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Bogomolov A, Zolotareva K, Filonov S, Chadaeva I, Rasskazov D, Sharypova E, Podkolodnyy N, Ponomarenko P, Savinkova L, Tverdokhleb N, Khandaev B, Kondratyuk E, Podkolodnaya O, Zemlyanskaya E, Kolchanov NA, Ponomarenko M. AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L. Int J Mol Sci 2024; 25:607. [PMID: 38203780 PMCID: PMC10779315 DOI: 10.3390/ijms25010607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/18/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.
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Affiliation(s)
- Anton Bogomolov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Sergey Filonov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Institute of Computational Mathematics and Mathematical Geophysics, Novosibirsk 630090, Russia
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Natalya Tverdokhleb
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Bato Khandaev
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina Kondratyuk
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk 630501, Novosibirsk Region, Russia
| | - Olga Podkolodnaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Elena Zemlyanskaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
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Wang M, Lu J, Liu R, Li Y, Ao D, Wu Y, Zhang L. Identification and validation of a major quantitative trait locus for spike length and compactness in the wheat ( Triticum aestivum L.) line Chuanyu12D7. FRONTIERS IN PLANT SCIENCE 2023; 14:1186183. [PMID: 37469784 PMCID: PMC10353862 DOI: 10.3389/fpls.2023.1186183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
Spike length (SL) and spike compactness (SC) are crucial traits related to wheat (Triticum aestivum L.) yield potential. In this study, a backcrossed inbred lines (BILs) population segregating for SL/SC was developed by using a commercial variety chuanyu25 as recurrent parent and a backbone parent Chuanyu12D7. Bulked segregant analysis (BSA) combined with the Wheat 660K SNP array was performed to conduct quantitative trait locus (QTL) mapping. A major and stable SL/SC QTL (designated as QSl/Sc.cib-2D.1) was identified on chromosome 2DS, explaining 45.63-59.72% of the phenotypic variation. QSl/Sc.cib-2D.1 was mapped to a 102.29-Kb interval by flanking SNPs AX-110276364 and AX-111593853 using a BC4F2:3 population. Since QSl/Sc.cib-2D.1 is linked to the Rht8 gene, their additive effects on plant type and spike type were analysed. Remarkably, the superior allele of QSl/Sc.cib-2D.1 combined with Rht8 can increase SL and TGW, and decrese SC without any apparent trade-offs in other yield-related traits. In addition, the closely linked kompetitive allele-specific PCR (KASP) markers of this locus were developed for marker-assisted selection (MAS) breeding. Four genes within the physical interval were considered as potential candidates based on expression patterns as well as orthologous gene functions. These results laid the foundation for map-based cloning of the gene(s) underlying QSl/Sc.cib-2D.1 and its potential application in wheat ideotype breeding.
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Affiliation(s)
- Mingxiu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- Department of Agriculture, Forestry and Food Engineering of Yibin University, Yibin, China
| | - Yunfang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Donghui Ao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Lei Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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An Overview of Molecular Basis and Genetic Modification of Floral Organs Genes: Impact of Next-Generation Sequencing. Mol Biotechnol 2022; 65:833-848. [DOI: 10.1007/s12033-022-00633-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
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Zhang X, Yang H, Li M, Bai Y, Chen C, Guo D, Guo C, Shu Y. A Pan-Transcriptome Analysis Indicates Efficient Downregulation of the FIB Genes Plays a Critical Role in the Response of Alfalfa to Cold Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:3148. [PMID: 36432878 PMCID: PMC9692835 DOI: 10.3390/plants11223148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/25/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Alfalfa (Medicago sativa L.) is a perennial forage legume that is widely distributed throughout the world, and cold stress is an important environmental factor limiting the growth and production of alfalfa in cold regions. However, little is known of the molecular mechanisms regarding cold tolerance in alfalfa. Here, we conducted physiological metabolism assays and pan-transcriptome sequencing on eight cultivars of alfalfa under cold stress conditions. The results of the RNA-seq analysis showed that the genes are "oxidoreductase activity" and "transcription regulator activity", suggesting that genes with such functions are more likely to play important roles in the response to cold stress by alfalfa. In addition, to identify specific gene modules and hub genes in response to alfalfa cold stress, we applied weighted gene co-expression network (WGCNA) analyses to the RNA-seq data. Our results indicate that the modules of genes that focus on the ATPase complex, ribosome biogenesis, are more likely to be involved in the alfalfa response to cold stress. It is important to note that we identified two fibronectin (FIB) genes as hub genes in alfalfa in response to cold stress and that they negatively regulate alfalfa response to chilling stress, and it is possible that dormant alfalfa is more effective at down-regulating FIB expression and therefore more resistant to cold stress.
