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Çelik S. Gene expression analysis of potato drought-responsive genes under drought stress in potato ( Solanum tuberosum L.) cultivars. PeerJ 2024; 12:e17116. [PMID: 38525286 PMCID: PMC10960530 DOI: 10.7717/peerj.17116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
The potato (Solanum tuberosum L.), an important field crop consumed extensively worldwide, is adversely affected by abiotic stress factors especially drought. Therefore, it is vital to understand the genetic mechanism under drought stress to decrease loose of yield and quality . This trial aimed to screen drought-responsive gene expressions of potato and determine the drought-tolerant potato cultivar. The trial pattern is a completely randomized block design (CRBD) with four replications under greenhouse conditions. Four cultivars (Brooke, Orwell, Vr808, Shc909) were irrigated with four different water regimes (control and three stress conditions), and the gene expression levels of 10 potato genes were investigated. The stress treatments as follows: Control = 100% field capacity; slight drought = 75% field capacity; moderate drought = 50% field capacity, and severe drought 25% field capacity. To understand the gene expression under drought stress in potato genotypes, RT-qPCR analysis was performed and results showed that the genes most associated with drought tolerance were the StRD22 gene, MYB domain transcription factor, StERD7, Sucrose Synthase (SuSy), ABC Transporter, and StDHN1. The StHSP100 gene had the lowest genetic expression in all cultivars. Among the cultivars, the Orwell exhibited the highest expression of the StRD22 gene under drought stress. Overall, the cultivar with the highest gene expression was the Vr808, closely followed by the Brooke cultivar. As a result, it was determined that potato cultivars Orwell, Vr808, and Brooke could be used as parents in breeding programs to develop drought tolerant potato cultivars.
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Affiliation(s)
- Sadettin Çelik
- Genç Vocational School, Forestry Department, Bingol University, Bingol, Turkey
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2
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Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads. Gene 2023; 852:147065. [PMID: 36435508 DOI: 10.1016/j.gene.2022.147065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) are common mechanisms in eukaryotes to increase the complexity of transcriptomes and subsequently proteomes. Analysis of long reads transcriptomics data can result in the discovery of novel transcripts, splice sites, AS or APA events. Gossypium arboreum is an important cultivated cotton species and a putative contributor of the A sub-genome to the modern tetraploid cotton; and inherently tolerant to several biotic and abiotic stresses. Specifically, its variety 'FDH228' is considered to be an important resistance source. In this study, we sequenced the G. arboreum (var. FDH228) transcriptome using PacBio IsoSeq and illumina short read sequencing under three different conditions i.e. untreated/healthy, treated with biotic stress through whitefly infestation, and treated with abiotic stress via water deprivation, for the discovery and surveying of canonical and non-canonical AS, APA and transcript fusion events. We were able to obtain 15,419 unique transcripts from all samples representing 11,343 genes, out of which 10,832 were annotated and 520 were novel with respect to the published reference genome. These transcripts were grouped into different structural categories including 60 Antisense, 11,959 having a full-splice match, 999 with incomplete-splice match, 30 fusion transcripts, 177 genic, 479 intergenic, 771 novels in the catalog, and 944 Novel but not found in the catalog. Subsequently, randomly selected candidate transcripts were experimentally validated using qRT-PCR. Our comprehensive identification of canonical and non-canonical splicing events, and novel and fusion transcripts aids in the understanding of the resistance mechanisms for this specific germplasm.
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Yu D, Li X, Li Y, Ali F, Li F, Wang Z. Dynamic roles and intricate mechanisms of ethylene in epidermal hair development in Arabidopsis and cotton. THE NEW PHYTOLOGIST 2022; 234:375-391. [PMID: 34882809 DOI: 10.1111/nph.17901] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Ethylene affects many aspects of plant growth and development, including root hairs and trichomes growth in Arabidopsis, as well as fiber development in cotton, though the underlying mechanism is unclear. In this article, we update the research progress associated with the main genes in ethylene biosynthesis and signaling pathway, and we propose a clear ethylene pathway based on genome-wide identification of homologues in cotton. Expression pattern analysis using transcriptome data revealed that some candidate genes may contribute to cotton fiber development through the ethylene pathway. Moreover, we systematically summarized the effects of ethylene on the development of epidermal hair and the underlying regulatory mechanisms in Arabidopsis. Based on the knowledge of ethylene-promoted cell differentiation, elongation, and development in different tissues or plants, we advised a possible regulatory network for cotton fiber development with ethylene as the hub. Importantly, we emphasized the roles of ethylene as an important node in regulating cotton vegetative growth, and stress resistance, and suggested utilizing multiple methods to subtly modify ethylene synthesis or signaling in a tissue or spatiotemporal-specific manner to clarify its exact effect on architecture, adaptability of the plant, and fiber development, paving the way for basic research and genetic improvement of the cotton crop.
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Affiliation(s)
- Daoqian Yu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaona Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yonghui Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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4
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Singh P, Kumar K, Jha AK, Yadava P, Pal M, Rakshit S, Singh I. Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.). Sci Rep 2022; 12:4211. [PMID: 35273237 PMCID: PMC8913646 DOI: 10.1038/s41598-022-07709-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
Abstract
Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88–97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ − 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.
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Affiliation(s)
- Prabha Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Krishan Kumar
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Abhishek Kumar Jha
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Pranjal Yadava
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Madan Pal
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Sujay Rakshit
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Ishwar Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.
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D’Oria A, Jing L, Arkoun M, Pluchon S, Pateyron S, Trouverie J, Etienne P, Diquélou S, Ourry A. Transcriptomic, Metabolomic and Ionomic Analyses Reveal Early Modulation of Leaf Mineral Content in Brassica napus under Mild or Severe Drought. Int J Mol Sci 2022; 23:781. [PMID: 35054964 PMCID: PMC8776245 DOI: 10.3390/ijms23020781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
While it is generally acknowledged that drought is one of the main abiotic factors affecting plant growth, how mineral nutrition is specifically and negatively affected by water deficit has received very little attention, other than being analyzed as a consequence of reduced growth. Therefore, Brassica napus plants were subjected to a gradual onset of water deficits (mild, severe, or severe extended), and leaves were analyzed at the ionomic, transcriptomic and metabolic levels. The number of Differentially Expressed Genes (DEGs) and of the most differentially accumulated metabolites increased from mild (525 DEGs, 57 metabolites) to severe (5454 DEGs, 78 metabolites) and severe extended (9346 DEGs, 95 metabolites) water deficit. Gene ontology enrichment analysis of the 11,747 DEGs identified revealed that ion transport was one of the most significant processes affected, even under mild water deficit, and this was also confirmed by the shift in ionomic composition (mostly micronutrients with a strong decrease in Mo, Fe, Zn, and Mn in leaves) that occurred well before growth reduction. The metabolomic data and most of the transcriptomic data suggested that well-known early leaf responses to drought such as phytohormone metabolism (ABA and JA), proline accumulation, and oxidative stress defense were induced later than repression of genes related to nutrient transport.
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Affiliation(s)
- Aurélien D’Oria
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
- Laboratoire de Nutrition Végétale, Agro Innovation International-TIMAC AGRO, 35400 Saint-Malo, France; (M.A.); (S.P.)
| | - Lun Jing
- Plateformes Analytiques de Recherche, Agro Innovation International-TIMAC AGRO, 35400 Saint-Malo, France;
| | - Mustapha Arkoun
- Laboratoire de Nutrition Végétale, Agro Innovation International-TIMAC AGRO, 35400 Saint-Malo, France; (M.A.); (S.P.)
| | - Sylvain Pluchon
- Laboratoire de Nutrition Végétale, Agro Innovation International-TIMAC AGRO, 35400 Saint-Malo, France; (M.A.); (S.P.)
| | - Stéphanie Pateyron
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France;
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Jacques Trouverie
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
| | - Philippe Etienne
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
| | - Sylvain Diquélou
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
| | - Alain Ourry
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
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Yang J, Gao L, Liu X, Zhang X, Wang X, Wang Z. Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum. Sci Rep 2021; 11:22833. [PMID: 34819523 PMCID: PMC8613186 DOI: 10.1038/s41598-021-01829-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 11/02/2021] [Indexed: 02/06/2023] Open
Abstract
Cotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.
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Affiliation(s)
- Jiangtao Yang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihua Gao
- School of Life Sciences, Langfang Normal University, Langfang, 065000, China
| | - Xiaojing Liu
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaochun Zhang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xujing Wang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhixing Wang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Physiological and Molecular Responses of 'Dusa' Avocado Rootstock to Water Stress: Insights for Drought Adaptation. PLANTS 2021; 10:plants10102077. [PMID: 34685886 PMCID: PMC8537572 DOI: 10.3390/plants10102077] [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: 09/01/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/17/2022]
Abstract
Avocado consumption is increasing year by year, and its cultivation has spread to many countries with low water availability, which threatens the sustainability and profitability of avocado orchards. However, to date, there is not much information on the behavior of commercial avocado rootstocks against drought. The aim of this research was to evaluate the physiological and molecular responses of ‘Dusa’ avocado rootstock to different levels of water stress. Plants were deficit irrigated until soil water content reached 50% (mild-WS) and 25% (severe-WS) of field capacity. Leaf water potential (Ψw), net CO2 assimilation rates (AN), transpiration rate (E), stomatal conductance (gs), and plant transpiration rates significantly decreased under both WS treatments, reaching significantly lower values in severe-WS plants. After rewatering, mild- and severe-WS plants showed a fast recovery in most physiological parameters measured. To analyze root response to different levels of drought stress, a cDNA avocado stress microarray was carried out. Plants showed a wide transcriptome response linked to the higher degree of water stress, and functional enrichment of differentially expressed genes (DEGs) revealed abundance of common sequences associated with water stress, as well as specific categories for mild-WS and severe-WS. DEGs previously linked to drought tolerance showed overexpression under both water stress levels, i.e., several transcription factors, genes related to abscisic acid (ABA) response, redox homeostasis, osmoprotection, and cell-wall organization. Taken altogether, physiological and molecular data highlight the good performance of ‘Dusa’ rootstock under low-water-availability conditions, although further water stress experiments must be carried out under field conditions.
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Genome-Wide Characterization and Expression Analysis of the HD-ZIP Gene Family in Response to Salt Stress in Pepper. Int J Genomics 2021; 2021:8105124. [PMID: 33604369 PMCID: PMC7869415 DOI: 10.1155/2021/8105124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/18/2020] [Accepted: 12/10/2020] [Indexed: 11/17/2022] Open
Abstract
HD-ZIP is a unique type of transcription factor in plants, which are closely linked to the regulation of plant growth and development, the response to abiotic stress, and disease resistance. However, there is little known about the HD-ZIP gene family of pepper. In this study, 40 HD-ZIP family members were analyzed in the pepper genome. The analysis indicated that the introns number of Ca-HD-ZIP varied from 1 to 17; the number of amino acids was between 119 and 841; the theoretical isoelectric point was between 4.54 and 9.85; the molecular weight was between 14.04 and 92.56; most of them were unstable proteins. The phylogenetic tree divided CaHD-ZIP into 4 subfamilies; 40 CaHD-ZIP genes were located on different chromosomes, and all of them contained the motif 1; two pairs of CaHD-ZIP parallel genes of six paralogism genes were fragment duplications which occurred in 58.28~88.24 million years ago. There were multiple pressure-related action elements upstream of the start codon of the HD-Z-IP family. Protein interaction network proved to be coexpression phenomenon between ATML1 (CaH-DZ22, CaHDZ32) and At4g048909 (CaHDZ12, CaHDZ31), and three regions of them were highly homology. The expression level of CaHD-ZIP gene was different with tissues and developmental stages, which suggested that CaHD-ZIP may be involved in biological functions during pepper progress. In addition, Pepper HD-ZIP I and II genes played a major role in salt stress. CaHDZ03, CaHDZ 10, CaHDZ17, CaHDZ25, CaHDZ34, and CaHDZ35 were significantly induced in response to salt stress. Notably, the expression of CaHDZ07, CaHDZ17, CaHDZ26, and CaHDZ30, homologs of Arabidopsis AtHB12 and AtHB7 genes, was significantly upregulated by salt stresses. CaHDZ03 possesses two closely linked ABA action elements, and its expression level increased significantly at 4 h under salt stress. qRT-P-CR and transcription analysis showed that the expression of CaHDZ03 and CaHDZ10 was upregulated under short-term salt stress, but CaHDZ10 was downregulated with long-term salt stress, which provided a theoretical basis for research the function of Ca-HDZIP in response to abiotic stress.
