displayed 71-96% similarity with Arabidopsis thaliana, Zea mays, and the Saccharum hybrid. To elucidate the function of the 5' regulatory region, the 1.1 kb promoter was isolated and validated in tobacco transgenics under Pi stress. The EaPHT1;2 promoter activity was detected using a β-glucuronidase (GUS) assay. The EaPHT1;2 promoter showed 3- to 4.2-fold higher expression than the most widely used CaMV35S promoter. The 5' deletion analysis with and without 5' UTRs revealed a small-sized 374 bp fragment with the highest promoter activity among 5' truncated fragments, which was 2.7 and 4.2 times higher than the well-used CaMV35S promoter under normal and Pi deprivation conditions, respectively. The strong and short promoter of EaPHT1;2 with 374 bp showed significant expression in low-Pi-stress conditions and it could be a valuable source for the development of stress-tolerant transgenic crops.
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Affiliation(s)
- Murugan Naveenarani
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; (M.N.); (H.K.M.S.); (S.S.K.); (C.M.); (R.V.); (G.H.)
- Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Huskur Kumaraswamy Mahadeva Swamy
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; (M.N.); (H.K.M.S.); (S.S.K.); (C.M.); (R.V.); (G.H.)
| | - Sakthivel Surya Krishna
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; (M.N.); (H.K.M.S.); (S.S.K.); (C.M.); (R.V.); (G.H.)
| | - Channappa Mahadevaiah
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; (M.N.); (H.K.M.S.); (S.S.K.); (C.M.); (R.V.); (G.H.)
- Division of Vegetable Crops, Indian Institute of Horticultural Research, Bengaluru 560089, Karnataka, India
| | - Ramanathan Valarmathi
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; (M.N.); (H.K.M.S.); (S.S.K.); (C.M.); (R.V.); (G.H.)
| | - Markandan Manickavasagam
- Department of Biotechnology, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India;
| | - Muthukrishnan Arun
- Department of Biotechnology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India;
| | - Govindakurup Hemaprabha
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; (M.N.); (H.K.M.S.); (S.S.K.); (C.M.); (R.V.); (G.H.)
| | - Chinnaswamy Appunu
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; (M.N.); (H.K.M.S.); (S.S.K.); (C.M.); (R.V.); (G.H.)
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A theory of mechanical stress-induced H 2O 2 signaling waveforms in Planta. J Math Biol 2022; 86:11. [PMID: 36478092 DOI: 10.1007/s00285-022-01835-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/10/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
Recent progress in nanotechnology-enabled sensors that can be placed inside of living plants has shown that it is possible to relay and record real-time chemical signaling stimulated by various abiotic and biotic stresses. The mathematical form of the resulting local reactive oxygen species (ROS) wave released upon mechanical perturbation of plant leaves appears to be conserved across a large number of species, and produces a distinct waveform from other stresses including light, heat and pathogen-associated molecular pattern (PAMP)-induced stresses. Herein, we develop a quantitative theory of the local ROS signaling waveform resulting from mechanical stress in planta. We show that nonlinear, autocatalytic production and Fickian diffusion of H2O2 followed by first order decay well describes the spatial and temporal properties of the waveform. The reaction-diffusion system is analyzed in terms of a new approximate solution that we introduce for such problems based on a single term logistic function ansatz. The theory is able to describe experimental ROS waveforms and degradation dynamics such that species-dependent dimensionless wave velocities are revealed, corresponding to subtle changes in higher moments of the waveform through an apparently conserved signaling mechanism overall. This theory has utility in potentially decoding other stress signaling waveforms for light, heat and PAMP-induced stresses that are similarly under investigation. The approximate solution may also find use in applied agricultural sensing, facilitating the connection between measured waveform and plant physiology.
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Mohr T, Horstman J, Gu YQ, Elarabi NI, Abdallah NA, Thilmony R. CRISPR-Cas9 Gene Editing of the Sal1 Gene Family in Wheat. PLANTS 2022; 11:plants11172259. [PMID: 36079639 PMCID: PMC9460255 DOI: 10.3390/plants11172259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
The highly conserved Sal1 encodes a bifunctional enzyme with inositol polyphosphate-1-phosphatase and 3′ (2′), 5′-bisphosphate nucleotidase activity and has been shown to alter abiotic stress tolerance in plants when disrupted. Precise gene editing techniques were used to generate Sal1 mutants in hexaploid bread wheat. The CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) Cas9 system with three guide RNAs (gRNAs) was used to inactivate six Sal1 homologous genes within the Bobwhite wheat genome. The resulting mutant wheat plants with all their Sal1 genes disabled had slimmer stems, had a modest reduction in biomass and senesced more slowly in water limiting conditions, but did not exhibit improved yield under drought conditions. Our results show that multiplexed gRNAs enabled effective targeted gene editing of the Sal1 gene family in hexaploid wheat. These Sal1 mutant wheat plants will be a resource for further research studying the function of this gene family in wheat.
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Affiliation(s)
- Toni Mohr
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - James Horstman
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - Yong Q. Gu
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - Nagwa I. Elarabi
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Naglaa A. Abdallah
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Roger Thilmony
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
- Correspondence: ; Tel.: +1-(510)-559-5761
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Koyro HW, Huchzermeyer B. From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity. PLANTS 2022; 11:plants11131654. [PMID: 35807605 PMCID: PMC9269222 DOI: 10.3390/plants11131654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/03/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022]
Abstract
Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.
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Affiliation(s)
- Hans-Werner Koyro
- Institute of Plantecology, Justus-Liebig-University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
- Correspondence:
| | - Bernhard Huchzermeyer
- Institute of Botany, Leibniz Universitaet Hannover, Herrenhaeuser Str. 2, 30416 Hannover, Germany; or
- AK Biotechnology, VDI-BV-Hannover, Hanomagstr. 12, 30449 Hannover, Germany
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Paes de Melo B, Carpinetti PDA, Fraga OT, Rodrigues-Silva PL, Fioresi VS, de Camargos LF, Ferreira MFDS. Abiotic Stresses in Plants and Their Markers: A Practice View of Plant Stress Responses and Programmed Cell Death Mechanisms. PLANTS (BASEL, SWITZERLAND) 2022; 11:1100. [PMID: 35567101 PMCID: PMC9103730 DOI: 10.3390/plants11091100] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 05/12/2023]
Abstract
Understanding how plants cope with stress and the intricate mechanisms thereby used to adapt and survive environmental imbalances comprise one of the most powerful tools for modern agriculture. Interdisciplinary studies suggest that knowledge in how plants perceive, transduce and respond to abiotic stresses are a meaningful way to design engineered crops since the manipulation of basic characteristics leads to physiological remodeling for plant adaption to different environments. Herein, we discussed the main pathways involved in stress-sensing, signal transduction and plant adaption, highlighting biochemical, physiological and genetic events involved in abiotic stress responses. Finally, we have proposed a list of practice markers for studying plant responses to multiple stresses, highlighting how plant molecular biology, phenotyping and genetic engineering interconnect for creating superior crops.
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Affiliation(s)
- Bruno Paes de Melo
- Trait Development Department, LongPing HighTech, Cravinhos 14140-000, SP, Brazil
| | - Paola de Avelar Carpinetti
- Genetics and Breeding Program, Universidade Federal do Espírito Santo, Alegre 29500-000, ES, Brazil; (P.d.A.C.); (V.S.F.); (M.F.d.S.F.)
| | - Otto Teixeira Fraga
- Applied Biochemistry Program, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil;
| | | | - Vinícius Sartori Fioresi
- Genetics and Breeding Program, Universidade Federal do Espírito Santo, Alegre 29500-000, ES, Brazil; (P.d.A.C.); (V.S.F.); (M.F.d.S.F.)
| | | | - Marcia Flores da Silva Ferreira
- Genetics and Breeding Program, Universidade Federal do Espírito Santo, Alegre 29500-000, ES, Brazil; (P.d.A.C.); (V.S.F.); (M.F.d.S.F.)
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Toulotte JM, Pantazopoulou CK, Sanclemente MA, Voesenek LACJ, Sasidharan R. Water stress resilient cereal crops: Lessons from wild relatives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:412-430. [PMID: 35029029 PMCID: PMC9255596 DOI: 10.1111/jipb.13222] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/10/2022] [Indexed: 05/20/2023]
Abstract
Cereal crops are significant contributors to global diets. As climate change disrupts weather patterns and wreaks havoc on crops, the need for generating stress-resilient, high-yielding varieties is more urgent than ever. One extremely promising avenue in this regard is to exploit the tremendous genetic diversity expressed by the wild ancestors of current day crop species. These crop wild relatives thrive in a range of environments and accordingly often harbor an array of traits that allow them to do so. The identification and introgression of these traits into our staple cereal crops can lessen yield losses in stressful environments. In the last decades, a surge in extreme drought and flooding events have severely impacted cereal crop production. Climate models predict a persistence of this trend, thus reinforcing the need for research on water stress resilience. Here we review: (i) how water stress (drought and flooding) impacts crop performance; and (ii) how identification of tolerance traits and mechanisms from wild relatives of the main cereal crops, that is, rice, maize, wheat, and barley, can lead to improved survival and sustained yields in these crops under water stress conditions.