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Affiliation(s)
| | | | | | | | | | | | - Changhong Guo
- Correspondence: (C.G.); (Y.S.); Tel.: +86-451-8806-0576 (Y.S. & C.G.)
| | - Yongjun Shu
- Correspondence: (C.G.); (Y.S.); Tel.: +86-451-8806-0576 (Y.S. & C.G.)
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5
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Cortijo S, Bhattarai M, Locke JCW, Ahnert SE. Co-expression Networks From Gene Expression Variability Between Genetically Identical Seedlings Can Reveal Novel Regulatory Relationships. FRONTIERS IN PLANT SCIENCE 2020; 11:599464. [PMID: 33384705 PMCID: PMC7770228 DOI: 10.3389/fpls.2020.599464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Co-expression networks are a powerful tool to understand gene regulation. They have been used to identify new regulation and function of genes involved in plant development and their response to the environment. Up to now, co-expression networks have been inferred using transcriptomes generated on plants experiencing genetic or environmental perturbation, or from expression time series. We propose a new approach by showing that co-expression networks can be constructed in the absence of genetic and environmental perturbation, for plants at the same developmental stage. For this, we used transcriptomes that were generated from genetically identical individual plants that were grown under the same conditions and for the same amount of time. Twelve time points were used to cover the 24-h light/dark cycle. We used variability in gene expression between individual plants of the same time point to infer a co-expression network. We show that this network is biologically relevant and use it to suggest new gene functions and to identify new targets for the transcriptional regulators GI, PIF4, and PRR5. Moreover, we find different co-regulation in this network based on changes in expression between individual plants, compared to the usual approach requiring environmental perturbation. Our work shows that gene co-expression networks can be identified using variability in gene expression between individual plants, without the need for genetic or environmental perturbations. It will allow further exploration of gene regulation in contexts with subtle differences between plants, which could be closer to what individual plants in a population might face in the wild.
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Affiliation(s)
- Sandra Cortijo
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- UMR5004 Biochimie et Physiologie Moléculaire des Plantes, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Marcel Bhattarai
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - James C. W. Locke
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Sebastian E. Ahnert
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, University of Cambridge, Cambridge, United Kingdom
- The Alan Turing Institute, British Library, London, United Kingdom
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6
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Ke M, Li Y, Qu Q, Ye Y, Peijnenburg WJGM, Zhang Z, Xu N, Lu T, Sun L, Qian H. Offspring toxicity of silver nanoparticles to Arabidopsis thaliana flowering and floral development. JOURNAL OF HAZARDOUS MATERIALS 2020; 386:121975. [PMID: 31884364 DOI: 10.1016/j.jhazmat.2019.121975] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Accepted: 12/23/2019] [Indexed: 05/16/2023]
Abstract
Many studies have considered silver nanoparticles (AgNPs) cytotoxicity to mammalian and human cell lines and plant growth. However, only few studies considered toxic effects of AgNPs on plant offspring, especially on flowering. Arabidopsis thaliana was treated with 12.5 mg/kg AgNPs employing parental-(P-AgNPs) and offspring-generation (O-AgNPs) exposure to study the effects of AgNPs on flowering and floral development. Exposure to P-AgNPs was found to significantly decrease petal and pollen viability and subsequently reduced pod production. The inhibition of A. thaliana vegetative growth caused by P-AgNPs exposure was transferred to offspring and even became more severe in the O-AgNPs group. Further, the transcription of genes related to flowering and floral organ development in P-AgNPs and O-Con plants was downregulated by approximately 10-40% compared to the transcription in P-Con plants and showed a stronger decrease in the O-AgNPs group to 30-50% of that in the P-AgNPs group. This resulted in a delay in flowering of 4, 3 and 8 days in P-AgNPs, O-Con and O-AgNPs plants, respectively. Our research shows that the negative effects on floral development can be transferred to the offspring in A. thaliana, which may have significant implications with regard to the risks posed by NPs to food safety and security.
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Affiliation(s)
- Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Yizhi Ye
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, RA Leiden 2300, the Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, the Netherlands
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China.
