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Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits. Biochem Soc Trans 2022; 50:583-596. [PMID: 35212360 PMCID: PMC9022969 DOI: 10.1042/bst20210908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 12/18/2022]
Abstract
DNA methylation is a chromatin modification that plays an essential role in regulating gene expression and genome stability and it is typically associated with gene silencing and heterochromatin. Owing to its heritability, alterations in the patterns of DNA methylation have the potential to provide for epigenetic inheritance of traits. Contemporary epigenomic technologies provide information beyond sequence variation and could supply alternative sources of trait variation for improvement in crops such as sorghum. Yet, compared with other species such as maize and rice, the sorghum DNA methylome is far less well understood. The distribution of CG, CHG, and CHH methylation in the genome is different compared with other species. CG and CHG methylation levels peak around centromeric segments in the sorghum genome and are far more depleted in the gene dense chromosome arms. The genes regulating DNA methylation in sorghum are also yet to be functionally characterised; better understanding of their identity and functional analysis of DNA methylation machinery mutants in diverse genotypes will be important to better characterise the sorghum methylome. Here, we catalogue homologous genes encoding methylation regulatory enzymes in sorghum based on genes in Arabidopsis, maize, and rice. Discovering variation in the methylome may uncover epialleles that provide extra information to explain trait variation and has the potential to be applied in epigenome-wide association studies or genomic prediction. DNA methylation can also improve genome annotations and discover regulatory elements underlying traits. Thus, improving our knowledge of the sorghum methylome can enhance our understanding of the molecular basis of traits and may be useful to improve sorghum performance.
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2
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Epigenome guided crop improvement: current progress and future opportunities. Emerg Top Life Sci 2022; 6:141-151. [PMID: 35072210 PMCID: PMC9023013 DOI: 10.1042/etls20210258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/14/2021] [Accepted: 01/04/2022] [Indexed: 12/22/2022]
Abstract
Epigenomics encompasses a broad field of study, including the investigation of chromatin states, chromatin modifications and their impact on gene regulation; as well as the phenomena of epigenetic inheritance. The epigenome is a multi-modal layer of information superimposed on DNA sequences, instructing their usage in gene expression. As such, it is an emerging focus of efforts to improve crop performance. Broadly, this might be divided into avenues that leverage chromatin information to better annotate and decode plant genomes, and into complementary strategies that aim to identify and select for heritable epialleles that control crop traits independent of underlying genotype. In this review, we focus on the first approach, which we term ‘epigenome guided’ improvement. This encompasses the use of chromatin profiles to enhance our understanding of the composition and structure of complex crop genomes. We discuss the current progress and future prospects towards integrating this epigenomic information into crop improvement strategies; in particular for CRISPR/Cas9 gene editing and precision genome engineering. We also highlight some specific opportunities and challenges for grain and horticultural crops.
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Crisp PA, Bhatnagar-Mathur P, Hundleby P, Godwin ID, Waterhouse PM, Hickey LT. Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future. Curr Opin Biotechnol 2021; 73:88-94. [PMID: 34348216 DOI: 10.1016/j.copbio.2021.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 12/20/2022]
Abstract
For millennia, natural and artificial selection has combined favourable alleles for desirable traits in crop species. While modern plant breeding has achieved steady increases in crop yields over the last century, on the current trajectory we will simply not meet demand by 2045. Novel breeding strategies and sources of genetic variation will be required to sustainably fill predicted yield gaps and meet new consumer preferences. Here, we highlight that stepping up to meet this grand challenge will increasingly require thinking 'beyond the gene'. Significant progress has been made in understanding the contributions of both epigenetic variation and cis-regulatory variation to plant traits. This non-genic variation has great potential in future breeding, synthetic biology and biotechnology applications.
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Affiliation(s)
- Peter A Crisp
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane QLD 4072, Australia.
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Penny Hundleby
- Crop Transformation Group, Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ian D Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
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Cascales J, Acevedo RM, Paiva DI, Gottlieb AM. Differential DNA methylation and gene expression during development of reproductive and vegetative organs in Ilex species. JOURNAL OF PLANT RESEARCH 2021; 134:559-575. [PMID: 33759060 DOI: 10.1007/s10265-021-01279-3] [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: 01/13/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Differential epigenetic (DNA cytosine methylation) and gene expression patterns were investigated in reproductive and vegetative organs from Ilex paraguariensis and I. dumosa, at distinct developmental stages. We aimed at contributing towards elucidating major molecular changes underlying the sexual differentiation processes which, in these dioecious species, are completely unknown. Simultaneously, as a first step towards the development of an early sexing system, we searched for promising molecular markers. This was assessed through Methylation Sensitive Amplified Polymorphism (MSAP) and Amplified Fragment Length Polymorphism on cDNA (cDNA-AFLP) techniques, applying discriminant multivariate analyses, and bioinformatic characterization of differential fragments. A significant positive correlation was found between epigenetic and indirect 'genetic' information for both species, indicating influence of the genetic background on the epigenetic variation. Higher epigenetic than genetic diversities were estimated. Our outcomes showed up to 1.86 times more representation of mCG subepiloci than mCCG in all organs sampled. Along the maturing stages of floral buds, the frequency of mCG evidenced an incremental trend, whereas mCCG and unmethylated conditions showed opposite tendencies. Reproductive and vegetative samples tended to cluster apart based on epigenetic patterns; at gene expression level, organs exhibited clear-cut distinctive patterns, nonetheless profiles of young leaves and floral primordia resemble. Epigenetic and expression data allowed discrimination of I. dumosa´s samples according to the gender of the donor; more elusive patterns were observed for I. paraguariensis. In total, 102 differentially methylated and expressed fragments were characterized bioinformatically. Forty-three were annotated in various functional categories; four candidate markers were validated through qPCR, finding statistical differences among organs but not among sexes. The methylation condition of epilocus C13m33 appears as indicative of gender in both species. Thirty-three organ-specific and 34 gender-specific methylated markers were discriminated and deserve further research, particularly those expressed in leaves. Our study contributes concrete candidate markers with potential for practical application.
