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Perveen S, Padula MP, Safdar N, Abbas S. Functional annotation of proteins in Catharanthus roseus shoot cultures under biogenic zinc nanotreatment. PLANT MOLECULAR BIOLOGY 2024; 114:26. [PMID: 38459275 DOI: 10.1007/s11103-024-01432-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/21/2024] [Indexed: 03/10/2024]
Abstract
Nano-interactions are well known for their positive as well as negative impacts on the morphological and physiological systems of plants. Keeping in mind, the conformational changes in plant proteins as one of the key mechanisms for stress adaptation responses, the current project was designed to explore the effect of glutathione-capped and uncapped zinc nano-entities on Catharanthus roseus shoot cultures. Zinc nanotreatment (0.05 μg/mL) significantly induced ester production in C. roseus shoots as detected by Gas Chromatography-Mass spectrometry. These nanotreated shoots were further subjected to peptide-centric nano-LC-MS/MS analysis. Mass spectrometry followed by a Heat map revealed a significant effect of zinc nanoparticles on 59 distinct classes of proteins as compared to control. Proteins involved in regulating stress scavenging, transport, and secondary metabolite biosynthesis were robustly altered under capped zinc nanotreatment. UniProt database identified majority of the localization of the abundantly altered protein in cell membranes and chloroplasts. STRING and Cytoscape analysis assessed inter and intra coordination of triosephosphate isomerase with other identified proteins and highlighted its role in the regulation of protein abundance under applied stress. This study highlights the understanding of complex underlying mechanisms and regulatory networks involved in proteomic alterations and interactions within the plant system to cope with the nano-effect.
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Affiliation(s)
- Shaghufta Perveen
- Microbiology and Biotechnology Research Lab, Fatima Jinnah Women University, Rawalpindi, Pakistan
| | - Matthew P Padula
- School of Life Sciences, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Naila Safdar
- Microbiology and Biotechnology Research Lab, Fatima Jinnah Women University, Rawalpindi, Pakistan.
| | - Sidra Abbas
- Microbiology and Biotechnology Research Lab, Fatima Jinnah Women University, Rawalpindi, Pakistan
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Guan C, Li W, Wang G, Yang R, Zhang J, Zhang J, Wu B, Gao R, Jia C. Transcriptomic analysis of ncRNAs and mRNAs interactions during drought stress in switchgrass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111930. [PMID: 38007196 DOI: 10.1016/j.plantsci.2023.111930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023]
Abstract
Switchgrass (Panicum virgatum L.) plays a pivotal role as a bioenergy feedstock in the production of cellulosic ethanol and contributes significantly to enhancing ecological grasslands and soil quality. The utilization of non-coding RNAs (ncRNAs) has gained momentum in deciphering the intricate genetic responses to abiotic stress in various plant species. Nevertheless, the current research landscape lacks a comprehensive exploration of the responses of diverse ncRNAs, including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), to drought stress in switchgrass. In this study, we employed whole transcriptome sequencing to comprehensively characterize the expression profiles of both mRNA and ncRNAs during episodes of drought stress in switchgrass. Our analysis identified a total of 12,511 mRNAs, 59 miRNAs, 38 circRNAs, and 368 lncRNAs that exhibited significant differential expression between normal and drought-treated switchgrass leaves. Notably, the majority of up-regulated mRNAs displayed pronounced enrichment within the starch and sucrose metabolism pathway, as validated through KEGG analysis. Co-expression analysis illuminated that differentially expressed (DE) lncRNAs conceivably regulated 1308 protein-coding genes in trans and 7110 protein-coding genes in cis. Furthermore, both cis- and trans-target mRNAs of DE lncRNAs exhibited enrichment in four common KEGG pathways. The intricate interplay between lncRNAs and circRNAs with miRNAs via miRNA response elements was explored within the competitive endogenous RNA (ceRNA) network framework. As a result, we constructed elaborate regulatory networks, including lncRNA-novel_miRNA480-mRNA, lncRNA-novel_miRNA304-mRNA, lncRNA/circRNA-novel_miRNA122-PvSS4, and lncRNA/circRNA-novel_miRNA14-PvSS4, and subsequently validated the functionality of the target gene, starch synthase 4 (PvSS4). Furthermore, through the overexpression of PvSS4, we ascertained its capacity to enhance drought tolerance in yeast. However, it is noteworthy that PvSS4 did not exhibit any discernible impact under salt stress conditions. These findings, as presented herein, not only contribute substantively to our understanding of ceRNA networks but also offer a basis for further investigations into their potential functions in response to drought stress in switchgrass.
