101
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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: 188] [Impact Index Per Article: 37.6] [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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102
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Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X, Schmitz RJ. The prevalence, evolution and chromatin signatures of plant regulatory elements. NATURE PLANTS 2019; 5:1250-1259. [PMID: 31740772 DOI: 10.1038/s41477-019-0548-z] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/09/2019] [Indexed: 05/03/2023]
Abstract
Chromatin accessibility and modification is a hallmark of regulatory DNA, the study of which led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants, especially in species with large and complex genomes. The majority of distal CREs have been moved away from their target genes by transposable-element (TE) proliferation, but a substantial number of distal CREs also seem to be created by TEs. Finally, plant distal CREs are associated with three major types of chromatin signatures that are distinct from metazoans. Taken together, these results suggest that CREs are prevalent in plants, highly dynamic during evolution and function through distinct chromatin pathways to regulate gene expression.
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Affiliation(s)
- Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | | | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, GA, USA.
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103
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Springer N, de León N, Grotewold E. Challenges of Translating Gene Regulatory Information into Agronomic Improvements. TRENDS IN PLANT SCIENCE 2019; 24:1075-1082. [PMID: 31377174 DOI: 10.1016/j.tplants.2019.07.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/26/2019] [Accepted: 07/05/2019] [Indexed: 06/10/2023]
Abstract
Improvement of agricultural species has exploited the genetic variation responsible for complex quantitative traits. Much of the functional variation is regulatory, in cis-regulatory elements and trans-acting factors that ultimately contribute to gene expression differences. However, the identification of gene regulatory network components that, when modulated, will increase plant productivity or resilience, is challenging, yet essential to provide increased predictive power for genome engineering approaches that are likely to benefit useful traits. Here, we discuss the opportunities and limitations of using data obtained from gene coexpression, transcription factor binding, and genome-wide association mapping analyses to predict regulatory interactions that impact crop improvement. It is apparent that a combination of information from these data types is necessary for the reliable identification and utilization of important regulatory interactions that underlie complex agronomic traits.
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Affiliation(s)
- Nathan Springer
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA.
| | - Natalia de León
- Department of Agronomy, University of Wisconsin, Madison, WI 56706, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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104
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Ho EKH, Bartkowska M, Wright SI, Agrawal AF. Population genomics of the facultatively asexual duckweed Spirodela polyrhiza. THE NEW PHYTOLOGIST 2019; 224:1361-1371. [PMID: 31298732 DOI: 10.1111/nph.16056] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Clonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome. We examine genome-wide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually. We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. A potential explanation for this observation is that a very low frequency of sex renders selection ineffective. However, there is a pronounced decay in linkage disequilibrium over 40 kb, suggesting that though sex may be rare at the individual level it is not too infrequent at the population level. In addition, neutral diversity is affected by the physical proximity of selected sites, which would be unexpected if sex was exceedingly rare at the population level. The amount of genetic mixing as assessed by the decay in linkage disequilibrium is not dissimilar from selfing species such as Arabidopsis thaliana, yet selection appears to be much less effective in duckweed. We discuss alternative explanations for the signature of weak purifying selection.
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Affiliation(s)
- Eddie K H Ho
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Magdalena Bartkowska
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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105
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Inference of plant gene regulatory networks using data-driven methods: A practical overview. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194447. [PMID: 31678628 DOI: 10.1016/j.bbagrm.2019.194447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/08/2019] [Accepted: 10/31/2019] [Indexed: 11/20/2022]
Abstract
Transcriptional regulation is a complex and dynamic process that plays a vital role in plant growth and development. A key component in the regulation of genes is transcription factors (TFs), which coordinate the transcriptional control of gene activity. A gene regulatory network (GRN) is a collection of regulatory interactions between TFs and their target genes. The accurate delineation of GRNs offers a significant contribution to our understanding about how plant cells are organized and function, and how individual genes are regulated in various conditions, organs or cell types. During the past decade, important progress has been made in the identification of GRNs using experimental and computational approaches. However, a detailed overview of available platforms supporting the analysis of GRNs in plants is missing. Here, we review current databases, platforms and tools that perform data-driven analyses of gene regulation in Arabidopsis. The platforms are categorized into two sections, 1) promoter motif analysis tools that use motif mapping approaches to find TF motifs in the regulatory sequences of genes of interest and 2) network analysis tools that identify potential regulators for a set of input genes using a range of data types in order to generate GRNs. We discuss the diverse datasets integrated and highlight the strengths and caveats of different platforms. Finally, we shed light on the limitations of the above approaches and discuss future perspectives, including the need for integrative approaches to unravel complex GRNs in plants.
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106
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Miller C, Wells R, McKenzie N, Trick M, Ball J, Fatihi A, Dubreucq B, Chardot T, Lepiniec L, Bevan MW. Variation in Expression of the HECT E3 Ligase UPL3 Modulates LEC2 Levels, Seed Size, and Crop Yields in Brassica napus. THE PLANT CELL 2019; 31:2370-2385. [PMID: 31439805 DOI: 10.1101/334581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/22/2019] [Accepted: 08/12/2019] [Indexed: 05/28/2023]
Abstract
Identifying genetic variation that increases crop yields is a primary objective in plant breeding. We used association analyses of oilseed rape/canola (Brassica napus) accessions to identify genetic variation that influences seed size, lipid content, and final crop yield. Variation in the promoter region of the HECT E3 ligase gene BnaUPL3 C03 made a major contribution to variation in seed weight per pod, with accessions exhibiting high seed weight per pod having lower levels of BnaUPL3 C03 expression. We defined a mechanism in which UPL3 mediated the proteasomal degradation of LEC2, a master transcriptional regulator of seed maturation. Accessions with reduced UPL3 expression had increased LEC2 protein levels, larger seeds, and prolonged expression of lipid biosynthetic genes during seed maturation. Natural variation in BnaUPL3 C03 expression appears not to have been exploited in current B napus breeding lines and could therefore be used as a new approach to maximize future yields in this important oil crop.
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Affiliation(s)
- Charlotte Miller
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Rachel Wells
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Neil McKenzie
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Martin Trick
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Joshua Ball
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Abdelhak Fatihi
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Thierry Chardot
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Loic Lepiniec
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Michael W Bevan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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107
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Miller C, Wells R, McKenzie N, Trick M, Ball J, Fatihi A, Dubreucq B, Chardot T, Lepiniec L, Bevan MW. Variation in Expression of the HECT E3 Ligase UPL3 Modulates LEC2 Levels, Seed Size, and Crop Yields in Brassica napus. THE PLANT CELL 2019; 31:2370-2385. [PMID: 31439805 PMCID: PMC6790077 DOI: 10.1105/tpc.18.00577] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/22/2019] [Accepted: 08/12/2019] [Indexed: 05/23/2023]
Abstract
Identifying genetic variation that increases crop yields is a primary objective in plant breeding. We used association analyses of oilseed rape/canola (Brassica napus) accessions to identify genetic variation that influences seed size, lipid content, and final crop yield. Variation in the promoter region of the HECT E3 ligase gene BnaUPL3 C03 made a major contribution to variation in seed weight per pod, with accessions exhibiting high seed weight per pod having lower levels of BnaUPL3 C03 expression. We defined a mechanism in which UPL3 mediated the proteasomal degradation of LEC2, a master transcriptional regulator of seed maturation. Accessions with reduced UPL3 expression had increased LEC2 protein levels, larger seeds, and prolonged expression of lipid biosynthetic genes during seed maturation. Natural variation in BnaUPL3 C03 expression appears not to have been exploited in current B napus breeding lines and could therefore be used as a new approach to maximize future yields in this important oil crop.