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Affiliation(s)
- Justine M. Toulotte
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Chrysoula K. Pantazopoulou
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Maria Angelica Sanclemente
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Laurentius A. C. J. Voesenek
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Rashmi Sasidharan
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
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Muslu T, Biyiklioglu-Kaya S, Akpinar BA, Yuce M, Budak H. Pan-Genome miRNomics in Brachypodium. PLANTS 2021; 10:plants10050991. [PMID: 34065739 PMCID: PMC8156279 DOI: 10.3390/plants10050991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/17/2021] [Accepted: 05/12/2021] [Indexed: 01/14/2023]
Abstract
Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying genomic regions in the pan-genome could include protein-coding genes as well as microRNA(miRNAs), small non-coding RNAs playing key roles in the regulation of gene expression. In this study, we performed in silico miRNA identification from the genomic sequences of 54 lineages of Brachypodium distachyon, aiming to explore varying miRNA contents and their functional interactions. A total of 115 miRNA families were identified in 54 lineages, 56 of which were found to be present in all lineages. The miRNA families were classified based on their conservation among lineages and potential mRNA targets were identified. Obtaining information about regulatory mechanisms stemming from these miRNAs offers strong potential to provide a better insight into the complex traits that were potentially present in some lineages. Future work could lead us to introduce these traits to different lineages or other economically important plant species in order to promote their survival in different environmental conditions.
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Affiliation(s)
- Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | - Sezgi Biyiklioglu-Kaya
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | | | - Meral Yuce
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey;
| | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT 59802, USA;
- Correspondence:
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Cai K, Zeng F, Wang J, Zhang G. Identification and characterization of HAK/KUP/KT potassium transporter gene family in barley and their expression under abiotic stress. BMC Genomics 2021; 22:317. [PMID: 33932999 PMCID: PMC8088664 DOI: 10.1186/s12864-021-07633-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 04/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HAK/KUP/KT (High-affinity K+ transporters/K+ uptake permeases/K+ transporters) is the largest potassium transporter family in plants, and plays pivotal roles in K+ uptake and transport, as well as biotic and abiotic stress responses. However, our understanding of the gene family in barley (Hordeum vulgare L.) is quite limited. RESULTS In the present study, we identified 27 barley HAK/KUP/KT genes (hereafter called HvHAKs) through a genome-wide analysis. These HvHAKs were unevenly distributed on seven chromosomes, and could be phylogenetically classified into four clusters. All HvHAK protein sequences possessed the conserved motifs and domains. However, the substantial difference existed among HAK members in cis-acting elements and tissue expression patterns. Wheat had the most orthologous genes to barley HAKs, followed by Brachypodium distachyon, rice and maize. In addition, six barley HAK genes were selected to investigate their expression profiling in response to three abiotic stresses by qRT-PCR, and their expression levels were all up-regulated under salt, hyperosmotic and potassium deficiency treatments. CONCLUSION Twenty seven HAK genes (HvHAKs) were identified in barley, and they differ in tissue expression patterns and responses to salt stress, drought stress and potassium deficiency.
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Affiliation(s)
- Kangfeng Cai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Fanrong Zeng
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Guoping Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
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Chu C, Wang S, Paetzold L, Wang Z, Hui K, Rudd JC, Xue Q, Ibrahim AMH, Metz R, Johnson CD, Rush CM, Liu S. RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars 'TAM 111' and 'TAM 112'. Sci Rep 2021; 11:4301. [PMID: 33619336 PMCID: PMC7900135 DOI: 10.1038/s41598-021-83372-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023] Open
Abstract
Wheat cultivars 'TAM 111' and 'TAM 112' have been dominantly grown in the Southern U.S. Great Plains for many years due to their high yield and drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. A total of 2254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars. TAM 111 had 593 and 1532 dry-wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1670 at heading and grain-filling stages, respectively. The two cultivars have 1214 (53.9%) dry-wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry-wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each has a specific mechanism to cope with drought. Annotations of all 2254 genes showed 1855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. TAM 112 showed more active than TAM 111 in response to drought and carried more specific genes with most of them were up-regulated in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation. In addition, 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption. Data of gene sequence and expression regulation from this study also provided useful information of annotating novel genes associated with drought tolerance in the wheat genome.
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Affiliation(s)
- Chenggen Chu
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA.
- Sugarbeet and Potato Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, 1616 Albrecht Blvd. N, Fargo, ND, 58102, USA.
| | - Shichen Wang
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | - Li Paetzold
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Zhen Wang
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Kele Hui
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Jackie C Rudd
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Amir M H Ibrahim
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX, 77843, USA
| | - Richard Metz
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | - Charles D Johnson
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | - Charles M Rush
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Shuyu Liu
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA.
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González-Morales S, Solís-Gaona S, Valdés-Caballero MV, Juárez-Maldonado A, Loredo-Treviño A, Benavides-Mendoza A. Transcriptomics of Biostimulation of Plants Under Abiotic Stress. Front Genet 2021; 12:583888. [PMID: 33613631 PMCID: PMC7888440 DOI: 10.3389/fgene.2021.583888] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Plant biostimulants are compounds, living microorganisms, or their constituent parts that alter plant development programs. The impact of biostimulants is manifested in several ways: via morphological, physiological, biochemical, epigenomic, proteomic, and transcriptomic changes. For each of these, a response and alteration occur, and these alterations in turn improve metabolic and adaptive performance in the environment. Many studies have been conducted on the effects of different biotic and abiotic stimulants on plants, including many crop species. However, as far as we know, there are no reviews available that describe the impact of biostimulants for a specific field such as transcriptomics, which is the objective of this review. For the commercial registration process of products for agricultural use, it is necessary to distinguish the specific impact of biostimulants from that of other legal categories of products used in agriculture, such as fertilizers and plant hormones. For the chemical or biological classification of biostimulants, the classification is seen as a complex issue, given the great diversity of compounds and organisms that cause biostimulation. However, with an approach focused on the impact on a particular field such as transcriptomics, it is perhaps possible to obtain a criterion that allows biostimulants to be grouped considering their effects on living systems, as well as the overlap of the impact on metabolism, physiology, and morphology occurring between fertilizers, hormones, and biostimulants.
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Keller I, Rodrigues CM, Neuhaus HE, Pommerrenig B. Improved resource allocation and stabilization of yield under abiotic stress. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153336. [PMID: 33360492 DOI: 10.1016/j.jplph.2020.153336] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Sugars are the main building blocks for carbohydrate storage, but also serve as signaling molecules and protective compounds during abiotic stress responses. Accordingly, sugar transport proteins fulfill multiple roles as they mediate long distance sugar allocation, but also shape the subcellular and tissue-specific carbohydrate profiles by balancing the levels of these molecules in various compartments. Accordingly, transporter activity represents a target by classical or directed breeding approaches, to either, directly increase phloem loading or to increase sink strength in crop species. The relative subcellular distribution of sugars is critical for molecular signaling affecting yield-relevant processes like photosynthesis, onset of flowering and stress responses, while controlled long-distance sugar transport directly impacts development and productivity of plants. However, long-distance transport is prone to become unbalanced upon adverse environmental conditions. Therefore, we highlight the influence of stress stimuli on sucrose transport in the phloem and include the role of stress induced cellular carbohydrate sinks, like raffinose or fructans, which possess important roles to build up tolerance against challenging environmental conditions. In addition, we report on recent breeding approaches that resulted in altered source and sink capacities, leading to increased phloem sucrose shuttling in crops. Finally, we present strategies integrating the need of cellular stress-protection into the general picture of long-distance transport under abiotic stress, and point to possible approaches improving plant performance and resource allocation under adverse environmental conditions, leading to stabilized or even increased crop yield.
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Affiliation(s)
- Isabel Keller
- Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - H Ekkehard Neuhaus
- Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany.
