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Repetitive Sequence Barcode Probe for Karyotype Analysis in Tripidium arundinaceum. Int J Mol Sci 2022; 23:ijms23126726. [PMID: 35743180 PMCID: PMC9224303 DOI: 10.3390/ijms23126726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
The barcode probe is a convenient and efficient tool for molecular cytogenetics. Tripidium arundinaceum, as a polyploid wild allied genus of Saccharum, is a useful genetic resource that confers biotic and abiotic stress resistance for sugarcane breeding. Unfortunately, the basic cytogenetic information is still unclear due to the complex genome. We constructed the Cot-20 library for screening moderately and highly repetitive sequences from T. arundinaceum, and the chromosomal distribution of these repetitive sequences was explored. We used the barcode of repetitive sequence probes to distinguish the ten chromosome types of T. arundinaceum by fluorescence in situ hybridization (FISH) with Ea-0907, Ea-0098, and 45S rDNA. Furthermore, the distinction among homology chromosomes based on repetitive sequences was constructed in T. arundinaceum by the repeated FISH using the barcode probes including Ea-0663, Ea-0267, EaCent, 5S rDNA, Ea-0265, Ea-0070, and 45S rDNA. We combined these probes to distinguish 37 different chromosome types, suggesting that the repetitive sequences may have different distributions on homologous chromosomes of T. arundinaceum. In summary, this method provide a basis for the development of similar applications for cytogenetic analysis in other species.
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De Vega JJ, Teshome A, Klaas M, Grant J, Finnan J, Barth S. Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:60. [PMID: 33676571 PMCID: PMC7937229 DOI: 10.1186/s13068-021-01915-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities make Miscanthus a particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed among Miscanthus species, which correlated to origin. In this study, we compared the physiological and molecular responses among Miscanthus species under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions. RESULTS A significant biomass loss was observed under drought conditions in all genotypes. M. x giganteus showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among four Miscanthus genotypes from different species. We observed the same biological processes were regulated across Miscanthus species during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. CONCLUSIONS Different phenotypic responses were observed during drought stress among Miscanthus genotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supported Miscanthus use in flooded land. The molecular processes regulated during drought were shared among Miscanthus species and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.
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Affiliation(s)
- Jose J De Vega
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Abel Teshome
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Teagasc Crop Science Department, Oak Park, Carlow, R93XE12, Ireland
- Feed and Forage Development, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Manfred Klaas
- Teagasc Crop Science Department, Oak Park, Carlow, R93XE12, Ireland
| | - Jim Grant
- Teagasc Statistics and Applied Physics Research Operations Group, Ashtown, Dublin 15, D15 DY05, Ireland
| | - John Finnan
- Teagasc Crop Science Department, Oak Park, Carlow, R93XE12, Ireland
| | - Susanne Barth
- Teagasc Crop Science Department, Oak Park, Carlow, R93XE12, Ireland.
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Zhong M, Yang X, Hu Y, Huang L, Peng Y, Li Z, Liu Q, Wang X, Zhang X, Nie G. Identification of candidate reference genes for quantitative RT-PCR in Miscanthus sinensis subjected to various abiotic stresses. Mol Biol Rep 2020; 47:2913-2927. [PMID: 32222917 DOI: 10.1007/s11033-020-05392-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/24/2020] [Indexed: 12/22/2022]
Abstract
Quantitative real-time PCR (qRT-PCR) has been widely used for studying gene expression at the transcript level. Its accuracy usually relies on the reference genes that are utilized for data normalization. Miscanthus sinensis, a perennial C4 grass with high biomass and strong resistance to adversities, is often utilized as a high value energy crop. However, no reliable reference genes have been investigated for normalizing gene expression for this species. In this study, 12 candidate reference genes were selected to identify their stability under five different abiotic stress treatments (drought, salt, cadmium, chromium and arsenic) by using geNorm, NormFinder, BestKeeper and RefFinder softwares. The results showed that 18S rRNA and Unigene33312 were the best reference genes under drought treatments. Unigene33312 and Unigene33024 were found to be the most stably expressed genes under salt stress and Cd stress. Moreover, Unigene33024 and PP2A were the most suitable reference genes under Cr stress and Unigene33024 and Sb09g019750 were deemed more suitable reference genes under As stress. In total, considering all the samples, Unigene33024 and PP2A were the most stable genes while ACTIN and Unigene26576 were the least stable reference genes for internal control. The expression patterns of two target genes (Cu/Zn SOD and CAT) were used to further verify those selected reference genes under different conditions. The results showed that the most and the least stable reference genes had clearly different expression patterns. This work comprehensively estimated the stability of reference genes in M. sinensis which may give insight to the reference genes selection in other tissues as well as other related varieties. These suggested reference genes would assist in further putative gene expression validation in M. sinensis.
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Affiliation(s)
- Minyi Zhong
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xinying Yang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yiyue Hu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhou Li
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiuxu Liu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xia Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Gang Nie
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Hennet L, Berger A, Trabanco N, Ricciuti E, Dufayard JF, Bocs S, Bastianelli D, Bonnal L, Roques S, Rossini L, Luquet D, Terrier N, Pot D. Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses. FRONTIERS IN PLANT SCIENCE 2020; 11:224. [PMID: 32194601 PMCID: PMC7064007 DOI: 10.3389/fpls.2020.00224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.
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Affiliation(s)
- Lauriane Hennet
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Angélique Berger
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Noemi Trabanco
- Parco Tecnologico Padano, Lodi, Italy
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Emeline Ricciuti
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Jean-François Dufayard
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Denis Bastianelli
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- CIRAD, UMR SELMET, Montpellier, France
| | - Laurent Bonnal
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- CIRAD, UMR SELMET, Montpellier, France
| | - Sandrine Roques
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Laura Rossini
- Parco Tecnologico Padano, Lodi, Italy
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Delphine Luquet
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nancy Terrier
- AGAP, CIRAD, INRAE, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
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Carvalho DS, Nishimwe AV, Schnable JC. IsoSeq transcriptome assembly of C 3 panicoid grasses provides tools to study evolutionary change in the Panicoideae. PLANT DIRECT 2020; 4:e00203. [PMID: 32128472 PMCID: PMC7047018 DOI: 10.1002/pld3.203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses-Poaceae-have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on alignments to the sorghum genome, we estimate that assembled consensus transcripts from each species capture between 54.2% and 65.7% of the conserved syntenic gene space in grasses. Genes co-opted into C4 were also well represented in this dataset, despite concerns that because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript-based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long-read sequences from these wild species was consistent with previously published phylogenies. It is hoped that these data, targeting underrepresented classes of species within the PACMAD grasses-wild species and species utilizing C3 photosynthesis-will aid in future studies of domestication and C4 evolution by decreasing the evolutionary distance between C4 and C3 species within this clade, enabling more accurate comparisons associated with evolution of the C4 pathway.