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Gundaraniya S, Ambalam PS, Tomar RS. Metabolomic Profiling of Drought-Tolerant and Susceptible Peanut ( Arachis hypogaea L.) Genotypes in Response to Drought Stress. ACS OMEGA 2020; 5:31209-31219. [PMID: 33324830 PMCID: PMC7726923 DOI: 10.1021/acsomega.0c04601] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/09/2020] [Indexed: 05/10/2023]
Abstract
Peanut is frequently constrained by extreme environmental conditions such as drought. To reveal the involvement of metabolites, TAG 24 (drought-tolerant) and JL 24 (drought-sensitive) peanut genotypes were investigated under control and 20% PEG 6000-mediated water scarcity conditions at the seedling stage. Samples were analyzed by gas chromatography-mass spectrometry (GC-MS) to identify untargeted metabolites and targeted metabolites, i.e., polyamines and polyphenols by high-performance liquid chromatography (HPLC) and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), respectively. The principal component analysis (PCA), partial least-squares discriminant analysis (PLS-DA), heat map, and cluster analysis were applied to the metabolomics data obtained by the GC-MS technique to determine the important metabolites for drought tolerance. Among 46 resulting metabolites, pentitol, phytol, xylonic acid, d-xylopyranose, stearic acid, and d-ribose were important drought-responsive metabolites. Agmatine and cadaverine were present in TAG 24 leaves and roots, respectively, during water-deficit conditions and believed to be the potential polyamines for drought tolerance. Polyphenols such as syringic acid and vanillic acid were produced more in the leaves of TAG 24, while catechin production was high in JL 24 during stress conditions. Seven metabolic pathways, namely, galactose metabolism, starch and sucrose metabolism, fructose and mannose metabolism, pentose and glucuronate interconversion, propanoate metabolism, amino sugar and nucleotide sugar metabolism, and biosynthesis of unsaturated fatty acids were significantly affected by water-deficit conditions. This study provides valuable information about the metabolic response of peanut to drought stress and metabolites identified, which encourages further study by transcriptome and proteomics to improve drought tolerance in peanut.
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Affiliation(s)
- Srutiben
A. Gundaraniya
- Department
of Biosciences, Saurashtra University, Rajkot, Gujarat 360005, India
- Christ
Campus, Vidya Niketan, Saurashtra University, Rajkot, Gujarat 360005, India
- Department
of Biotechnology and Biochemistry, Junagadh
Agricultural University, Junagadh, Gujarat 362001, India
| | - Padma S. Ambalam
- Christ
Campus, Vidya Niketan, Saurashtra University, Rajkot, Gujarat 360005, India
| | - Rukam S. Tomar
- Department
of Biotechnology and Biochemistry, Junagadh
Agricultural University, Junagadh, Gujarat 362001, India
- . Tel: +91 94260 37195
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Comparative transcriptomic analysis of contrasting hybrid cultivars reveal key drought-responsive genes and metabolic pathways regulating drought stress tolerance in maize at various stages. PLoS One 2020; 15:e0240468. [PMID: 33057352 PMCID: PMC7561095 DOI: 10.1371/journal.pone.0240468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 09/25/2020] [Indexed: 02/01/2023] Open
Abstract
Drought stress is the primary environmental factor that negatively influences plant growth and yield in cereal grain crops such as maize (Zea mays L.). Crop breeding efforts for enhanced drought resistance require improved knowledge of plant drought stress responses. In this study, we applied a 12-day water-deficit stress treatment to maize plants of two contrasting (drought tolerant ND476 and drought sensitive ZX978) hybrid cultivars at four (V12, VT, R1, and R4) crop growth stages and we report key cultivar-specific and growth-stage-specific molecular mechanisms regulating drought stress responses in maize. Based on the transcriptome analysis, a total of 3451 and 4088 differentially expressed genes (DEGs) were identified in ND476 and ZX978 from the four experimental comparisons, respectively. These gene expression changes effected corresponding metabolic pathway responses related to drought tolerance in maize. In ND476, the DEGs associated with the ribosome, starch and sucrose metabolism, phenylpropanoid biosynthesis and phenylpropanoid metabolism pathways were predominant at the V12, VT, R2, and R4 stages, respectively, whereas those in ZX978 were related to ribosome, pentose and glucuronate interconversions (PGI), MAPK signaling and sulfur metabolism pathways, respectively. MapMan analysis revealed that DEGs related to secondary metabolism, lipid metabolism, and amino acid metabolism were universal across the four growth stages in ND476. Meanwhile, the DEGs involved in cell wall, photosynthesis and amino acid metabolism were universal across the four growth stages in ZX978. However, K-means analysis clustered those DEGs into clear and distinct expression profiles in ND476 and ZX978 at each stage. Several functional and regulatory genes were identified in the special clusters related to drought defense response. Our results affirmed that maize drought stress adaptation is a cultivar-specific response as well as a stage-specific response process. Additionally, our findings enrich the maize genetic resources and enhance our further understanding of the molecular mechanisms regulating drought stress tolerance in maize. Further, the DEGs screened in this study may provide a foundational basis for our future targeted cloning studies.
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Gu H, Yang Y, Xing M, Yue C, Wei F, Zhang Y, Zhao W, Huang J. Physiological and transcriptome analyses of Opisthopappus taihangensis in response to drought stress. Cell Biosci 2019; 9:56. [PMID: 31312427 PMCID: PMC6611040 DOI: 10.1186/s13578-019-0318-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/25/2019] [Indexed: 11/15/2022] Open
Abstract
Background Water scarcity is considered to be a severe environmental constraint to plant survival and productivity. Studies on drought-tolerant plants would definitely promote a better understanding of the regulatory mechanism lying behind the adaptive response of plants to drought. Opisthopappus taihangensis (ling) shih is a typical drought-tolerant perennial plant species endemically distributed across the Taihang Mountains in China, but the underlying mechanism for drought tolerance of this particular species remains elusive. Results To mimic natural drought stress, O. taihangensis plants were treated with two different concentrations (25% and 5%) of polyethylene glycol (PEG6000), which represent the H group (high salinity) and the L group (low salinity), respectively. The physiological characteristics of these two groups of plants, including relative water content maintenance (RWC), proline content and chlorophyll content were assessed and compared with plants in the control group (CK), which had normal irrigation. There was not a significant difference in RWC when comparing plants in the L group with the control group. Proline was accumulated to a higher level, and chlorophyll content was decreased slightly in plants under low drought stress. In plants from the H group, a lower RWC was observed. Proline was accumulated to an even higher level when compared with plants from the L group, and chlorophyll content was further reduced in plants under high drought stress. Transcriptomic analysis was carried out to look for genes that are differentially expressed (DEGs) in O. taihangensis plants coping adaptively with the two levels of drought stress. A total of 23,056 genes are differentially expressed between CK and L, among which 12,180 genes are up-regulated and 10,876 genes are down-regulated. Between H and L, 6182 genes are up-regulated and 1850 genes are down-regulated, which gives a total of 8032 genes. The highest number of genes, that are differentially expressed, was obtained when a comparison was made between CK and H. A total of 43,074 genes were found to be differentially expressed with 26,977 genes up-regulated and 16,097 genes down-regulated. Further analysis of these genes suggests that many of the up-regulated genes are enriched in pathways involved in amino acid metabolism. Besides, 39 transcription factors (TFs) were found to be continuously up-regulated with the increase of drought stress level. Conclusion Taken together, the results indicate that O. taihangensis plants are able to live adaptively under drought stress by responding physiologically and regulating the expression of a substantial number of drought-responsive genes and TFs to avoid adverse effects. Electronic supplementary material The online version of this article (10.1186/s13578-019-0318-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huihui Gu
- 1School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China.,2School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China
| | - Yan Yang
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China.,3School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China
| | - Minghui Xing
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China
| | - Caipeng Yue
- 3School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China
| | - Fang Wei
- 3School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China
| | - Yanjie Zhang
- 3School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China
| | - Wenen Zhao
- 1School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China
| | - Jinyong Huang
- 3School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001 People's Republic of China
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12
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Zhao D, Shi Y, Senthilkumar HA, Qiao Q, Wang Q, Shen Y, Hu G. Enriched networks 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' potentially conferred to drought adaptation of the epiphytic orchid Dendrobium wangliangii. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:31-45. [PMID: 30804628 PMCID: PMC6352522 DOI: 10.1007/s12298-018-0607-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 08/12/2018] [Accepted: 09/24/2018] [Indexed: 05/17/2023]
Abstract
Dendrobium wangliangii is an endangered and epiphytic orchid with tolerance to seasonally extreme arid conditions and occurs exclusively in the hot-dry valley area of southwestern China. To reveal its molecular basis responsible for ecological adaptation, large-scale transcriptome sequencing was performed using Illumina sequencing with pooled mRNA extracted from whole plants and pseudobulbs during drought and rainy seasons. Based on the target transcript selection, the differentially expressed genes were related to 8 well-known drought-tolerant categories, and to morphological traits in resistance to water stress including pseudobulbs and roots. Further gene ontology enrichment analysis revealed that 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' were the two most important aspects in resistance to drought stress with respect to the whole plant. In addition, the difference in the number and category of differentially expressed genes in whole plant and stem suggested the involvement of genes specifically localized in the stem, such as GTP-binding protein, lipases, signaling related transcripts and those involved in the ATP metabolic process. The comprehensive analysis of the epiphytic orchid in response to water deprivation indicates that integral tactics lead to active adaptation as a basal defense response to drought stress by the endangered epiphyte, including the collaboration of metabolic processes, responses to a various stimulus and other candidate genes contribute to its extreme drought tolerance. Insights from this study can be further utilized to understand stress-responsive genes in other medicinally important species and to improve the drought tolerance of food crops.
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Affiliation(s)
- Dake Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, China
| | - Yana Shi
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, China
| | | | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, China
| | - Qiuxia Wang
- Key Laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan Province, Kunming University, Kunming, China
| | - Yong Shen
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Guangwan Hu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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13
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Bielsa B, Hewitt S, Reyes-Chin-Wo S, Dhingra A, Rubio-Cabetas MJ. Identification of water use efficiency related genes in 'Garnem' almond-peach rootstock using time-course transcriptome analysis. PLoS One 2018; 13:e0205493. [PMID: 30308016 PMCID: PMC6181374 DOI: 10.1371/journal.pone.0205493] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/26/2018] [Indexed: 11/19/2022] Open
Abstract
Drought is one of the main abiotic stresses with far-reaching ecological and socioeconomic impacts, especially in perennial food crops such as Prunus. There is an urgent need to identify drought resilient rootstocks that can adapt to changes in water availability. In this study, we tested the hypothesis that PEG-induced water limitation stress will simulate drought conditions and drought-related genes, including transcription factors (TFs), will be differentially expressed in response to this stress. 'Garnem' genotype, an almond × peach hybrid [P. amygdalus Batsch, syn P. dulcis (Mill.) x P. persica (L.) Batsch] was exposed to PEG-6000 solution, and a time-course transcriptome analysis of drought-stressed roots was performed at 0, 2 and 24 h time points post-stress. Transcriptome analysis resulted in the identification of 12,693 unique differentially expressed contigs (DECs) at the 2 h time point, and 7,705 unique DECs at the 24 h time point after initiation of the drought treatment. Interestingly, three drought-induced genes, directly related to water use efficiency (WUE) namely, ERF023 TF; LRR receptor-like serine/threonine-kinase ERECTA; and NF-YB3 TF, were found induced under stress. The RNAseq results were validated with quantitative RT-PCR analysis of eighteen randomly selected differentially expressed contigs (DECs). Pathway analysis in the present study provides valuable information regarding metabolic events that occur during stress-induced signalling in 'Garnem' roots. This information is expected to be useful in understanding the potential mechanisms underlying drought stress responses and drought adaptation strategies in Prunus species.