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Sun MY, Li JY, Li D, Huang FJ, Wang D, Li H, Xing Q, Zhu HB, Shi L. Full-Length Transcriptome Sequencing and Modular Organization Analysis of the Naringin/Neoeriocitrin-Related Gene Expression Pattern in Drynaria roosii. PLANT & CELL PHYSIOLOGY 2018; 59:1398-1414. [PMID: 29660070 DOI: 10.1093/pcp/pcy072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/31/2018] [Indexed: 05/28/2023]
Abstract
Drynaria roosii (Nakaike) is a traditional Chinese medicinal fern, known as 'GuSuiBu'. The effective components, naringin and neoeriocitrin, share a highly similar chemical structure and medicinal function. Our HPLC-tandem mass spectrometry (MS/MS) results showed that the accumulation of naringin/neoeriocitrin depended on specific tissues or ages. However, little was known about the expression patterns of naringin/neoeriocitrin-related genes involved in their regulatory pathways. Due to a lack of basic genetic information, we applied a combination of single molecule real-time (SMRT) sequencing and second-generation sequencing (SGS) to generate the complete and full-length transcriptome of D. roosii. According to the SGS data, the differentially expressed gene (DEG)-based heat map analysis revealed that naringin/neoeriocitrin-related gene expression exhibited obvious tissue- and time-specific transcriptomic differences. Using the systems biology method of modular organization analysis, we clustered 16,472 DEGs into 17 gene modules and studied the relationships between modules and tissue/time point samples, as well as modules and naringin/neoeriocitrin contents. We found that naringin/neoeriocitrin-related DEGs distributed in nine distinct modules, and DEGs in these modules showed significantly different patterns of transcript abundance to be linked to specific tissues or ages. Moreover, weighted gene co-expression network analysis (WGCNA) results further identified that PAL, 4CL and C4H, and C3H and HCT acted as the major hub genes involved in naringin and neoeriocitrin synthesis, respectively, and exhibited high co-expression with MYB- and basic helix-leucine-helix (bHLH)-regulated genes. In this work, modular organization and co-expression networks elucidated the tissue and time specificity of the gene expression pattern, as well as hub genes associated with naringin/neoeriocitrin synthesis in D. roosii. Simultaneously, the comprehensive transcriptome data set provided important genetic information for further research on D. roosii.
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Affiliation(s)
- Mei-Yu Sun
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jing-Yi Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Feng-Jie Huang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Di Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hui Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Quan Xing
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hui-Bin Zhu
- Hangzhou1gene Technology Co., Ltd., HangZhou, China
| | - Lei Shi
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Di Silvestre D, Bergamaschi A, Bellini E, Mauri P. Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World. Proteomes 2018; 6:proteomes6020027. [PMID: 29865292 PMCID: PMC6027444 DOI: 10.3390/proteomes6020027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022] Open
Abstract
The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.
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Affiliation(s)
- Dario Di Silvestre
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Andrea Bergamaschi
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Edoardo Bellini
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - PierLuigi Mauri
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
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9
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Yang Y, Wang Y, Jia L, Yang G, Xu X, Zhai H, He S, Li J, Dai X, Qin N, Zhu C, Liu Q. Involvement of an ABI-like protein and a Ca2+-ATPase in drought tolerance as revealed by transcript profiling of a sweetpotato somatic hybrid and its parents Ipomoea batatas (L.) Lam. and I. triloba L. PLoS One 2018; 13:e0193193. [PMID: 29466419 PMCID: PMC5821372 DOI: 10.1371/journal.pone.0193193] [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: 07/05/2017] [Accepted: 02/06/2018] [Indexed: 12/14/2022] Open
Abstract
Previously, we obtained the sweetpotato somatic hybrid KT1 from a cross between sweetpotato (Ipomoea batatas (L.) Lam.) cv. Kokei No. 14 and its drought-tolerant wild relative I. triloba L. KT1 not only inherited the thick storage root characteristic of Kokei No. 14 but also the drought-tolerance trait of I. triloba L. The aim of this study was to explore the molecular mechanism of the drought tolerance of KT1. Four-week-old in vitro-grown plants of KT1, Kokei No. 14, and I. triloba L. were subjected to a simulated drought stress treatment (30% PEG6000) for 0, 6, 12 and 24 h. Total RNA was extracted from samples at each time point, and then used for transcriptome sequencing. The gene transcript profiles of KT1 and its parents were compared to identify differentially expressed genes, and drought-related modules were screened by a weighted gene co-expression network analysis. The functions of ABI-like protein and Ca2+-ATPase, two proteins screened from the cyan and light yellow modules, were analyzed in terms of their potential roles in drought tolerance in KT1 and its parents. These analyses of the drought responses of KT1 and its somatic donors at the transcriptional level provide new annotations for the molecular mechanism of drought tolerance in the somatic hybrid KT1 and its parents.