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Affiliation(s)
- Daniel S. Carvalho
- Department of Agronomy and HorticultureCenter for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Aime V. Nishimwe
- Department of Agronomy and HorticultureCenter for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - James C. Schnable
- Department of Agronomy and HorticultureCenter for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
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Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing. Int J Genomics 2017; 2017:9184731. [PMID: 29318138 PMCID: PMC5727683 DOI: 10.1155/2017/9184731] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/18/2017] [Indexed: 11/23/2022] Open
Abstract
Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly. Furthermore, 95,897 (83.57%) unigenes were annotated to at least one database including NR, Swiss-Prot, KEGG, COG, GO, and NT, supporting that the sequences obtained were annotated properly. Differentially expressed gene analysis indicates that drought stress 15 days could be a critical period for M. sinensis response to drought stress. The high-throughput transcriptome sequencing of M. sinensis under drought stress has greatly enriched the current genomic available resources. The comparison of DEGs under different periods of drought stress identified a wealth of candidate genes involved in drought tolerance regulatory networks, which will facilitate further genetic improvement and molecular studies of the M. sinensis.
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7
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Transcriptomics and proteomics reveal genetic and biological basis of superior biomass crop Miscanthus. Sci Rep 2017; 7:13777. [PMID: 29062090 PMCID: PMC5653860 DOI: 10.1038/s41598-017-14151-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/05/2017] [Indexed: 12/18/2022] Open
Abstract
Miscanthus is a rhizomatous C4 grass which is considered as potential high-yielding energy crop with the low-nutrient requirements, high water-use efficiency, and capability of C mitigation. To better understand the genetic basis, an integrative analysis of the transcriptome and proteome was performed to identify important genes and pathways involved in Miscanthus leaves. At the transcript level, 64,663 transcripts in M. lutarioriparius, 97,043 in M. sacchariflorus, 97,043 in M. sinensis, 67,323 in M. floridulus and 70,021 in M. × giganteus were detected by an RNA sequencing approach. At the protein level, 1964 peptide-represented proteins were identified and 1933 proteins differed by 1.5-fold or more in their relative abundance, as indicated by iTRAQ (isobaric tags for relative and absolute quantitation) analysis. Phylogenies were constructed from the nearly taxa of Miscanthus. A large number of genes closely related to biomass production were found. And SSR markers and their corresponding primers were derived from Miscanthus transcripts and 90% of them were successfully detected by PCR amplification among Miacanthus species. These similarities and variations on the transcriptional and proteomic level between Miscanthus species will serve as a resource for research in Miscanthus and other lignocellulose crops.
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8
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Bhatia R, Gallagher JA, Gomez LD, Bosch M. Genetic engineering of grass cell wall polysaccharides for biorefining. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1071-1092. [PMID: 28557198 PMCID: PMC5552484 DOI: 10.1111/pbi.12764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/17/2017] [Accepted: 05/24/2017] [Indexed: 05/10/2023]
Abstract
Grasses represent an abundant and widespread source of lignocellulosic biomass, which has yet to fulfil its potential as a feedstock for biorefining into renewable and sustainable biofuels and commodity chemicals. The inherent recalcitrance of lignocellulosic materials to deconstruction is the most crucial limitation for the commercial viability and economic feasibility of biomass biorefining. Over the last decade, the targeted genetic engineering of grasses has become more proficient, enabling rational approaches to modify lignocellulose with the aim of making it more amenable to bioconversion. In this review, we provide an overview of transgenic strategies and targets to tailor grass cell wall polysaccharides for biorefining applications. The bioengineering efforts and opportunities summarized here rely primarily on (A) reprogramming gene regulatory networks responsible for the biosynthesis of lignocellulose, (B) remodelling the chemical structure and substitution patterns of cell wall polysaccharides and (C) expressing lignocellulose degrading and/or modifying enzymes in planta. It is anticipated that outputs from the rational engineering of grass cell wall polysaccharides by such strategies could help in realizing an economically sustainable, grass-derived lignocellulose processing industry.
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Affiliation(s)
- Rakesh Bhatia
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Joe A. Gallagher
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | | | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
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9
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Field Guide to Plant Model Systems. Cell 2017; 167:325-339. [PMID: 27716506 DOI: 10.1016/j.cell.2016.08.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/28/2016] [Accepted: 08/15/2016] [Indexed: 12/20/2022]
Abstract
For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.
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Pignon CP, Jaiswal D, McGrath JM, Long SP. Loss of photosynthetic efficiency in the shade. An Achilles heel for the dense modern stands of our most productive C4 crops? JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:335-345. [PMID: 28110277 PMCID: PMC5441902 DOI: 10.1093/jxb/erw456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The wild progenitors of major C4 crops grew as individuals subjected to little shading. Today they are grown in dense stands where most leaves are shaded. Do they maintain photosynthetic efficiency in these low light conditions produced by modern cultivation? The apparent maximum quantum yield of CO2 assimilation (ΦCO2max,app), a key determinant of light-limited photosynthesis, has not been systematically studied in field stands of C4 crops. ΦCO2max,app was derived from the initial slope of the response of leaf CO2 uptake (A) to photon flux (Q). Leaf fractional light absorptance (α) was measured to determine the absolute maximum quantum yield of CO2 assimilation on an absorbed light basis (ΦCO2max,abs). Light response curves were determined on sun and shade leaves of 49 field plants of Miscanthus × giganteus and Zea mays following canopy closure. ΦCO2max,app and ΦCO2max,abs declined significantly by 15-27% (P<0.05) with canopy depth. Experimentally, leaf age was shown unlikely to cause this loss. Modeling canopy CO2 assimilation over diurnal courses suggested that the observed decline in ΦCO2max,app with canopy depth costs 10% of potential carbon gain. Overcoming this limitation could substantially increase the productivity of major C4 crops.