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Tiwari P, Indoliya Y, Chauhan AS, Singh P, Singh PK, Singh PC, Srivastava S, Pande V, Chakrabarty D. Auxin-salicylic acid cross-talk ameliorates OsMYB-R1 mediated defense towards heavy metal, drought and fungal stress. JOURNAL OF HAZARDOUS MATERIALS 2020; 399:122811. [PMID: 32540701 DOI: 10.1016/j.jhazmat.2020.122811] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/18/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
The MYB TF family is an immensely large and functionally diverse class of proteins involved in the regulation of cell cycle, cell morphogenesis to stress signaling mechanism. The present study deciphered the hormonal cross-talk of wound inducible and stress-responsive OsMYB-R1 transcription factor in combating abiotic [Cr(VI) and drought/PEG] as well as biotic (Rhizoctonia solani) stress. OsMYB-R1 over-expressing rice transgenics exhibit a significant increase in lateral roots, which may be associated with increased tolerance under Cr(VI) and drought exposure. In contrast, its loss-of-function reduces stress tolerance. Higher auxin accumulation in the OsMYB-R1 over-expressed lines further strengthens the protective role of lateral roots under stress conditions. RNA-seq. data reveals over-representation of salicylic acid signaling molecule calcium-dependent protein kinases, which probably activate the stress-responsive downstream genes (Peroxidases, Glutathione S-transferases, Osmotins, Heat Shock Proteins, Pathogenesis Related-Proteins). Enzymatic studies further confirm OsMYB-R1 mediated robust antioxidant system as catalase, guaiacol peroxidase and superoxide dismutase activities were found to be increased in the over-expressed lines. Our results suggest that OsMYB-R1 is part of a complex network of transcription factors controlling the cross-talk of auxin and salicylic acid signaling and other genes in response to multiple stresses by modifying molecular signaling, internal cellular homeostasis and root morphology.
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Affiliation(s)
- Poonam Tiwari
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India; Department of Biotechnology, Kumaun University, Nainital 26300, India
| | - Yuvraj Indoliya
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Abhishek Singh Chauhan
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Puja Singh
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pradyumna Kumar Singh
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Poonam C Singh
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Suchi Srivastava
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital 26300, India
| | - Debasis Chakrabarty
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Proteomic profiling of developing wheat heads under water-stress. Funct Integr Genomics 2020; 20:695-710. [PMID: 32681185 DOI: 10.1007/s10142-020-00746-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 10/23/2022]
Abstract
A replicated iTRAQ (isobaric tags for relative and absolute quantification) study on developing wheat heads from two doubled haploid (DH) lines identified from a cross between cv Westonia x cv Kauz characterized the proteome changes influenced by reproductive stage water-stress. All lines were exposed to 10 days of water-stress from early booting (Zadok 40), with sample sets taken from five head developmental stages. Two sample groups (water-stressed and control) account for 120 samples that required 18 eight-plex iTRAQ runs. Based on the IWGSC RefSeq v1 wheat assembly, among the 4592 identified proteins, a total of 132 proteins showed a significant response to water-stress, including the down-regulation of a mitochondrial Rho GTPase, a regulator of intercellular fundamental biological processes (7.5 fold) and cell division protein FtsZ at anthesis (6.0 fold). Up-regulated proteins included inosine-5'-monophosphate dehydrogenase (3.83 fold) and glycerophosphodiester phosphodiesterase (4.05 fold). The Pre-FHE and FHE stages (full head emerged) of head development were differentiated by 391 proteins and 270 proteins differentiated the FHE and Post-FHE stages. Water-stress during meiosis affected seed setting with 27% and 6% reduction in the progeny DH105 and DH299 respectively. Among the 77 proteins that differentiated between the two DH lines, 7 proteins were significantly influenced by water-stress and correlated with the seed set phenotype response of the DH lines to water-stress (e.g. the up-regulation of a subtilisin-like protease in DH 299 relative to DH 105). This study provided unique insights into the biological changes in developing wheat head that occur during water-stress.
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Thayale Purayil F, Rajashekar B, S. Kurup S, Cheruth AJ, Subramaniam S, Hassan Tawfik N, M.A. Amiri K. Transcriptome Profiling of Haloxylon persicum (Bunge ex Boiss and Buhse) an Endangered Plant Species under PEG-Induced Drought Stress. Genes (Basel) 2020; 11:genes11060640. [PMID: 32531994 PMCID: PMC7349776 DOI: 10.3390/genes11060640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 01/06/2023] Open
Abstract
Haloxylon persicum is an endangered western Asiatic desert plant species, which survives under extreme environmental conditions. In this study, we focused on transcriptome analysis of H. persicum to understand the molecular mechanisms associated with drought tolerance. Two different periods of polyethylene glycol (PEG)-induced drought stress (48 h and 72 h) were imposed on H. persicum under in vitro conditions, which resulted in 18 million reads, subsequently assembled by de novo method with more than 8000 transcripts in each treatment. The N50 values were 1437, 1467, and 1524 for the control sample, 48 h samples, and 72 h samples, respectively. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis resulted in enrichment of mitogen-activated protein kinase (MAPK) and plant hormone signal transduction pathways under PEG-induced drought conditions. The differential gene expression analysis (DGEs) revealed significant changes in the expression pattern between the control and the treated samples. The KEGG analysis resulted in mapping transcripts with 138 different pathways reported in plants. The differential expression of drought-responsive transcription factors depicts the possible signaling cascades involved in drought tolerance. The present study provides greater insight into the fundamental transcriptome reprogramming of desert plants under drought.
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Affiliation(s)
- Fayas Thayale Purayil
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, P.O. Box. Al-Ain 15551, UAE; (F.T.P.); (A.J.C.); (N.H.T.)
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, UAE
| | - Balaji Rajashekar
- Institute of Computer Science, University of Tartu, 50409 Tartu, Estonia;
- Celixa, Bangalore, Karnataka 560020, India
| | - Shyam S. Kurup
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, P.O. Box. Al-Ain 15551, UAE; (F.T.P.); (A.J.C.); (N.H.T.)
- Correspondence: (S.S.K.); (K.M.A.)
| | - Abdul Jaleel Cheruth
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, P.O. Box. Al-Ain 15551, UAE; (F.T.P.); (A.J.C.); (N.H.T.)
| | - Sreeramanan Subramaniam
- School of Biological Sciences, Universiti Sains Malaysia (USM), Minden Heights, Georgetown, Penang 11800, Malaysia;
| | - Nadia Hassan Tawfik
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, P.O. Box. Al-Ain 15551, UAE; (F.T.P.); (A.J.C.); (N.H.T.)
| | - Khaled M.A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, UAE
- Department of Biology, College of Science, United Arab Emirates University, P.O. Box. Al Ain 15551, UAE
- Correspondence: (S.S.K.); (K.M.A.)
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15
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Nawaz M, Wang Z. Abscisic Acid and Glycine Betaine Mediated Tolerance Mechanisms under Drought Stress and Recovery in Axonopus compressus: A New Insight. Sci Rep 2020; 10:6942. [PMID: 32332777 PMCID: PMC7181621 DOI: 10.1038/s41598-020-63447-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
Changing climatic scenarios affect plant growth and consequences are more malicious in drought conditions. This study was performed for better understanding of tolerance mechanisms under prevailing drought stress and succeeding recovery in Axonopus compressus by exogenously applied abscisic acid (ABA) and glycine betaine (GB). Three A. compressus accessions (A-38, A-58 and A-59) were subjected to well-watered (100% field capacity) and drought (40% field capacity) conditions. Two weeks later, plants were recovered from drought by re-watering. Water (control), GB, ABA and their combination were foliar applied on plants under drought twice a week until recovery. Drought stress decreased photosynthetic pigments and increased reactive oxygen species, lipid peroxidation, osmolytes and antioxidants in all accessions of A. compressus. Nonetheless, exogenous ABA and GB alone or in combination improved drought tolerance in all accessions which was maintained even after recovery. Maximum decrease in hydrogen peroxide and malondialdehyde, and increase in soluble sugars, proteins, proline, phenolics and chlorophyll contents, and superoxide dismutase, catalase, peroxidase and ascorbate peroxidase activity was recorded when GB was applied alone under drought. Order of improvement in drought tolerance among accessions was A-58 > A-59 > A-38. In conclusion, improved drought tolerance mechanisms by ABA and GB in A. compressus were retained even after recovery.
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Affiliation(s)
- Mohsin Nawaz
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, 570228, P.R. China
| | - Zhiyong Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, 570228, P.R. China.
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Lew TTS, Koman VB, Silmore KS, Seo JS, Gordiichuk P, Kwak SY, Park M, Ang MCY, Khong DT, Lee MA, Chan-Park MB, Chua NH, Strano MS. Real-time detection of wound-induced H 2O 2 signalling waves in plants with optical nanosensors. NATURE PLANTS 2020; 6:404-415. [PMID: 32296141 DOI: 10.1038/s41477-020-0632-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 03/10/2020] [Indexed: 05/21/2023]
Abstract
Decoding wound signalling in plants is critical for understanding various aspects of plant sciences, from pest resistance to secondary metabolite and phytohormone biosynthesis. The plant defence responses are known to primarily involve NADPH-oxidase-mediated H2O2 and Ca2+ signalling pathways, which propagate across long distances through the plant vasculature and tissues. Using non-destructive optical nanosensors, we find that the H2O2 concentration profile post-wounding follows a logistic waveform for six plant species: lettuce (Lactuca sativa), arugula (Eruca sativa), spinach (Spinacia oleracea), strawberry blite (Blitum capitatum), sorrel (Rumex acetosa) and Arabidopsis thaliana, ranked in order of wave speed from 0.44 to 3.10 cm min-1. The H2O2 wave tracks the concomitant surface potential wave measured electrochemically. We show that the plant RbohD glutamate-receptor-like channels (GLR3.3 and GLR3.6) are all critical to the propagation of the wound-induced H2O2 wave. Our findings highlight the utility of a new type of nanosensor probe that is species-independent and capable of real-time, spatial and temporal biochemical measurements in plants.