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Affiliation(s)
- Yufeng Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Yannan Wang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Licong Jia
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Guohong Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xinzhi Xu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hong Zhai
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Shaozhen He
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Junxia Li
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaodong Dai
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Na Qin
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Cancan Zhu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qingchang Liu
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
- * E-mail:
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Tan M, Cheng D, Yang Y, Zhang G, Qin M, Chen J, Chen Y, Jiang M. Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes. BMC PLANT BIOLOGY 2017; 17:194. [PMID: 29115926 PMCID: PMC5678563 DOI: 10.1186/s12870-017-1143-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/30/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The migration of cadmium (Cd) from contaminated soil to rice is a cause for concern. However, the molecular mechanism underlying the response of rice roots to various Cd stresses remains to be clarified from the viewpoint of the co-expression network at a system-wide scale. RESULTS We employed a comparative RNAseq-based approach to identify early Cd-responsive differentially expressed genes (DEGs) in rice 'Nipponbare' seedling roots after 1 h of high-Cd treatment. A multiplicity of the identified 1772 DEGs were implicated in hormone signaling and transcriptional regulation, particularly NACs and WRKYs were all upregulated under Cd stress. All of the 6 Cd-upregulated ABC transporters were pleiotropic drug resistance proteins (PDRs), whereas all of the 6 ZRT/IRT-like proteins (ZIPs) were consistently downregulated by Cd treatment. To further confirm our results of this early transcriptomic response to Cd exposure, we then conducted weighted gene co-expression network analysis (WGCNA) to re-analyze our RNAseq data in combination with other 11 previously published RNAseq datasets for rice roots exposed to diverse concentrations of Cd for extended treatment periods. This integrative approach identified 271 transcripts as universal Cd-regulated DEGs that are key components of the Cd treatment coupled co-expression module. A global view of the 164 transcripts with annotated functions in pathway networks revealed several Cd-upregulated key functional genes, including transporter ABCG36/OsPDR9, 12-oxo-phytodienoic acid reductases (OPRs) for JA synthesis, and ZIM domain proteins JAZs in JA signaling, as well as OsWRKY10, NAC, and ZFP transcription factors. More importantly, 104 of these, including ABCG36/OsPDR9, OsNAC3, as well as several orthologs in group metalloendoproteinase, plastocyanin-like domain containing proteins and pectin methylesterase inhibitor, may respond specifically to various Cd pressures, after subtracting the 60 general stress-responsive genes reported to be commonly upregulated following multiple stresses. CONCLUSION An integrative approach was implemented to identify DEGs and co-expression network modules in response to various Cd pressures, and 104 of the 164 annotatable universal Cd-responsive DEGs may specifically respond to various Cd pressures. These results provide insight into the universal molecular mechanisms beneath the Cd response in rice roots, and suggest many promising targets for improving the rice acclimation process against Cd toxicity.
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Affiliation(s)
- Mingpu Tan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dan Cheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yuening Yang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Guoqiang Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengjie Qin
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mingyi Jiang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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11
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Ren Z, Yu D, Yang Z, Li C, Qanmber G, Li Y, Li J, Liu Z, Lu L, Wang L, Zhang H, Chen Q, Li F, Yang Z. Genome-Wide Identification of the MIKC-Type MADS-Box Gene Family in Gossypium hirsutum L. Unravels Their Roles in Flowering. FRONTIERS IN PLANT SCIENCE 2017; 8:384. [PMID: 28382045 PMCID: PMC5360754 DOI: 10.3389/fpls.2017.00384] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 03/06/2017] [Indexed: 05/22/2023]
Abstract
Cotton is one of the major world oil crops. Cottonseed oil meets the increasing demand of fried food, ruminant feed, and renewable bio-fuels. MADS intervening keratin-like and C-terminal (MIKC)-type MADS-box genes encode transcription factors that have crucial roles in various plant developmental processes. Nevertheless, this gene family has not been characterized, nor its functions investigated, in cotton. Here, we performed a comprehensive analysis of MIKC-type MADS genes in the tetraploid Gossypium hirsutum L., which is the most widely cultivated cotton species. In total, 110 GhMIKC genes were identified and phylogenetically classified into 13 subfamilies. The Flowering locus C (FLC) subfamily was absent in the Gossypium hirsutum L. genome but is found in Arabidopsis and Vitis vinifera L. Among the genes, 108 were distributed across the 13 A and 12 of the D genome's chromosomes, while two were located in scaffolds. GhMIKCs within subfamilies displayed similar exon/intron characteristics and conserved motif compositions. According to RNA-sequencing, most MIKC genes exhibited high flowering-associated expression profiles. A quantitative real-time PCR analysis revealed that some crucial MIKC genes determined the identities of the five flower organs. Furthermore, the overexpression of GhAGL17.9 in Arabidopsis caused an early flowering phenotype. Meanwhile, the expression levels of the flowering-related genes CONSTANS (CO), LEAFY (LFY) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) were significantly increased in these lines. These results provide useful information for future studies of GhMIKCs' regulation of cotton flowering.