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Affiliation(s)
- Beatriz Bielsa
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
| | - Seanna Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | | | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - María José Rubio-Cabetas
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
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14
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Multiple Regression Analysis Reveals MicroRNA Regulatory Networks in Oryza sativa under Drought Stress. Int J Genomics 2018; 2018:9395261. [PMID: 30402456 PMCID: PMC6196795 DOI: 10.1155/2018/9395261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/14/2018] [Accepted: 09/10/2018] [Indexed: 01/17/2023] Open
Abstract
Drought is a major abiotic stress that reduces rice development and yield. miRNAs (microRNAs) are known to mediate posttranscriptional regulation under drought stress. Although the importance of individual miRNAs has been established, the crosstalks between miRNAs and mRNAs remain unearthed. Here we performed microarray analysis of miRNAs and matched mRNA expression profiles of drought-treated rice cultivar Nipponbare. Drought-responsive miRNA-mRNA regulations were identified by a combination of a partial least square (PLS) regression approach and sequence-based target prediction. A drought-induced network with 13 miRNAs and 58 target mRNAs was constructed, and four miRNA coregulatory modules were revealed. Functional analysis suggested that drought-response miRNA targets are enriched in hormone signaling, lipid and carbohydrate metabolism, and antioxidant defense. 13 candidate miRNAs and target genes were validated by RT-qPCR, hierarchical clustering, and ROC analysis. Two target genes (DWARF-3 and P0651G05.2) of miRNA coregulatory modules were further verified by RLM-5' RACE. Together, our integrative study of miRNA-mRNA interaction provided attractive candidates that will help elucidate the drought-response mechanisms in Oryza sativa.
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15
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Yan J, Li G, Guo X, Li Y, Cao X. Genome-wide classification, evolutionary analysis and gene expression patterns of the kinome in Gossypium. PLoS One 2018; 13:e0197392. [PMID: 29768506 PMCID: PMC5955557 DOI: 10.1371/journal.pone.0197392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 05/01/2018] [Indexed: 11/18/2022] Open
Abstract
The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122-24 subfamilies using software HMMER v3.0 scanning and neighbor-joining (NJ) phylogenetic analysis. Some conserved exon-intron structures were identified not only in cotton species but also in primitive plants, ferns and moss, suggesting the significant function and ancient origination of these PK genes. Collinearity analysis revealed that 16.6 million years ago (Mya) cotton-specific whole genome duplication (WGD) events may have played a partial role in the expansion of the cotton kinomes, whereas tandem duplication (TD) events mainly contributed to the expansion of the cotton RLK group. Synteny analysis revealed that tetraploidization of G. hirsutum and G. barbadense contributed to the expansion of G. hirsutum and G. barbadense PKs. Global expression analysis of cotton PKs revealed stress-specific and fiber development-related expression patterns, suggesting that many cotton PKs might be involved in the regulation of the stress response and fiber development processes. This study provides foundational information for further studies on the evolution and molecular function of cotton PKs.
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Affiliation(s)
- Jun Yan
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, PR China
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Guilin Li
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Xingqi Guo
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Yang Li
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Xuecheng Cao
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, PR China
- * E-mail:
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16
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Tiwari S, Lata C, Chauhan PS, Prasad V, Prasad M. A Functional Genomic Perspective on Drought Signalling and its Crosstalk with Phytohormone-mediated Signalling Pathways in Plants. Curr Genomics 2017; 18:469-482. [PMID: 29204077 PMCID: PMC5684651 DOI: 10.2174/1389202918666170605083319] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/03/2016] [Accepted: 10/15/2016] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Drought stress is one of the most important abiotic stresses that negatively influence crop performance and productivity. Plants acclimatize to drought stress conditions through altered molecular, biochemical and physiological responses. Gene and/or protein expression and regulation are thought to be modulated upon stress perception and signal transduction for providing requisite endurance to plants.Plant growth regulators or phytohormones are important molecules required for various biological processes in plants and are also central to stress signalling pathways. Among various phytohormones, Abscisic Acid (ABA) and Ethylene (ET) are considered to be the most vital growth regulators implicated in drought stress signalling and tolerance. Besides the above two known classical phytohormones, Salicylic Acid (SA) and Jasmonic Acid (JA) have also been found to potentially enhance abiotic stress tolerance particularly that of drought, salinity, and heat stress tolerance in plants. Apart from these several other growth regulators such as Cytokinins (CKs), Auxin (AUX), Gibberellic Acid (GA), Brassinosteroids (BRs) and Strigolactones (SLs) have also been reported to actively participate in abiotic stress responses and tolerance in plants. The abiotic stress signalling in plants regulated by these hormones further depends upon the nature, intensity, and duration of exposure to various environmental stresses. It has been reported that all these phytohormones are also involved in extensive crosstalk and signal transduction among themselves and/or with other factors. CONCLUSION This review thus summarizes the molecular mechanism of drought signalling and its crosstalk with various phytohormone signalling pathways implicated in abiotic stress response and tolerance.
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Affiliation(s)
- Shalini Tiwari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, India
- Department of Botany, University of Lucknow, Lucknow-226007, India
| | - Charu Lata
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, India
| | - Puneet Singh Chauhan
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, India
| | - Vivek Prasad
- Department of Botany, University of Lucknow, Lucknow-226007, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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17
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Zhao Q, Ma D, Huang Y, He W, Li Y, Vasseur L, You M. Genome-wide investigation of transcription factors provides insights into transcriptional regulation in Plutella xylostella. Mol Genet Genomics 2017; 293:435-449. [PMID: 29147778 DOI: 10.1007/s00438-017-1389-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023]
Abstract
Transcription factors (TFs), which play a vital role in regulating gene expression, are prevalent in all organisms and characterization of them may provide important clues for understanding regulation in vivo. The present study reports a genome-wide investigation of TFs in the diamondback moth, Plutella xylostella (L.), a worldwide pest of crucifers. A total of 940 TFs distributed among 133 families were identified. Phylogenetic analysis of insect species showed that some of these families were found to have expanded during the evolution of P. xylostella or Lepidoptera. RNA-seq analysis showed that some of the TF families, such as zinc fingers, homeobox, bZIP, bHLH, and MADF_DNA_bdg genes, were highly expressed in certain tissues including midgut, salivary glands, fat body, and hemocytes, with an obvious sex-biased expression pattern. In addition, a number of TFs showed significant differences in expression between insecticide susceptible and resistant strains, suggesting that these TFs play a role in regulating genes related to insecticide resistance. Finally, we identified an expansion of the HOX cluster in Lepidoptera, which might be related to Lepidoptera-specific evolution. Knockout of this cluster using CRISPR/Cas9 showed that the egg cannot hatch, indicating that this cluster may be related to egg development and maturation. This is the first comprehensive study on identifying and characterizing TFs in P. xylostella. Our results suggest that some TF families are expanded in the P. xylostella genome, and these TFs may have important biological roles in growth, development, sexual dimorphism, and resistance to insecticides. The present work provides a solid foundation for understanding regulation via TFs in P. xylostella and insights into the evolution of the P. xylostella genome.
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Affiliation(s)
- Qian Zhao
- State Key Laboratory for Ecological Pest Control of Fujian - Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, People's Republic of China
| | - Dongna Ma
- State Key Laboratory for Ecological Pest Control of Fujian - Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, People's Republic of China
| | - Yuping Huang
- State Key Laboratory for Ecological Pest Control of Fujian - Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, People's Republic of China
| | - Weiyi He
- State Key Laboratory for Ecological Pest Control of Fujian - Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, People's Republic of China
| | - Yiying Li
- State Key Laboratory for Ecological Pest Control of Fujian - Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Liette Vasseur
- State Key Laboratory for Ecological Pest Control of Fujian - Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.,Department of Biological Sciences, Brock University, 500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
| | - Minsheng You
- State Key Laboratory for Ecological Pest Control of Fujian - Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China. .,Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, People's Republic of China.
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18
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Vital CE, Giordano A, de Almeida Soares E, Rhys Williams TC, Mesquita RO, Vidigal PMP, de Santana Lopes A, Pacheco TG, Rogalski M, de Oliveira Ramos HJ, Loureiro ME. An integrative overview of the molecular and physiological responses of sugarcane under drought conditions. PLANT MOLECULAR BIOLOGY 2017; 94:577-594. [PMID: 28409321 DOI: 10.1007/s11103-017-0611-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/26/2017] [Indexed: 06/07/2023]
Abstract
Drought is the main abiotic stress constraining sugarcane production. However, our limited understanding of the molecular mechanisms involved in the drought stress responses of sugarcane impairs the development of new technologies to increase sugarcane drought tolerance. Here, an integrated approach was performed to reveal the molecular and physiological changes in two closely related sugarcane cultivars, including the most extensively planted cultivar in Brazil (cv. RB867515), in response to moderate (-0.5 MPa) and severe (-1 MPa) drought stress at the transcriptional, translational, and posttranslational levels. The results show common and cultivar exclusive changes in specific genes related to photosynthesis, carbohydrate, amino acid, and phytohormone metabolism. The novel phosphoproteomics and redox proteomic analysis revealed the importance of posttranslational regulation mechanisms during sugarcane drought stress. The shift to soluble sugar, secondary metabolite production, and activation of ROS eliminating processes in response to drought tolerance were mechanisms exclusive to cv. RB867515, helping to explain the better performance and higher production of this cultivar under these stress conditions.
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Affiliation(s)
- Camilo Elber Vital
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Andrea Giordano
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Thomas Christopher Rhys Williams
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Departamento de Botânica, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Rosilene Oliveira Mesquita
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Departamento de Fitotecnia, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Centro de Ciências Biológicas, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Amanda de Santana Lopes
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Túlio Gomes Pacheco
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcelo Rogalski
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Marcelo Ehlers Loureiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Farooq M, Mansoor S, Guo H, Amin I, Chee PW, Azim MK, Paterson AH. Identification and Characterization of miRNA Transcriptome in Asiatic Cotton ( Gossypium arboreum) Using High Throughput Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 8:969. [PMID: 28663752 PMCID: PMC5471329 DOI: 10.3389/fpls.2017.00969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/23/2017] [Indexed: 05/22/2023]
Abstract
MicroRNAs (miRNAs) are small 20-24nt molecules that have been well studied over the past decade due to their important regulatory roles in different cellular processes. The mature sequences are more conserved across vast phylogenetic scales than their precursors and some are conserved within entire kingdoms, hence, their loci and function can be predicted by homology searches. Different studies have been performed to elucidate miRNAs using de novo prediction methods but due to complex regulatory mechanisms or false positive in silico predictions, not all of them express in reality and sometimes computationally predicted mature transcripts differ from the actual expressed ones. With the availability of a complete genome sequence of Gossypium arboreum, it is important to annotate the genome for both coding and non-coding regions using high confidence transcript evidence, for this cotton species that is highly resistant to various biotic and abiotic stresses. Here we have analyzed the small RNA transcriptome of G. arboreum leaves and provided genome annotation of miRNAs with evidence from miRNA/miRNA∗ transcripts. A total of 446 miRNAs clustered into 224 miRNA families were found, among which 48 families are conserved in other plants and 176 are novel. Four short RNA libraries were used to shortlist best predictions based on high reads per million. The size, origin, copy numbers and transcript depth of all miRNAs along with their isoforms and targets has been reported. The highest gene copy number was observed for gar-miR7504 followed by gar-miR166, gar-miR8771, gar-miR156, and gar-miR7484. Altogether, 1274 target genes were found in G. arboreum that are enriched for 216 KEGG pathways. The resultant genomic annotations are provided in UCSC, BED format.