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Affiliation(s)
- Cong Guan
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Wei Li
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing 100193, China
| | - Guoliang Wang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Ruimei Yang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing 100193, China
| | - Jinglei Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Jinhong Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Bo Wu
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Run Gao
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Chunlin Jia
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China.
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Tiedge K, Li X, Merrill AT, Davisson D, Chen Y, Yu P, Tantillo DJ, Last RL, Zerbe P. Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum). THE NEW PHYTOLOGIST 2022; 236:1393-1408. [PMID: 36028985 PMCID: PMC9912200 DOI: 10.1111/nph.18443] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/09/2022] [Indexed: 05/13/2023]
Abstract
Switchgrass (Panicum virgatum) is a bioenergy model crop valued for its energy efficiency and drought tolerance. The related monocot species rice (Oryza sativa) and maize (Zea mays) deploy species-specific, specialized metabolites as core stress defenses. By contrast, specialized chemical defenses in switchgrass are largely unknown. To investigate specialized metabolic drought responses in switchgrass, we integrated tissue-specific transcriptome and metabolite analyses of the genotypes Alamo and Cave-in-Rock that feature different drought tolerance. The more drought-susceptible Cave-in-Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo. Specialized pathways showed moderate differential expression compared to pronounced transcriptomic alterations in carbohydrate and amino acid metabolism. However, diterpenoid-biosynthetic genes showed drought-inducible expression in Alamo roots, contrasting largely unaltered triterpenoid and phenylpropanoid pathways. Metabolomic analyses identified common and genotype-specific flavonoids and terpenoids. Consistent with transcriptomic alterations, several root diterpenoids showed significant drought-induced accumulation, whereas triterpenoid abundance remained predominantly unchanged. Structural analysis verified select drought-responsive diterpenoids as oxygenated furanoditerpenoids. Drought-dependent transcriptome and metabolite profiles provide the foundation to understand the molecular mechanisms underlying switchgrass drought responses. Accumulation of specialized root diterpenoids and corresponding pathway transcripts supports a role in drought stress tolerance.
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Affiliation(s)
- Kira Tiedge
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
- Groningen Institute for Evolutionary Life SciencesUniversity of Groningen9747AG Groningenthe Netherlands
| | - Xingxing Li
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
| | - Amy T. Merrill
- Department of ChemistryUniversity of California, DavisDavisCA95616USA
| | - Danielle Davisson
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
| | - Yuxuan Chen
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
| | - Ping Yu
- NMR FacilityUniversity of California, DavisDavisCA95616USA
| | - Dean J. Tantillo
- Department of ChemistryUniversity of California, DavisDavisCA95616USA
| | - Robert L. Last
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
- Department Plant BiologyMichigan State UniversityEast LansingMI48824USA
| | - Philipp Zerbe
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
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Hayford RK, Serba DD, Xie S, Ayyappan V, Thimmapuram J, Saha MC, Wu CH, Kalavacharla VK. Global analysis of switchgrass (Panicum virgatum L.) transcriptomes in response to interactive effects of drought and heat stresses. BMC PLANT BIOLOGY 2022; 22:107. [PMID: 35260072 PMCID: PMC8903725 DOI: 10.1186/s12870-022-03477-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Sustainable production of high-quality feedstock has been of great interest in bioenergy research. Despite the economic importance, high temperatures and water deficit are limiting factors for the successful cultivation of switchgrass in semi-arid areas. There are limited reports on the molecular basis of combined abiotic stress tolerance in switchgrass, particularly the combination of drought and heat stress. We used transcriptomic approaches to elucidate the changes in the response of switchgrass to drought and high temperature simultaneously. RESULTS We conducted solely drought treatment in switchgrass plant Alamo AP13 by withholding water after 45 days of growing. For the combination of drought and heat effect, heat treatment (35 °C/25 °C day/night) was imposed after 72 h of the initiation of drought. Samples were collected at 0 h, 72 h, 96 h, 120 h, 144 h, and 168 h after treatment imposition, total RNA was extracted, and RNA-Seq conducted. Out of a total of 32,190 genes, we identified 3912, as drought (DT) responsive genes, 2339 and 4635 as, heat (HT) and drought and heat (DTHT) responsive genes, respectively. There were 209, 106, and 220 transcription factors (TFs) differentially expressed under DT, HT and DTHT respectively. Gene ontology annotation identified the metabolic process as the significant term enriched in DTHT genes. Other biological processes identified in DTHT responsive genes included: response to water, photosynthesis, oxidation-reduction processes, and response to stress. KEGG pathway enrichment analysis on DT and DTHT responsive genes revealed that TFs and genes controlling phenylpropanoid pathways were important for individual as well as combined stress response. For example, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) from the phenylpropanoid pathway was induced by single DT and combinations of DTHT stress. CONCLUSION Through RNA-Seq analysis, we have identified unique and overlapping genes in response to DT and combined DTHT stress in switchgrass. The combination of DT and HT stress may affect the photosynthetic machinery and phenylpropanoid pathway of switchgrass which negatively impacts lignin synthesis and biomass production of switchgrass. The biological function of genes identified particularly in response to DTHT stress could further be confirmed by techniques such as single point mutation or RNAi.