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Affiliation(s)
- Zhongying Ren
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Daoqian Yu
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Zhaoen Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Changfeng Li
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
- Cotton Research Institute, Anhui Academy of Agricultural SciencesHefei, China
| | - Ghulam Qanmber
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Yi Li
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Jie Li
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Zhao Liu
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Lili Lu
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Lingling Wang
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Hua Zhang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
| | - Quanjia Chen
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
| | - Fuguang Li
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
- *Correspondence: Zuoren Yang
| | - Zuoren Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
- Fuguang Li
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12
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Samad AFA, Sajad M, Nazaruddin N, Fauzi IA, Murad AMA, Zainal Z, Ismail I. MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network. FRONTIERS IN PLANT SCIENCE 2017; 8:565. [PMID: 28446918 PMCID: PMC5388764 DOI: 10.3389/fpls.2017.00565] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/29/2017] [Indexed: 05/14/2023]
Abstract
Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions. This present review focuses on the regulatory relationships between miRNAs and different families of TFs like; NF-Y, MYB, AP2, TCP, WRKY, NAC, GRF, and SPL. For instance NF-Y play important role during drought tolerance and flower development, MYB are involved in signal transduction and biosynthesis of secondary metabolites, AP2 regulate the floral development and nodule formation, TCP direct leaf development and growth hormones signaling. WRKY have known roles in multiple stress tolerances, NAC regulate lateral root formation, GRF are involved in root growth, flower, and seed development, and SPL regulate plant transition from juvenile to adult. We also studied the relation between miRNAs and TFs by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.
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Affiliation(s)
- Abdul F. A. Samad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Muhammad Sajad
- Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, PunjabPakistan
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Nazaruddin Nazaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Darussalam, Banda AcehIndonesia
| | - Izzat A. Fauzi
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Abdul M. A. Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Zamri Zainal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
- *Correspondence: Ismanizan Ismail,
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Li C, Wang Y, Xu L, Nie S, Chen Y, Liang D, Sun X, Karanja BK, Luo X, Liu L. Genome-Wide Characterization of the MADS-Box Gene Family in Radish ( Raphanus sativus L.) and Assessment of Its Roles in Flowering and Floral Organogenesis. FRONTIERS IN PLANT SCIENCE 2016; 7:1390. [PMID: 27703461 PMCID: PMC5028395 DOI: 10.3389/fpls.2016.01390] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 09/01/2016] [Indexed: 05/08/2023]
Abstract
The MADS-box gene family is an important transcription factor (TF) family that is involved in various aspects of plant growth and development, especially flowering time and floral organogenesis. Although it has been reported in many plant species, the systematic identification and characterization of MADS-box TF family is still limited in radish (Raphanus sativus L.). In the present study, a comprehensive analysis of MADS-box genes was performed, and a total of 144 MADS-box family members were identified from the whole radish genome. Meanwhile, a detailed list of MADS-box genes from other 28 plant species was also investigated. Through the phylogenetic analysis between radish and Arabidopsis thaliana, all the RsMADS genes were classified into two groups including 68 type I (31 Mα, 12 Mβ and 25Mγ) and 76 type II (70 MIKCC and 6 MIKC∗). Among them, 41 (28.47%) RsMADS genes were located in nine linkage groups of radish from R1 to R9. Moreover, the homologous MADS-box gene pairs were identified among radish, A. thaliana, Chinese cabbage and rice. Additionally, the expression profiles of RsMADS genes were systematically investigated in different tissues and growth stages. Furthermore, quantitative real-time PCR analysis was employed to validate expression patterns of some crucial RsMADS genes. These results could provide a valuable resource to explore the potential functions of RsMADS genes in radish, and facilitate dissecting MADS-box gene-mediated molecular mechanisms underlying flowering and floral organogenesis in root vegetable crops.
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Affiliation(s)
- Chao Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Shanshan Nie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yinglong Chen
- School of Earth and Environment, The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Dongyi Liang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Xiaochuan Sun
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Benard K. Karanja
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Liwang Liu,
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