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Affiliation(s)
- Muhammad Farooq
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Shahid Mansoor
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
- Plant Genome Mapping Laboratory, University of Georgia, AthensGA, United States
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, AthensGA, United States
| | - Imran Amin
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Peng W. Chee
- Plant Genome Mapping Laboratory, University of Georgia, AthensGA, United States
| | - M. Kamran Azim
- Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences, University of KarachiKarachi, Pakistan
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, AthensGA, United States
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20
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Kong X, Luo Z, Dong H, Li W, Chen Y. Non-uniform salinity in the root zone alleviates salt damage by increasing sodium, water and nutrient transport genes expression in cotton. Sci Rep 2017; 7:2879. [PMID: 28588258 PMCID: PMC5460137 DOI: 10.1038/s41598-017-03302-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/25/2017] [Indexed: 11/09/2022] Open
Abstract
Non-uniform salinity alleviates salt damage through sets of physiological adjustments in Na+ transport in leaf and water and nutrient uptake in the non-saline root side. However, little is known of how non-uniform salinity induces these adjustments. In this study, RNA sequencing (RNA-Seq) analysis shown that the expression of sodium transport and photosynthesis related genes in the non-uniform treatment were higher than that in the uniform treatment, which may be the reason for the increased photosynthetic (Pn) rate and decreased Na+ content in leaves of the non-uniform salinity treatment. Most of the water and nutrient transport related genes were up-regulated in the non-saline root side but down-regulated in roots of the high-saline side, which might be the key reason for the increased water and nutrient uptake in the non-saline root side. Furthermore, the expression pattern of most differentially expressed transcription factor and hormone related genes in the non-saline root side was similar to that in the high-saline side. The alleviated salt damage by non-uniform salinity was probably attributed to the increased expression of salt tolerance related genes in the leaf and that of water and nutrient uptake genes in the non-saline root side.
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Affiliation(s)
- Xiangqiang Kong
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China
| | - Zhen Luo
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China
| | - Hezhong Dong
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China.
| | - Weijiang Li
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China
| | - Yizhen Chen
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China
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Carvalho LC, Silva M, Coito JL, Rocheta MP, Amâncio S. Design of a Custom RT-qPCR Array for Assignment of Abiotic Stress Tolerance in Traditional Portuguese Grapevine Varieties. FRONTIERS IN PLANT SCIENCE 2017; 8:1835. [PMID: 29118776 PMCID: PMC5660995 DOI: 10.3389/fpls.2017.01835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 10/10/2017] [Indexed: 05/21/2023]
Abstract
Widespread agricultural losses attributed to drought, often combined with high temperatures, frequently occur in the field, namely in Mediterranean climate areas, where the existing scenarios for climate change indicate an increase in the frequency of heat waves and severe drought events in summer. Grapevine (Vitis vinifera L.) is the most cultivated fruit species in the world and the most valuable one and is a traditional Mediterranean species. Currently, viticulture must adjust to impending climate changes that are already pushing vine-growers toward the use of ancient and resilient varieties. Portugal is very rich in grapevine biodiversity, however, currently, 90% of the total producing area is planted with only 16 varieties. There is a pressing need to understand the existing genetic diversity and the physiological potential of the varieties/genotypes available to be able to respond to climate changes. With the above scenario in mind, an assembly of 65 differentially expresses genes (DEGs) previously identified as responsive to abiotic stresses in two well studied genotypes, 'Touriga Nacional' and 'Trincadeira,' was designed to scan the gene expression of leaf samples from 10 traditional Portuguese varieties growing in two regions with distinct environmental conditions. Forty-five of those DEGs proved to be associated to "abiotic stress" and were chosen to build a custom qPCR array to identify uncharacterized genotypes as sensitive or tolerant to abiotic stress. According to the experimental set-up behind the array design these DEGs can also be used as indicators of the main abiotic stress that the plant is subjected and responding to (drought, heat, or excess light).
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22
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Yang Y, Mo Y, Yang X, Zhang H, Wang Y, Li H, Wei C, Zhang X. Transcriptome Profiling of Watermelon Root in Response to Short-Term Osmotic Stress. PLoS One 2016; 11:e0166314. [PMID: 27861528 PMCID: PMC5115733 DOI: 10.1371/journal.pone.0166314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022] Open
Abstract
Osmotic stress adversely affects the growth, fruit quality and yield of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai). Increasing the tolerance of watermelon to osmotic stress caused by factors such as high salt and water deficit is an effective way to improve crop survival in osmotic stress environments. Roots are important organs in water absorption and are involved in the initial response to osmosis stress; however, few studies have examined the underlying mechanism of tolerance to osmotic stress in watermelon roots. For better understanding of this mechanism, the inbred watermelon accession M08, which exhibits relatively high tolerance to water deficits, was treated with 20% polyethylene glycol (PEG) 6000. The root samples were harvested at 6 h after PEG treatment and untreated samples were used as controls. Transcriptome analyses were carried out by Illumina RNA sequencing. A total of 5246 differentially expressed genes were identified. Gene ontology enrichment and biochemical pathway analyses of these 5246 genes showed that short-term osmotic stress affected osmotic adjustment, signal transduction, hormone responses, cell division, cell cycle and ribosome, and M08 may repress root growth to adapt osmotic stress. The results of this study describe the watermelon root transcriptome under osmotic stress and propose new insight into watermelon root responses to osmotic stress at the transcriptome level. Accordingly, these results allow us to better understand the molecular mechanisms of watermelon in response to drought stress and will facilitate watermelon breeding projects to improve drought tolerance.
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Affiliation(s)
- Yongchao Yang
- College of Horticulture, Northwest A&F University, Yangling, China
- Wenshan Academy of Agricultural Sciences, Wenshan, China
| | - Yanling Mo
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Xiaozheng Yang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Haifei Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Yongqi Wang
- College of Horticulture, Northwest A&F University, Yangling, China
- Hanzhong City Agro-technology Extension Center, Hanzhong, China
| | - Hao Li
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Chunhua Wei
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Xian Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
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23
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Liang C, Meng Z, Meng Z, Malik W, Yan R, Lwin KM, Lin F, Wang Y, Sun G, Zhou T, Zhu T, Li J, Jin S, Guo S, Zhang R. GhABF2, a bZIP transcription factor, confers drought and salinity tolerance in cotton (Gossypium hirsutum L.). Sci Rep 2016; 6:35040. [PMID: 27713524 PMCID: PMC5054369 DOI: 10.1038/srep35040] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/23/2016] [Indexed: 11/16/2022] Open
Abstract
The bZIP transcription factor (TF) act as an important regulator for the abscisic acid (ABA) mediated abiotic stresses signaling pathways in plants. Here, we reported the cloning and characterization of GhABF2, encoding for typical cotton bZIP TF. Overexpression of GhABF2 significantly improved drought and salt stress tolerance both in Arabidopsis and cotton. However, silencing of GhABF2 made transgenic cotton sensitive to PEG osmotic and salt stress. Expression of GhABF2 was induced by drought and ABA treatments but repressed by high salinity. Transcriptome analysis indicated that GhABF2 increases drought and salt tolerance by regulating genes related to ABA, drought and salt response. The proline contents, activity of superoxide dismutase (SOD) and catalase (CAT) were also significantly increased in GhABF2-overexpression cottons in comparison to wild type after drought and salt treatment. Further, an increase in fiber yield under drought and saline-alkali wetland exhibited the important role of GhABF2 in enhancing the drought and salt tolerance in transgenic lines. In conclusion, manipulation of GhABF2 by biotechnological tools could be a sustainable strategy to deploy drought and salt tolerance in cotton.
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Affiliation(s)
- Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaohong Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Waqas Malik
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Rong Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Khin Myat Lwin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Biotechnology Research Department, Ministry of Science and Technology, Naypyidaw, Myanmar
| | - Fazhuang Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Genome-Wide Characterization and Expression Profiles of the Superoxide Dismutase Gene Family in Gossypium. Int J Genomics 2016; 2016:8740901. [PMID: 27660755 PMCID: PMC5021877 DOI: 10.1155/2016/8740901] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/03/2016] [Indexed: 01/01/2023] Open
Abstract
Superoxide dismutase (SOD) as a group of significant and ubiquitous enzymes plays a critical function in plant growth and development. Previously this gene family has been investigated in Arabidopsis and rice; it has not yet been characterized in cotton. In our study, it was the first time for us to perform a genome-wide analysis of SOD gene family in cotton. Our results showed that 10 genes of SOD gene family were identified in Gossypium arboreum and Gossypium raimondii, including 6 Cu-Zn-SODs, 2 Fe-SODs, and 2 Mn-SODs. The chromosomal distribution analysis revealed that SOD genes are distributed across 7 chromosomes in Gossypium arboreum and 8 chromosomes in Gossypium raimondii. Segmental duplication is predominant duplication event and major contributor for expansion of SOD gene family. Gene structure and protein structure analysis showed that SOD genes have conserved exon/intron arrangement and motif composition. Microarray-based expression analysis revealed that SOD genes have important function in abiotic stress. Moreover, the tissue-specific expression profile reveals the functional divergence of SOD genes in different organs development of cotton. Taken together, this study has imparted new insights into the putative functions of SOD gene family in cotton. Findings of the present investigation could help in understanding the role of SOD gene family in various aspects of the life cycle of cotton.
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25
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Kumar S, Kanakachari M, Gurusamy D, Kumar K, Narayanasamy P, Kethireddy Venkata P, Solanke A, Gamanagatti S, Hiremath V, Katageri IS, Leelavathi S, Kumar PA, Reddy VS. Genome-wide transcriptomic and proteomic analyses of bollworm-infested developing cotton bolls revealed the genes and pathways involved in the insect pest defence mechanism. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1438-55. [PMID: 26799171 PMCID: PMC5066800 DOI: 10.1111/pbi.12508] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 05/31/2023]
Abstract
Cotton bollworm, Helicoverpa armigera, is a major insect pest that feeds on cotton bolls causing extensive damage leading to crop and productivity loss. In spite of such a major impact, cotton plant response to bollworm infection is yet to be witnessed. In this context, we have studied the genome-wide response of cotton bolls infested with bollworm using transcriptomic and proteomic approaches. Further, we have validated this data using semi-quantitative real-time PCR. Comparative analyses have revealed that 39% of the transcriptome and 35% of the proteome were differentially regulated during bollworm infestation. Around 36% of significantly regulated transcripts and 45% of differentially expressed proteins were found to be involved in signalling followed by redox regulation. Further analysis showed that defence-related stress hormones and their lipid precursors, transcription factors, signalling molecules, etc. were stimulated, whereas the growth-related counterparts were suppressed during bollworm infestation. Around 26% of the significantly up-regulated proteins were defence molecules, while >50% of the significantly down-regulated were related to photosynthesis and growth. Interestingly, the biosynthesis genes for synergistically regulated jasmonate, ethylene and suppressors of the antagonistic factor salicylate were found to be up-regulated, suggesting a choice among stress-responsive phytohormone regulation. Manual curation of the enzymes and TFs highlighted the components of retrograde signalling pathways. Our data suggest that a selective regulatory mechanism directs the reallocation of metabolic resources favouring defence over growth under bollworm infestation and these insights could be exploited to develop bollworm-resistant cotton varieties.