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Affiliation(s)
- Charlotte Miller
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Rachel Wells
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Neil McKenzie
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Martin Trick
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Joshua Ball
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Abdelhak Fatihi
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Thierry Chardot
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Loic Lepiniec
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Michael W Bevan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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108
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Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays. G3-GENES GENOMES GENETICS 2019; 9:3023-3033. [PMID: 31337639 PMCID: PMC6723120 DOI: 10.1534/g3.119.400549] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modern improvement of complex traits in agricultural species relies on successful associations of heritable molecular variation with observable phenotypes. Historically, this pursuit has primarily been based on easily measurable genetic markers. The recent advent of new technologies allows assaying and quantifying biological intermediates (hereafter endophenotypes) which are now readily measurable at a large scale across diverse individuals. The usefulness of endophenotypes for delineating the regulatory landscape of the genome and genetic dissection of complex trait variation remains underexplored in plants. The work presented here illustrated the utility of a large-scale (299-genotype and seven-tissue) gene expression resource to dissect traits across multiple levels of biological organization. Using single-tissue- and multi-tissue-based transcriptome-wide association studies (TWAS), we revealed that about half of the functional variation acts through altered transcript abundance for maize kernel traits, including 30 grain carotenoid abundance traits, 20 grain tocochromanol abundance traits, and 22 field-measured agronomic traits. Comparing the efficacy of TWAS with genome-wide association studies (GWAS) and an ensemble approach that combines both GWAS and TWAS, we demonstrated that results of TWAS in combination with GWAS increase the power to detect known genes and aid in prioritizing likely causal genes. Using a variance partitioning approach in the largely independent maize Nested Association Mapping (NAM) population, we also showed that the most strongly associated genes identified by combining GWAS and TWAS explain more heritable variance for a majority of traits than the heritability captured by the random genes and the genes identified by GWAS or TWAS alone. This not only improves the ability to link genes to phenotypes, but also highlights the phenotypic consequences of regulatory variation in plants.
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109
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Brown K, Takawira LT, O'Neill MM, Mizrachi E, Myburg AA, Hussey SG. Identification and functional evaluation of accessible chromatin associated with wood formation in Eucalyptus grandis. THE NEW PHYTOLOGIST 2019; 223:1937-1951. [PMID: 31063599 DOI: 10.1111/nph.15897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/29/2019] [Indexed: 05/03/2023]
Abstract
Accessible chromatin changes dynamically during development and harbours functional regulatory regions which are poorly understood in the context of wood development. We explored the importance of accessible chromatin in Eucalyptus grandis in immature xylem generally, and MYB transcription factor-mediated transcriptional programmes specifically. We identified biologically reproducible DNase I Hypersensitive Sites (DHSs) and assessed their functional significance in immature xylem through their associations with gene expression, epigenomic data and DNA sequence conservation. We identified in vitro DNA binding sites for six secondary cell wall-associated Eucalyptus MYB (EgrMYB) transcription factors using DAP-seq, reconstructed protein-DNA networks of predicted targets based on binding sites within or outside DHSs and assessed biological enrichment of these networks with published datasets. 25 319 identified immature xylem DHSs were associated with increased transcription and significantly enriched for various epigenetic signatures (H3K4me3, H3K27me3, RNA pol II), conserved noncoding sequences and depleted single nucleotide variants. Predicted networks built from EgrMYB binding sites located in accessible chromatin were significantly enriched for systems biology datasets relevant to wood formation, whereas those occurring in inaccessible chromatin were not. Our study demonstrates that DHSs in E. grandis immature xylem, most of which are intergenic, are of functional significance to gene regulation in this tissue.
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Affiliation(s)
- Katrien Brown
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Lazarus T Takawira
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Marja M O'Neill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Steven G Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
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110
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Washburn JD, McElfresh MJ, Birchler JA. Progressive heterosis in genetically defined tetraploid maize. J Genet Genomics 2019; 46:389-396. [PMID: 31444136 DOI: 10.1016/j.jgg.2019.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 01/24/2019] [Accepted: 02/20/2019] [Indexed: 12/30/2022]
Abstract
Progressive heterosis, i.e., the additional hybrid vigor in double-cross tetraploid hybrids not found in their single-cross tetraploid parents, has been documented in a number of species including alfalfa, potato, and maize. In this study, four artificially induced maize tetraploids, directly derived from standard inbred lines, were crossed in pairs to create two single-cross hybrids. These hybrids were then crossed to create double-cross hybrids containing genetic material from all four original lines. Replicated field-based phenotyping of the materials over four years indicated a strong progressive heterosis phenotype in tetraploids but not in their diploid counterparts. In particular, the above ground dry weight phenotype of double-cross tetraploid hybrids was on average 34% and 56% heavier than that of the single-cross tetraploid hybrids and the double-cross diploid counterparts, respectively. Additionally, whole-genome resequencing of the original inbred lines and further analysis of these data did not show the expected spectrum of alleles to explain tetraploid progressive heterosis under the complementation of complete recessive model. These results underscore the reality of the progressive heterosis phenotype, its potential utility for increasing crop biomass production, and the need for exploring alternative hypothesis to explain it at a molecular level.
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Affiliation(s)
- Jacob D Washburn
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA
| | - Mitchell J McElfresh
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA.
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111
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Chen J, Li E, Lai J. The coupled effect of nucleosome organization on gene transcription level and transcriptional plasticity. Nucleus 2019; 8:605-612. [PMID: 29202635 DOI: 10.1080/19491034.2017.1402152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Nucleosomes are the fundamental units of eukaryotic chromatin and can modulate the DNA accessibility for transcriptional regulatory elements. Many studies have demonstrated the effect of nucleosome organization on gene transcription level and transcriptional plasticity upon different conditions. Our recent study showed that nucleosome organization also plays an important role in modulating the plasticity of gene transcriptional status in maize. Here, we integrated our findings with previous studies on the role of nucleosome organization in regulation of gene transcription. We highlighted our recent finding that nucleosome organization plays an important role in determining the plasticity of gene transcription, beyond its role in regulating gene transcription level, particularly for intrinsically DNA-encoded nucleosome organization. We also discussed the features of sequence and structure of genes involved in affecting nucleosome organization around genes, as well as the potential mechanisms for overcoming the coupled effect of nucleosome organization on gene transcription level and transcriptional plasticity.
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Affiliation(s)
- Jian Chen
- a State Key Laboratory of Agrobiotechnology and National Maize Improvement Center , Department of Plant Genetics and Breeding , China Agricultural University , Beijing , P. R. China
| | - En Li
- a State Key Laboratory of Agrobiotechnology and National Maize Improvement Center , Department of Plant Genetics and Breeding , China Agricultural University , Beijing , P. R. China
| | - Jinsheng Lai
- a State Key Laboratory of Agrobiotechnology and National Maize Improvement Center , Department of Plant Genetics and Breeding , China Agricultural University , Beijing , P. R. China
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112
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Wei J, Xie W, Li R, Wang S, Qu H, Ma R, Zhou X, Jia Z. Analysis of trait heritability in functionally partitioned rice genomes. Heredity (Edinb) 2019; 124:485-498. [PMID: 31253955 DOI: 10.1038/s41437-019-0244-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 06/05/2019] [Accepted: 06/08/2019] [Indexed: 01/10/2023] Open
Abstract
Knowledge of the genetic architecture of importantly agronomical traits can speed up genetic improvement in cultivated rice (Oryza sativa L.). Many recent investigations have leveraged genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs), associated with agronomic traits in various rice populations. The reported trait-relevant SNPs appear to be arbitrarily distributed along the genome, including genic and nongenic regions. Whether the SNPs in different genomic regions play different roles in trait heritability and which region is more responsible for phenotypic variation remains opaque. We analyzed a natural rice population of 524 accessions with 3,616,597 SNPs to compare the genetic contributions of functionally distinct genomic regions for five agronomic traits, i.e., yield, heading date, plant height, grain length, and grain width. An analysis of heritability in the functionally partitioned rice genome showed that regulatory or intergenic regions account for the most trait heritability. A close look at the trait-associated SNPs (TASs) indicated that the majority of the TASs are located in nongenic regions, and the genetic effects of the TASs in nongenic regions are generally greater than those in genic regions. We further compared the predictabilities using the genetic variants from genic regions with those using nongenic regions. The results revealed that nongenic regions play a more important role than genic regions in trait heritability in rice, which is consistent with findings in humans and maize. This conclusion not only offers clues for basic research to disclose genetics behind these agronomic traits, but also provides a new perspective to facilitate genomic selection in rice.
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Affiliation(s)
- Julong Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ruidong Li
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA
| | - Shibo Wang
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA
| | - Han Qu
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA
| | - Renyuan Ma
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA.,Department of Mathematics, Bowdoin College, Brunswick, ME, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Zhenyu Jia
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA.