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Affiliation(s)
- Tedrick Thomas Salim Lew
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Disruptive & Sustainable Technologies for Agricultural Precision IRG, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #03-06/07/08 Research Wing, Singapore, Singapore
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin S Silmore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jun Sung Seo
- Disruptive & Sustainable Technologies for Agricultural Precision IRG, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #03-06/07/08 Research Wing, Singapore, Singapore
- Temasek Life Sciences Laboratory Limited, 1 Research Link National University of Singapore, Singapore, Singapore
| | - Pavlo Gordiichuk
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Seon-Yeong Kwak
- Department of Biosystems and Biomaterials Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Minkyung Park
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Disruptive & Sustainable Technologies for Agricultural Precision IRG, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #03-06/07/08 Research Wing, Singapore, Singapore
| | - Mervin Chun-Yi Ang
- Disruptive & Sustainable Technologies for Agricultural Precision IRG, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #03-06/07/08 Research Wing, Singapore, Singapore
| | - Duc Thinh Khong
- Disruptive & Sustainable Technologies for Agricultural Precision IRG, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #03-06/07/08 Research Wing, Singapore, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Michael A Lee
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mary B Chan-Park
- Disruptive & Sustainable Technologies for Agricultural Precision IRG, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #03-06/07/08 Research Wing, Singapore, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Nam-Hai Chua
- Disruptive & Sustainable Technologies for Agricultural Precision IRG, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #03-06/07/08 Research Wing, Singapore, Singapore
- Temasek Life Sciences Laboratory Limited, 1 Research Link National University of Singapore, Singapore, Singapore
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Disruptive & Sustainable Technologies for Agricultural Precision IRG, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #03-06/07/08 Research Wing, Singapore, Singapore.
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17
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Identification and quantitation of genetically modified (GM) ingredients in maize, rice, soybean and wheat-containing retail foods and feeds in Turkey. Journal of Food Science and Technology 2019; 57:787-793. [PMID: 32116387 DOI: 10.1007/s13197-019-04080-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/27/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
The cultivation area and diversity of genetically modified (GM) crop varieties worldwide is increasing rapidly. Taking Turkey as an example of a country with tight restrictions on the import and use of GM crops but limited resources for product monitoring, we developed a cost-effective 3-tier screening protocol, and tested 110 retail food products and 13 animal feeds available in 2016-2017 for GM ingredients. No evidence was found for the presence of GM wheat or rice in the foodstuffs tested; however, 6 feeds and 3 food products containing soybean and/or maize were positive for one or more GM elements. GM events present in positive samples were identified by event-specific PCR and quantified by real-time PCR. We also compared the results with previous surveys in Turkey. Overall, we observed consistent use of GM animal feeds; however, these were not labelled as GM at the point of sale. Occasional food products also tested positive for GM ingredients, usually at low concentrations that could be attributed to accidental contamination.
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Rojas M, Jimenez-Bremont F, Villicaña C, Carreón-Palau L, Arredondo-Vega BO, Gómez-Anduro G. Involvement of OpsLTP1 from Opuntia streptacantha in abiotic stress adaptation and lipid metabolism. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:816-829. [PMID: 31138396 DOI: 10.1071/fp18280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/27/2019] [Indexed: 06/09/2023]
Abstract
Plant lipid transfer proteins (LTPs) exhibit the ability to transfer lipids between membranes in vitro, and have been implicated in diverse physiological processes associated to plant growth, reproduction, development, biotic and abiotic stress responses. However, their mode of action is not yet fully understood. To explore the functions of the OpsLTP1 gene encoding a LTP from cactus pear Opuntia streptacantha Lem., we generated transgenic Arabidopsis thaliana (L.) Heynh. plants to overexpress OpsLTP1 and contrasted our results with the loss-of-function mutant ltp3 from A. thaliana under abiotic stress conditions. The ltp3 mutant seeds showed impaired germination under salt and osmotic treatments, in contrast to OpsLTP1 overexpressing lines that displayed significant increases in germination rate. Moreover, stress recovery assays showed that ltp3 mutant seedlings were more sensitive to salt and osmotic treatments than wild-type plants suggesting that AtLTP3 is required for stress-induced responses, while the OpsLTP1 overexpressing line showed no significant differences. In addition, OpsLTP1 overexpressing and ltp3 mutant seeds stored lower amount of total lipids compared with wild-type seeds, showing changes primarily on 16C and 18C fatty acids. However, ltp3 mutant also lead changes in lipid profile and no over concrete lipids which may suggest a compensatory activation of other LTPs. Interestingly, linoleic acid (18:2ω6) was consistently increased in neutral, galactoglycerolipids and phosphoglycerolipids of OpsLTP1 overexpressing line indicating a role of OpsLTP1 in the modulation of lipid composition in A. thaliana.
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Affiliation(s)
- Mario Rojas
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Apdo, Postal 128, 23096 La Paz, B.C.S., México
| | - Francisco Jimenez-Bremont
- Instituto Potosino de Investigación Científica y Tecnológica. Camino a la Presa San José 2055, Col. Lomas 4 sección CP. 78216, San Luis Potosí, S.L.P., México
| | - Claudia Villicaña
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a Eldorado Km. 5.5, Apartado Postal 32-A. C. P. 80110, Culiacán, Sinaloa, México
| | - Laura Carreón-Palau
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Apdo, Postal 128, 23096 La Paz, B.C.S., México
| | - Bertha Olivia Arredondo-Vega
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Apdo, Postal 128, 23096 La Paz, B.C.S., México
| | - Gracia Gómez-Anduro
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Apdo, Postal 128, 23096 La Paz, B.C.S., México; and Corresponding author.
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19
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Han X, Mao L, Lu W, Wei X, Ying T, Luo Z. Positive Regulation of the Transcription of AchnKCS by a bZIP Transcription Factor in Response to ABA-Stimulated Suberization of Kiwifruit. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7390-7398. [PMID: 31244202 DOI: 10.1021/acs.jafc.9b01609] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Wound-induced suberization is an essentially protective healing process for wounded fruit to reduce water loss and microbial infection. It has been demonstrated that abscisic acid (ABA) could promote wound suberization, but the molecular mechanism of ABA regulation remains little known. In this study, the transcript level of Achn030011 (designated as AchnKCS), coding a β-ketoacyl-coenzyme A synthase (KCS) involved in suberin biosynthesis, was found to be significantly upregulated by ABA in wounded kiwifruit. A bZIP transcription factor (Achn270881), a possible downstream transcription factor in the ABA signaling pathway, was screened and designated as AchnbZIP12 according to its homology with related Arabidopsis transcription factors. A yeast one-hybrid assay demonstrated that AchnbZIP12 could interact with the AchnKCS promoter. Furthermore, significant trans-activation of AchnbZIP12 on AchnKCS was verified. The transcript level of AchnbZIP12 was also upregulated upon treatment with ABA. These results imply that AchnbZIP12 acts as a positive regulator in ABA-mediated AchnKCS transcription during wound suberization of kiwifruit.
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Affiliation(s)
- Xueyuan Han
- School of Life Sciences , Shaoxing University , Shaoxing , Zhejiang Province 312000 , People's Republic of China
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
- Ningbo Research Institute , Zhejiang University , Ningbo 315100 , People's Republic of China
| | - Wenjing Lu
- Institute of Food Science , Zhejiang Academy of Agricultural Sciences , Hangzhou 310021 , People's Republic of China
| | - Xiaopeng Wei
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Tiejin Ying
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of AgroFood Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs , Zhejiang University , Hangzhou 310058 , People's Republic of China
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20
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Cao J, Ye C, Hao G, Dabney-Smith C, Hunt AG, Li QQ. Root Hair Single Cell Type Specific Profiles of Gene Expression and Alternative Polyadenylation Under Cadmium Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:589. [PMID: 31134121 PMCID: PMC6523994 DOI: 10.3389/fpls.2019.00589] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/23/2019] [Indexed: 05/15/2023]
Abstract
Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic stress by increasing the heterogeneity at mRNA 3'-ends. Heavy metals like cadmium pollute water and soil due to mining and industry applications. Understanding how plants cope with heavy metal stress remains an interesting question. The Arabidopsis root hair was chosen as a single cell model to investigate the functional role of APA in cadmium stress response. Primary root growth inhibition and defective root hair morphotypes were observed. Poly(A) tag (PAT) libraries from single cell types, i.e., root hair cells, non-hair epidermal cells, and whole root tip under cadmium stress were prepared and sequenced. Interestingly, a root hair cell type-specific gene expression under short term cadmium exposure, but not related to the prolonged treatment, was detected. Differentially expressed poly(A) sites were identified, which largely contributed to altered gene expression, and enriched in pentose and glucuronate interconversion pathways as well as phenylpropanoid biosynthesis pathways. Numerous genes with poly(A) site switching were found, particularly for functions in cell wall modification, root epidermal differentiation, and root hair tip growth. Our findings suggest that APA plays a functional role as a potential stress modulator in root hair cells under cadmium treatment.