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Affiliation(s)
- Jimena Cascales
- Laboratorio de Citogenética y Evolución, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA, CONICET-UBA), Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, Ciudad Universitaria, C1428EHA, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Raúl Maximiliano Acevedo
- Laboratorio de Biotecnología Aplicada y Genómica Funcional, Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (IBONE, UNNE-CONICET), Universidad Nacional del Nordeste, Sargento Juan Bautista Cabral 2131, Corrientes, W3402BKG, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Daniela Ivana Paiva
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Montecarlo (INTA EEA Montecarlo), Av. El Libertador 2472, Misiones, N3384, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Alexandra Marina Gottlieb
- Laboratorio de Citogenética y Evolución, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA, CONICET-UBA), Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, Ciudad Universitaria, C1428EHA, Ciudad Autónoma de Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina.
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Zhang Y, Restall J, Crisp P, Godwin I, Liu G. Current status and prospects of plant genome editing in Australia. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2021; 57:574-583. [PMID: 34054265 PMCID: PMC8143062 DOI: 10.1007/s11627-021-10188-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 04/13/2021] [Indexed: 05/22/2023]
Abstract
Plant genome editing, particularly CRISPR-Cas biotechnologies, has rapidly evolved and drawn enormous attention all around the world in the last decade. The cutting-edge technologies have had substantial impact on precise genome editing for manipulating gene expression, stacking gene mutations, and improving crop agronomic traits. Following the global trends, investigations on CRISPR-Cas have been thriving in Australia, especially in agriculture sciences. Importantly, CRISPR-edited plants, classified as SDN-1 organisms (SDN: site-directed nuclease), have been given a green light in Australia, with regulatory bodies indicating they will not be classified as a genetically modified organism (GMO) if no foreign DNA is present in an edited plant. As a result, genome-edited products would not attract the onerous regulation required for the introduction of a GMO, which could mean more rapid deployment of new varieties and products that could be traded freely in Australia, and potentially to export markets. In the present review, we discuss the current status and prospects of plant genome editing in Australia by highlighting several species of interest. Using these species as case studies, we discuss the priorities and potential of plant genome editing, as well as the remaining challenges.
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Affiliation(s)
- Yan Zhang
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072 Australia
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Jemma Restall
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Peter Crisp
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Ian Godwin
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Guoquan Liu
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072 Australia
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Galli M, Feng F, Gallavotti A. Mapping Regulatory Determinants in Plants. Front Genet 2020; 11:591194. [PMID: 33193733 PMCID: PMC7655918 DOI: 10.3389/fgene.2020.591194] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022] Open
Abstract
The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.
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Affiliation(s)
- Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Fan Feng
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States.,Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
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7
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Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proc Natl Acad Sci U S A 2020; 117:23991-24000. [PMID: 32879011 DOI: 10.1073/pnas.2010250117] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.
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8
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Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ, Zhang X. Widespread long-range cis-regulatory elements in the maize genome. NATURE PLANTS 2019; 5:1237-1249. [PMID: 31740773 PMCID: PMC6904520 DOI: 10.1038/s41477-019-0547-0] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/09/2019] [Indexed: 05/03/2023]
Abstract
Genetic mapping studies on crops suggest that agronomic traits can be controlled by gene-distal intergenic loci. Despite the biological importance and the potential agronomic utility of these loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic and functional molecular evidence to support the widespread existence of gene-distal (hereafter, distal) loci that act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. Such loci are enriched for euchromatic features that suggest their regulatory functions. Chromatin loops link together putative CREs with genes and recapitulate genetic interactions. Putative CREs also display elevated transcriptional enhancer activities, as measured by self-transcribing active regulatory region sequencing. These results provide functional support for the widespread existence of CREs that act over large genomic distances to control gene expression.
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Affiliation(s)
- William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | | | | | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
| | | | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Plant Science, Technical University of Munich, Freising, Germany
| | - Frank Johannes
- Department of Plant Science, Technical University of Munich, Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | | | | | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Edward S Buckler
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- US Department of Agriculture-Agricultural Research Service, Robert Holley Center, Ithaca, NY, USA
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, USA.
- Institute for Advanced Study, Technical University of Munich, Garching, Germany.
| | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, GA, USA.
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