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Affiliation(s)
- Charles P Pignon
- University of Illinois, Carl Woese Institute for Genomic Biology and Departments of Crop Sciences and of Plant Biology, 1206 W Gregory Drive, Urbana, IL 61801, USA
| | - Deepak Jaiswal
- University of Illinois, Carl Woese Institute for Genomic Biology and Departments of Crop Sciences and of Plant Biology, 1206 W Gregory Drive, Urbana, IL 61801, USA
| | - Justin M McGrath
- University of Illinois, Carl Woese Institute for Genomic Biology and Departments of Crop Sciences and of Plant Biology, 1206 W Gregory Drive, Urbana, IL 61801, USA
| | - Stephen P Long
- University of Illinois, Carl Woese Institute for Genomic Biology and Departments of Crop Sciences and of Plant Biology, 1206 W Gregory Drive, Urbana, IL 61801, USA
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
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11
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Estrela R, Cate JHD. Energy biotechnology in the CRISPR-Cas9 era. Curr Opin Biotechnol 2016; 38:79-84. [DOI: 10.1016/j.copbio.2016.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/20/2016] [Indexed: 12/18/2022]
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12
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Figala J, Vranová V, Rejšek K, Formánek P. Giant miscanthus (Miscantus × Giganteus Greef Et Deu.) - A Promising Plant for Soil Remediation: A Mini Review. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2016. [DOI: 10.11118/actaun201563062241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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13
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Hu G, Ji S, Yu Y, Wang S, Zhou G, Li F. Organisms for biofuel production: natural bioresources and methodologies for improving their biosynthetic potentials. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 147:185-224. [PMID: 24085385 DOI: 10.1007/10_2013_245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
In order to relieve the pressure of energy supply and environment contamination that humans are facing, there are now intensive worldwide efforts to explore natural bioresources for production of energy storage compounds, such as lipids, alcohols, hydrocarbons, and polysaccharides. Around the world, many plants have been evaluated and developed as feedstock for bioenergy production, among which several crops have successfully achieved industrialization. Microalgae are another group of photosynthetic autotroph of interest due to their superior growth rates, relatively high photosynthetic conversion efficiencies, and vast metabolic capabilities. Heterotrophic microorganisms, such as yeast and bacteria, can utilize carbohydrates from lignocellulosic biomass directly or after pretreatment and enzymatic hydrolysis to produce liquid biofuels such as ethanol and butanol. Although finding a suitable organism for biofuel production is not easy, many naturally occurring organisms with good traits have recently been obtained. This review mainly focuses on the new organism resources discovered in the last 5 years for production of transport fuels (biodiesel, gasoline, jet fuel, and alkanes) and hydrogen, and available methods to improve natural organisms as platforms for the production of biofuels.
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Affiliation(s)
- Guangrong Hu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
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14
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Ji L, Hu R, Jiang J, Qi G, Yang X, Zhu M, Fu C, Zhou G, Yi Z. Molecular cloning and expression analysis of 13 NAC transcription factors in Miscanthus lutarioriparius. PLANT CELL REPORTS 2014; 33:2077-2092. [PMID: 25224554 DOI: 10.1007/s00299-014-1682-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/30/2014] [Accepted: 09/01/2014] [Indexed: 06/03/2023]
Abstract
The 13 MlNAC genes could respond to various abiotic stresses, suggesting their crucial roles in stress response. Overexpression of MlNAC2 in Arabidopsis led to improved drought tolerance. NAC (NAM, ATAF1/2 and CUC2) proteins are plant-specific transcription factors that play crucial roles in plant development, growth and stress responses. In this study, 13 stress-responsive NAC genes were identified from Miscanthus lutarioriparius. Full-length cDNA sequences were obtained for 11 MlNAC genes, which were phylogenetically classified into six subfamilies. Sequence alignment revealed the highly conserved NAC domain in the N-terminus of these MlNACs, while the C-terminus was highly divergent. We performed quantitative real-time RT-PCR to examine the expression profiles of MlNAC genes in different tissues including root, rhizome, mature stem, young stem, leaf and sheath. The 13 MlNAC genes displayed distinct tissue-specific patterns in six tissues examined. To gain further insight into their roles in response to abiotic stresses, expressions of MlNAC genes were analyzed under different stresses and hormone treatments including salt, drought, cold, wounding, abscisic acid, Methyl jasmonate and salicylic acid. The 13 MlNAC genes could respond to at least five stress treatments, and over 100-fold variations in transcript levels of MlNAC1, MlNAC2, MlNAC4, and MlNAC12 were observed in salt, drought and MeJA treatments, which indicated that MlNACs play crucial roles in stress response. Crosstalk among various abiotic stress and hormone responses was also discussed based on the expression of MlNAC genes. Overexpression of MlNAC2 in Arabidopsis (Col-0) led to improved drought tolerance. The water loss rate was significantly lower, and the recovery rate after a 60-min dehydration stress treatment was significantly higher in the MlNAC2 overexpression lines than the control.
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Affiliation(s)
- Lu Ji
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China
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15
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Nie G, Zhang XQ, Huang LK, Xu WZ, Wang JP, Zhang YW, Ma X, Yan YH, Yan HD. Genetic variability and population structure of the potential bioenergy crop Miscanthus sinensis (Poaceae) in Southwest China based on SRAP markers. Molecules 2014; 19:12881-97. [PMID: 25153884 PMCID: PMC6271393 DOI: 10.3390/molecules190812881] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 11/16/2022] Open
Abstract
The genus Miscanthus has great potential as a biofuel feedstock because of its high biomass, good burning quality, environmental tolerance, and good adaptability to marginal land. In this study, the genetic diversity and the relationship of 24 different natural Miscanthus sinensis populations collected from Southwestern China were analyzed by using 33 pairs of Sequence Related Amplified Polymorphism (SRAP) primers. A total of 688 bands were detected with 646 polymorphic bands, an average of 19.58 polymorphic bands per primer pair. The average percentage of polymorphic loci (P), gene diversity (H), and Shannon's diversity index (I) among the 24 populations are 70.59%, 0.2589, and 0.3836, respectively. The mean value of total gene diversity (HT) was 0.3373±0.0221, while the allelic diversity within populations (HS) was 0.2589±0.0136 and the allelic diversity among populations (DST) was 0.0784. The mean genetic differentiation coefficient (Gst=0.2326) estimated from the detected 688 loci indicated that there was 76.74% genetic differentiation within the populations, which is consistent with the results from Analysis of Molecular Variance (AMOVA) analysis. Based upon population structure and phylogenetic analysis, five groups were formed and a special population with mixed ancestry was inferred indicating that human-mediated dispersal may have had a significant effect on population structure of M. sinensis. Evaluating the genetic structure and genetic diversity at morphological and molecular levels of the wild M. sinensis in Southwest China is critical to further utilize the wild M. sinensis germplasm in the breeding program. The results in this study will facilitate the biofuel feedstock breeding program and germplasm conservation.