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113
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Chromatin interaction maps reveal genetic regulation for quantitative traits in maize. Nat Commun 2019; 10:2632. [PMID: 31201335 PMCID: PMC6572838 DOI: 10.1038/s41467-019-10602-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 05/20/2019] [Indexed: 12/21/2022] Open
Abstract
Chromatin loops connect regulatory elements to their target genes. They serve as bridges between transcriptional regulation and phenotypic variation in mammals. However, spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, we characterize epigenetic features of active promoter proximal regions and candidate distal regulatory elements to construct high-resolution chromatin interaction maps for maize via long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). The maps indicate that chromatin loops are formed between regulatory elements, and that gene pairs between promoter proximal regions tend to be co-expressed. The maps also demonstrated the topological basis of quantitative trait loci which influence gene expression and phenotype. Many promoter proximal regions are involved in chromatin loops with distal regulatory elements, which regulate important agronomic traits. Collectively, these maps provide a high-resolution view of 3D maize genome architecture, and its role in gene expression and phenotypic variation. Spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, the authors construct maize chromatin interaction maps using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and show their associations with gene expression and agronomic traits.
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114
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Mejía-Guerra MK, Buckler ES. A k-mer grammar analysis to uncover maize regulatory architecture. BMC PLANT BIOLOGY 2019; 19:103. [PMID: 30876396 PMCID: PMC6419808 DOI: 10.1186/s12870-019-1693-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 02/21/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Only a small percentage of the genome sequence is involved in regulation of gene expression, but to biochemically identify this portion is expensive and laborious. In species like maize, with diverse intergenic regions and lots of repetitive elements, this is an especially challenging problem that limits the use of the data from one line to the other. While regulatory regions are rare, they do have characteristic chromatin contexts and sequence organization (the grammar) with which they can be identified. RESULTS We developed a computational framework to exploit this sequence arrangement. The models learn to classify regulatory regions based on sequence features - k-mers. To do this, we borrowed two approaches from the field of natural language processing: (1) "bag-of-words" which is commonly used for differentially weighting key words in tasks like sentiment analyses, and (2) a vector-space model using word2vec (vector-k-mers), that captures semantic and linguistic relationships between words. We built "bag-of-k-mers" and "vector-k-mers" models that distinguish between regulatory and non-regulatory regions with an average accuracy above 90%. Our "bag-of-k-mers" achieved higher overall accuracy, while the "vector-k-mers" models were more useful in highlighting key groups of sequences within the regulatory regions. CONCLUSIONS These models now provide powerful tools to annotate regulatory regions in other maize lines beyond the reference, at low cost and with high accuracy.
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Affiliation(s)
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, 14853 NY USA
- USDA-ARS, Research Geneticist, USDA ARS Robert Holley Center, Ithaca, 14853 NY USA
- Department of Plant Breeding and Genetics, Cornell University, 159 Biotechnology Building, Ithaca, 14853 NY USA
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115
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Alexandre CM, Urton JR, Jean-Baptiste K, Huddleston J, Dorrity MW, Cuperus JT, Sullivan AM, Bemm F, Jolic D, Arsovski AA, Thompson A, Nemhauser JL, Fields S, Weigel D, Bubb KL, Queitsch C. Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana. Mol Biol Evol 2019; 35:837-854. [PMID: 29272536 DOI: 10.1093/molbev/msx326] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Variation in regulatory DNA is thought to drive phenotypic variation, evolution, and disease. Prior studies of regulatory DNA and transcription factors across animal species highlighted a fundamental conundrum: Transcription factor binding domains and cognate binding sites are conserved, while regulatory DNA sequences are not. It remains unclear how conserved transcription factors and dynamic regulatory sites produce conserved expression patterns across species. Here, we explore regulatory DNA variation and its functional consequences within Arabidopsis thaliana, using chromatin accessibility to delineate regulatory DNA genome-wide. Unlike in previous cross-species comparisons, the positional homology of regulatory DNA is maintained among A. thaliana ecotypes and less nucleotide divergence has occurred. Of the ∼50,000 regulatory sites in A. thaliana, we found that 15% varied in accessibility among ecotypes. Some of these accessibility differences were associated with extensive, previously unannotated sequence variation, encompassing many deletions and ancient hypervariable alleles. Unexpectedly, for the majority of such regulatory sites, nearby gene expression was unaffected. Nevertheless, regulatory sites with high levels of sequence variation and differential chromatin accessibility were the most likely to be associated with differential gene expression. Finally, and most surprising, we found that the vast majority of differentially accessible sites show no underlying sequence variation. We argue that these surprising results highlight the necessity to consider higher-order regulatory context in evaluating regulatory variation and predicting its phenotypic consequences.
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Affiliation(s)
| | - James R Urton
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Ken Jean-Baptiste
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, Seattle, WA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dino Jolic
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | | | - Stan Fields
- Department of Genome Sciences, University of Washington, Seattle, WA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Christin Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA
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116
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Crisp PA, Noshay JM, Anderson SN, Springer NM. Opportunities to Use DNA Methylation to Distil Functional Elements in Large Crop Genomes. MOLECULAR PLANT 2019; 12:282-284. [PMID: 30797889 DOI: 10.1016/j.molp.2019.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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117
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Ramstein GP, Jensen SE, Buckler ES. Breaking the curse of dimensionality to identify causal variants in Breeding 4. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:559-567. [PMID: 30547185 PMCID: PMC6439136 DOI: 10.1007/s00122-018-3267-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 12/07/2018] [Indexed: 05/18/2023]
Abstract
In the past, plant breeding has undergone three major transformations and is currently transitioning to a new technological phase, Breeding 4. This phase is characterized by the development of methods for biological design of plant varieties, including transformation and gene editing techniques directed toward causal loci. The application of such technologies will require to reliably estimate the effect of loci in plant genomes by avoiding the situation where the number of loci assayed (p) surpasses the number of plant genotypes (n). Here, we discuss approaches to avoid this curse of dimensionality (n ≪ p), which will involve analyzing intermediate phenotypes such as molecular traits and component traits related to plant morphology or physiology. Because these approaches will rely on novel data types such as DNA sequences and high-throughput phenotyping images, Breeding 4 will call for analyses that are complementary to traditional quantitative genetic studies, being based on machine learning techniques which make efficient use of sequence and image data. In this article, we will present some of these techniques and their application for prioritizing causal loci and developing improved varieties in Breeding 4.
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Affiliation(s)
- Guillaume P Ramstein
- Institute for Genomic Diversity, Institute of Biotechnology, Cornell University, 175 Biotechnology Building, Ithaca, NY, 14853, USA.
| | - Sarah E Jensen
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Edward S Buckler
- Institute for Genomic Diversity, Institute of Biotechnology, Cornell University, 175 Biotechnology Building, Ithaca, NY, 14853, USA
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture, Agricultural Research Service, Ithaca, NY, 14853, USA
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118
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Vaattovaara A, Leppälä J, Salojärvi J, Wrzaczek M. High-throughput sequencing data and the impact of plant gene annotation quality. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1069-1076. [PMID: 30590678 PMCID: PMC6382340 DOI: 10.1093/jxb/ery434] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/28/2018] [Indexed: 06/02/2023]
Abstract
The use of draft genomes of different species and re-sequencing of accessions and populations are now common tools for plant biology research. The de novo assembled draft genomes make it possible to identify pivotal divergence points in the plant lineage and provide an opportunity to investigate the genomic basis and timing of biological innovations by inferring orthologs between species. Furthermore, re-sequencing facilitates the mapping and subsequent molecular characterization of causative loci for traits, such as those for plant stress tolerance and development. In both cases high-quality gene annotation-the identification of protein-coding regions, gene promoters, and 5'- and 3'-untranslated regions-is critical for investigation of gene function. Annotations are constantly improving but automated gene annotations still require manual curation and experimental validation. This is particularly important for genes with large introns, genes located in regions rich with transposable elements or repeats, large gene families, and segmentally duplicated genes. In this opinion paper, we highlight the impact of annotation quality on evolutionary analyses, genome-wide association studies, and the identification of orthologous genes in plants. Furthermore, we predict that incorporating accurate information from manual curation into databases will dramatically improve the performance of automated gene predictors.