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Affiliation(s)
- Jingyi Cao
- Department of Biology, Miami University, Oxford, OH, United States
- Cell, Molecular, Structural Biology Graduate Program, Miami University, Oxford, OH, United States
| | - Congting Ye
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guijie Hao
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Carole Dabney-Smith
- Cell, Molecular, Structural Biology Graduate Program, Miami University, Oxford, OH, United States
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, United States
| | - Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Qingshun Q. Li
- Department of Biology, Miami University, Oxford, OH, United States
- Cell, Molecular, Structural Biology Graduate Program, Miami University, Oxford, OH, United States
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
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Agarwal P, Khurana P. Functional characterization of HSFs from wheat in response to heat and other abiotic stress conditions. Funct Integr Genomics 2019; 19:497-513. [PMID: 30868385 DOI: 10.1007/s10142-019-00666-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 10/27/2022]
Abstract
High temperature stress is known to be one of the major limiting factors for wheat productivity worldwide. HSFs are known to play a central role in heat stress response in plants. Hence, the current study is an attempt to explore an in-depth involvement of TaHSFs in stress responses mainly in heat and other abiotic responses like salinity, drought, and cold stress. Effort was made to understand as how the expression of HSF is able to define the differential robustness of wheat varieties. Subsequent studies were done to establish the involvement of any temporal or spatial cue on the behavior of these TaHSFs under heat stress conditions. A total of 53 HSFs have been reported until date and out of these, few TaHSFs including one identified in our library, i.e., TaHsfA2d (Traes_4AS_52EB860E7.2), were selected for the expression analysis studies. The expressions of these HSFs were found to differ in both magnitude and sensitivity to the heat as well as other abiotic stresses. Moreover, these TaHSFs displayed wide range of expression in different tissues like anther, ovary, lemma, palea, awn, glume, and different stages of seed development. Thus, TaHSFs appear to be under dynamic expression as they respond in a unique manner to spatial, temporal, and environmental cues. Therefore, these HSFs can be used as candidate genes for understanding the molecular mechanism under heat stress and can be utilized for improving crop yield by enhancing the tolerance and survival of the crop plants under adverse environment conditions.
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Affiliation(s)
- Preeti Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, 110021, India.
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Yan H, Zhou B, He W, Nie Y, Li Y. Expression characterisation of cyclophilin BrROC1 during light treatment and abiotic stresses response in Brassica rapa subsp. rapa 'Tsuda'. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:1223-1232. [PMID: 32291012 DOI: 10.1071/fp18029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 07/02/2018] [Indexed: 05/20/2023]
Abstract
ROC1 is a prototypic peptidyl prolyl cis/trans isomerase (PPIase) of the plant cytosol belonging to the large subfamily of cyclophilins that are associated with diverse functions through foldase, scaffolding, chaperoning or other unknown activities. Although many functions of plant cyclophilins have been reported, the molecular basis of stress-responsive expression of plant cyclophilins is still largely unknown. To characterise the roles of BrROC1 during light treatment and their responses in various abiotic stresses, we identified BrROC1 genes and characterised their expression patterns in Brassica rapa subsp. rapa 'Tsuda'. Our results showed that BrROC1 genes are multi-family genes. Transcript level analysis showed BrROC1-2 expressed higher than BrROC1-1 in 0 to 6-day-old seedlings under natural light. Moreover, BrROC1-2 genes were also induced to highly express in the cotyledon, upper hypocotyls and lower hypocotyls of seedlings under UV-A and blue-light treatment. In addition, the transcript level of BrROC1-1 was higher in pigment tissues than that in unpigment tissues (cotyledon and lower hypocotyl) under UV-A and blue-light treatment. Furthermore, when the unpigment epidermis (shaded light) of 2-month-old 'Tsuda' turnip roots was exposed to UV-A light, transcript levels of the BrROC1-1 and BrROC1-2 were significantly increased with time prolongation. These two BrROC1 genes might be involved in UV-A-induced anthocyanin synthesis in the root epidermis of 'Tsuda' turnip, which accumulates high levels of anthocyanin. These two BrROC1 genes were also induced to be regulated by abiotic stresses such as high or low temperature, dehydration, osmotic and salt stresses. Then, the results indicate that BrROC1 genes are involved in light induction response and may play important roles in adaptation of plants to various environmental stresses.
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Affiliation(s)
- Haifang Yan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Bo Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Wei He
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yuzhe Nie
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yuhua Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
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Ullah N, Yüce M, Neslihan Öztürk Gökçe Z, Budak H. Comparative metabolite profiling of drought stress in roots and leaves of seven Triticeae species. BMC Genomics 2017; 18:969. [PMID: 29246190 PMCID: PMC5731210 DOI: 10.1186/s12864-017-4321-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/21/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Drought is a lifestyle disease. Plant metabolomics has been exercised for understanding the fine-tuning of the potential pathways to surmount the adverse effects of drought stress. A broad spectrum of morphological and metabolic responses from seven Triticeae species including wild types with different drought tolerance/susceptibility level was investigated under control and water scarcity conditions. RESULTS Significant morphological parameters measured were root length, surface area, average root diameter and overall root development. Principal Component Analysis, Partial Least-Squares-Discriminant Analysis and Hierarchical Cluster Analysis were applied to the metabolomic data obtained by Gas Chromatography-Mass Spectrometry technique in order to determine the important metabolites of the drought tolerance across seven different Triticeae species. The metabolites showing significant accumulation under the drought stress were considered as the key metabolites and correlated with potential biochemical pathways, enzymes or gene locations for a better understanding of the tolerance mechanisms. In all tested species, 45 significantly active metabolites with possible roles in drought stress were identified. Twenty-one metabolites out of forty-five including sugars, amino acids, organic acids and low molecular weight compounds increased in both leaf and root samples of TR39477, IG132864 and Bolal under the drought stress, contrasting to TTD-22, Tosunbey, Ligustica and Meyeri samples. Three metabolites including succinate, aspartate and trehalose were selected for further genome analysis due to their increased levels in TR39477, IG132864, and Bolal upon drought stress treatment as well as their significant role in energy producing biochemical pathways. CONCLUSION These results demonstrated that the genotypes with high drought tolerance skills, especially wild emmer wheat, have a great potential to be a genetic model system for experiments aiming to validate metabolomics-genomics networks.
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Affiliation(s)
- Naimat Ullah
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Meral Yüce
- Nanotechnology Research and Application Centre, Sabanci University, 34956, Istanbul, Turkey
| | - Z Neslihan Öztürk Gökçe
- Ayhan Sahenk Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey
| | - Hikmet Budak
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, USA.
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Hussain B, Lucas SJ, Ozturk L, Budak H. Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stagein wheat. Sci Rep 2017. [PMID: 29142238 DOI: 10.1038/s41598‐017‐15726‐6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder's Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity. Of 49 mapped QTLs, six were for Na+ exclusion (NAX) and two QTLs (qSNAX.2 A.1, qSNAX.2 A.2) on chromosome 2 A coincided with a reported major NAX QTL (Nax1 or HKT1;4). Two other major NAX QTLs were mapped on 7 A, which contributed 11.23 and 18.79% of the salt tolerance respectively. In addition to Ca+2 and Mg+2 QTLs, twenty-seven QTLs for tissue Phosphorus, Zinc, Iron, Manganese, Copper, Sulphur and Boron concentrations under salinity were also mapped. The 1293 segregating SNPs were annotated/located within genes for various ion channels, signalling pathways, transcription factors (TFs), metabolic pathways and 258 of them showed differential expression in silico under salinity. These findings will create new opportunities for salt tolerance breeding programs.