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Affiliation(s)
- Gang Nie
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Xin-Quan Zhang
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Lin-Kai Huang
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Wen-Zhi Xu
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Jian-Ping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA.
| | - Yun-Wei Zhang
- Grassland Institute, China Agricultural University, Beijing 100193, China.
| | - Xiao Ma
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Yan-Hong Yan
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Hai-Dong Yan
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
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16
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Meineke T, Manisseri C, Voigt CA. Phylogeny in defining model plants for lignocellulosic ethanol production: a comparative study of Brachypodium distachyon, wheat, maize, and Miscanthus x giganteus leaf and stem biomass. PLoS One 2014; 9:e103580. [PMID: 25133818 PMCID: PMC4136770 DOI: 10.1371/journal.pone.0103580] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/04/2014] [Indexed: 12/26/2022] Open
Abstract
The production of ethanol from pretreated plant biomass during fermentation is a strategy to mitigate climate change by substituting fossil fuels. However, biomass conversion is mainly limited by the recalcitrant nature of the plant cell wall. To overcome recalcitrance, the optimization of the plant cell wall for subsequent processing is a promising approach. Based on their phylogenetic proximity to existing and emerging energy crops, model plants have been proposed to study bioenergy-related cell wall biochemistry. One example is Brachypodium distachyon, which has been considered as a general model plant for cell wall analysis in grasses. To test whether relative phylogenetic proximity would be sufficient to qualify as a model plant not only for cell wall composition but also for the complete process leading to bioethanol production, we compared the processing of leaf and stem biomass from the C3 grasses B. distachyon and Triticum aestivum (wheat) with the C4 grasses Zea mays (maize) and Miscanthus x giganteus, a perennial energy crop. Lambda scanning with a confocal laser-scanning microscope allowed a rapid qualitative analysis of biomass saccharification. A maximum of 108-117 mg ethanol·g(-1) dry biomass was yielded from thermo-chemically and enzymatically pretreated stem biomass of the tested plant species. Principal component analysis revealed that a relatively strong correlation between similarities in lignocellulosic ethanol production and phylogenetic relation was only given for stem and leaf biomass of the two tested C4 grasses. Our results suggest that suitability of B. distachyon as a model plant for biomass conversion of energy crops has to be specifically tested based on applied processing parameters and biomass tissue type.
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Affiliation(s)
- Till Meineke
- Phytopathology & Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Chithra Manisseri
- Phytopathology & Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Christian A. Voigt
- Phytopathology & Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
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17
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Spence AK, Boddu J, Wang D, James B, Swaminathan K, Moose SP, Long SP. Transcriptional responses indicate maintenance of photosynthetic proteins as key to the exceptional chilling tolerance of C4 photosynthesis in Miscanthus × giganteus. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3737-47. [PMID: 24958895 PMCID: PMC4085969 DOI: 10.1093/jxb/eru209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Miscanthus × giganteus is exceptional among C4 plants in its ability to acclimate to chilling (≤14 °C) and maintain a high photosynthetic capacity, in sharp contrast to maize, leading to very high productivity even in cool temperate climates. To identify the mechanisms that underlie this acclimation, RNA was isolated from M × giganteus leaves in chilling and nonchilling conditions and hybridized to microarrays developed for its close relative Zea mays. Among 21 000 array probes that yielded robust signals, 723 showed significant expression change under chilling. Approximately half of these were for annotated genes. Thirty genes associated with chloroplast membrane function were all upregulated. Increases in transcripts for the lhcb5 (chlorophyll a/b-binding protein CP26), ndhF (NADH dehydrogenase F, chloroplast), atpA (ATP synthase alpha subunit), psbA (D1), petA (cytochrome f), and lhcb4 (chlorophyll a/b-binding protein CP29), relative to housekeeping genes in M. × giganteus, were confirmed by quantitative reverse-transcription PCR. In contrast, psbo1, lhcb5, psbA, and lhcb4 were all significantly decreased in Z. mays after 14 days of chilling. Western blot analysis of the D1 protein and LHCII type II chlorophyll a/b-binding protein also showed significant increases in M. × giganteus during chilling and significant decreases in Z. mays. Compared to other C4 species, M. × giganteus grown in chilling conditions appears to counteract the loss of photosynthetic proteins and proteins protecting photosystem II typically observed in other species by increasing mRNA levels for their synthesis.
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Affiliation(s)
- Ashley K Spence
- Proctor and Gamble, 8700 South Mason-Montgomery Road Mason, OH 45040, USA
| | - Jay Boddu
- Department of Crop Sciences, University of Illinois, 389 Edward R. Madigan Laboratory, 1201W Gregory Drive, Urbana, IL 61801, USA
| | - Dafu Wang
- Monsanto Company, Chesterfield Village Research Center, 700 Chesterfield Parkway North, Chesterfield, MO 63017, USA
| | - Brandon James
- Department of Crop Sciences, University of Illinois, 389 Edward R. Madigan Laboratory, 1201W Gregory Drive, Urbana, IL 61801, USA
| | - Kankshita Swaminathan
- Energy Biosciences Institute, University of Illinois, 1200 Institute for Genomic Biology, 1206W. Gregory Drive, Urbana, IL 61801, USA
| | - Stephen P Moose
- Department of Crop Sciences, University of Illinois, 389 Edward R. Madigan Laboratory, 1201W Gregory Drive, Urbana, IL 61801, USA
| | - Stephen P Long
- Department of Crop Sciences, University of Illinois, 389 Edward R. Madigan Laboratory, 1201W Gregory Drive, Urbana, IL 61801, USA
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18
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Zhao H, Huai Z, Xiao Y, Wang X, Yu J, Ding G, Peng J. Natural variation and genetic analysis of the tiller angle gene MsTAC1 in Miscanthus sinensis. PLANTA 2014; 240:161-75. [PMID: 24771021 DOI: 10.1007/s00425-014-2070-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 03/21/2014] [Indexed: 05/25/2023]
Abstract
Biomass yield is an important target trait in Miscanthus breeding for desirable energy crops. Tiller angle is a key trait of plant architecture because it determines planting density and further influences biomass yield through affecting photosynthesis efficiency. TAC1, a major gene involved in tiller and leaf angle control in rice and maize, respectively, has been extensively studied. Nucleotide variation at this gene, MsTAC1, was investigated in 33 Miscanthus sinensis accessions collected from different areas in China, and one genotype of Miscanthus × giganteus. A total of 136 loci, including 129 single base substitutions and seven InDels, occurred within the MsTAC1 gene of 1,874 bp. The genetic diversity at MsTAC1 is characterized by high nucleotide diversity (π value) and high heterozygosity. Clustering analysis indicated that the phylogenetic tree of the 33 M. sinensis accessions was correlated with their geographical sites of origin. The neutrality test revealed no strong selection pressure on coding and non-coding region variations of the MsTAC1 gene in the accessions. Phenotype evaluations were conducted for tiller angle and five other traits in the Miscanthus panels in the first two growth years of 2009 and 2010. Analysis of variance showed significant phenotypic variations in the examined traits. Association analysis using 246 markers detected 88 loci associated with all the test traits in either 1 or 2 years, and 11 of the 88 were year reproducible and thus reliable. These associations indicate that the variation of MsTAC1 affects the phenotypic value of the tiller angle, tiller number and biomass yield, suggesting that allelic variation in MsTAC1 affects multiple traits and demonstrates its significance in Miscanthus breeding programs.