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Affiliation(s)
- Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
| | - Johanna Leppälä
- Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 6, Umeå, Sweden
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
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119
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Borrill P, Harrington SA, Uauy C. Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:56-72. [PMID: 30407665 PMCID: PMC6378701 DOI: 10.1111/tpj.14150] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/23/2018] [Accepted: 10/30/2018] [Indexed: 05/10/2023]
Abstract
Improving traits in wheat has historically been challenging due to its large and polyploid genome, limited genetic diversity and in-field phenotyping constraints. However, within recent years many of these barriers have been lowered. The availability of a chromosome-level assembly of the wheat genome now facilitates a step-change in wheat genetics and provides a common platform for resources, including variation data, gene expression data and genetic markers. The development of sequenced mutant populations and gene-editing techniques now enables the rapid assessment of gene function in wheat directly. The ability to alter gene function in a targeted manner will unmask the effects of homoeolog redundancy and allow the hidden potential of this polyploid genome to be discovered. New techniques to identify and exploit the genetic diversity within wheat wild relatives now enable wheat breeders to take advantage of these additional sources of variation to address challenges facing food production. Finally, advances in phenomics have unlocked rapid screening of populations for many traits of interest both in greenhouses and in the field. Looking forwards, integrating diverse data types, including genomic, epigenetic and phenomics data, will take advantage of big data approaches including machine learning to understand trait biology in wheat in unprecedented detail.
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Affiliation(s)
- Philippa Borrill
- School of BiosciencesThe University of BirminghamBirminghamB15 2TTUK
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120
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Lyra DH, Galli G, Alves FC, Granato ÍSC, Vidotti MS, Bandeira E Sousa M, Morosini JS, Crossa J, Fritsche-Neto R. Modeling copy number variation in the genomic prediction of maize hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:273-288. [PMID: 30382311 DOI: 10.1007/s00122-018-3215-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 10/20/2018] [Indexed: 06/08/2023]
Abstract
Our study indicates that copy variants may play an essential role in the phenotypic variation of complex traits in maize hybrids. Moreover, predicting hybrid phenotypes by combining additive-dominance effects with copy variants has the potential to be a viable predictive model. Non-additive effects resulting from the actions of multiple loci may influence trait variation in single-cross hybrids. In addition, complementation of allelic variation could be a valuable contributor to hybrid genetic variation, especially when crossing inbred lines with higher contents of copy gains. With this in mind, we aimed (1) to study the association between copy number variation (CNV) and hybrid phenotype, and (2) to compare the predictive ability (PA) of additive and additive-dominance genomic best linear unbiased prediction model when combined with the effects of CNV in two datasets of maize hybrids (USP and HELIX). In the USP dataset, we observed a significant negative phenotypic correlation of low magnitude between copy number loss and plant height, revealing a tendency that more copy losses lead to lower plants. In the same set, when CNV was combined with the additive plus dominance effects, the PA significantly increased only for plant height under low nitrogen. In this case, CNV effects explicitly capture relatedness between individuals and add extra information to the model. In the HELIX dataset, we observed a pronounced difference in PA between additive (0.50) and additive-dominance (0.71) models for predicting grain yield, suggesting a significant contribution of dominance. We conclude that copy variants may play an essential role in the phenotypic variation of complex traits in maize hybrids, although the inclusion of CNVs into datasets does not return significant gains concerning PA.
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Affiliation(s)
- Danilo Hottis Lyra
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil.
- Department of Computational and Analytical Sciences, Rothamsted Research, West Common, Harpenden, AL52JQ, UK.
| | - Giovanni Galli
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Filipe Couto Alves
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Ítalo Stefanine Correia Granato
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Miriam Suzane Vidotti
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Massaine Bandeira E Sousa
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Júlia Silva Morosini
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - José Crossa
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), 06600, Texcoco, D.F, Mexico
| | - Roberto Fritsche-Neto
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
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121
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Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
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Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Clémentine M François
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France.
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122
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Zaidem ML, Groen SC, Purugganan MD. Evolutionary and ecological functional genomics, from lab to the wild. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:40-55. [PMID: 30444573 DOI: 10.1111/tpj.14167] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/10/2018] [Accepted: 11/13/2018] [Indexed: 05/12/2023]
Abstract
Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.
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Affiliation(s)
- Maricris L Zaidem
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Simon C Groen
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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123
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Dluzewska J, Szymanska M, Ziolkowski PA. Where to Cross Over? Defining Crossover Sites in Plants. Front Genet 2018; 9:609. [PMID: 30619450 PMCID: PMC6299014 DOI: 10.3389/fgene.2018.00609] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022] Open
Abstract
It is believed that recombination in meiosis serves to reshuffle genetic material from both parents to increase genetic variation in the progeny. At the same time, the number of crossovers is usually kept at a very low level. As a consequence, many organisms need to make the best possible use from the one or two crossovers that occur per chromosome in meiosis. From this perspective, the decision of where to allocate rare crossover events becomes an important issue, especially in self-pollinating plant species, which experience limited variation due to inbreeding. However, the freedom in crossover allocation is significantly limited by other, genetic and non-genetic factors, including chromatin structure. Here we summarize recent progress in our understanding of those processes with a special emphasis on plant genomes. First, we focus on factors which influence the distribution of recombination initiation sites and discuss their effects at both, the single hotspot level and at the chromosome scale. We also briefly explain the aspects of hotspot evolution and their regulation. Next, we analyze how recombination initiation sites translate into the development of crossovers and their location. Moreover, we provide an overview of the sequence polymorphism impact on crossover formation and chromosomal distribution.
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Affiliation(s)
- Julia Dluzewska
- Department of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Maja Szymanska
- Department of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Piotr A Ziolkowski
- Department of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
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124
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Wallace JG, Rodgers-Melnick E, Buckler ES. On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics. Annu Rev Genet 2018; 52:421-444. [DOI: 10.1146/annurev-genet-120116-024846] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.
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Affiliation(s)
- Jason G. Wallace
- Department of Crop and Soil Sciences, The University of Georgia, Athens, Georgia 30602, USA
| | | | - Edward S. Buckler
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
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125
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Grattapaglia D, Silva-Junior OB, Resende RT, Cappa EP, Müller BSF, Tan B, Isik F, Ratcliffe B, El-Kassaby YA. Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding. FRONTIERS IN PLANT SCIENCE 2018; 9:1693. [PMID: 30524463 PMCID: PMC6262028 DOI: 10.3389/fpls.2018.01693] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/31/2018] [Indexed: 05/18/2023]
Abstract
Forest tree breeding has been successful at delivering genetically improved material for multiple traits based on recurrent cycles of selection, mating, and testing. However, long breeding cycles, late flowering, variable juvenile-mature correlations, emerging pests and diseases, climate, and market changes, all pose formidable challenges. Genetic dissection approaches such as quantitative trait mapping and association genetics have been fruitless to effectively drive operational marker-assisted selection (MAS) in forest trees, largely because of the complex multifactorial inheritance of most, if not all traits of interest. The convergence of high-throughput genomics and quantitative genetics has established two new paradigms that are changing contemporary tree breeding dogmas. Genomic selection (GS) uses large number of genome-wide markers to predict complex phenotypes. It has the potential to accelerate breeding cycles, increase selection intensity and improve the accuracy of breeding values. Realized genomic relationships matrices, on the other hand, provide innovations in genetic parameters' estimation and breeding approaches by tracking the variation arising from random Mendelian segregation in pedigrees. In light of a recent flow of promising experimental results, here we briefly review the main concepts, analytical tools and remaining challenges that currently underlie the application of genomics data to tree breeding. With easy and cost-effective genotyping, we are now at the brink of extensive adoption of GS in tree breeding. Areas for future GS research include optimizing strategies for updating prediction models, adding validated functional genomics data to improve prediction accuracy, and integrating genomic and multi-environment data for forecasting the performance of genetic material in untested sites or under changing climate scenarios. The buildup of phenotypic and genome-wide data across large-scale breeding populations and advances in computational prediction of discrete genomic features should also provide opportunities to enhance the application of genomics to tree breeding.