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Affiliation(s)
- Babar Hussain
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Stuart James Lucas
- SU Nanotechnology Research and Application Centre, Sabanci University, Istanbul, Turkey
| | - Levent Ozturk
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. .,Cereal genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stagein wheat. Sci Rep 2017; 7:15662. [PMID: 29142238 PMCID: PMC5688110 DOI: 10.1038/s41598-017-15726-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 11/01/2017] [Indexed: 11/16/2022] Open
Abstract
Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder’s Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity. Of 49 mapped QTLs, six were for Na+ exclusion (NAX) and two QTLs (qSNAX.2 A.1, qSNAX.2 A.2) on chromosome 2 A coincided with a reported major NAX QTL (Nax1 or HKT1;4). Two other major NAX QTLs were mapped on 7 A, which contributed 11.23 and 18.79% of the salt tolerance respectively. In addition to Ca+2 and Mg+2 QTLs, twenty-seven QTLs for tissue Phosphorus, Zinc, Iron, Manganese, Copper, Sulphur and Boron concentrations under salinity were also mapped. The 1293 segregating SNPs were annotated/located within genes for various ion channels, signalling pathways, transcription factors (TFs), metabolic pathways and 258 of them showed differential expression in silico under salinity. These findings will create new opportunities for salt tolerance breeding programs.
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26
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Exploring the heat-responsive chaperones and microsatellite markers associated with terminal heat stress tolerance in developing wheat. Funct Integr Genomics 2017; 17:621-640. [PMID: 28573536 DOI: 10.1007/s10142-017-0560-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 04/06/2017] [Accepted: 04/17/2017] [Indexed: 10/19/2022]
Abstract
Global warming is a major threat for agriculture and food security, and in many cases the negative impacts are already apparent. Wheat is one of the most important staple food crops and is highly sensitive to the heat stress (HS) during reproductive and grain-filling stages. Here, whole transcriptome analysis of thermotolerant wheat cv. HD2985 was carried out at the post-anthesis stage under control (22 ± 3 °C) and HS-treated (42 °C, 2 h) conditions using Illumina Hiseq and Roche GS-FLX 454 platforms. We assembled ~24 million (control) and ~23 million (HS-treated) high-quality trimmed reads using different assemblers with optimal parameters. De novo assembly yielded 52,567 (control) and 59,658 (HS-treated) unigenes. We observed 785 transcripts to be upregulated and 431 transcripts to be downregulated under HS; 78 transcripts showed >10-fold upregulation such as HSPs, metabolic pathway-related genes, etc. Maximum number of upregulated genes was observed to be associated with processes such as HS-response, protein-folding, oxidation-reduction and photosynthesis. We identified 2008 and 2483 simple sequence repeats (SSRs) markers from control and HS-treated samples; 243 SSRs were observed to be overlying on stress-associated genes. Polymorphic study validated four SSRs to be heat-responsive in nature. Expression analysis of identified differentially expressed transcripts (DETs) showed very high fold increase in the expression of catalytic chaperones (HSP26, HSP17, and Rca) in contrasting wheat cvs. HD2985 and HD2329 under HS. We observed positive correlation between RNA-seq and qRT-PCR expression data. The present study culminated in greater understanding of the heat-response of tolerant genotype and has provided good candidate genes for the marker development and screening of wheat germplasm for thermotolerance.
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Alptekin B, Langridge P, Budak H. Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 2017; 17:145-170. [PMID: 27665284 PMCID: PMC5383695 DOI: 10.1007/s10142-016-0525-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.
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Affiliation(s)
- Burcu Alptekin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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28
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Arshad M, Feyissa BA, Amyot L, Aung B, Hannoufa A. MicroRNA156 improves drought stress tolerance in alfalfa (Medicago sativa) by silencing SPL13. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 258:122-136. [PMID: 28330556 DOI: 10.1016/j.plantsci.2017.01.018] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 01/26/2017] [Accepted: 01/30/2017] [Indexed: 05/20/2023]
Abstract
Alfalfa (Medicago sativa) is an important forage crop that is often grown in areas that frequently experience drought and water shortage. MicroRNA156 (miR156) is an emerging tool for improving various traits in plants. We tested the role of miR156d in drought response of alfalfa, and observed a significant improvement in drought tolerance of miR156 overexpression (miR156OE) alfalfa genotypes compared to the wild type control (WT). In addition to higher survival and reduced water loss, miR156OE genotypes also maintained higher stomatal conductance compared to WT during drought stress. Furthermore, we observed an enhanced accumulation of compatible solute (proline) and increased levels of abscisic acid (ABA) and antioxidants in miR156OE genotypes. Similarly, alfalfa plants with reduced expression of miR156-targeted SPL13 showed reduced water loss and enhanced stomatal conductance, chlorophyll content and photosynthetic assimilation. Several genes known to be involved in drought tolerance were differentially expressed in leaf and root of miR156 overexpression plants. Taken together, our findings reveal that miR156 improves drought tolerance in alfalfa at least partially by silencing SPL13.
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Affiliation(s)
- Muhammad Arshad
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada.
| | - Biruk A Feyissa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada; Biology Department, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.
| | - Lisa Amyot
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada.
| | - Banyar Aung
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada.
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada; Biology Department, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.
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29
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Ben Romdhane W, Ben-Saad R, Meynard D, Verdeil JL, Azaza J, Zouari N, Fki L, Guiderdoni E, Al-Doss A, Hassairi A. Ectopic Expression of Aeluropus littoralis Plasma Membrane Protein Gene AlTMP1 Confers Abiotic Stress Tolerance in Transgenic Tobacco by Improving Water Status and Cation Homeostasis. Int J Mol Sci 2017; 18:E692. [PMID: 28338609 PMCID: PMC5412278 DOI: 10.3390/ijms18040692] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/12/2017] [Accepted: 03/20/2017] [Indexed: 01/15/2023] Open
Abstract
We report here the isolation and functional analysis of AlTMP1 gene encoding a member of the PMP3 protein family. In Aeluropus littoralis, AlTMP1 is highly induced by abscisic acid (ABA), cold, salt, and osmotic stresses. Transgenic tobacco expressing AlTMP1 exhibited enhanced tolerance to salt, osmotic, H₂O₂, heat and freezing stresses at the seedling stage. Under greenhouse conditions, the transgenic plants showed a higher level of tolerance to drought than to salinity. Noteworthy, AlTMP1 plants yielded two- and five-fold more seeds than non-transgenic plants (NT) under salt and drought stresses, respectively. The leaves of AlTMP1 plants accumulated lower Na⁺ but higher K⁺ and Ca2+ than those of NT plants. Tolerance to osmotic and salt stresses was associated with higher membrane stability, low electrolyte leakage, and improved water status. Finally, accumulation of AlTMP1 in tobacco altered the regulation of some stress-related genes in either a positive (NHX1, CAT1, APX1, and DREB1A) or negative (HKT1 and KT1) manner that could be related to the observed tolerance. These results suggest that AlTMP1 confers stress tolerance in tobacco through maintenance of ion homeostasis, increased membrane integrity, and water status. The observed tolerance may be due to a direct or indirect effect of AlTMP1 on the expression of stress-related genes which could stimulate an adaptive potential not present in NT plants.
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Affiliation(s)
- Walid Ben Romdhane
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia.
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
- Current Address: Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia..
| | - Rania Ben-Saad
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
| | - Donaldo Meynard
- CIRAD-UMR AGAP (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement), Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Jean-Luc Verdeil
- CIRAD-UMR AGAP (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement), Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Jalel Azaza
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
| | - Nabil Zouari
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
| | - Lotfi Fki
- Laboratory of Plant Biotechnology Applied to Crop Improvement, Faculty of Sciences of Sfax, University of Sfax, B.P 802, 3038 Sfax, Tunisia.
| | - Emmanuel Guiderdoni
- CIRAD-UMR AGAP (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement), Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Abdullah Al-Doss
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia.
| | - Afif Hassairi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia.
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018 Sfax, Tunisia.
- Current Address: Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Saudi Arabia..
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Mukhi N, Kundu S, Kaur J. NO dioxygenase- and peroxidase-like activity of Arabidopsis phytoglobin 3 and its role in Sclerotinia sclerotiorum defense. Nitric Oxide 2017; 68:150-162. [PMID: 28315469 DOI: 10.1016/j.niox.2017.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/17/2017] [Accepted: 03/13/2017] [Indexed: 01/05/2023]
Abstract
Phytoglobin 3 appears to be ubiquitous in plants, yet there has been dearth of evidence for their potent physiological functions. Previous crystallographic studies suggest a potential NO dioxygenase like activity of Arabidopsis phytoglobin 3 (AHb3). The present work examined the in vivo function of AHb3 in plant physiology and its role in biotic stress using Arabidopsis- Sclerotinia sclerotorium pathosystem. The gene was found to be ubiquitously expressed in all plant tissues, with moderately increased expression in roots. Its expression was induced upon NO, H2O2 and biotic stress. A C-terminal tagged GFP version of the wild type protein revealed its enhanced accumulation in the guard cells. AHb3-GFP was found to be partitioned majorly into the nucleus while residual amounts were present in the cytoplasm. The loss of function AHb3 mutant exhibited reduced root length and fresh weight. AHb3 knockout lines also displayed enhanced susceptibility towards the S. sclerotiorum. Interestingly, these lines displayed enhanced ROS accumulation upon pathogen challenge as suggested by DAB staining. Furthermore, enhanced/decreased NO accumulation in AHb3 knockout/overexpression lines upon treatment with multiple NO donors suggests a potent NO dioxygenase like activity for the protein. Taken together, our data indicate that AHb3 play a crucial role in regulating root length as well as in mediating defense response against S. sclerotiorum, possibly by modulating NO and ROS levels.