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Affiliation(s)
- Saravanan Kumar
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mogilicherla Kanakachari
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Dhandapani Gurusamy
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Krishan Kumar
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Prabhakaran Narayanasamy
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | | | - Amolkumar Solanke
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | | | | | | | - Sadhu Leelavathi
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Polumetla Ananda Kumar
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Vanga Siva Reddy
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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26
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Li C, Nong Q, Solanki MK, Liang Q, Xie J, Liu X, Li Y, Wang W, Yang L, Li Y. Differential expression profiles and pathways of genes in sugarcane leaf at elongation stage in response to drought stress. Sci Rep 2016; 6:25698. [PMID: 27170459 PMCID: PMC4864372 DOI: 10.1038/srep25698] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/21/2016] [Indexed: 01/06/2023] Open
Abstract
Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, a pot experiment was performed with the sugarcane variety GT21 at three water-deficit levels (mild, moderate, and severe) during the elongation stage and gene expression was analyzed using microarray technology. Physiological parameters of sugarcane showed significant alterations in response to drought stress. Based on the expression profile of 15,593 sugarcane genes, 1,501 (9.6%) genes were differentially expressed under different water-level treatments; 821 genes were upregulated and 680 genes were downregulated. A gene similarity analysis showed that approximately 62.6% of the differentially expressed genes shared homology with functional proteins. In a Gene Ontology (GO) analysis, 901 differentially expressed genes were assigned to 36 GO categories. Moreover, 325 differentially expressed genes were classified into 101 pathway categories involved in various processes, such as the biosynthesis of secondary metabolites, ribosomes, carbon metabolism, etc. In addition, some unannotated genes were detected; these may provide a basis for studies of water-deficit tolerance. The reliability of the observed expression patterns was confirmed by RT-PCR. The results of this study may help identify useful genes for improving drought tolerance in sugarcane.
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Affiliation(s)
- Changning Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Qian Nong
- Microbiology Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Manoj Kumar Solanki
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Qiang Liang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Jinlan Xie
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Xiaoyan Liu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Yijie Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Weizan Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Litao Yang
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi 530004, China
| | - Yangrui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
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27
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Guo K, Du X, Tu L, Tang W, Wang P, Wang M, Liu Z, Zhang X. Fibre elongation requires normal redox homeostasis modulated by cytosolic ascorbate peroxidase in cotton (Gossypium hirsutum). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3289-301. [PMID: 27091877 PMCID: PMC4892722 DOI: 10.1093/jxb/erw146] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
High-quality cotton fibre equates to a more comfortable textile. Fibre length is an important index of fibre quality. Hydrogen peroxide (H2O2) acts as a signalling molecule in the regulation of fibre elongation. Results from in vitro ovule culture suggest that the alteration of fibre cell H2O2 levels affects fibre development. Ascorbate peroxidase (APX) is an important reactive oxygen species (ROS) scavenging enzyme, and we found that GhAPX1AT/DT encoded one member of the previously unrealized group of cytosolic APXs (cAPXs) that were preferentially expressed during the fibre elongation stage. Transgenic cottons with up- and down-regulation of GhAPX1AT/DT were generated to control fibre endogenous levels of H2O2 Suppression of all cAPX (IAO) resulted in a 3.5-fold increase in H2O2 level in fibres and oxidative stress, which significantly suppressed fibre elongation. The fibre length of transgenic lines with over-expression or specific down-regulation of GhAPX1AT/DT did not show any obvious change. However, the fibres in the over-expression lines exhibited higher tolerance to oxidative stress. Differentially expressed genes (DEGs) in fibres at 10 days post-anthesis (DPA) of IAO lines identified by RNA-seq were related to redox homeostasis, signalling pathways, stress responses and cell wall synthesis, and the DEGs that were up-regulated in IAO lines were also up-regulated in the 10 DPA and 20 DPA fibres of wild cotton compared with domesticated cotton. These results suggest that optimal H2O2 levels and redox state regulated by cytosolic APX are key mechanisms regulating fibre elongation, and dysregulation of the increase in H2O2 induces oxidative stress and results in shorter fibres by initiating secondary cell wall-related gene expression.
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Affiliation(s)
- Kai Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xueqiong Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Wenxin Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zhen Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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28
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Gunapati S, Naresh R, Ranjan S, Nigam D, Hans A, Verma PC, Gadre R, Pathre UV, Sane AP, Sane VA. Expression of GhNAC2 from G. herbaceum, improves root growth and imparts tolerance to drought in transgenic cotton and Arabidopsis. Sci Rep 2016; 6:24978. [PMID: 27113714 PMCID: PMC4844984 DOI: 10.1038/srep24978] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/22/2016] [Indexed: 02/07/2023] Open
Abstract
NAC proteins are plant-specific transcription factors that play essential roles in regulating development and responses to abiotic and biotic stresses. We show that over-expression of the cotton GhNAC2 under the CaMV35S promoter increases root growth in both Arabidopsis and cotton under unstressed conditions. Transgenic Arabidopsis plants also show improved root growth in presence of mannitol and NaCl while transgenic cotton expressing GhNAC2 show reduced leaf abscission and wilting upon water stress compared to control plants. Transgenic Arabidopsis plants also have larger leaves, higher seed number and size under well watered conditions, reduced transpiration and higher relative leaf water content. Micro-array analysis of transgenic plants over-expressing GhNAC2 reveals activation of the ABA/JA pathways and a suppression of the ethylene pathway at several levels to reduce expression of ERF6/ERF1/WRKY33/ MPK3/MKK9/ACS6 and their targets. This probably suppresses the ethylene-mediated inhibition of organ expansion, leading to larger leaves, better root growth and higher yields under unstressed conditions. Suppression of the ethylene pathway and activation of the ABA/JA pathways also primes the plant for improved stress tolerance by reduction in transpiration, greater stomatal control and suppression of growth retarding factors.
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Affiliation(s)
- Samatha Gunapati
- Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow-226001, India
| | - Ram Naresh
- Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow-226001, India
| | - Sanjay Ranjan
- Dept. of Plant Physiology, CSIR- National Botanical Research Institute, Lucknow-226001, India
| | - Deepti Nigam
- Dept. of Bioinformatics, CSIR- National Botanical Research Institute, Lucknow-226001, India
| | - Aradhana Hans
- Plant tissue culture, CSIR- National Botanical Research Institute, Lucknow-226001, India
| | - Praveen C Verma
- Plant tissue culture, CSIR- National Botanical Research Institute, Lucknow-226001, India
| | - Rekha Gadre
- Dept of Biochemistry, DeviAhilyaBai University, Indore-452001, India
| | - Uday V Pathre
- Dept. of Plant Physiology, CSIR- National Botanical Research Institute, Lucknow-226001, India
| | - Aniruddha P Sane
- Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow-226001, India
| | - Vidhu A Sane
- Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow-226001, India
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29
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Imadi SR, Kazi AG, Ahanger MA, Gucel S, Ahmad P. Plant transcriptomics and responses to environmental stress: an overview. J Genet 2016; 94:525-37. [PMID: 26440096 DOI: 10.1007/s12041-015-0545-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Different stresses include nutrient deficiency, pathogen attack, exposure to toxic chemicals etc. Transcriptomic studies have been mainly applied to only a few plant species including the model plant, Arabidopsis thaliana. These studies have provided valuable insights into the genetic networks of plant stress responses. Transcriptomics applied to cash crops including barley, rice, sugarcane, wheat and maize have further helped in understanding physiological and molecular responses in terms of genome sequence, gene regulation, gene differentiation, posttranscriptional modifications and gene splicing. On the other hand, comparative transcriptomics has provided more information about plant's response to diverse stresses. Thus, transcriptomics, together with other biotechnological approaches helps in development of stress tolerance in crops against the climate change.
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Affiliation(s)
- Sameen Ruqia Imadi
- Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, H-12 Campus, Islamabad 25000,
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30
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Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4182071. [PMID: 27088086 PMCID: PMC4818802 DOI: 10.1155/2016/4182071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/18/2016] [Accepted: 02/28/2016] [Indexed: 11/17/2022]
Abstract
The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. In this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.
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31
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Wang X, Xin C, Cai J, Zhou Q, Dai T, Cao W, Jiang D. Heat Priming Induces Trans-generational Tolerance to High Temperature Stress in Wheat. FRONTIERS IN PLANT SCIENCE 2016; 7:501. [PMID: 27148324 PMCID: PMC4830833 DOI: 10.3389/fpls.2016.00501] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/29/2016] [Indexed: 05/20/2023]
Abstract
Wheat plants are very sensitive to high temperature stress during grain filling. Effects of heat priming applied to the first generation on tolerance of the successive generation to post-anthesis high temperature stress were investigated. Compared with the progeny of non-heat primed plants (NH), the progeny of heat-primed plants (PH) possessed higher grain yield, leaf photosynthesis and activities of antioxidant enzymes and lower cell membrane damage under high temperature stress. In the transcriptome profile, 1430 probes showed obvious difference in expression between PH and NH. These genes were related to signal transduction, transcription, energy, defense, and protein destination and storage, respectively. The gene encoding the lysine-specific histone demethylase 1 (LSD1) which was involved in histone demethylation related to epigenetic modification was up-regulated in the PH compared with NH. The proteome analysis indicated that the proteins involved in photosynthesis, energy production and protein destination and storage were up-regulated in the PH compared with NH. In short, thermos-tolerance was induced through heritable epigenetic alternation and signaling transduction, both processes further triggered prompt modifications of defense related responses in anti-oxidation, transcription, energy production, and protein destination and storage in the progeny of the primed plants under high temperature stress. It was concluded that trans-generation thermo-tolerance was induced by heat priming in the first generation, and this might be an effective measure to cope with severe high-temperature stresses during key growth stages in wheat production.
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Affiliation(s)
- Xiao Wang
- National Technology Innovation Center for Regional Wheat Production/National Engineering and Technology Center for Information Agriculture/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
| | - Caiyun Xin
- National Technology Innovation Center for Regional Wheat Production/National Engineering and Technology Center for Information Agriculture/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- Rice Research Institute, Shandong Academy of Agricultural SciencesJinan, China
| | - Jian Cai
- National Technology Innovation Center for Regional Wheat Production/National Engineering and Technology Center for Information Agriculture/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
| | - Qin Zhou
- National Technology Innovation Center for Regional Wheat Production/National Engineering and Technology Center for Information Agriculture/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Dong Jiang, ; Qin Zhou,
| | - Tingbo Dai
- National Technology Innovation Center for Regional Wheat Production/National Engineering and Technology Center for Information Agriculture/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
| | - Weixing Cao
- National Technology Innovation Center for Regional Wheat Production/National Engineering and Technology Center for Information Agriculture/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
| | - Dong Jiang
- National Technology Innovation Center for Regional Wheat Production/National Engineering and Technology Center for Information Agriculture/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Dong Jiang, ; Qin Zhou,
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Mittal A, Jiang Y, Ritchie GL, Burke JJ, Rock CD. AtRAV1 and AtRAV2 overexpression in cotton increases fiber length differentially under drought stress and delays flowering. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:78-95. [PMID: 26706061 DOI: 10.1016/j.plantsci.2015.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/11/2015] [Accepted: 09/16/2015] [Indexed: 05/23/2023]
Abstract
There is a longstanding problem of an inverse relationship between cotton fiber qualities versus high yields. To better understand drought stress signaling and adaptation in cotton (Gossypium hirsutum) fiber development, we expressed the Arabidopsis transcription factors RELATED_TO_ABA-INSENSITIVE3/VIVIPAROUS1/(RAV1) and AtRAV2, which encode APETALA2-Basic3 domain proteins shown to repress transcription of FLOWERING_LOCUS_T (FT) and to promote stomatal opening cell-autonomously. In three years of field trials, we show that AtRAV1 and AtRAV2-overexpressing cotton had ∼5% significantly longer fibers with only marginal decreases in yields under well-watered or drought stress conditions that resulted in 40-60% yield penalties and 3-7% fiber length penalties in control plants. The longer transgenic fibers from drought-stressed transgenics could be spun into yarn which was measurably stronger and more uniform than that from well-watered control fibers. The transgenic AtRAV1 and AtRAV2 lines flowered later and retained bolls at higher nodes, which correlated with repression of endogenous GhFT-Like (FTL) transcript accumulation. Elevated expression early in development of ovules was observed for GhRAV2L, GhMYB25-Like (MYB25L) involved in fiber initiation, and GhMYB2 and GhMYB25 involved in fiber elongation. Altered expression of RAVs controlling critical nodes in developmental and environmental signaling hierarchies has the potential for phenotypic modification of crops.