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Affiliation(s)
- Dario Grattapaglia
- EMBRAPA Recursos Genéticos e BiotecnologiaBrasília, Brazil
- Programa de Ciências Genômicas e BiotecnologiaUniversidade Católica de Brasília, Brasília, Brazil
- Departamento de Biologia CelularUniversidade de Brasília, Brasília, Brazil
- Department of Forestry and Environmental Resources, North Carolina State UniversityRaleigh, NC, United States
| | - Orzenil B. Silva-Junior
- EMBRAPA Recursos Genéticos e BiotecnologiaBrasília, Brazil
- Programa de Ciências Genômicas e BiotecnologiaUniversidade Católica de Brasília, Brasília, Brazil
| | | | - Eduardo P. Cappa
- Centro de Investigación de Recursos Naturales, Instituto de Recursos BiológicosINTA, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y TécnicasBuenos Aires, Argentina
| | - Bárbara S. F. Müller
- EMBRAPA Recursos Genéticos e BiotecnologiaBrasília, Brazil
- Departamento de Biologia CelularUniversidade de Brasília, Brasília, Brazil
| | - Biyue Tan
- Biomaterials DivisionStora Enso AB, Stockholm, Sweden
| | - Fikret Isik
- Department of Forestry and Environmental Resources, North Carolina State UniversityRaleigh, NC, United States
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British ColumbiaVancouver, BC, Canada
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British ColumbiaVancouver, BC, Canada
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126
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Tock AJ, Henderson IR. Hotspots for Initiation of Meiotic Recombination. Front Genet 2018; 9:521. [PMID: 30467513 PMCID: PMC6237102 DOI: 10.3389/fgene.2018.00521] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/15/2018] [Indexed: 11/13/2022] Open
Abstract
Homologous chromosomes must pair and recombine to ensure faithful chromosome segregation during meiosis, a specialized type of cell division that occurs in sexually reproducing eukaryotes. Meiotic recombination initiates by programmed induction of DNA double-strand breaks (DSBs) by the conserved type II topoisomerase-like enzyme SPO11. A subset of meiotic DSBs are resolved as crossovers, whereby reciprocal exchange of DNA occurs between homologous chromosomes. Importantly, DSBs are non-randomly distributed along eukaryotic chromosomes, forming preferentially in permissive regions known as hotspots. In many species, including plants, DSB hotspots are located within nucleosome-depleted regions. DSB localization is governed by interconnected factors, including cis-regulatory elements, transcription factor binding, and chromatin accessibility, as well as by higher-order chromosome architecture. The spatiotemporal control of DSB formation occurs within a specialized chromosomal structure characterized by sister chromatids organized into linear arrays of chromatin loops that are anchored to a proteinaceous axis. Although SPO11 and its partner proteins required for DSB formation are bound to the axis, DSBs occur preferentially within the chromatin loops, which supports the "tethered-loop/axis model" for meiotic recombination. In this mini review, we discuss insights gained from recent efforts to define and profile DSB hotspots at high resolution in eukaryotic genomes. These advances are deepening our understanding of how meiotic recombination shapes genetic diversity and genome evolution in diverse species.
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Affiliation(s)
- Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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127
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Galli M, Khakhar A, Lu Z, Chen Z, Sen S, Joshi T, Nemhauser JL, Schmitz RJ, Gallavotti A. The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family. Nat Commun 2018; 9:4526. [PMID: 30375394 PMCID: PMC6207667 DOI: 10.1038/s41467-018-06977-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/23/2018] [Indexed: 01/19/2023] Open
Abstract
AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants. As with many large TF families, a key question is whether individual members determine developmental specificity by binding distinct target genes. We use DAP-seq to generate genome-wide in vitro TF:DNA interaction maps for fourteen maize ARFs from the evolutionarily conserved A and B clades. Comparative analysis reveal a high degree of binding site overlap for ARFs of the same clade, but largely distinct clade A and B binding. Many sites are however co-occupied by ARFs from both clades, suggesting transcriptional coordination for many genes. Among these, we investigate known QTLs and use machine learning to predict the impact of cis-regulatory variation. Overall, large-scale comparative analysis of ARF binding suggests that auxin response specificity may be determined by factors other than individual ARF binding site selection.
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Affiliation(s)
- Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Arjun Khakhar
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Zefu Lu
- Department of Genetics, The University of Georgia, Athens, GA, 30602, USA
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Sidharth Sen
- Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Trupti Joshi
- Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.,Department of Health Management and Informatics and Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | | | - Robert J Schmitz
- Department of Genetics, The University of Georgia, Athens, GA, 30602, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA. .,Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
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128
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Gould BA, Chen Y, Lowry DB. Gene regulatory divergence between locally adapted ecotypes in their native habitats. Mol Ecol 2018; 27:4174-4188. [PMID: 30168223 DOI: 10.1111/mec.14852] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 01/04/2023]
Abstract
Local adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Expression plasticity of alleles across habitats (G × E interactions) appears to be relatively common (affecting 18% of transcripts) and could minimize fitness trade-offs at loci that contribute to local adaptation. We also found evidence that at least one chromosomal inversion may act as supergene by holding together haplotypes of differentially expressed genes, but this pattern depends on habitat context. Our results highlight multiple key patterns regarding the relationship between gene expression and the evolution of locally adapted populations.
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Affiliation(s)
- Billie A Gould
- Department of Plant Biology, Michigan State University, East Lansing, Michigan.,Myriad Women's Health, South San Francisco, California
| | - Yani Chen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan.,Plant Resilience Institute, Michigan State University, East Lansing, Michigan
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129
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Li B, Kremling KAG, Wu P, Bukowski R, Romay MC, Xie E, Buckler ES, Chen M. Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation. Genome Res 2018; 28:1555-1565. [PMID: 30166407 PMCID: PMC6169892 DOI: 10.1101/gr.229716.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 08/29/2018] [Indexed: 12/16/2022]
Abstract
Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variation present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA (rDNA) copy number and ribosomal RNA (rRNA) expression for a population of maize inbred lines and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variation was found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We have not found that the rDNA gene dosage has a regulatory role in gene expression; however, thousands of genes are identified to be coregulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We further investigated the potential roles of copy number and the expression level of rDNA on agronomic traits and found that both correlated with flowering time but through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is a valuable source of functional diversity that affects gene expression variation and field-based phenotypic changes.
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Affiliation(s)
- Bo Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Karl A G Kremling
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Penghao Wu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- College of Agronomy, Xinjiang Agriculture University, Urumqi, China 830052
| | - Robert Bukowski
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York 14853, USA
| | - Maria C Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - En Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
- US Department of Agriculture-Agricultural Research Service (USDA-ARS), Ithaca, New York 14853, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
- University of Chinese Academy of Sciences, Beijing, China 100049
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130
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Turpin ZM, Vera DL, Savadel SD, Lung PY, Wear EE, Mickelson-Young L, Thompson WF, Hanley-Bowdoin L, Dennis JH, Zhang J, Bass HW. Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize ( Zea mays L). Data Brief 2018; 20:358-363. [PMID: 30175199 PMCID: PMC6117953 DOI: 10.1016/j.dib.2018.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/12/2018] [Accepted: 08/06/2018] [Indexed: 11/17/2022] Open
Abstract
Presented here are data from Next-Generation Sequencing of differential micrococcal nuclease digestions of formaldehyde-crosslinked chromatin in selected tissues of maize (Zea mays) inbred line B73. Supplemental materials include a wet-bench protocol for making DNS-seq libraries, the DNS-seq data processing pipeline for producing genome browser tracks. This report also includes the peak-calling pipeline using the iSeg algorithm to segment positive and negative peaks from the DNS-seq difference profiles. The data repository for the sequence data is the NCBI SRA, BioProject Accession PRJNA445708.
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Affiliation(s)
- Zachary M. Turpin
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Daniel L. Vera
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL, USA
| | - Savannah D. Savadel
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL, 32306, USA
| | - Emily E. Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh 27606, USA
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh 27606, USA
| | - William F. Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh 27606, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh 27606, USA
| | - Jonathan H. Dennis
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL, 32306, USA
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
- Corresponding author.
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131
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Genome-Wide TSS Identification in Maize. Methods Mol Biol 2018. [PMID: 30043374 DOI: 10.1007/978-1-4939-8657-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Regulation of gene expression is a fundamental biological process that relies on transcription factors (TF) recognizing specific cis motifs in the regulatory regions of the genes that they control. In most eukaryotic organisms, cis-regulatory elements are significantly enriched around the transcription start site (TSS). However, different from other genic features, TSSs need to be experimentally determined, becoming then important components of genome annotations. One of the methods for experimentally determining TSSs at the genome-wide level is CAGE (cap analysis of gene expression). This chapter describes how to prepare a CAGE library for sequencing, starting with RNA extraction, library construction, and quality controls before proceed to sequencing in the Illumina platform. We then describe how to use a computational pipeline to determine, from the alignment of CAGE tags, the genome-wide location of TSSs, followed with statistical approaches required to cluster TSSs that operate as transcriptional units, and to determine core promoter properties such as shape. The analyses described here focus on maize, since its large and yet deficiently annotated genome creates some unique challenges, but with some modifications can be easily adopted for other organisms as well.