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Affiliation(s)
- Nitika Mukhi
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Jagreet Kaur
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India.
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Transcription dynamics of Saltol QTL localized genes encoding transcription factors, reveals their differential regulation in contrasting genotypes of rice. Funct Integr Genomics 2016; 17:69-83. [PMID: 27848097 DOI: 10.1007/s10142-016-0529-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/02/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Salinity is one of the major environmental factors affecting the growth and yield of rice crop. Salinity stress response is a multigenic trait and numerous approaches have been used to dissect out the key determinants of complex salt tolerance trait and their regulation in plant. In the current study, we have investigated expression dynamics of the genes encoding transcription factors (SalTFs) localized within a major salinity tolerance related QTL-'Saltol' in the contrasting cultivars of rice. SalTFs were found to be differentially regulated between the contrasting genotypes of rice, with higher constitutive expression in the salt tolerant landrace, Pokkali than the cultivar IR64. Moreover, SalTFs were found to exhibit inducibility in the salt sensitive cultivar at late duration (after 24 h) of salinity stress. Further, the transcript abundance analysis of these SalTFs at various developmental stages of rice revealed that low expressing genes may be involved in developmental responses, while high expressing genes can be linked with the salt stress response. Grouping of these genes was well supported by in silico protein-protein interaction studies and distribution of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the promoter and genic regions of these genes. Taken together, we propose that out of 14 SalTFs, eight members are strongly correlated with the salinity stress tolerance in rice and six are involved in plant growth and development.
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Exploring drought stress-regulated genes in senna (Cassia angustifolia Vahl.): a transcriptomic approach. Funct Integr Genomics 2016; 17:1-25. [PMID: 27709374 DOI: 10.1007/s10142-016-0523-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 01/08/2023]
Abstract
De novo assembly of reads produced by next-generation sequencing (NGS) technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Senna (Cassia angustifolia Vahl.) is a drought-tolerant annual undershrub of Caesalpiniaceae, a subfamily of Fabaceae. There are insufficient transcriptomic and genomic data in public databases for understanding the molecular mechanism underlying the drought tolerance of senna. Therefore, the main purpose of this study was to know the transcriptome profile of senna, with special reference to drought stress. RNA from two different stages of leaf development was extracted and sequenced separately using the Illumina technology. A total of 200 million reads were generated, and a de novo assembly of processed reads in the pooled transcriptome using Trinity yielded 43,413 transcripts which were further annotated using NCBI BLAST with "green plant database (txid 33090)," Swiss Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Out of the total transcripts, 42,280 (95.0 %) were annotated by BLASTX against the green plant database of NCBI. Senna transcriptome showed the highest similarity to Glycine max (41 %), followed by Phaseolus vulgaris (16 %), Cicer arietinum (15 %), and Medicago trancatula (5 %). The highest number of GO terms were enriched for the molecular functions category; of these "catalytic activity" (GO: 0003824) (25.10 %) and "binding activity" (GO: 0005488) (20.10 %) were most abundantly represented. We used InterProscan to see protein similarity at domain level; a total of 33,256 transcripts were annotated against the Pfam domains. The transcripts were assigned with various KEGG pathways. Coding DNA sequences (CDS) encoding various drought stress-regulated pathways such as signaling factors, protein-modifying/degrading enzymes, biosynthesis of phytohormone, phytohormone signaling, osmotically active compounds, free radical scavengers, chlorophyll metabolism, leaf cuticular wax, polyamines, and protective proteins were identified through BLASTX search. The lucine-rich repeat kinase family was the most abundantly found group of protein kinases. Orphan, bHLH, and bZIP family TFs were the most abundantly found in senna. Six genes encoding MYC2 transcription factor, 9-cis-epoxycarotenoid dioxygenase (NCED), l -ascorbate peroxidase (APX), aminocyclopropane carboxylate oxidase (ACO), abscisic acid 8'-hydroxylase (ABA), and WRKY transcription factor were confirmed through reverse transcriptase-PCR (RT-PCR) and Sanger sequencing for the first time in senna. The potential drought stress-related transcripts identified in this study provide a good start for further investigation into the drought adaptation in senna. Additionally, our transcriptome sequences are the valuable resource for accelerated genomics-assisted genetic improvement programs and facilitate manipulation of biochemical pathways for developing drought-tolerant genotypes of crop plants.
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Chen X, Tian D, Kong X, Chen Q, E F AA, Hu X, Jia A. The role of nitric oxide signalling in response to salt stress in Chlamydomonas reinhardtii. PLANTA 2016; 244:651-69. [PMID: 27116428 DOI: 10.1007/s00425-016-2528-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/11/2016] [Indexed: 05/23/2023]
Abstract
Nitric oxide signal and GSNOR activity play an essential role for Chlamydomonas reinhardtii response to salt stress. The unicellular alga Chlamydomonas reinhardtii is one of the most important model organisms phylogenetically situated between higher plants and animals. In the present study, we used comparative proteomics and physiological approaches to study the mechanisms underlying the response to salt stress in C. reinhardtii. We identified 74 proteins that accumulated differentially after salt stress, including oxidative enzymes and enzymes associated with nitric oxide (NO) metabolism, cell damage, and cell autophagy processes. A set of antioxidant enzymes, as well as S-nitrosoglutathione reductase (GSNOR) activity, were induced to balance the cellular redox status during short-term salt stress. Enzymes involved in DNA repair and cell autophagy also contribute to adaptation to short-term salt stress. However, under long-term salt stress, antioxidant enzymes and GSNOR were gradually inactivated through protein S-nitrosylation, leading to oxidative damage and a reduction in cell viability. Modulating the protein S-nitrosylation levels by suppressing GSNOR activity or adding thioredoxin affected the plant's adaptation to salt stress, through altering the redox status and DNA damage and autophagy levels. Based on these data, we propose that unicellular algae use multiple strategies to adapt to salt stress, and that, during this process, GSNOR activity and protein S-nitrosylation levels play important roles.
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Affiliation(s)
- Xiaodong Chen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Dagang Tian
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
| | - Xiangxiang Kong
- The Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China
| | - Qian Chen
- The Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China
| | - Abd Allah E F
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China.
| | - Aiqun Jia
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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Alptekin B, Budak H. Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors. Funct Integr Genomics 2016; 17:171-187. [PMID: 27032785 DOI: 10.1007/s10142-016-0487-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/06/2016] [Accepted: 03/14/2016] [Indexed: 12/24/2022]
Abstract
MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and exploiting their roles on a functional context, providing valuable clues into the regulation of important biological processes, such as stress tolerance or environmental adaptation. Wheat is a hardy crop, extensively harvested in temperate regions, and is a major component of the human diet. With the advent of the next generation sequencing technologies considerably decreasing sequencing costs per base-pair, genomic, and transcriptomic data from several wheat species, including the progenitors and wild relatives have become available. In this study, we performed in silico identification and comparative analysis of microRNA repertoires of bread wheat (Triticum aestivum L.) and its diploid progenitors and relatives, Aegilops sharonensis, Aegilops speltoides, Aegilops tauschii, Triticum monococcum, and Triticum urartu through the utilization of publicly available transcriptomic data. Over 200 miRNA families were identified, majority of which have not previously been reported. Ancestral relationships expanded our understanding of wheat miRNA evolution, while T. monococcum miRNAs delivered important clues on the effects of domestication on miRNA expression. Comparative analyses on wild Ae. sharonensis accessions highlighted candidate miRNAs that can be linked to stress tolerance. The miRNA repertoires of bread wheat and its diploid progenitors and relatives provide important insight into the diversification and distribution of miRNA genes, which should contribute to the elucidation of miRNA evolution of Poaceae family. A thorough understanding of the convergent and divergent expression profiles of miRNAs in different genetic backgrounds can provide unique opportunities to modulation of gene regulation for better crop performance.
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Affiliation(s)
- Burcu Alptekin
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956, Istanbul, Turkey
| | - Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956, Istanbul, Turkey.