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Affiliation(s)
- Amandeep Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, United States.
| | - Yingwen Jiang
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, United States.
| | - Glen L Ritchie
- Department of Plant and Soils Science, Texas Tech University, Lubbock, TX 79409-2122, United States.
| | - John J Burke
- USDA-ARS Plant Stress and Germplasm Laboratory, Lubbock, TX 79415, United States.
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, United States.
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Sun H, Chen ZH, Chen F, Xie L, Zhang G, Vincze E, Wu F. DNA microarray revealed and RNAi plants confirmed key genes conferring low Cd accumulation in barley grains. BMC PLANT BIOLOGY 2015; 15:259. [PMID: 26503017 PMCID: PMC4623906 DOI: 10.1186/s12870-015-0648-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/20/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND Understanding the mechanism of low Cd accumulation in crops is crucial for sustainable safe food production in Cd-contaminated soils. RESULTS Confocal microscopy, atomic absorption spectrometry, gas exchange and chlorophyll fluorescence analyses revealed a distinct difference in Cd accumulation and tolerance between the two contrasting barley genotypes: W6nk2 (a low-grain-Cd-accumulating and Cd-sensitive genotype) and Zhenong8 (a high-grain-Cd-accumulating and tolerant genotype). A DNA microarray analysis detected large-scale changes of gene expression in response to Cd stress with a substantial difference between the two genotypes. Cd stress led to higher expression of genes involved in transport, carbohydrate metabolism and signal transduction in the low-grain-Cd-accumulating genotype. Novel transporter genes such as zinc transporter genes were identified as being associated with low Cd accumulation. Quantitative RT-PCR confirmed our microarray data. Furthermore, suppression of the zinc transporter genes HvZIP3 and HvZIP8 by RNAi silencing showed increased Cd accumulation and reduced Zn and Mn concentrations in barley grains. Thus, HvZIP3 and HvZIP8 could be candidate genes related to low-grain-Cd-accumulation. CONCLUSION Novel transporter genes such as HvZIP3 and HvZIP8 were identified as being associated with low-grain-Cd-accumulation. In addition to advancing academic knowledge, our findings may also result in potential economic benefits for molecular breeding of low Cd accumulating barley and other crops.
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Affiliation(s)
- Hongyan Sun
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, PR China.
| | - Zhong-Hua Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, PR China.
| | - Fei Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, PR China.
| | - Lupeng Xie
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, PR China.
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, PR China.
| | - Eva Vincze
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark.
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, PR China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Kanakachari M, Solanke AU, Prabhakaran N, Ahmad I, Dhandapani G, Jayabalan N, Kumar PA. Evaluation of Suitable Reference Genes for Normalization of qPCR Gene Expression Studies in Brinjal (Solanum melongena L.) During Fruit Developmental Stages. Appl Biochem Biotechnol 2015; 178:433-50. [DOI: 10.1007/s12010-015-1884-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 10/02/2015] [Indexed: 12/18/2022]
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Hyun TK, Albacete A, van der Graaff E, Eom SH, Großkinsky DK, Böhm H, Janschek U, Rim Y, Ali WW, Kim SY, Roitsch T. The Arabidopsis PLAT domain protein1 promotes abiotic stress tolerance and growth in tobacco. Transgenic Res 2015; 24:651-63. [PMID: 25757741 DOI: 10.1007/s11248-015-9868-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 03/04/2015] [Indexed: 11/25/2022]
Abstract
Plant growth and consequently crop yield can be severely compromised by abiotic and biotic stress conditions. Transgenic approaches that resulted in increased tolerance against abiotic stresses often were typically accompanied by adverse effects on plant growth and fitness under optimal growing conditions. Proteins that belong to the PLAT-plant-stress protein family harbour a single PLAT (Polycystin, Lipoxygenase, Alpha-toxin and Triacylglycerol lipase) domain and are ubiquitously present in monocot and dicot plant species. Until now, only limited data is available for PLAT-plant-stress family members, which suggested that these proteins in general could promote tolerance towards stress responses. We studied the function of the Arabidopsis PLAT-plant-stress protein AtPLAT1 employing heterologous gain-of-function analysis in tobacco. AtPLAT1 conferred increased abiotic stress tolerance in tobacco, evident by improved tolerance towards cold, drought and salt stresses, and promoted growth, reflected by a faster development under non-stressed conditions. However, the overexpression of AtPLAT1 in tobacco reduced the tolerance towards biotic stress conditions and, therefore, could be involved in regulating the crosstalk between abiotic and biotic stress responses. Thus, we showed that heterologously expressed AtPLAT1 functions as positive regulator of abiotic stress tolerance and plant growth, which could be an important new asset for strategies to develop plants with improved abiotic stress tolerance, without growth and subsequent yield penalties under optimal growth conditions.
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Affiliation(s)
- Tae Kyung Hyun
- Institute of Plant Sciences, University of Graz, 8010, Graz, Austria
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Gong L, Zhang H, Gan X, Zhang L, Chen Y, Nie F, Shi L, Li M, Guo Z, Zhang G, Song Y. Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions. PLoS One 2015; 10:e0128041. [PMID: 26010543 PMCID: PMC4444143 DOI: 10.1371/journal.pone.0128041] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/21/2015] [Indexed: 01/04/2023] Open
Abstract
Drought stress can seriously affect tuberization, yield and quality of potato plant. However, the precise molecular mechanisms governing potato stolon’s response to drought stress and water supply are not very well understood. In this work, a potato (Solanum tuberosum L.) variant, Ningshu 4, was subjected to severe drought stress treatment (DT) and re-watering treatment (RWT) at tuber bulking stage. Strand-specific cDNA libraries of stolon materials were constructed for paired-end transcriptome sequencing analyses and differentially expressed gene (DEG) examination. In comparison to untreated-control (CT) plants, 3189 and 1797 DEGs were identified in DT and RWT plants and 4154 solely expressed DEGs were screened out from these two comparison groups. Interestingly, 263 genes showed opposite expression patterns in DT and RWT plants. Among them, genes homologous to Protein Phosphatase 2C (PP2C), Aspartic protease in guard cell 1 (ASPG1), auxin-responsive protein, Arabidopsis pseudo response regualtor 2 (APRR2), GA stimulated transcripts in Arabidopsis 6 (GASA6), Calmodulin-like protein 19 (CML19), abscisic acid 8'-hydroxylases and calcium-transporting ATPase, et al. were related with drought-stress and water stimulus response. Sixteen DEGs involved in starch synthesis, accumulation and tuber formation exhibited significantly different expression upon re-watering. In addition, 1630, 1527 and 1596 transcription factor encoding genes were detected in CT, DT and RWT. DEGs of ERF, bHLH, MYB, NAC, WRKY, C2H2, bZIP and HD-ZIP families accounted for 50% in three comparison groups, respectively. Furthermore, characteristics of 565 gene ontology (GO) and 108 Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were analyzed with the 4154 DEGs. All these results suggest that the drought- and water-stimulus response could be implemented by the regulated expression of metabolic pathway DEGs, and these genes were involved in the endogenous hormone biosynthesis and signal transduction pathways. Our data provide more direct information for future study on the interaction between key genes involved in various metabolic pathways under drought stress in potato.
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Affiliation(s)
- Lei Gong
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia Hui Nationality Autonomous Region, China
| | - Hongxia Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyan Gan
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia Hui Nationality Autonomous Region, China
| | - Li Zhang
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia Hui Nationality Autonomous Region, China
| | - Yuchao Chen
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia Hui Nationality Autonomous Region, China
| | - Fengjie Nie
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia Hui Nationality Autonomous Region, China
| | - Lei Shi
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia Hui Nationality Autonomous Region, China
| | - Miao Li
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia Hui Nationality Autonomous Region, China
| | - Zhiqian Guo
- Guyuan sub-centers of National Potato Improvement Center, Ningxia Academy of Agriculture and Forestry Science, Guyuan, Ningxia Hui Nationality Autonomous Region, China
| | - Guohui Zhang
- Guyuan sub-centers of National Potato Improvement Center, Ningxia Academy of Agriculture and Forestry Science, Guyuan, Ningxia Hui Nationality Autonomous Region, China
| | - Yuxia Song
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia Hui Nationality Autonomous Region, China
- * E-mail:
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Chen T, Li W, Hu X, Guo J, Liu A, Zhang B. A Cotton MYB Transcription Factor, GbMYB5, is Positively Involved in Plant Adaptive Response to Drought Stress. PLANT & CELL PHYSIOLOGY 2015; 56:917-29. [PMID: 25657343 DOI: 10.1093/pcp/pcv019] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 02/02/2015] [Indexed: 05/19/2023]
Abstract
Drought stress negatively affects plant growth and limits plant productivity. Genes functioning in plant responses to drought stress are essential for the development of drought-tolerant crops. Here, we report that an R2R3-type MYB transcription factor gene in Gossypium barbadense, GbMYB5, confers drought tolerance in cotton and transgenic tobacco. Virus-induced gene silencing of GbMYB5 compromised the tolerance of cotton plantlets to drought stress and reduced the post-rewatering water recovery survival rate to 50% as compared with the 90% survival rate in the wild type (WT). Silencing GbMYB5 decreased proline content and antioxidant enzyme activities and increased malondialdehyde (MDA) content in cotton under drought stress. The expression levels of drought-inducible genes NCED3, RD22 and RD26 were not affected by the silencing of GbMYB5. However, GbMYB5-overexpressing tobacco lines displayed hypersensitivity to ABA and improved survival rates as well as reduced water loss rates under drought stress. Furthermore, stomatal size and the rate of opening of stomata were markedly decreased in transgenic tobacco. The overexpression of GbMYB5 enhanced the accumulation of proline and antioxidant enzymes while it reduced production of MDA in transgenic tobacco as compared with the WT under drought stress. The transcript levels of the antioxidant genes SOD, CAT and GST, polyamine biosynthesis genes ADC1 and SAMDC, the late embryogenesis abundant protein-encoding gene ERD10D and drought-responsive genes NCED3, BG and RD26 were generally higher in GbMYB5-overexpressing tobacco than in the WT under drought stress. Collectively, our data suggested that GbMYB5 was positively involved in the plant adaptive response to drought stress.