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132
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Li M, Xu X, Chang CW, Zheng L, Shen B, Liu Y. SUMO2 conjugation of PCNA facilitates chromatin remodeling to resolve transcription-replication conflicts. Nat Commun 2018; 9:2706. [PMID: 30006506 PMCID: PMC6045570 DOI: 10.1038/s41467-018-05236-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 06/14/2018] [Indexed: 12/27/2022] Open
Abstract
During DNA synthesis, DNA replication and transcription machinery can collide, and the replication fork may temporarily dislodge RNA polymerase II (RNAPII) to resolve the transcription-replication conflict (TRC), a major source of endogenous DNA double-strand breaks (DSBs) and common fragile site (CFS) instability. However, the mechanism of TRC resolution remains unclear. Here, we show that conjugation of SUMO2, but not SUMO1 or SUMO3, to the essential replication factor PCNA is induced on transcribed chromatin by the RNAPII-bound helicase RECQ5. Proteomic analysis reveals that SUMO2-PCNA enriches histone chaperones CAF1 and FACT in the replication complex via interactions with their SUMO-interacting motifs. SUMO2-PCNA enhances CAF1-dependent histone deposition, which correlates with increased histone H3.1 at CFSs and repressive histone marks in the chromatin to reduce chromatin accessibility. Hence, SUMO2-PCNA dislodges RNAPII at CFSs, and overexpressing either SUMO2-PCNA or CAF1 reduces the incidence of DSBs in TRC-prone RECQ5-deficient cells.
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Affiliation(s)
- Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Xiaohua Xu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Chou-Wei Chang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA.
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133
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Kianian PMA, Wang M, Simons K, Ghavami F, He Y, Dukowic-Schulze S, Sundararajan A, Sun Q, Pillardy J, Mudge J, Chen C, Kianian SF, Pawlowski WP. High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize. Nat Commun 2018; 9:2370. [PMID: 29915302 PMCID: PMC6006299 DOI: 10.1038/s41467-018-04562-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 05/04/2018] [Indexed: 12/19/2022] Open
Abstract
Meiotic crossovers (COs) are not uniformly distributed across the genome. Factors affecting this phenomenon are not well understood. Although many species exhibit large differences in CO numbers between sexes, sex-specific aspects of CO landscape are particularly poorly elucidated. Here, we conduct high-resolution CO mapping in maize. Our results show that CO numbers as well as their overall distribution are similar in male and female meioses. There are, nevertheless, dissimilarities at local scale. Male and female COs differ in their locations relative to transcription start sites in gene promoters and chromatin marks, including nucleosome occupancy and tri-methylation of lysine 4 of histone H3 (H3K4me3). Our data suggest that sex-specific factors not only affect male–female CO number disparities but also cause fine differences in CO positions. Differences between male and female CO landscapes indicate that recombination has distinct implications for population structure and gene evolution in male and in female meioses. Sex-specific meiotic crossover (CO) landscapes have been identified in multiple species. Here, the authors show that male and female meioses in maize have similar CO landscapes, and differences between COs in the two sexes only exists in their location relative to transcription start sites and some chromatin marks.
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Affiliation(s)
- Penny M A Kianian
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Minghui Wang
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.,Bioinformatics Facility, Cornell University, Ithaca, NY, 14853, USA
| | - Kristin Simons
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA.,Eurofins BioDiagnostics, River Falls, WI, 54022, USA
| | - Yan He
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.,National Maize Improvement Center, China Agricultural University, Beijing, China
| | | | | | - Qi Sun
- Bioinformatics Facility, Cornell University, Ithaca, NY, 14853, USA
| | | | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Wojciech P Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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134
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Dong X, Chen J, Li T, Li E, Zhang X, Zhang M, Song W, Zhao H, Lai J. Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize. Genome Res 2018; 28:1020-1028. [PMID: 29903724 PMCID: PMC6028132 DOI: 10.1101/gr.230201.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 05/31/2018] [Indexed: 12/23/2022]
Abstract
Genomic imprinting refers to allele-specific expression of genes depending on their parental origin. Nucleosomes, the fundamental units of chromatin, play a critical role in gene transcriptional regulation. However, it remains unknown whether differential nucleosome organization is related to the allele-specific expression of imprinted genes. Here, we generated a genome-wide map of allele-specific nucleosome occupancy in maize endosperm and presented an integrated analysis of its relationship with parent-of-origin-dependent gene expression and DNA methylation. We found that ∼2.3% of nucleosomes showed significant parental bias in maize endosperm. The parent-of-origin-dependent nucleosomes mostly exist as single isolated nucleosomes. Parent-of-origin-dependent nucleosomes were significantly associated with the allele-specific expression of imprinted genes, with nucleosomes positioned preferentially in the promoter of nonexpressed alleles of imprinted genes. Furthermore, we found that most of the paternal specifically positioned nucleosomes (pat-nucleosomes) were associated with parent-of-origin-dependent differential methylated regions, suggesting a functional link between the maternal demethylation and the occurrence of pat-nucleosome. Maternal specifically positioned nucleosomes (mat-nucleosomes) were independent of allele-specific DNA methylation but seem to be associated with allele-specific histone modification. Our study provides the first genome-wide map of allele-specific nucleosome occupancy in plants and suggests a mechanistic connection between chromatin organization and genomic imprinting.
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Affiliation(s)
- Xiaomei Dong
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Tong Li
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - En Li
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xiangbo Zhang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Mei Zhang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, People's Republic of China.,Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
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135
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Srivastava R, Li Z, Russo G, Tang J, Bi R, Muppirala U, Chudalayandi S, Severin A, He M, Vaitkevicius SI, Lawrence-Dill CJ, Liu P, Stapleton AE, Bassham DC, Brandizzi F, Howell SH. Response to Persistent ER Stress in Plants: A Multiphasic Process That Transitions Cells from Prosurvival Activities to Cell Death. THE PLANT CELL 2018; 30:1220-1242. [PMID: 29802214 PMCID: PMC6048783 DOI: 10.1105/tpc.18.00153] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 05/09/2023]
Abstract
The unfolded protein response (UPR) is a highly conserved response that protects plants from adverse environmental conditions. The UPR is elicited by endoplasmic reticulum (ER) stress, in which unfolded and misfolded proteins accumulate within the ER. Here, we induced the UPR in maize (Zea mays) seedlings to characterize the molecular events that occur over time during persistent ER stress. We found that a multiphasic program of gene expression was interwoven among other cellular events, including the induction of autophagy. One of the earliest phases involved the degradation by regulated IRE1-dependent RNA degradation (RIDD) of RNA transcripts derived from a family of peroxidase genes. RIDD resulted from the activation of the promiscuous ribonuclease activity of ZmIRE1 that attacks the mRNAs of secreted proteins. This was followed by an upsurge in expression of the canonical UPR genes indirectly driven by ZmIRE1 due to its splicing of Zmbzip60 mRNA to make an active transcription factor that directly upregulates many of the UPR genes. At the peak of UPR gene expression, a global wave of RNA processing led to the production of many aberrant UPR gene transcripts, likely tempering the ER stress response. During later stages of ER stress, ZmIRE1's activity declined, as did the expression of survival modulating genes, Bax inhibitor1 and Bcl-2-associated athanogene7, amid a rising tide of cell death. Thus, in response to persistent ER stress, maize seedlings embark on a course of gene expression and cellular events progressing from adaptive responses to cell death.