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Affiliation(s)
- Hua Zhao
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China,
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19
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de Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GMQ, Del Bem LE, Vicentini R, Nogueira FTS, Campos RA, Nunes SL, Turrini PCG, Vieira AP, Ochoa Cruz EA, Corrêa TCS, Hotta CT, de Mello Varani A, Vautrin S, da Trindade AS, de Mendonça Vilela M, Lembke CG, Sato PM, de Andrade RF, Nishiyama MY, Cardoso-Silva CB, Scortecci KC, Garcia AAF, Carneiro MS, Kim C, Paterson AH, Bergès H, D'Hont A, de Souza AP, Souza GM, Vincentz M, Kitajima JP, Van Sluys MA. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics 2014; 15:540. [PMID: 24984568 PMCID: PMC4122759 DOI: 10.1186/1471-2164-15-540] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 06/19/2014] [Indexed: 01/24/2023] Open
Abstract
Background Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome. Results Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences. Conclusion This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marie-Anne Van Sluys
- Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, SP, Brazil.
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20
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Shakoor N, Nair R, Crasta O, Morris G, Feltus A, Kresovich S. A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums. BMC PLANT BIOLOGY 2014; 14:35. [PMID: 24456189 PMCID: PMC3925131 DOI: 10.1186/1471-2229-14-35] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/15/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Effective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced in 2009, a comprehensive annotation of the sorghum genome and the development of functional genomics resources is key to enable the discovery and deployment of regulatory and metabolic genes and gene networks for crop improvement. RESULTS This study utilizes the first commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast, and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (maize and sugarcane) were also included in our array design. We generated expression data for 78 samples with a combination of four different tissue types (shoot, root, leaf and stem), two dissected stem tissues (pith and rind) and six diverse genotypes, which included 6 public sorghum lines (R159, Atlas, Fremont, PI152611, AR2400 and PI455230) representing grain, sweet, forage, and high biomass ideotypes. CONCLUSIONS Here we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways. With an aim to enable identification and functional characterization of genes in sorghum, this expression atlas presents a new and valuable resource to the research community.
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Affiliation(s)
- Nadia Shakoor
- Chromatin Inc, Chicago, Illinois, USA
- Department of Biological Sciences, The University of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | | | - Oswald Crasta
- Chromatin Inc, Chicago, Illinois, USA
- Current address: Dow AgroSciences, Indianapolis, Indiana, USA
| | - Geoffrey Morris
- Department of Biological Sciences, The University of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | - Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Stephen Kresovich
- Department of Biological Sciences, The University of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
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21
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Barling A, Swaminathan K, Mitros T, James BT, Morris J, Ngamboma O, Hall MC, Kirkpatrick J, Alabady M, Spence AK, Hudson ME, Rokhsar DS, Moose SP. A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes. BMC Genomics 2013; 14:864. [PMID: 24320546 PMCID: PMC4046694 DOI: 10.1186/1471-2164-14-864] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 12/04/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates. However, few genomic resources exist for Miscanthus, which limits understanding of its interesting biology and future genetic improvement. A comprehensive catalog of expressed sequences were generated from a variety of Miscanthus species and tissue types, with an emphasis on characterizing gene expression changes in spring compared to fall rhizomes. RESULTS Illumina short read sequencing technology was used to produce transcriptome sequences from different tissues and organs during distinct developmental stages for multiple Miscanthus species, including Miscanthus sinensis, Miscanthus sacchariflorus, and their interspecific hybrid Miscanthus × giganteus. More than fifty billion base-pairs of Miscanthus transcript sequence were produced. Overall, 26,230 Sorghum gene models (i.e., ~ 96% of predicted Sorghum genes) had at least five Miscanthus reads mapped to them, suggesting that a large portion of the Miscanthus transcriptome is represented in this dataset. The Miscanthus × giganteus data was used to identify genes preferentially expressed in a single tissue, such as the spring rhizome, using Sorghum bicolor as a reference. Quantitative real-time PCR was used to verify examples of preferential expression predicted via RNA-Seq. Contiguous consensus transcript sequences were assembled for each species and annotated using InterProScan. Sequences from the assembled transcriptome were used to amplify genomic segments from a doubled haploid Miscanthus sinensis and from Miscanthus × giganteus to further disentangle the allelic and paralogous variations in genes. CONCLUSIONS This large expressed sequence tag collection creates a valuable resource for the study of Miscanthus biology by providing detailed gene sequence information and tissue preferred expression patterns. We have successfully generated a database of transcriptome assemblies and demonstrated its use in the study of genes of interest. Analysis of gene expression profiles revealed biological pathways that exhibit altered regulation in spring compared to fall rhizomes, which are consistent with their different physiological functions. The expression profiles of the subterranean rhizome provides a better understanding of the biological activities of the underground stem structures that are essentials for perenniality and the storage or remobilization of carbon and nutrient resources.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Stephen P Moose
- Energy Biosciences Institute, Institute for Genomic Biology, University of Illinois Urbana, 1206 West Gregory Drive, Urbana, IL 61801, USA.