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Affiliation(s)
- Rita K Hayford
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology, Delaware State University, Dover, DE, USA
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA
| | - Desalegn D Serba
- USDA-ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, IN, USA
| | - Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology, Delaware State University, Dover, DE, USA
| | | | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, OK, USA.
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA
| | - Venu Kal Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology, Delaware State University, Dover, DE, USA.
- Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE, USA.
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Wang Y, Li X, Wang C, Gao L, Wu Y, Ni X, Sun J, Jiang J. Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms. BMC Genomics 2021; 22:690. [PMID: 34551715 PMCID: PMC8459517 DOI: 10.1186/s12864-021-07971-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work on its biology and genetic improvement. Results In this study, through analyzing the transcriptome of mixed samples of leaves and stems using the latest PacBio Iso-Seq sequencing technology combined with Illumina HiSeq, we report the first full-length transcriptome dataset of M. sinensis with a total of 58.21 Gb clean data. An average of 15.75 Gb clean reads of each sample were obtained from the PacBio Iso-Seq system, which doubled the data size (6.68 Gb) obtained from the Illumina HiSeq platform. The integrated analyses of PacBio- and Illumina-based transcriptomic data uncovered 408,801 non-redundant transcripts with an average length of 1,685 bp. Of those, 189,406 transcripts were commonly identified by both methods, 169,149 transcripts with an average length of 619 bp were uniquely identified by Illumina HiSeq, and 51,246 transcripts with an average length of 2,535 bp were uniquely identified by PacBio Iso-Seq. Approximately 96 % of the final combined transcripts were mapped back to the Miscanthus genome, reflecting the high quality and coverage of our sequencing results. When comparing our data with genomes of four species of Andropogoneae, M. sinensis showed the closest relationship with sugarcane with up to 93 % mapping ratios, followed by sorghum with up to 80 % mapping ratios, indicating a high conservation of orthologs in these three genomes. Furthermore, 306,228 transcripts were successfully annotated against public databases including cell wall related genes and transcript factor families, thus providing many new insights into gene functions. The PacBio Iso-Seq data also helped identify 3,898 alternative splicing events and 2,963 annotated AS isoforms within 10 function categories. Conclusions Taken together, the present study provides a rich data set of full-length transcripts that greatly enriches our understanding of M. sinensis transcriptomic resources, thus facilitating further genetic improvement and molecular studies of the Miscanthus species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07971-x.
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Affiliation(s)
- Yongli Wang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Xia Li
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Congsheng Wang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Lu Gao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Yanfang Wu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Xingnan Ni
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China.
| | - Jianxiong Jiang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China.