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Affiliation(s)
- Renu Srivastava
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
| | - Zhaoxia Li
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
| | - Giulia Russo
- MSU-DOE Plant Research Laboratories, Department of Plant Biology, East Lansing, Michigan 48824
| | - Jie Tang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Ran Bi
- Department of Statistics, Iowa State University, Ames, Iowa 50011
| | - Usha Muppirala
- Genome Informatics Facility, Iowa State University, Ames, Iowa 50011
| | | | - Andrew Severin
- Genome Informatics Facility, Iowa State University, Ames, Iowa 50011
| | - Mingze He
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Samuel I Vaitkevicius
- MSU-DOE Plant Research Laboratories, Department of Plant Biology, East Lansing, Michigan 48824
| | - Carolyn J Lawrence-Dill
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, Iowa 50011
| | - Ann E Stapleton
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina 28403
| | - Diane C Bassham
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Federica Brandizzi
- MSU-DOE Plant Research Laboratories, Department of Plant Biology, East Lansing, Michigan 48824
| | - Stephen H Howell
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
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136
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Girimurugan SB, Liu Y, Lung PY, Vera DL, Dennis JH, Bass HW, Zhang J. iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. BMC Bioinformatics 2018; 19:131. [PMID: 29642840 PMCID: PMC5896135 DOI: 10.1186/s12859-018-2140-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/26/2018] [Indexed: 11/16/2022] Open
Abstract
Background Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments where adjacent segments have different properties, such as different mean values. Despite dozens of algorithms developed to address this problem in genomics research, methods with improved accuracy and speed are still needed to effectively tackle both existing and emerging genomic and epigenomic segmentation problems. Results We designed an efficient algorithm, called iSeg, for segmentation of genomic and epigenomic profiles. iSeg first utilizes dynamic programming to identify candidate segments and test for significance. It then uses a novel data structure based on two coupled balanced binary trees to detect overlapping significant segments and update them simultaneously during searching and refinement stages. Refinement and merging of significant segments are performed at the end to generate the final set of segments. By using an objective function based on the p-values of the segments, the algorithm can serve as a general computational framework to be combined with different assumptions on the distributions of the data. As a general segmentation method, it can segment different types of genomic and epigenomic data, such as DNA copy number variation, nucleosome occupancy, nuclease sensitivity, and differential nuclease sensitivity data. Using simple t-tests to compute p-values across multiple datasets of different types, we evaluate iSeg using both simulated and experimental datasets and show that it performs satisfactorily when compared with some other popular methods, which often employ more sophisticated statistical models. Implemented in C++, iSeg is also very computationally efficient, well suited for large numbers of input profiles and data with very long sequences. Conclusions We have developed an efficient general-purpose segmentation tool and showed that it had comparable or more accurate results than many of the most popular segment-calling algorithms used in contemporary genomic data analysis. iSeg is capable of analyzing datasets that have both positive and negative values. Tunable parameters allow users to readily adjust the statistical stringency to best match the biological nature of individual datasets, including widely or sparsely mapped genomic datasets or those with non-normal distributions. Electronic supplementary material The online version of this article (10.1186/s12859-018-2140-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Yuhang Liu
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Daniel L Vera
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL, USA
| | - Jonathan H Dennis
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL, USA.
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137
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Zhao H, Zhang W, Chen L, Wang L, Marand AP, Wu Y, Jiang J. Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome. PLANT PHYSIOLOGY 2018; 176:2789-2803. [PMID: 29463772 PMCID: PMC5884613 DOI: 10.1104/pp.17.01467] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/09/2018] [Indexed: 05/05/2023]
Abstract
Genomic regions free of nucleosomes, which are hypersensitive to DNase I digestion, are known as DNase I hypersensitive sites (DHSs) and frequently contain cis-regulatory DNA elements. To investigate their prevalence and characteristics in maize (Zea mays), we developed high-resolution genome-wide DHS maps using a modified DNase-seq technique. Maize DHSs exhibit depletion of nucleosomes and low levels of DNA methylation and are enriched with conserved noncoding sequences (CNSs). We developed a protoplast-based transient transformation assay to assess the potential gene expression enhancer and/or promoter functions associated with DHSs, which showed that more than 80% of DHSs overlapping with CNSs showed an enhancer function. Strikingly, nearly 25% of maize DHSs were derived from transposable elements (TEs), including both class I and class II transposons. Interestingly, TE-derived DHSs (teDHSs) homologous to retrotransposons were enriched with sequences related to the intrinsic cis-regulatory elements within the long terminal repeats of retrotransposons. We demonstrate that more than 80% of teDHSs can drive transcription of a reporter gene in protoplast assays. These results reveal the widespread occurrence of TE-derived cis-regulatory sequences and suggest that teDHSs play a major role in transcriptional regulation in maize.
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Affiliation(s)
- Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Lifen Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Lei Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Alexandre P Marand
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
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138
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Affiliation(s)
- Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA.
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA.
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139
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Choi K, Zhao X, Tock AJ, Lambing C, Underwood CJ, Hardcastle TJ, Serra H, Kim J, Cho HS, Kim J, Ziolkowski PA, Yelina NE, Hwang I, Martienssen RA, Henderson IR. Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res 2018; 28:532-546. [PMID: 29530928 PMCID: PMC5880243 DOI: 10.1101/gr.225599.117] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 02/08/2018] [Indexed: 02/02/2023]
Abstract
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes and allows SPO11-1 access. A positive relationship was observed between SPO11-1-oligos and crossovers genome-wide, although fine-scale correlations were weaker. This may reflect the influence of interhomolog polymorphism on crossover formation, downstream from DSB formation. Although H3K4me3 is enriched in proximity to SPO11-1-oligo hotspots at gene 5' ends, H3K4me3 levels do not correlate with DSBs. Repetitive transposons are thought to be recombination silenced during meiosis, to prevent nonallelic interactions and genome instability. Unexpectedly, we found high SPO11-1-oligo levels in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. High SPO11-1-oligo transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin in SPO11-1-oligo distributions. Epigenetic activation of meiotic DSBs in proximity to centromeres and transposons occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription, and H3K4me3. Together, our work reveals a complex relationship between chromatin and meiotic DSBs within A. thaliana genes and transposons, with significance for the diversity and evolution of plant genomes.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom;,Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Andrew J. Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Charles J. Underwood
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom;,Howard Hughes Medical Institute–Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Thomas J. Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Juhyun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Piotr A. Ziolkowski
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Nataliya E. Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Robert A. Martienssen
- Howard Hughes Medical Institute–Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R. Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
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140
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Lu Z, Ricci WA, Schmitz RJ, Zhang X. Identification of cis-regulatory elements by chromatin structure. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:90-94. [PMID: 29704803 DOI: 10.1016/j.pbi.2018.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 05/22/2023]
Abstract
The systematic identification of cis-regulatory elements (CREs) in plant genomes is critically important in understanding transcriptional regulation during development and in response to environmental cues. Several genome-wide structure-based methods have been successfully applied to plant genomes in the past few years. Here, we review recent results on the identification and characterization of CREs in multiple plant species and in different biological processes and discuss future applications of chromatin accessibility data to understand the mechanism, function and evolution of transcriptional regulation networks.
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Affiliation(s)
- Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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141
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Choi K, Zhao X, Tock AJ, Lambing C, Underwood CJ, Hardcastle TJ, Serra H, Kim J, Cho HS, Kim J, Ziolkowski PA, Yelina NE, Hwang I, Martienssen RA, Henderson IR. Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res 2018. [PMID: 29530928 DOI: 10.1101/gr.225599.117.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes and allows SPO11-1 access. A positive relationship was observed between SPO11-1-oligos and crossovers genome-wide, although fine-scale correlations were weaker. This may reflect the influence of interhomolog polymorphism on crossover formation, downstream from DSB formation. Although H3K4me3 is enriched in proximity to SPO11-1-oligo hotspots at gene 5' ends, H3K4me3 levels do not correlate with DSBs. Repetitive transposons are thought to be recombination silenced during meiosis, to prevent nonallelic interactions and genome instability. Unexpectedly, we found high SPO11-1-oligo levels in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. High SPO11-1-oligo transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin in SPO11-1-oligo distributions. Epigenetic activation of meiotic DSBs in proximity to centromeres and transposons occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription, and H3K4me3. Together, our work reveals a complex relationship between chromatin and meiotic DSBs within A. thaliana genes and transposons, with significance for the diversity and evolution of plant genomes.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Charles J Underwood
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Juhyun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Piotr A Ziolkowski
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Robert A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
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142
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Massive crossover elevation via combination of HEI10 and recq4a recq4b during Arabidopsis meiosis. Proc Natl Acad Sci U S A 2018; 115:2437-2442. [PMID: 29463699 DOI: 10.1073/pnas.1713071115] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
During meiosis, homologous chromosomes undergo reciprocal crossovers, which generate genetic diversity and underpin classical crop improvement. Meiotic recombination initiates from DNA double-strand breaks (DSBs), which are processed into single-stranded DNA that can invade a homologous chromosome. The resulting joint molecules can ultimately be resolved as crossovers. In Arabidopsis, competing pathways balance the repair of ∼100-200 meiotic DSBs into ∼10 crossovers per meiosis, with the excess DSBs repaired as noncrossovers. To bias DSB repair toward crossovers, we simultaneously increased dosage of the procrossover E3 ligase gene HEI10 and introduced mutations in the anticrossovers helicase genes RECQ4A and RECQ4B As HEI10 and recq4a recq4b increase interfering and noninterfering crossover pathways, respectively, they combine additively to yield a massive meiotic recombination increase. Interestingly, we also show that increased HEI10 dosage increases crossover coincidence, which indicates an effect on interference. We also show that patterns of interhomolog polymorphism and heterochromatin drive recombination increases distally towards the subtelomeres in both HEI10 and recq4a recq4b backgrounds, while the centromeres remain crossover suppressed. These results provide a genetic framework for engineering meiotic recombination landscapes in plant genomes.