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22
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Yu Y, Hu R, Wang H, Cao Y, He G, Fu C, Zhou G. MlWRKY12, a novel Miscanthus transcription factor, participates in pith secondary cell wall formation and promotes flowering. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 212:1-9. [PMID: 24094048 DOI: 10.1016/j.plantsci.2013.07.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/18/2013] [Accepted: 07/20/2013] [Indexed: 05/19/2023]
Abstract
WRKY proteins play crucial roles in various plant processes. An AtWRKY12 homologous gene, named MlWRKY12, was isolated from Miscanthus lutarioriparius. The MlWRKY12 gene encodes a WRKY transcription factor belonging to the group IIc subfamily. MlWRKY12 is a nuclear protein. Gene expression pattern analysis revealed a relatively high MlWRKY12 expression level in rhizomes, stems and leaf sheaths. In situ hybridization analysis further demonstrated that MlWRKY12 was expressed in vascular bundle sheath, sclerenchyma and parenchyma tissues. The heterologous expression of MlWRKY12 in an atwrky12 background mutant successfully rescued the phenotype of pith cell walls caused by the defect of AtWRKY12. Most strikingly, the transgenic Arabidopsis plants overexpressing MlWRKY12 exhibited early flowering. The transcript abundance of flowering related genes was measured by quantitative RT-PCR analysis, suggesting that overexpression of MlWRKY12 in Arabidopsis had a significant impact on the expression level of CONSTANS (CO). Moreover, the expression levels of FLOWERING LOCUS T (FT), LFY (LEAFY), APETALA1 (AP1), CAULIFLOWER (CAL) and FRUITFULL (FUL) were upregulated in transgenic plants. These results demonstrated the conserved function of MlWRKY12 existing in secondary cell wall formation of monocotyledonous species and implied a possible impact of MlWRKY12 on flowering control.
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Affiliation(s)
- Yanchong Yu
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS), Qingdao, Shandong, China
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23
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Natali L, Cossu RM, Barghini E, Giordani T, Buti M, Mascagni F, Morgante M, Gill N, Kane NC, Rieseberg L, Cavallini A. The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads. BMC Genomics 2013; 14:686. [PMID: 24093210 PMCID: PMC3852528 DOI: 10.1186/1471-2164-14-686] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 10/03/2013] [Indexed: 11/12/2022] Open
Abstract
Background Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage Illumina or 454 libraries. Results By varying sequencing technology (Illumina or 454), coverage (0.55 x-1.25 x), assemblers and assembly procedures, six different genomic databases were produced. The annotation of these databases showed that they were composed of different proportions of repetitive DNA families. The final assembly of the sequences belonging to the six databases produced a whole genome set of 283,800 contigs. The redundancy of each contig was estimated by mapping the whole genome set with a large Illumina read set and measuring the number of matched Illumina reads. The repetitive component amounted to 81% of the sunflower genome, that is composed mainly of numerous families of Gypsy and Copia retrotransposons. Also many families of non autonomous retrotransposons and DNA transposons (especially of the Helitron superfamily) were identified. Conclusions The results substantially matched those previously obtained by using a Sanger-sequenced shotgun library and a standard 454 whole-genome-shotgun approach, indicating the reliability of the proposed procedures also for other species. The repetitive sequences were collected to produce a database, SUNREP, that will be useful for the annotation of the sunflower genome sequence and for studying the genome evolution in dicotyledons.
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Affiliation(s)
- Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy.
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24
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Żur I, Dubas E, Słomka A, Dubert F, Kuta E, Płażek A. Failure of androgenesis in Miscanthus × giganteus in vitro culture of cytologically unbalanced microspores. PLANT REPRODUCTION 2013; 26:297-307. [PMID: 23824237 PMCID: PMC3747323 DOI: 10.1007/s00497-013-0219-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 06/23/2013] [Indexed: 05/13/2023]
Abstract
Miscanthus × giganteus is a popular energy crop, which due to its hybrid origin is only vegetatively reproduced. Asexual embryogenesis in anther and microspore culture leading to double haploids production could allow to regain the ability for sexual reproduction and to increase the biodiversity of the species. Therefore, the goal of this paper was to investigate the requirements of androgenesis in Miscanthus. The standard protocols used for monocotyledonous plants were applied with many modifications regarding the developmental stage of the explants at the time of culture initiation, stress treatment applied to panicles and isolated anthers as well as various chemical and physical parameters of in vitro culture conditions. Our results indicated that the induction of androgenesis in M. × giganteus is possible. However, the very low efficiency of the process and the lack of regeneration ability of the androgenic structures presently prevent the use of this technique.
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Affiliation(s)
- Iwona Żur
- Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Krakow, Poland
| | - Ewa Dubas
- Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Krakow, Poland
| | - Aneta Słomka
- Department of Plant Cytology and Embryology, Jagiellonian University, Grodzka 52, 31-044 Krakow, Poland
| | - Franciszek Dubert
- Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Krakow, Poland
| | - Elżbieta Kuta
- Department of Plant Cytology and Embryology, Jagiellonian University, Grodzka 52, 31-044 Krakow, Poland
| | - Agnieszka Płażek
- Department of Plant Physiology, University of Agriculture, Podłużna 3, 30-239 Krakow, Poland
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de Siqueira Ferreira S, Nishiyama MY, Paterson AH, Souza GM. Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era. Genome Biol 2013; 14:210. [PMID: 23805917 PMCID: PMC3707038 DOI: 10.1186/gb-2013-14-6-210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Herein, we review knowledge useful for their improvement and synergies gained by their parallel study.
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Affiliation(s)
- Savio de Siqueira Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
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Wei H, Zhou B, Zhang F, Tu Y, Hu Y, Zhang B, Zhai Q. Profiling and identification of small rDNA-derived RNAs and their potential biological functions. PLoS One 2013; 8:e56842. [PMID: 23418607 PMCID: PMC3572043 DOI: 10.1371/journal.pone.0056842] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/14/2013] [Indexed: 12/13/2022] Open
Abstract
Small non-coding RNAs constitute a large family of regulatory molecules with diverse functions. Notably, some small non-coding RNAs matched to rDNA have been identified as qiRNAs and small guide RNAs involved in various biological processes. However, a large number of small rDNA-derived RNAs (srRNAs) are usually neglected and yet to be investigated. We systematically investigated srRNAs using small RNA datasets generated by high-throughput sequencing, and found srRNAs are mainly mapped to rRNA coding regions in sense direction. The datasets from immunoprecipitation and high-throughput sequencing demonstrate that srRNAs are co-immunoprecipitated with Argonaute (AGO) proteins. Furthermore, the srRNA expression profile in mouse liver is affected by diabetes. Overexpression or inhibition of srRNAs in cultured cells shows that srRNAs are involved in various signaling pathways. This study presents a global view of srRNAs in total small RNA and AGO protein complex from different species, and demonstrates that srRNAs are correlated with diabetes, and involved in some biological processes. These findings provide new insights into srRNAs and their functions in various physiological and pathological processes.