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Affiliation(s)
- Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China These authors contributed equally to this work
| | - Wenjuan Li
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China These authors contributed equally to this work
| | - Xuehong Hu
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaru Guo
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aimin Liu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Dhandapani G, Lakshmi Prabha A, Kanakachari M, Phanindra MLV, Prabhakaran N, Gothandapani S, Padmalatha KV, Solanke AU, Kumar PA. GhDRIN1, a novel drought-induced gene of upland cotton (Gossypium hirsutum L.) confers abiotic and biotic stress tolerance in transgenic tobacco. Biotechnol Lett 2015; 37:907-19. [PMID: 25413882 DOI: 10.1007/s10529-014-1733-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/11/2014] [Indexed: 10/24/2022]
Abstract
A novel stress tolerance cDNA fragment encoding GhDRIN1 protein was identified and its regulation was studied in cotton boll tissues and seedlings subjected to various biotic and abiotic stresses. Phylogenetic and conserved domain prediction indicated that GhDRIN1 was annotated with a hypothetical protein of unknown function. Subcellular localization showed that GhDRIN1 is localized in the chloroplasts. The promoter sequence was isolated and subjected to in silico study. Various cis-acting elements responsive to biotic and abiotic stresses and hormones were found. Transgenic tobacco seedlings exhibited better growth on amended MS medium and showed minimal leaf damage in insect bioassays carried out with Helicoverpa armigera larvae. Transgenic tobacco showed better tolerance to water-deficit and fast recovered upon rewatering. Present work demonstrated that GhDRIN1, a novel stress tolerance gene of cotton, positively regulates the response to biotic and abiotic stresses in transgenic tobacco.
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Affiliation(s)
- Gurusamy Dhandapani
- National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
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Singh R, Pandey N, Naskar J, Shirke PA. Physiological performance and differential expression profiling of genes associated with drought tolerance in contrasting varieties of two Gossypium species. PROTOPLASMA 2015; 252:423-38. [PMID: 25149149 DOI: 10.1007/s00709-014-0686-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/01/2014] [Indexed: 05/26/2023]
Abstract
Cotton is mostly cultivated under rain-fed conditions in India, thus faces frequent drought conditions during its life cycle. Drought being a major stress factor responsible for yield penalty, there has always been a high priority to generate knowledge on adaptation and tolerance of cotton. In the present study, four cotton varieties, JKC-770 and KC-2 (Gossypium hirsutum), and JKC-717 and RAHS-187(Gossypium herbaceum), were imposed to drought. Under drought condition, differential changes in physiological characters like net photosynthesis, transpiration, stomatal conductance, chlorophyll fluorescence, relative water content (RWC), and predawn water potential (ψ 0) showed a change. While proline, malondialdehyde (MDA), and glutathione-S-transferase (GST) content increased along with a concomitant change in the expression of their associated genes. Under moderate stress, tolerant varieties maintain lower ψ 0 probably due to higher proline content as compared to sensitive varieties. Cyclic electron flow (CEF) also plays an important role in tolerance under mild water stress in G. hirsutum varieties. CEF not only activates at high light but also initiates at a very low light intensity. Expression analysis of genes reveals that drought-tolerant varieties showed enhanced detoxifying mechanism by up-regulation of asparagine synthase (AS), glutathione-S-transferase (GST), and methyl glyoxalase (GlyI) genes under drought stress. Up-regulation of Δ(1)-pyrroline-5-carboxylase synthase (Δ(1)P5CS) enhanced accumulation of proline, an osmolyte, under drought in tolerant varieties. While the drought-sensitive varieties showed up-regulation of ethylene responsive factor (ERF) and down-regulation of WRKY70 responsible for senescence of the leaf which correlated well with the high rate of leaf fall in sensitive varieties under water stress.
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Affiliation(s)
- Ruchi Singh
- Plant Physiology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
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Hyun TK, van der Graaff E, Albacete A, Eom SH, Großkinsky DK, Böhm H, Janschek U, Rim Y, Ali WW, Kim SY, Roitsch T. The Arabidopsis PLAT domain protein1 is critically involved in abiotic stress tolerance. PLoS One 2014; 9:e112946. [PMID: 25396746 PMCID: PMC4232524 DOI: 10.1371/journal.pone.0112946] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/17/2014] [Indexed: 11/19/2022] Open
Abstract
Despite the completion of the Arabidopsis genome sequence, for only a relatively low percentage of the encoded proteins experimental evidence concerning their function is available. Plant proteins that harbour a single PLAT (Polycystin, Lipoxygenase, Alpha-toxin and Triacylglycerol lipase) domain and belong to the PLAT-plant-stress protein family are ubiquitously present in monocot and dicots. However, the function of PLAT-plant-stress proteins is still poorly understood. Therefore, we have assessed the function of the uncharacterised Arabidopsis PLAT-plant-stress family members through a combination of functional genetic and physiological approaches. PLAT1 overexpression conferred increased abiotic stress tolerance, including cold, drought and salt stress, while loss-of-function resulted in opposite effects on abiotic stress tolerance. Strikingly, PLAT1 promoted growth under non-stressed conditions. Abiotic stress treatments induced PLAT1 expression and caused expansion of its expression domain. The ABF/ABRE transcription factors, which are positive mediators of abscisic acid signalling, activate PLAT1 promoter activity in transactivation assays and directly bind to the ABRE elements located in this promoter in electrophoretic mobility shift assays. This suggests that PLAT1 represents a novel downstream target of the abscisic acid signalling pathway. Thus, we showed that PLAT1 critically functions as positive regulator of abiotic stress tolerance, but also is involved in regulating plant growth, and thereby assigned a function to this previously uncharacterised PLAT domain protein. The functional data obtained for PLAT1 support that PLAT-plant-stress proteins in general could be promising targets for improving abiotic stress tolerance without yield penalty.
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Affiliation(s)
- Tae Kyung Hyun
- Institute of Plant Sciences, University of Graz, Graz, Austria
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Eric van der Graaff
- Institute of Plant Sciences, University of Graz, Graz, Austria
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Taastrup, Denmark
| | - Alfonso Albacete
- Institute of Plant Sciences, University of Graz, Graz, Austria
- Departamento de Nutrición Vegetal, CEBAS-CSIC, Campus Espinardo, Murcia, Spain
| | - Seung Hee Eom
- Institute of Plant Sciences, University of Graz, Graz, Austria
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Dominik K. Großkinsky
- Institute of Plant Sciences, University of Graz, Graz, Austria
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Taastrup, Denmark
| | - Hannah Böhm
- Institute of Plant Sciences, University of Graz, Graz, Austria
| | - Ursula Janschek
- Institute of Plant Sciences, University of Graz, Graz, Austria
| | - Yeonggil Rim
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Walid Wahid Ali
- Department of Pharmaceutical Biology, University of Würzburg, Würzburg, Germany
| | - Soo Young Kim
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Thomas Roitsch
- Institute of Plant Sciences, University of Graz, Graz, Austria
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Taastrup, Denmark
- Global Change Research Centre, CzechGlobe AS CR, v.v.i., Drásov, Czech Republic
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Doğramacı M, Horvath DP, Anderson JV. Dehydration-induced endodormancy in crown buds of leafy spurge highlights involvement of MAF3- and RVE1-like homologs, and hormone signaling cross-talk. PLANT MOLECULAR BIOLOGY 2014; 86:409-424. [PMID: 25150409 DOI: 10.1007/s11103-014-0237-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 08/12/2014] [Indexed: 06/03/2023]
Abstract
Vegetative shoot growth from underground adventitious buds of leafy spurge is critical for survival of this invasive perennial weed after episodes of severe abiotic stress. To determine the impact that dehydration-stress has on molecular mechanisms associated with vegetative reproduction of leafy spurge, greenhouse plants were exposed to mild- (3-day), intermediate- (7-day), severe- (14-day) and extended- (21-day) dehydration treatments. Aerial tissues of treated plants were then decapitated and soil was rehydrated to determine the growth potential of underground adventitious buds. Compared to well-watered plants, mild-dehydration accelerated new vegetative shoot growth, whereas intermediate- through extended-dehydration treatments both delayed and reduced shoot growth. Results of vegetative regrowth further confirmed that 14 days of dehydration induced a full-state of endodormancy in crown buds, which was correlated with a significant (P < 0.05) change in abundance of 2,124 transcripts. Sub-network enrichment analyses of transcriptome data obtained from the various levels of dehydration treatment also identified central hubs of over-represented genes involved in processes such as hormone signaling (i.e., ABA, auxin, ethylene, GA, and JA), response to abiotic stress (DREB1A/2A, RD22) and light (PIF3), phosphorylation (MPK4/6), circadian regulation (CRY2, PHYA), and flowering (AGL20, AP2, FLC). Further, results from this and previous studies highlight homologs most similar to Arabidopsis HY5, MAF3, RVE1 and RD22 as potential molecular markers for endodormancy in crown buds of leafy spurge. Early response to mild dehydration also highlighted involvement of upstream ethylene and JA-signaling, whereas severe dehydration impacted ABA-signaling. The identification of conserved ABRE- and MYC-consensus, cis-acting elements in the promoter of leafy spurge genomic clones similar to Arabidopsis RVE1 (AT5G17300) implicates a potential role for ABA-signaling in its dehydration-induced expression. Response of these molecular mechanisms to dehydration-stress provides insights on the ability of invasive perennial weeds to adapt and survive under harsh environments, which will be beneficial for addressing future management practices.
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Affiliation(s)
- Münevver Doğramacı
- Biosciences Research Laboratory, USDA-ARS, 1605 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
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Genome-wide investigation and transcriptome analysis of the WRKY gene family in Gossypium. Mol Genet Genomics 2014; 290:151-71. [DOI: 10.1007/s00438-014-0904-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 08/19/2014] [Indexed: 10/24/2022]
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Peng Z, He S, Gong W, Sun J, Pan Z, Xu F, Lu Y, Du X. Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes. BMC Genomics 2014; 15:760. [PMID: 25189468 PMCID: PMC4169805 DOI: 10.1186/1471-2164-15-760] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/04/2014] [Indexed: 12/26/2022] Open
Abstract
Background Cotton (Gossypium spp.) is one of the major fibre crops of the world. Although it is classified as salt tolerant crop, cotton growth and productivity are adversely affected by high salinity, especially at germination and seedling stages. Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology. Results We investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions. The expression patterns of differentially co-expressed unigenes were divided into six groups using short time-servies expression miner software. During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype. We further analyzed the predicted target genes of these miRNAs along with the transcriptome for each time point. Important expressed genes encoding membrane receptors, transporters, and pathways involved in biosynthesis and signal transduction of calcium-dependent protein kinase, mitogen-activated protein kinase, and hormones (abscisic acid and ethylene) were up-regulated. We also analyzed the salt stress response of some key miRNAs and their target genes and found that the expressions of five of nine target genes exhibited significant inverse correlations with their corresponding miRNAs. On the basis of these results, we constructed molecular regulatory pathways and a potential regulatory network for these salt-responsive miRNAs. Conclusions Our comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-760) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Yanli Lu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000 Anyang, Henan, China.
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Reddy SK, Liu S, Rudd JC, Xue Q, Payton P, Finlayson SA, Mahan J, Akhunova A, Holalu SV, Lu N. Physiology and transcriptomics of water-deficit stress responses in wheat cultivars TAM 111 and TAM 112. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1289-98. [PMID: 25014264 DOI: 10.1016/j.jplph.2014.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 05/05/2023]
Abstract
Hard red winter wheat crops on the U.S. Southern Great Plains often experience moderate to severe drought stress, especially during the grain filling stage, resulting in significant yield losses. Cultivars TAM 111 and TAM 112 are widely cultivated in the region, share parentage and showed superior but distinct adaption mechanisms under water-deficit (WD) conditions. Nevertheless, the physiological and molecular basis of their adaptation remains unknown. A greenhouse study was conducted to understand the differences in the physiological and transcriptomic responses of TAM 111 and TAM 112 to WD stress. Whole-plant data indicated that TAM 112 used more water, produced more biomass and grain yield under WD compared to TAM 111. Leaf-level data at the grain filling stage indicated that TAM 112 had elevated abscisic acid (ABA) content and reduced stomatal conductance and photosynthesis as compared to TAM 111. Sustained WD during the grain filling stage also resulted in greater flag leaf transcriptome changes in TAM 112 than TAM 111. Transcripts associated with photosynthesis, carbohydrate metabolism, phytohormone metabolism, and other dehydration responses were uniquely regulated between cultivars. These results suggested a differential role for ABA in regulating physiological and transcriptomic changes associated with WD stress and potential involvement in the superior adaptation and yield of TAM 112.