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
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Zhou J, Wang J, Zheng Z, Fan B, Yu JQ, Chen Z. Characterization of the promoter and extended C-terminal domain of Arabidopsis WRKY33 and functional analysis of tomato WRKY33 homologues in plant stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4567-83. [PMID: 25969555 PMCID: PMC4507763 DOI: 10.1093/jxb/erv221] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Arabidopsis AtWRKY33 plays a critical role in broad plant stress responses. Whether there are evolutionarily conserved homologues of AtWRKY33 in other plants and what make AtWRKY33 such an important protein in plant stress responses are largely unknown. We compared AtWRKY33 with its close homologues to identify AtWRKY33-specific regulatory and structural elements, which were then functionally analysed through complementation. We also performed phylogenetic analysis to identify structural AtWRKY33 homologues in other plants and functionally analysed two tomato homologues through complementation and gene silencing. AtWRKY33 has an extended C-terminal domain (CTD) absent in its close homologue AtWRKY25. Both its CTD and the strong pathogen/stress-responsive expression of AtWRKY33 are necessary to complement the critical phenotypes of atwrky33. Structural AtWRKY33 homologues were identified in both dicot and monocot plants including two (SlWRKY33A and SlWRKY33B) in tomato. Molecular complementation and gene silencing confirmed that the two tomato WRKY genes play a critical role similar to that of AtWRKY33 in plant stress responses. Thus, WRKY33 proteins are evolutionarily conserved with a critical role in broad plant stress responses. Both its CTD and promoter are critical for the uniquely important roles of WRKY33 in plant stress responses.
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Affiliation(s)
- Jie Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China Department of Botany and Plant Pathology, 915W. State Street, Purdue University, West Lafayette, IN 47907-2054, USA
| | - Jian Wang
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Zuyu Zheng
- Department of Botany and Plant Pathology, 915W. State Street, Purdue University, West Lafayette, IN 47907-2054, USA Present address: Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92036, USA
| | - Baofang Fan
- Department of Botany and Plant Pathology, 915W. State Street, Purdue University, West Lafayette, IN 47907-2054, USA
| | - Jing-Quan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Zhixiang Chen
- Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China Department of Botany and Plant Pathology, 915W. State Street, Purdue University, West Lafayette, IN 47907-2054, USA
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36
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Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress. Funct Integr Genomics 2015; 15:587-98. [PMID: 26174050 DOI: 10.1007/s10142-015-0453-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/26/2015] [Accepted: 07/01/2015] [Indexed: 01/09/2023]
Abstract
MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.
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Budak H, Hussain B, Khan Z, Ozturk NZ, Ullah N. From Genetics to Functional Genomics: Improvement in Drought Signaling and Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2015; 6:1012. [PMID: 26635838 PMCID: PMC4652017 DOI: 10.3389/fpls.2015.01012] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/02/2015] [Indexed: 05/18/2023]
Abstract
Drought being a yield limiting factor has become a major threat to international food security. It is a complex trait and drought tolerance response is carried out by various genes, transcription factors (TFs), microRNAs (miRNAs), hormones, proteins, co-factors, ions, and metabolites. This complexity has limited the development of wheat cultivars for drought tolerance by classical breeding. However, attempts have been made to fill the lost genetic diversity by crossing wheat with wild wheat relatives. In recent years, several molecular markers including single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs) associated with genes for drought signaling pathways have been reported. Screening of large wheat collections by marker assisted selection (MAS) and transformation of wheat with different genes/TFs has improved drought signaling pathways and tolerance. Several miRNAs also provide drought tolerance to wheat by regulating various TFs/genes. Emergence of OMICS techniques including transcriptomics, proteomics, metabolomics, and ionomics has helped to identify and characterize the genes, proteins, metabolites, and ions involved in drought signaling pathways. Together, all these efforts helped in understanding the complex drought tolerance mechanism. Here, we have reviewed the advances in wide hybridization, MAS, QTL mapping, miRNAs, transgenic technique, genome editing system, and above mentioned functional genomics tools for identification and utility of signaling molecules for improvement in wheat drought tolerance.
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Affiliation(s)
- Hikmet Budak
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
- *Correspondence: Hikmet Budak,
| | - Babar Hussain
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Zaeema Khan
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Neslihan Z. Ozturk
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niǧde UniversityNiǧde, Turkey
| | - Naimat Ullah
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
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Budak H, Akpinar BA, Unver T, Turktas M. Proteome changes in wild and modern wheat leaves upon drought stress by two-dimensional electrophoresis and nanoLC-ESI-MS/MS. PLANT MOLECULAR BIOLOGY 2013; 83:89-103. [PMID: 23443681 DOI: 10.1007/s11103-013-0024-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/04/2013] [Indexed: 05/18/2023]
Abstract
To elucidate differentially expressed proteins and to further understand post-translational modifications of transcripts, full leaf proteome profiles of two wild emmer (Triticum turgidum ssp. dicoccoides TR39477 and TTD22) and one modern durum wheat (Triticum turgidum ssp. durum cv. Kızıltan) genotypes were compared upon 9-day drought stress using two-dimensional gel electrophoresis and nano-scale liquid chromatographic electrospray ionization tandem mass spectrometry methods. The three genotypes compared exhibit distinctive physiological responses to drought as previously shown by our group. Results demonstrated that many of the proteins were common in both wild emmer and modern wheat proteomes; of which, 75 were detected as differentially expressed proteins. Several proteins identified in all proteomes exhibited drought regulated patterns of expression. A number of proteins were observed with higher expression levels in response to drought in wild genotypes compared to their modern relative. Eleven protein spots with low peptide matches were identified as candidate unique drought responsive proteins. Of the differentially expressed proteins, four were selected and further analyzed by quantitative real-time PCR at the transcriptome level to compare with the proteomic data. The present study provides protein level differences in response to drought in modern and wild genotypes of wheat that may account for the differences of the overall responses of these genotypes to drought. Such comparative proteomics analyses may aid in the better understanding of complex drought response and may suggest candidate genes for molecular breeding studies to improve tolerance against drought stress and, thus, to enhance yields.
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Affiliation(s)
- Hikmet Budak
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul 34956, Turkey.
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Budak H, Akpinar BA, Unver T, Turktas M. Proteome changes in wild and modern wheat leaves upon drought stress by two-dimensional electrophoresis and nanoLC-ESI-MS/MS. PLANT MOLECULAR BIOLOGY 2013; 83:89-103. [PMID: 23443681 DOI: 10.1007/s11103-013-0024-25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/04/2013] [Indexed: 05/27/2023]
Abstract
To elucidate differentially expressed proteins and to further understand post-translational modifications of transcripts, full leaf proteome profiles of two wild emmer (Triticum turgidum ssp. dicoccoides TR39477 and TTD22) and one modern durum wheat (Triticum turgidum ssp. durum cv. Kızıltan) genotypes were compared upon 9-day drought stress using two-dimensional gel electrophoresis and nano-scale liquid chromatographic electrospray ionization tandem mass spectrometry methods. The three genotypes compared exhibit distinctive physiological responses to drought as previously shown by our group. Results demonstrated that many of the proteins were common in both wild emmer and modern wheat proteomes; of which, 75 were detected as differentially expressed proteins. Several proteins identified in all proteomes exhibited drought regulated patterns of expression. A number of proteins were observed with higher expression levels in response to drought in wild genotypes compared to their modern relative. Eleven protein spots with low peptide matches were identified as candidate unique drought responsive proteins. Of the differentially expressed proteins, four were selected and further analyzed by quantitative real-time PCR at the transcriptome level to compare with the proteomic data. The present study provides protein level differences in response to drought in modern and wild genotypes of wheat that may account for the differences of the overall responses of these genotypes to drought. Such comparative proteomics analyses may aid in the better understanding of complex drought response and may suggest candidate genes for molecular breeding studies to improve tolerance against drought stress and, thus, to enhance yields.
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Affiliation(s)
- Hikmet Budak
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul 34956, Turkey.
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40
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Marder M. Plant intelligence and attention. PLANT SIGNALING & BEHAVIOR 2013; 8:e23902. [PMID: 23425923 PMCID: PMC3906434 DOI: 10.4161/psb.23902] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 02/06/2013] [Indexed: 05/19/2023]
Abstract
This article applies the phenomenological model of attention to plant monitoring of environmental stimuli and signal perception. Three complementary definitions of attention as selectivity, modulation and perdurance are explained with reference to plant signaling and behaviors, including foraging, ramet placement and abiotic stress communication. Elements of animal and human attentive attitudes are compared with plant attention at the levels of cognitive focus, context and margin. It is argued that the concept of attention holds the potential of becoming a cornerstone of plant intelligence studies.
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Affiliation(s)
- Michael Marder
- Department of Philosophy; The University of the Basque Country; UPV-EHU; Ikerbasque: Basque Foundation for Science; Vitoria-Gasteiz, Basque Country
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