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Saha P, Lin F, Thibivilliers S, Xiong Y, Pan C, Bartley LE. Phenylpropanoid Biosynthesis Gene Expression Precedes Lignin Accumulation During Shoot Development in Lowland and Upland Switchgrass Genotypes. FRONTIERS IN PLANT SCIENCE 2021; 12:640930. [PMID: 34434200 PMCID: PMC8380989 DOI: 10.3389/fpls.2021.640930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/14/2021] [Indexed: 06/13/2023]
Abstract
Efficient conversion of lignocellulosic biomass into biofuels is influenced by biomass composition and structure. Lignin and other cell wall phenylpropanoids, such as para-coumaric acid (pCA) and ferulic acid (FA), reduce cell wall sugar accessibility and hamper biochemical fuel production. Toward identifying the timing and key parameters of cell wall recalcitrance across different switchgrass genotypes, this study measured cell wall composition and lignin biosynthesis gene expression in three switchgrass genotypes, A4 and AP13, representing the lowland ecotype, and VS16, representing the upland ecotype, at three developmental stages [Vegetative 3 (V3), Elongation 4 (E4), and Reproductive 3 (R3)] and three segments (S1-S3) of the E4 stage under greenhouse conditions. A decrease in cell wall digestibility and an increase in phenylpropanoids occur across development. Compared with AP13 and A4, VS16 has significantly less lignin and greater cell wall digestibility at the V3 and E4 stages; however, differences among genotypes diminish by the R3 stage. Gini correlation analysis across all genotypes revealed that lignin and pCA, but also pectin monosaccharide components, show the greatest negative correlations with digestibility. Lignin and pCA accumulation is delayed compared with expression of phenylpropanoid biosynthesis genes, while FA accumulation coincides with expression of these genes. The different cell wall component accumulation profiles and gene expression correlations may have implications for system biology approaches to identify additional gene products with cell wall component synthesis and regulation functions.
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Affiliation(s)
- Prasenjit Saha
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Fan Lin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Sandra Thibivilliers
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Yi Xiong
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Chongle Pan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
- School of Computer Science, University of Oklahoma, Norman, OK, United States
| | - Laura E. Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
- Research Institute for the Sustainable Humanosphere, Kyoto University, Kyoto, Japan
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
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Ayyappan V, Sripathi VR, Kalavacharla V(K, Saha MC, Thimmapuram J, Bhide KP, Fiedler E. Genome-wide identification of histone methylation (H3K9 me2) and acetylation (H4K12 ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). BMC Genomics 2019; 20:667. [PMID: 31438854 PMCID: PMC6704705 DOI: 10.1186/s12864-019-6038-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/16/2019] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns) and transcriptomic studies are currently available in switchgrass, the genome-wide distribution of histone modifications has not yet been studied to help elucidate gene regulation and its application to switchgrass improvement. RESULTS This study provides a comprehensive epigenomic analyses of two contrasting switchgrass ecotypes, lowland (AP13) and upland (VS16), by employing chromatin immunoprecipitation sequencing (ChIP-Seq) with two histone marks (suppressive- H3K9me2 and active- H4K12ac). In this study, most of the histone binding was in non-genic regions, and the highest enrichment was seen between 0 and 2 kb regions from the transcriptional start site (TSS). Considering the economic importance and potential of switchgrass as a bioenergy crop, we focused on genes, transcription factors (TFs), and pathways that were associated with C4-photosynthesis, biomass, biofuel production, biotic stresses, and abiotic stresses. Using quantitative real-time PCR (qPCR) the relative expression of five genes selected from the phenylpropanoid-monolignol pathway showed preferential binding of acetylation marks in AP13 rather than in VS16. CONCLUSIONS The genome-wide histone modifications reported here can be utilized in understanding the regulation of genes important in the phenylpropanoid-monolignol biosynthesis pathway, which in turn, may help understand the recalcitrance associated with conversion of biomass to biofuel, a major roadblock in utilizing lignocellulosic feedstocks.