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Affiliation(s)
- Srirama Krishna Reddy
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, 6500 Amarillo Blvd W, Amarillo, TX 79106 USA
| | - Shuyu Liu
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, 6500 Amarillo Blvd W, Amarillo, TX 79106 USA.
| | - Jackie C Rudd
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, 6500 Amarillo Blvd W, Amarillo, TX 79106 USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, 6500 Amarillo Blvd W, Amarillo, TX 79106 USA
| | - Paxton Payton
- United States Department of Agriculture - Agriculture Research Services, Cropping Systems Research Laboratory, Lubbock, TX 79415 USA.
| | - Scott A Finlayson
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX 77843 USA
| | - James Mahan
- United States Department of Agriculture - Agriculture Research Services, Cropping Systems Research Laboratory, Lubbock, TX 79415 USA
| | - Alina Akhunova
- Integrated Genomics Facility, Kansas State University, 4024 Throckmorton, Manhattan, KS 66506 USA
| | - Srinidhi V Holalu
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX 77843 USA
| | - Nanyan Lu
- Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS 66506 USA
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Huang TL, Huang LY, Fu SF, Trinh NN, Huang HJ. Genomic profiling of rice roots with short- and long-term chromium stress. PLANT MOLECULAR BIOLOGY 2014; 86:157-70. [PMID: 25056418 DOI: 10.1007/s11103-014-0219-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/20/2014] [Indexed: 05/19/2023]
Abstract
Cr(VI) is the most toxic valency form of Cr, but its toxicity targets and the cellular systems contributing to acquisition of tolerance remain to be resolved at the molecular level in plants. We used microarray assay to analyze the transcriptomic profiles of rice roots in response to Cr(VI) stress. Gene ontology analysis revealed that the 2,688 Cr-responsive genes were involved in binding activity, metabolic process, biological regulation, cellular process and catalytic activity. More transcripts were responsive to Cr(VI) during long-term exposure (24 h, 2,097 genes), than short-term exposure (1- and 3-h results pooled, 1,181 genes). Long-term Cr(VI)-regulated genes are involved in cytokinin signaling, the ubiquitin-proteasome system pathway, DNA repair and Cu transportation. The expression of AS2 transcription factors was specifically modulated by long-term Cr(VI) stress. The protein kinases receptor-like cytoplasmic kinase and receptor-like kinase in flowers 3 were significantly upregulated with only short-term Cr(VI) exposure. In addition, 4 mitogen-activated protein kinase kinase kinases, 1 mitogen-activated protein kinase (MAPK) and 1 calcium-dependent protein kinase (CDPK) were upregulated with short-term Cr(VI) treatment. Expression of reactive oxygen species and calcium and activity of MAPKs and CDPK-like kinases were induced with increasing Cr(VI) concentration. These results may provide new insights into understanding the mechanisms of Cr toxicity and tolerance during different stages in rice roots.
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Affiliation(s)
- Tsai-Lien Huang
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City, 701, Taiwan
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47
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Genome-wide analysis of the WRKY gene family in cotton. Mol Genet Genomics 2014; 289:1103-21. [PMID: 24942461 DOI: 10.1007/s00438-014-0872-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/26/2014] [Indexed: 12/23/2022]
Abstract
WRKY proteins are major transcription factors involved in regulating plant growth and development. Although many studies have focused on the functional identification of WRKY genes, our knowledge concerning many areas of WRKY gene biology is limited. For example, in cotton, the phylogenetic characteristics, global expression patterns, molecular mechanisms regulating expression, and target genes/pathways of WRKY genes are poorly characterized. Therefore, in this study, we present a genome-wide analysis of the WRKY gene family in cotton (Gossypium raimondii and Gossypium hirsutum). We identified 116 WRKY genes in G. raimondii from the completed genome sequence, and we cloned 102 WRKY genes in G. hirsutum. Chromosomal location analysis indicated that WRKY genes in G. raimondii evolved mainly from segmental duplication followed by tandem amplifications. Phylogenetic analysis of alga, bryophyte, lycophyta, monocot and eudicot WRKY domains revealed family member expansion with increasing complexity of the plant body. Microarray, expression profiling and qRT-PCR data revealed that WRKY genes in G. hirsutum may regulate the development of fibers, anthers, tissues (roots, stems, leaves and embryos), and are involved in the response to stresses. Expression analysis showed that most group II and III GhWRKY genes are highly expressed under diverse stresses. Group I members, representing the ancestral form, seem to be insensitive to abiotic stress, with low expression divergence. Our results indicate that cotton WRKY genes might have evolved by adaptive duplication, leading to sensitivity to diverse stresses. This study provides fundamental information to inform further analysis and understanding of WRKY gene functions in cotton species.
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48
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Fang L, Tian R, Chen J, Wang S, Li X, Wang P, Zhang T. Transcriptomic analysis of fiber strength in upland cotton chromosome introgression lines carrying different Gossypium barbadense chromosomal segments. PLoS One 2014; 9:e94642. [PMID: 24762562 PMCID: PMC3998979 DOI: 10.1371/journal.pone.0094642] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/17/2014] [Indexed: 01/09/2023] Open
Abstract
Fiber strength is the key trait that determines fiber quality in cotton, and it is closely related to secondary cell wall synthesis. To understand the mechanism underlying fiber strength, we compared fiber transcriptomes from different G. barbadense chromosome introgression lines (CSILs) that had higher fiber strengths than their recipient, G. hirsutum acc. TM-1. A total of 18,288 differentially expressed genes (DEGs) were detected between CSIL-35431 and CSIL-31010, two CSILs with stronger fiber and TM-1 during secondary cell wall synthesis. Functional classification and enrichment analysis revealed that these DEGs were enriched for secondary cell wall biogenesis, glucuronoxylan biosynthesis, cellulose biosynthesis, sugar-mediated signaling pathways, and fatty acid biosynthesis. Pathway analysis showed that these DEGs participated in starch and sucrose metabolism (328 genes), glycolysis/gluconeogenesis (122 genes), phenylpropanoid biosynthesis (101 genes), and oxidative phosphorylation (87 genes), etc. Moreover, the expression of MYB- and NAC-type transcription factor genes were also dramatically different between the CSILs and TM-1. Being different to those of CSIL-31134, CSIL-35431 and CSIL-31010, there were many genes for fatty acid degradation and biosynthesis, and also for carbohydrate metabolism that were down-regulated in CSIL-35368. Metabolic pathway analysis in the CSILs showed that different pathways were changed, and some changes at the same developmental stage in some pathways. Our results extended our understanding that carbonhydrate metabolic pathway and secondary cell wall biosynthesis can affect the fiber strength and suggested more genes and/or pathways be related to complex fiber strength formation process.
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Affiliation(s)
- Lei Fang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Ruiping Tian
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Jiedan Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Sen Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Xinghe Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Peng Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
- * E-mail:
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49
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Nigam D, Kavita P, Tripathi RK, Ranjan A, Goel R, Asif M, Shukla A, Singh G, Rana D, Sawant SV. Transcriptome dynamics during fibre development in contrasting genotypes of Gossypium hirsutum L. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:204-218. [PMID: 24119257 DOI: 10.1111/pbi.12129] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/29/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
Understanding the contribution of genetic background in fibre quality traits is important for the development of future cotton varieties with superior fibre quality. We used Affymetrix microarray (Santa Clara, CA) and Roche 454 GSFLX (Branford, CT) for comparative transcriptome analysis between two superior and three inferior genotypes at six fibre developmental stages. Microarray-based analysis of variance (ANOVA) for 89 microarrays encompassing five contrasting genotypes and six developmental stages suggests that the stages of the fibre development have a more pronounced effect on the differentially expressed genes (DEGs) than the genetic background of genotypes. Superior genotypes showed enriched activity of cell wall enzymes, such as pectin methyl esterase, at early elongation stage, enriched metabolic activities such as lipid, amino acid and ribosomal protein subunits at peak elongation, and prolonged combinatorial regulation of brassinosteroid and auxin at later stages. Our efforts on transcriptome sequencing were focused on changes in gene expression at 25 DPA. Transcriptome sequencing resulted in the generation of 475 658 and 429 408 high-quality reads from superior and inferior genotypes, respectively. A total of 24 609 novel transcripts were identified manually for Gossypium hirsutum with no hits in NCBI 'nr' database. Gene ontology analyses showed that the genes for ribosome biogenesis, protein transport and fatty acid biosynthesis were over-represented in superior genotype, whereas salt stress, abscisic acid stimuli and water deprivation leading to the increased proteolytic activity were more pronounced in inferior genotype.
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Affiliation(s)
- Deepti Nigam
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, India
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50
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Yoo MJ, Wendel JF. Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome. PLoS Genet 2014; 10:e1004073. [PMID: 24391525 PMCID: PMC3879233 DOI: 10.1371/journal.pgen.1004073] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/15/2013] [Indexed: 01/05/2023] Open
Abstract
The single-celled cotton (Gossypium hirsutum) fiber provides an excellent model to investigate how human selection affects phenotypic evolution. To gain insight into the evolutionary genomics of cotton domestication, we conducted comparative transcriptome profiling of developing cotton fibers using RNA-Seq. Analysis of single-celled fiber transcriptomes from four wild and five domesticated accessions from two developmental time points revealed that at least one-third and likely one-half of the genes in the genome are expressed at any one stage during cotton fiber development. Among these, ∼5,000 genes are differentially expressed during primary and secondary cell wall synthesis between wild and domesticated cottons, with a biased distribution among chromosomes. Transcriptome data implicate a number of biological processes affected by human selection, and suggest that the domestication process has prolonged the duration of fiber elongation in modern cultivated forms. Functional analysis suggested that wild cottons allocate greater resources to stress response pathways, while domestication led to reprogrammed resource allocation toward increased fiber growth, possibly through modulating stress-response networks. This first global transcriptomic analysis using multiple accessions of wild and domesticated cottons is an important step toward a more comprehensive systems perspective on cotton fiber evolution. The understanding that human selection over the past 5,000+ years has dramatically re-wired the cotton fiber transcriptome sets the stage for a deeper understanding of the genetic architecture underlying cotton fiber synthesis and phenotypic evolution. Ever since Darwin biologists have recognized that comparative study of crop plants and their wild relatives offers a powerful framework for generating insights into the mechanisms that underlie evolutionary change. Here, we study the domestication process in cotton, Gossypium hirsutum, an allopolyploid species (containing two different genomes) which initially was domesticated approximately 5000 years ago, and which primarily is grown for its single-celled seed fibers. Strong directional selection over the millennia was accompanied by transformation of the short, coarse, and brown fibers of wild plants into the long, strong, and fine white fibers of the modern cotton crop plant. To explore the evolutionary genetics of cotton domestication, we conducted transcriptome profiling of developing cotton fibers from multiple accessions of wild and domesticated cottons. Comparative analysis revealed that the domestication process dramatically rewired the transcriptome, affecting more than 5,000 genes, and with a more evenly balanced usage of the duplicated copies arising from genome doubling. We identify many different biological processes that were involved in this transformation, including those leading to a prolongation of fiber elongation and a reallocation of resources toward increased fiber growth in modern forms. The data provide a rich resource for future functional analyses targeting crop improvement and evolutionary objectives.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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