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Affiliation(s)
- Haibin Wei
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Ben Zhou
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Fang Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yanyang Tu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yanan Hu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Baoguo Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Qiwei Zhai
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- * E-mail:
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Abstract
C(4) photosynthesis under optimal conditions enables higher-efficiency use of light, water, and nitrogen than the C(3) form used by many crops. It is associated with the most productive terrestrial plants and crops but is largely limited to the tropics and subtropics. It has been argued that the C(4) photosynthetic apparatus is inherently limited to warm environments. A small group of C(4) species appear to have overcome this, and in contrast to the major C(4) crop, maize, these species are able to acclimate their photosynthetic apparatus to chilling conditions. This review explores the mechanisms underlying this difference as well as the potential of introducing these changes into maize and other warm-climate C(4) crops.
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Affiliation(s)
- Stephen P Long
- Institute for Genomic Biology, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
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Slavov G, Allison G, Bosch M. Advances in the genetic dissection of plant cell walls: tools and resources available in Miscanthus. FRONTIERS IN PLANT SCIENCE 2013; 4:217. [PMID: 23847628 PMCID: PMC3701120 DOI: 10.3389/fpls.2013.00217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 06/05/2013] [Indexed: 05/19/2023]
Abstract
Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass crops. However, Miscanthus species are essentially undomesticated, and genetic, molecular and bioinformatics tools are in very early stages of development. Furthermore, similar to other crops targeted as lignocellulosic feedstocks, the efficient utilization of biomass is hampered by our limited knowledge of the structural organization of the plant cell wall and the underlying genetic components that control this organization. The Institute of Biological, Environmental and Rural Sciences (IBERS) has assembled an extensive collection of germplasm for several species of Miscanthus. In addition, an integrated, multidisciplinary research programme at IBERS aims to inform accelerated breeding for biomass productivity and composition, while also generating fundamental knowledge. Here we review recent advances with respect to the genetic characterization of the cell wall in Miscanthus. First, we present a summary of recent and on-going biochemical studies, including prospects and limitations for the development of powerful phenotyping approaches. Second, we review current knowledge about genetic variation for cell wall characteristics of Miscanthus and illustrate how phenotypic data, combined with high-density arrays of single-nucleotide polymorphisms, are being used in genome-wide association studies to generate testable hypotheses and guide biological discovery. Finally, we provide an overview of the current knowledge about the molecular biology of cell wall biosynthesis in Miscanthus and closely related grasses, discuss the key conceptual and technological bottlenecks, and outline the short-term prospects for progress in this field.
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Affiliation(s)
- Gancho Slavov
- *Correspondence: Gancho Slavov, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EB, UK e-mail:
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Swaminathan K, Chae WB, Mitros T, Varala K, Xie L, Barling A, Glowacka K, Hall M, Jezowski S, Ming R, Hudson M, Juvik JA, Rokhsar DS, Moose SP. A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. BMC Genomics 2012; 13:142. [PMID: 22524439 PMCID: PMC3355032 DOI: 10.1186/1471-2164-13-142] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 04/24/2012] [Indexed: 11/24/2022] Open
Abstract
Background Miscanthus (subtribe Saccharinae, tribe Andropogoneae, family Poaceae) is a genus of temperate perennial C4 grasses whose high biomass production makes it, along with its close relatives sugarcane and sorghum, attractive as a biofuel feedstock. The base chromosome number of Miscanthus (x = 19) is different from that of other Saccharinae and approximately twice that of the related Sorghum bicolor (x = 10), suggesting large-scale duplications may have occurred in recent ancestors of Miscanthus. Owing to the complexity of the Miscanthus genome and the complications of self-incompatibility, a complete genetic map with a high density of markers has not yet been developed. Results We used deep transcriptome sequencing (RNAseq) from two M. sinensis accessions to define 1536 single nucleotide variants (SNVs) for a GoldenGate™ genotyping array, and found that simple sequence repeat (SSR) markers defined in sugarcane are often informative in M. sinensis. A total of 658 SNP and 210 SSR markers were validated via segregation in a full sibling F1 mapping population. Using 221 progeny from this mapping population, we constructed a genetic map for M. sinensis that resolves into 19 linkage groups, the haploid chromosome number expected from cytological evidence. Comparative genomic analysis documents a genome-wide duplication in Miscanthus relative to Sorghum bicolor, with subsequent insertional fusion of a pair of chromosomes. The utility of the map is confirmed by the identification of two paralogous C4-pyruvate, phosphate dikinase (C4-PPDK) loci in Miscanthus, at positions syntenic to the single orthologous gene in Sorghum. Conclusions The genus Miscanthus experienced an ancestral tetraploidy and chromosome fusion prior to its diversification, but after its divergence from the closely related sugarcane clade. The recent timing of this tetraploidy complicates discovery and mapping of genetic markers for Miscanthus species, since alleles and fixed differences between paralogs are comparable. These difficulties can be overcome by careful analysis of segregation patterns in a mapping population and genotyping of doubled haploids. The genetic map for Miscanthus will be useful in biological discovery and breeding efforts to improve this emerging biofuel crop, and also provide a valuable resource for understanding genomic responses to tetraploidy and chromosome fusion.
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Affiliation(s)
- Kankshita Swaminathan
- Energy Biosciences Institute, Institute for Genomic Biology, University of Illinois Urbana, Urbana, IL 61801, USA
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Ma XF, Jensen E, Alexandrov N, Troukhan M, Zhang L, Thomas-Jones S, Farrar K, Clifton-Brown J, Donnison I, Swaller T, Flavell R. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis. PLoS One 2012; 7:e33821. [PMID: 22439001 PMCID: PMC3306302 DOI: 10.1371/journal.pone.0033821] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 02/17/2012] [Indexed: 11/19/2022] Open
Abstract
We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.
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Affiliation(s)
- Xue-Feng Ma
- Ceres, Inc., Thousand Oaks, California, United States of America
| | - Elaine Jensen
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | | | - Maxim Troukhan
- Ceres, Inc., Thousand Oaks, California, United States of America
| | - Liping Zhang
- Ceres, Inc., Thousand Oaks, California, United States of America
| | - Sian Thomas-Jones
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Kerrie Farrar
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - John Clifton-Brown
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Iain Donnison
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Timothy Swaller
- Ceres, Inc., Thousand Oaks, California, United States of America
- * E-mail:
| | - Richard Flavell
- Ceres, Inc., Thousand Oaks, California, United States of America
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Kelly LJ, Leitch IJ. Exploring giant plant genomes with next-generation sequencing technology. Chromosome Res 2012; 19:939-53. [PMID: 21987187 DOI: 10.1007/s10577-011-9246-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Genome size in plants is characterised by its extraordinary range. Although it appears that the majority of plants have small genomes, in several lineages genome size has reached giant proportions. The recent advent of next-generation sequencing (NGS) methods has for the first time made detailed analysis of even the largest of plant genomes a possibility. In this review, we highlight investigations that have utilised NGS for the study of plants with large genomes, as well as describing ongoing work that aims to harness the power of these technologies to gain insights into their evolution. In addition, we emphasise some areas of research where the use of NGS has the potential to generate significant advances in our current understanding of how plant genomes evolve. Finally, we discuss some of the future developments in sequencing technology that may further improve our ability to explore the content and evolutionary dynamics of the very largest genomes.