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Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
| | - Venkateswara R. Sripathi
- Molecular Biology and Bioinformatics Laboratory, College of Agricultural, Life and Natural Sciences, Alabama A&M University, Normal, AL USA
| | - Venu ( Kal) Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
- Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE USA
| | | | | | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN USA
| | - Elizabeth Fiedler
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
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Comparative transcriptome analysis of pigeonpea, Cajanus cajan (L.) and one of its wild relatives Cajanus platycarpus (Benth.) Maesen. PLoS One 2019; 14:e0218731. [PMID: 31269083 PMCID: PMC6609033 DOI: 10.1371/journal.pone.0218731] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 06/08/2019] [Indexed: 11/19/2022] Open
Abstract
Pigeonpea is a major source of dietary protein to the vegetarian population of the Indian sub-continent. Crop improvement to mitigate biotic and abiotic stresses for realization of its potential yield and bridging yield gap is the need of the hour. Availability of limited genomic resources in the cultivated germplasm, however, is a serious bottleneck towards successful molecular breeding for the development of superior genotypes in pigeonpea. In view of this, improvement of pigeonpea can be attempted through transgenesis or by exploiting genetic resources from its wild relatives. Pigeonpea wild relatives are known to be bestowed with agronomic traits of importance; discovery and deployment of genes from them can provide a lucrative option for crop improvement. Understanding molecular signatures of wild relatives would not only provide information about the mechanism behind desired traits but also enable us to extrapolate the information to cultivated pigeonpea. The present study deals with the characterization of leaf transcriptomes of Cajanus cajan and one of its wild relatives, Cajanus platycarpus. Illumina sequencing revealed 0.11 million transcripts in both the species with an annotation of 0.09 million (82%) transcripts using BLASTX. Comparative transcriptome analyses on the whole, divulged cues about the wild relative being vigilant and agile. Gene ontology and Mapman analysis depicted higher number of transcripts in the wild relative pertaining to signaling, transcription factors and stress responsive genes. Further, networking between the differentially expressed MapMan bins demonstrated conspicuous interactions between different bins through 535 nodes (512 Genes and 23 Pathways) and 1857 edges. The authenticity of RNA-seq analysis was confirmed by qRT-PCR. The information emanating from this study can provide valuable information and resource for future translational research including genome editing to alleviate varied stresses. Further, this learning can be a platform for in-depth investigations to decipher molecular mechanisms for mitigation of various stresses in the wild relative.
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Wu Q, Zhao G, Bai X, Zhao W, Xiang D, Wan Y, Wu X, Sun Y, Tan M, Peng L, Zhao J. Characterization of the transcriptional profiles in common buckwheat (Fagopyrum esculentum) under PEG-mediated drought stress. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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10
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Pournosrat R, Kaya S, Shaaf S, Kilian B, Ozkan H. Geographical and environmental determinants of the genetic structure of wild barley in southeastern Anatolia. PLoS One 2018; 13:e0192386. [PMID: 29420597 PMCID: PMC5805283 DOI: 10.1371/journal.pone.0192386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/21/2018] [Indexed: 11/29/2022] Open
Abstract
Despite the global value of barley, compared to its wild progenitor, genetic variation in this crop has been drastically reduced due to the process of domestication, selection and improvement. In the medium term, this will negatively impact both the vulnerability and yield stability of barley against biotic and abiotic stresses under climate change. Returning to the crop wild relatives (CWR) as sources of new and beneficial alleles is a clear option for enhancing the resilience of diversity and adaptation to climate change. Southeastern Anatolia constitutes an important part of the natural distribution of wild barley in the Fertile Crescent where important crops were initially domesticated. In this study, we investigated genetic diversity in a comprehensive collection of 281 geo-referenced wild barley individuals from 92 collection sites with sample sizes ranging from 1 to 9 individuals per site, collected from southeastern Anatolia and 131 domesticated genotypes from 49 different countries using 40 EST-SSR markers. A total of 375 alleles were detected across entire collection, of which 283 were carried by domesticated genotypes and 316 alleles were present in the wild gene pool. The number of unique alleles in the wild and in the domesticated gene pool was 92 and 59, respectively. The population structure at K = 3 suggested two groups of wild barley namely G1-W consisting wild barley genotypes from the western part and G1-E comprising those mostly from the eastern part of the study area, with a sharp separation from the domesticated gene pool. The geographic and climatic factors jointly showed significant effects on the distribution of wild barley. Using a Latent Factor Mixed Model, we identified four candidate loci potentially involved in adaptation of wild barley to three environmental factors: temperature seasonality, mean temperature of driest quarter, and precipitation of coldest quarter. These loci are probably the targets of genomic regions, with potential roles against abiotic stresses.
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Affiliation(s)
- Reza Pournosrat
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Selma Kaya
- University of Çukurova, Faculty of Agriculture, Department of Field Crops, Adana, Turkey
| | - Salar Shaaf
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
- * E-mail: (HO); (BK); (SS)
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Genebank Department, Genome Diversity Group, Seeland, Germany
- * E-mail: (HO); (BK); (SS)
| | - Hakan Ozkan
- University of Çukurova, Faculty of Agriculture, Department of Field Crops, Adana, Turkey
- * E-mail: (HO); (BK); (SS)
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