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143
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Renny-Byfield S, Rodgers-Melnick E, Ross-Ibarra J. Gene Fractionation and Function in the Ancient Subgenomes of Maize. Mol Biol Evol 2018; 34:1825-1832. [PMID: 28430989 DOI: 10.1093/molbev/msx121] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The maize genome experienced an ancient whole genome duplication ∼10 MYA and the duplicate subgenomes have since experienced reciprocal gene loss such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here, we use published data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared with their lowly expressed counterparts. Furthermore, paralogous genes in the least-fractionated subgenome account for a greater degree of phenotypic diversity than those resident on the more-fractionated subgenome. Intriguingly, analysis of singleton genes reveals this difference persists even after fractionation is complete. Additionally, we show that the two subgenomes of maize may differ in their epigenetic profiles.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Plant Sciences, University of California, Davis, CA.,DuPont Pioneer, Johnston, IA
| | - Eli Rodgers-Melnick
- DuPont Pioneer, Johnston, IA.,Institute for Genomic Diversity, Cornell University, Ithaca, NY
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, CA.,Center for Population Biology and Genome Center, University of California, Davis, CA
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144
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Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West DA, Zumstein K, Woodhouse M, Bubb K, Dorrity MW, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal RB. Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules. THE PLANT CELL 2018. [PMID: 29229750 DOI: 10.1101/167932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the assay for transposase-accessible chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell-type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell-type-specific transcriptomes during development.
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Affiliation(s)
- Kelsey A Maher
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Marko Bajic
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia 30322
| | - Kaisa Kajala
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mauricio Reynoso
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Germain Pauluzzi
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Donnelly A West
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, California 95616
| | - Margaret Woodhouse
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kerry Bubb
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Michael W Dorrity
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Christine Queitsch
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
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145
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Manchanda N, Snodgrass SJ, Ross-Ibarra J, Hufford MB. Evolution and Adaptation in the Maize Genome. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-97427-9_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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146
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Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West DA, Zumstein K, Woodhouse M, Bubb K, Dorrity MW, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal RB. Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules. THE PLANT CELL 2018; 30:15-36. [PMID: 29229750 PMCID: PMC5810565 DOI: 10.1105/tpc.17.00581] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/30/2017] [Accepted: 12/06/2017] [Indexed: 05/19/2023]
Abstract
The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the assay for transposase-accessible chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell-type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell-type-specific transcriptomes during development.
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Affiliation(s)
- Kelsey A Maher
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Marko Bajic
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia 30322
| | - Kaisa Kajala
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mauricio Reynoso
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Germain Pauluzzi
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Donnelly A West
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, California 95616
| | - Margaret Woodhouse
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kerry Bubb
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Michael W Dorrity
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Christine Queitsch
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
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147
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Mo Y, Howell T, Vasquez-Gross H, de Haro LA, Dubcovsky J, Pearce S. Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study. Mol Genet Genomics 2017. [PMID: 29188438 DOI: 10.1007/s00438‐017‐1401‐6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes.
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Affiliation(s)
- Youngjun Mo
- Department of Plant Sciences, University of California, Davis, CA, USA
- National Institute of Crop Science, Rural Development Administration, Wanju, South Korea
| | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Luis Alejandro de Haro
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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148
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Mo Y, Howell T, Vasquez-Gross H, de Haro LA, Dubcovsky J, Pearce S. Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study. Mol Genet Genomics 2017; 293:463-477. [PMID: 29188438 PMCID: PMC5854723 DOI: 10.1007/s00438-017-1401-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/23/2017] [Indexed: 11/23/2022]
Abstract
Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes.
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Affiliation(s)
- Youngjun Mo
- Department of Plant Sciences, University of California, Davis, CA, USA.,National Institute of Crop Science, Rural Development Administration, Wanju, South Korea
| | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Luis Alejandro de Haro
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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149
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Mazumdar P, Binti Othman R, Mebus K, Ramakrishnan N, Ann Harikrishna J. Codon usage and codon pair patterns in non-grass monocot genomes. ANNALS OF BOTANY 2017; 120:893-909. [PMID: 29155926 PMCID: PMC5710610 DOI: 10.1093/aob/mcx112] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 09/19/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Studies on codon usage in monocots have focused on grasses, and observed patterns of this taxon were generalized to all monocot species. Here, non-grass monocot species were analysed to investigate the differences between grass and non-grass monocots. METHODS First, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available. Measurements were taken regarding relative synonymous codon usage, effective number of codons, derived optimal codon and GC content and then the relationships investigated to infer the underlying evolutionary forces. KEY RESULTS The research identified optimal codons, rare codons and preferred codon-pair context in the non-grass monocot species studied. In contrast to the bimodal distribution of GC3 (GC content in third codon position) in grasses, non-grass monocots showed a unimodal distribution. Disproportionate use of G and C (and of A and T) in two- and four-codon amino acids detected in the analysis rules out the mutational bias hypothesis as an explanation of genomic variation in GC content. There was found to be a positive relationship between CAI (codon adaptation index; predicts the level of expression of a gene) and GC3. In addition, a strong correlation was observed between coding and genomic GC content and negative correlation of GC3 with gene length, indicating a strong impact of GC-biased gene conversion (gBGC) in shaping codon usage and nucleotide composition in non-grass monocots. CONCLUSION Optimal codons in these non-grass monocots show a preference for G/C in the third codon position. These results support the concept that codon usage and nucleotide composition in non-grass monocots are mainly driven by gBGC.
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Affiliation(s)
- Purabi Mazumdar
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - RofinaYasmin Binti Othman
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Katharina Mebus
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - N Ramakrishnan
- Electrical and Computer System Engineering, School of Engineering, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- For correspondence. E-mail:
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150
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Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, Murray JAH. Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet 2017; 13:e1006988. [PMID: 28902852 PMCID: PMC5597176 DOI: 10.1371/journal.pgen.1006988] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes. The genome-wide profile of these subNSPs has not been previously analysed in plants and this study investigates the relationship of dynamic bound particles with transcriptional control. Here we combine differential micrococcal nuclease (MNase) digestion and a modified paired-end sequencing protocol to reveal the chromatin structure landscape of Arabidopsis cells across a wide particle size range. Linking this data to RNAseq expression analysis provides detailed insight into the relationship of identified DNA-bound particles with transcriptional activity. The use of differential digestion reveals sensitive positions, including a labile -1 nucleosome positioned upstream of the transcription start site (TSS) of active genes. We investigated the response of the chromatin landscape to changes in environmental conditions using light and dark growth, given the large transcriptional changes resulting from this simple alteration. The resulting shifts in the suites of expressed and repressed genes show little correspondence to changes in nucleosome positioning, but led to significant alterations in the profile of subNSPs upstream of TSS both globally and locally. We examined previously mapped positions for the TFs PIF3, PIF4 and CCA1, which regulate light responses, and found that changes in subNSPs co-localized with these binding sites. This small particle structure is detected only under low levels of MNase digestion and is lost on more complete digestion of chromatin to nucleosomes. We conclude that wide-spectrum analysis of the Arabidopsis genome by differential MNase digestion allows detection of sensitive features hereto obscured, and the comparisons between genome-wide subNSP profiles reveals dynamic changes in their distribution, particularly at distinct genomic locations (i.e. 5'UTRs). The method here employed allows insight into the complex influence of genetic and extrinsic factors in modifying the sub-nucleosomal landscape in association with transcriptional changes.
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Affiliation(s)
- Daniel Antony Pass
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Emily Sornay
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Angela Marchbank
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Margaret R. Crawford
- Genome Centre, University of Sussex, Sussex House, Falmer, Brighton, United Kingdom
| | - Konrad Paszkiewicz
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Nicholas A. Kent
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
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