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Affiliation(s)
- Laura J Kelly
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK.
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Chouvarine P, Cooksey AM, McCarthy FM, Ray DA, Baldwin BS, Burgess SC, Peterson DG. Transcriptome-based differentiation of closely-related Miscanthus lines. PLoS One 2012; 7:e29850. [PMID: 22253803 PMCID: PMC3254643 DOI: 10.1371/journal.pone.0029850] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 12/05/2011] [Indexed: 01/28/2023] Open
Abstract
Background Distinguishing between individuals is critical to those conducting animal/plant breeding, food safety/quality research, diagnostic and clinical testing, and evolutionary biology studies. Classical genetic identification studies are based on marker polymorphisms, but polymorphism-based techniques are time and labor intensive and often cannot distinguish between closely related individuals. Illumina sequencing technologies provide the detailed sequence data required for rapid and efficient differentiation of related species, lines/cultivars, and individuals in a cost-effective manner. Here we describe the use of Illumina high-throughput exome sequencing, coupled with SNP mapping, as a rapid means of distinguishing between related cultivars of the lignocellulosic bioenergy crop giant miscanthus (Miscanthus × giganteus). We provide the first exome sequence database for Miscanthus species complete with Gene Ontology (GO) functional annotations. Results A SNP comparative analysis of rhizome-derived cDNA sequences was successfully utilized to distinguish three Miscanthus × giganteus cultivars from each other and from other Miscanthus species. Moreover, the resulting phylogenetic tree generated from SNP frequency data parallels the known breeding history of the plants examined. Some of the giant miscanthus plants exhibit considerable sequence divergence. Conclusions Here we describe an analysis of Miscanthus in which high-throughput exome sequencing was utilized to differentiate between closely related genotypes despite the current lack of a reference genome sequence. We functionally annotated the exome sequences and provide resources to support Miscanthus systems biology. In addition, we demonstrate the use of the commercial high-performance cloud computing to do computational GO annotation.
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Affiliation(s)
- Philippe Chouvarine
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America.
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Genetic and Molecular Approaches to Assess MicroRNA Function. MICRORNAS IN PLANT DEVELOPMENT AND STRESS RESPONSES 2012. [DOI: 10.1007/978-3-642-27384-1_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Calviño M, Messing J. Sweet sorghum as a model system for bioenergy crops. Curr Opin Biotechnol 2011; 23:323-9. [PMID: 22204822 DOI: 10.1016/j.copbio.2011.12.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 12/07/2011] [Accepted: 12/07/2011] [Indexed: 01/20/2023]
Abstract
Bioenergy is the reduction of carbon via photosynthesis. Currently, this energy is harvested as liquid fuel through fermentation. A major concern, however, is input cost, in particular use of excess water and nitrogen, derived from an energy-negative process, the Haber-Bosch method. Furthermore, the shortage of arable land creates competition between uses for food and fuel, resulting in increased living expenses. This review seeks to summarize recent knowledge in genetics, genomics, and gene expression of a rising model species for bioenergy applications, sorghum. Its diploid genome has been sequenced, it has favorable low-input cost traits, and genetic crosses between different cultivars can be used to study allelic variations of genes involved in stem sugar metabolism and incremental biomass.
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Affiliation(s)
- Martín Calviño
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, United States
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Wong MML, Cannon CH, Wickneswari R. Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing. BMC Genomics 2011; 12:342. [PMID: 21729267 PMCID: PMC3161972 DOI: 10.1186/1471-2164-12-342] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 07/05/2011] [Indexed: 01/11/2023] Open
Abstract
Background Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants. Results We sequenced transcriptomes of A. auriculiformis and A. mangium from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. De novo assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for A. auriculiformis and A. mangium respectively. The assemblies of A. auriculiformis and A. mangium had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3-MYB proteins in other plant species that are involved in transcriptional regulation of secondary cell wall formation and lignin deposition. We searched the contigs against public microRNA database and predicted the stem-loop structures of six highly conserved microRNA families (miR319, miR396, miR160, miR172, miR162 and miR168) and one legume-specific family (miR2086). Three microRNA target genes were predicted to be involved in wood formation and flavonoid biosynthesis. By using the assemblies as a reference, we discovered 16,648 and 9,335 high quality putative Single Nucleotide Polymorphisms (SNPs) in the transcriptomes of A. auriculiformis and A. mangium, respectively, thus yielding useful markers for population genetics studies and marker-assisted selection. Conclusion We have produced the first comprehensive transcriptome-wide analysis in A. auriculiformis and A. mangium using de novo assembly techniques. Our high quality and comprehensive assemblies allowed the identification of many genes in the lignin biosynthesis and secondary cell wall formation in Acacia hybrids. Our results demonstrated that Next Generation Sequencing is a cost-effective method for gene discovery, identification of regulatory sequences, and informative markers in a non-model plant.
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Affiliation(s)
- Melissa M L Wong
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor, Malaysia
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Straub SCK, Fishbein M, Livshultz T, Foster Z, Parks M, Weitemier K, Cronn RC, Liston A. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genomics 2011; 12:211. [PMID: 21542930 PMCID: PMC3116503 DOI: 10.1186/1471-2164-12-211] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 05/04/2011] [Indexed: 01/05/2023] Open
Abstract
Background Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first step in the development of a community resource for further study of plant-insect co-evolution, anti-herbivore defense, floral developmental genetics, reproductive biology, chemical evolution, population genetics, and comparative genomics using milkweeds, and A. syriaca in particular, as ecological and evolutionary models.
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Affiliation(s)
- Shannon C K Straub
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.
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Parry MAJ, Jing HC. Bioenergy plants: Hopes, concerns and prospectives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:94-95. [PMID: 21205192 DOI: 10.1111/j.1744-7909.2010.01029.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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Paszkiewicz K, Studholme DJ. De novo assembly of short sequence reads. Brief Bioinform 2010; 11:457-72. [DOI: 10.1093/bib/bbq020] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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